| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | AA | AB | AC | AD | AE | AF | AG | AH | AI | AJ | AK | AL | AM | AN | AO | AP | AQ | AR | AS | AT | AU | AV | AW | AX | AY | AZ | BA | BB | BC | BD | BE | |
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1 | Gephe ID | Gene-Gephebase | Username | Generic Gene Name | UniProtKB_ID | UniProtKB_Species | String | Sequence Similarities | Synonyms | GO Molecular | GO Cellular | GO Biological | GenBankID | Trait Category | Trait | State A | State B | Taxon A ID | Latin Name A | Common Name A | Rank A | Taxon A Lineage | A=Infraspecies | Taxon A Description | Taxon B ID | Latin Name B | Common Name B | Rank B | Taxon B Lineage | B=Infraspecies | Taxon B Description | Ancestral State | Taxonomic Status | Empirical Evidence | Molecular Details | Molecular Type | Presumptive Null | SNP Coding Change | Student | Codon-Taxon-A | Codon-Position | Codon-TaxonB | Codon-Site | transition-transversion | AminoAcid-Taxon A | AA-Position | AminoAcid-Taxon B | Aberration Type | Aberration Size | Reference Title | Reference Abstract | Publication Year | Main PMID | RefLink | Additional PMID | Comments | User Feedback |
2 | GP00000958 | Rc | Martin | Rc | A7J5U6 | Oryza sativa subsp. japonica | CTN5;CYR3;GLC5;TSL7;ASC1;YNL098C;N2198 | GO:0046983 | GO:0005886;GO:0005634;GO:0005739;GO:0005789 | GO:0007165;GO:0032880;GO:0016236;GO:0007190;GO:0030437;GO:0045762;GO:2000222;GO:0000411;GO:0032258;GO:0097271;GO:0010603;GO:0001302 | ADR01106 | Morphology | Coloration (seed) | Oryza glaberrima (Africa; wild strains with red pericarp) | Oryza glaberrima (Africa; domesticated strains with white pericarp) | 4538 | Oryza glaberrima | African rice | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza | 1 | 4538 | Oryza glaberrima | African rice | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza | 1 | Data not curated | Domesticated | Candidate Gene | Premature stop codon in exon 7 | Coding | Yes | Nonsense | SNP | The molecular basis of white pericarps in African domesticated rice: novel mutations at the Rc gene. | Repeated phenotypic evolution can occur at both the inter- and intraspecific level and is especially prominent in domesticated plants; where artificial selection has favoured the same traits in many different species and varieties. The question of whether repeated evolution reflects changes at the same or different genes in each lineage can now be addressed using the domestication and improvement genes that have been identified in a variety of crops. Here; we document the genetic basis of nonpigmented ('white') pericarps in domesticated African rice (Oryza glaberrima) and compare it with the known genetic basis of the same trait in domesticated Asian rice (Oryza sativa). In some cases; white pericarps in African rice are apparently caused by unique mutations at the Rc gene; which also controls pericarp colour variation in Asian rice. In one case; white pericarps appear to reflect changes at a different gene or potentially a cis-regulatory region. © 2010 The Authors. Journal Compilation © 2010 European Society For Evolutionary Biology. | 2010 | 21121088,1 | ND | |||||||||||||||||
3 | GP00001026 | scd-2 | Martin | scd-2 | O76411 | Caenorhabditis elegans | 6239.T10H9.2 | Belongs to the protein kinase superfamily. Tyr protein kinase family. Insulin receptor subfamily. | T10H9.2 | GO:0005524;GO:0004714 | GO:0016021;GO:0005886 | GO:0006935;GO:0040024;GO:0007606;GO:0050893 | BX284605 | Physiology | Diapause | C. elegans - desert strain | C. elegans - N2 | 6239 | Caenorhabditis elegans | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis | 1 | 6239 | Caenorhabditis elegans | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis | 1 | Data not curated | Intraspecific | Linkage Mapping | Gly985Arg, G to A | Coding | No | Nonsynonymous | Courtier | GGR | nd | AGR | 1 | transition | Gly | 985 | Arg | SNP | C. elegans anaplastic lymphoma kinase ortholog SCD-2 controls dauer formation by modulating TGF-beta signaling. | Different environmental stimuli; including exposure to dauer pheromone; food deprivation; and high temperature; can induce C. elegans larvae to enter the dauer stage; a developmentally arrested diapause state. Although molecular and cellular pathways responsible for detecting dauer pheromone and temperature have been defined in part; other sensory inputs are poorly understood; as are the mechanisms by which these diverse sensory inputs are integrated to achieve a consistent developmental outcome. In this paper; we analyze a wild C. elegans strain isolated from a desert oasis. Unlike wild-type laboratory strains; the desert strain fails to respond to dauer pheromone at 25 degrees C; but it does respond at higher temperatures; suggesting a unique adaptation to the hot desert environment. We map this defect in dauer response to a mutation in the scd-2 gene; which; we show; encodes the nematode anaplastic lymphoma kinase (ALK) homolog; a proto-oncogene receptor tyrosine kinase. scd-2 acts in a genetic pathway shown here to include the HEN-1 ligand; the RTK adaptor SOC-1; and the MAP kinase SMA-5. The SCD-2 pathway modulates TGF-beta signaling; which mediates the response to dauer pheromone; but SCD-2 might mediate a nonpheromone sensory input; such as food. Our studies identify a new sensory pathway controlling dauer formation and shed light on ALK signaling; integration of signaling pathways; and adaptation to extreme environmental conditions. | 2008 | 18674914,1 | https://sci-hub.tw/10.1016/j.cub.2008.06.060 | @GxE | |||||||
4 | GP00001237 | ETC2 | Arnoult | ETC2 | Q84RD1 | Arabidopsis thaliana | 3702.AT2G30420.1 | ENHANCER OF TRY AND CPC 2;T9D9.23;T9D9_23;At2g30420;T6B20;T9D9 | GO:0003700;GO:0043565;GO:0000981;GO:0044212;GO:0001135 | GO:0005634 | GO:0006355;GO:0006351;GO:0006357;GO:0048629;GO:1900033;GO:0080147 | NM_179814.3 | Morphology | Trichome density (leaf) | Arabidopsis thaliana- Gr-1 | Arabidopsis thaliana Can-0 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Intraspecific | Linkage Mapping | K19E | Coding | No | Nonsynonymous | Courtier | GAR | nd | AAR | 1 | transition | Lys | 19 | Glu | SNP | A single amino acid replacement in ETC2 shapes trichome patterning in natural Arabidopsis populations. | Our understanding of the evolution of organismal diversity is restricted by the current resolution of the genotype-phenotype map. In particular; the genetic basis of environmentally relevant phenotypic variation among natural populations remains poorly understood. Trichomes are single-cell outgrowths on the surface of plant leaves and other above-ground organs. Consistent with trichomes' suggested function to protect plants from predators and abiotic stressors [1-3]; trichome density is strikingly variable among natural populations (e.g.; [2; 4]). Despite substantial progress in the genetic dissection of trichome development [5]; how trichome number is modulated in natural populations remains enigmatic. Here; we show that the ENHANCER OF TRY AND CPC 2 (ETC2) from the single-repeat R3 MYB family is the major locus determining trichome patterning in natural Arabidopsis populations. Our study identifies a single amino acid substitution in ETC2 (K19E) as the causal quantitative trait nucleotide (QTN). We suggest that this amino acid replacement might affect the stability of the ETC2 repressor; which results in a reduced trichome number. This is consistent with the view that morphology can evolve by coding changes that can subtly modulate protein activity as well as cis-regulatory changes that alter expression patterns. | 2009 | 19818620,1 | https://sci-hub.tw/10.1016/j.cub.2009.08.057 | functional test of QTN + mutant complementation | ||||||
5 | GP00000195 | CYC8 | Martin | CYC8 | P14922 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | 4932.YBR112C | Belongs to the CYC8/SSN6 family. | CRT8;SSN6;YBR112C;YBR0908 | GO:0042826;GO:0003714;GO:0003713 | GO:0005634;GO:0017053 | GO:0045944;GO:0006351;GO:0000122;GO:0006338;GO:0035955;GO:0016584;GO:2000531;GO:2001020 | X78993 | Physiology | Salt tolerance (experimental evolution) | Saccharomyces cerevisiae | Saccharomyces cerevisiae | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | Data not curated | Experimental Evolution | Association Mapping | 1bp substitution resulting in premature stop codon | Coding | Yes | Nonsense | Courtier | TAR | 464706 | TAY | 3 | transversion | Tyr | nd | STP | SNP | Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. | Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here; whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations; six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt; two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose; one mutation occurred in MDS3; which modulates growth at high pH; and one in MKT1; a global regulator of mRNAs encoding mitochondrial proteins; the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong. Copyright (c) 2010 Elsevier Ltd. All rights reserved. | 2010 | 20637622,1 | https://sci-hub.tw/10.1016/j.cub.2010.06.022 | 21856932,1 | |||||
6 | GP00000641 | MDS3 | Martin | MDS3 | P53094 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | 4932.YGL197W | YGL197W;G1307 | GO:0004977 | GO:0005737 | GO:0051321;GO:0007124;GO:0030435;GO:0075297;GO:0031929 | Z72719 | Physiology | Low-glucose adaptation (experimental evolution) | Saccharomyces cerevisiae | Saccharomyces cerevisiae | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | Data not curated | Experimental Evolution | Association Mapping | Phe - Val substitution | Coding | No | Nonsynonymous | Courtier | TTY | 126872 | GTY | 1 | transversion | Phe | nd | Val | SNP | Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. | Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here; whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations; six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt; two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose; one mutation occurred in MDS3; which modulates growth at high pH; and one in MKT1; a global regulator of mRNAs encoding mitochondrial proteins; the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong. Copyright (c) 2010 Elsevier Ltd. All rights reserved. | 2010 | 20637622,1 | https://sci-hub.tw/10.1016/j.cub.2010.06.022 | 21856932,1 | ||||||
7 | GP00000662 | MKT1 | Martin | MKT1 | P40850 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | 4932.YNL085W | YNL085W;N2302 | GO:0004520 | GO:0034399;GO:0010494;GO:0000932;GO:0005844 | GO:0006974;GO:0006281;GO:0044419 | X03534 | Physiology | Low-glucose adaptation (experimental evolution) | Saccharomyces cerevisiae - 30G laboratory strain | Saccharomyces cerevisiae - experimentally evolved lines | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 1 | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | Data not curated | Experimental Evolution | Association Mapping | D30G (reversion; functionally verified); evolved independently in 3 lines | Coding | No | Nonsynonymous | Courtier | GAC | 467221 | GGC | 2 | transition | Asp | 30 | Gly | SNP | Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. | Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here; whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations; six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt; two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose; one mutation occurred in MDS3; which modulates growth at high pH; and one in MKT1; a global regulator of mRNAs encoding mitochondrial proteins; the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong. Copyright (c) 2010 Elsevier Ltd. All rights reserved. | 2010 | 20637622,1 | https://sci-hub.tw/10.1016/j.cub.2010.06.022 | 21856932,1 | @& | |||||
8 | GP00000900 | PMA1 | Martin | PMA1 | P05030 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | 4932.YGL008C | Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIIA subfamily. | KTI10;YGL008C | GO:0005524;GO:0046872;GO:0008553 | GO:0016021;GO:0005886;GO:0045121 | GO:0055085;GO:0006885;GO:1902906;GO:0120029;GO:1902600 | X03534 | Physiology | Salt tolerance (experimental evolution) | Saccharomyces cerevisiae | Saccharomyces cerevisiae - after 500 generations of selective pressure | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | Taxon A | Experimental Evolution | Association Mapping | Leu363Trp | Coding | No | Nonsynonymous | Courtier | TTG | 481584 | TGG | 2 | transversion | Leu | 363 | Trp | SNP | Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. | Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here; whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations; six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt; two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose; one mutation occurred in MDS3; which modulates growth at high pH; and one in MKT1; a global regulator of mRNAs encoding mitochondrial proteins; the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong. Copyright (c) 2010 Elsevier Ltd. All rights reserved. | 2010 | 20637622,1 | https://sci-hub.tw/10.1016/j.cub.2010.06.022 | 21856932.1;25016004.1 | PMID 25016004 includes nucleotidic changes | ||||
9 | GP00000901 | PMA1 | Martin | PMA1 | P05030 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | 4932.YGL008C | Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIIA subfamily. | KTI10;YGL008C | GO:0005524;GO:0046872;GO:0008553 | GO:0016021;GO:0005886;GO:0045121 | GO:0055085;GO:0006885;GO:1902906;GO:0120029;GO:1902600 | X03534 | Physiology | Salt tolerance (experimental evolution) | Saccharomyces cerevisiae | Saccharomyces cerevisiae - after 500 generations of selective pressure | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | Taxon A | Experimental Evolution | Association Mapping | Ser234Cys | Coding | No | Nonsynonymous | Courtier | TCY | 481971 | TGY | 2 | transversion | Ser | 234 | Cys | SNP | Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. | Divergent adaptation can be associated with reproductive isolation in speciation [1]. We recently demonstrated the link between divergent adaptation and the onset of reproductive isolation in experimental populations of the yeast Saccharomyces cerevisiae evolved from a single progenitor in either a high-salt or a low-glucose environment [2]. Here; whole-genome resequencing and comparative genome hybridization of representatives of three populations revealed 17 mutations; six of which explained the adaptive increases in mitotic fitness. In two populations evolved in high salt; two different mutations occurred in the proton efflux pump gene PMA1 and the global transcriptional repressor gene CYC8; the ENA genes encoding sodium efflux pumps were overexpressed once through expansion of this gene cluster and once because of mutation in the regulator CYC8. In the population from low glucose; one mutation occurred in MDS3; which modulates growth at high pH; and one in MKT1; a global regulator of mRNAs encoding mitochondrial proteins; the latter recapitulating a naturally occurring variant. A Dobzhansky-Muller (DM) incompatibility between the evolved alleles of PMA1 and MKT1 strongly depressed fitness in the low-glucose environment. This DM interaction is the first reported between experimentally evolved alleles of known genes and shows how reproductive isolation can arise rapidly when divergent selection is strong. Copyright (c) 2010 Elsevier Ltd. All rights reserved. | 2010 | 20637622,1 | https://sci-hub.tw/10.1016/j.cub.2010.06.022 | 21856932.1;25016004.1 | PMID 25016004 includes nucleotidic changes | ||||
10 | GP00001174 | Vkorc1 | Martin | VKORC1 | Q9BQB6 | Homo sapiens | 9606.ENSP00000378426 | Belongs to the VKOR family. | VKOR;MST134;MST576;VKCFD2;EDTP308;MSTP134;MSTP576;UNQ308/PRO351 | GO:0048038;GO:0047057 | GO:0016021;GO:0005783;GO:0005789 | GO:0017144;GO:0007596;GO:0060348;GO:0017187;GO:0042373 | ADN94694 | Physiology | Xenobiotic resistance (rodenticide; warfarin) | Mus musculus | Mus spretus (North Africa) and Mus musculus (Spain) | 10090 | Mus musculus | house mouse | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus | 0 | 10096 | Mus spretus | western wild mouse | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus | 0 | Data not curated | Intraspecific | Candidate Gene | Multiple coding changes | Coding | No | Nonsynonymous | SNP | Adaptive introgression of anticoagulant rodent poison resistance by hybridization between old world mice. | Polymorphisms in the vitamin K 2;3-epoxide reductase subcomponent 1 (vkorc1) of house mice (Mus musculus domesticus) can cause resistance to anticoagulant rodenticides such as warfarin [1-3]. Here we show that resistant house mice can also originate from selection on vkorc1 polymorphisms acquired from the Algerian mouse (M. spretus) through introgressive hybridization. We report on a polymorphic introgressed genomic region in European M. m. domesticus that stems from M. spretus; spans >10 Mb on chromosome 7; and includes the molecular target of anticoagulants vkorc1 [1-4]. We show that in the laboratory; the homozygous complete vkorc1 allele of M. spretus confers resistance when introgressed into M. m. domesticus. Consistent with selection on the introgressed allele after the introduction of rodenticides in the 1950s; we found signatures of selection in patterns of variation in M. m. domesticus. Furthermore; we detected adaptive protein evolution of vkorc1 in M. spretus (Ka/Ks = 1.54-1.93) resulting in radical amino acid substitutions that apparently cause anticoagulant tolerance in M. spretus as a pleiotropic effect. Thus; positive selection produced an adaptive; divergent; and pleiotropic vkorc1 allele in the donor species; M. spretus; which crossed a species barrier and produced an adaptive polymorphic trait in the recipient species; M. m. domesticus. Copyright © 2011 Elsevier Ltd. All rights reserved. | 2011 | 21782438,1 | https://sci-hub.tw/10.1016/j.cub.2011.06.043 | @& @Introgression @Pleiotropy | ||||||||||||||
11 | GP00001062 | SLC45A2=MATP | Martin | SLC45A2 | Q9UMX9 | Homo sapiens | 9606.ENSP00000296589 | Belongs to the glycoside-pentoside-hexuronide (GPH) cation symporter transporter (TC 2.A.2) family. | 1A1;AIM1;MATP;OCA4;SHEP5 | GO:0008506 | GO:0016021;GO:0033162 | GO:0042438;GO:0048066;GO:0007601;GO:0050896;GO:0015770 | XP_005506068 | Morphology | Coloration (feathers) | Columba livia - blue/black | Columba livia - recessive dilute (Dun) | 8932 | Columba livia | rock pigeon | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba | 0 | 8932 | Columba livia | rock pigeon | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba | 0 | Taxon A | Domesticated | Linkage Mapping | His341Arg | Coding | No | Nonsynonymous | Dupuis | CAY | CGY | 2 | transition | His | 341 | Arg | SNP | Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. | Understanding the molecular basis of phenotypic diversity is a critical challenge in biology; yet we know little about the mechanistic effects of different mutations and epistatic relationships among loci that contribute to complex traits. Pigmentation genetics offers a powerful model for identifying mutations underlying diversity and for determining how additional complexity emerges from interactions among loci. Centuries of artificial selection in domestic rock pigeons (Columba livia) have cultivated tremendous variation in plumage pigmentation through the combined effects of dozens of loci. The dominance and epistatic hierarchies of key loci governing this diversity are known through classical genetic studies; but their molecular identities and the mechanisms of their genetic interactions remain unknown. Here we identify protein-coding and cis-regulatory mutations in Tyrp1; Sox10; and Slc45a2 that underlie classical color phenotypes of pigeons and present a mechanistic explanation of their dominance and epistatic relationships. We also find unanticipated allelic heterogeneity at Tyrp1 and Sox10; indicating that color variants evolved repeatedly though mutations in the same genes. These results demonstrate how a spectrum of coding and regulatory mutations in a small number of genes can interact to generate substantial phenotypic diversity in a classic Darwinian model of evolution. Copyright © 2014 Elsevier Ltd. All rights reserved. | 2014 | 24508169,1 | https://sci-hub.tw/10.1016/j.cub.2014.01.020 | @Epistasis | ||||||
12 | GP00001148 | tyrosinase-related protein 1 (TYRP1) | Martin | Tyrp1 | P07147 | Mus musculus | 10090.ENSMUSP00000006151 | Belongs to the tyrosinase family. | b;isa;Oca3;TRP1;Tyrp;TRP-1;brown;Tyrp-1 | GO:0042803;GO:0046982;GO:0046872;GO:0004497 | GO:0016021;GO:0030669;GO:0010008;GO:0042470;GO:0033162 | GO:0032438;GO:0043473;GO:0048023;GO:0006583;GO:0030318;GO:0043438;GO:0006582 | NP_001302454 | Morphology | Coloration (coat) | Columba livia - blue/black | Columba livia - ash-red | 8932 | Columba livia | rock pigeon | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba | 0 | 8932 | Columba livia | rock pigeon | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba | 0 | Taxon A | Domesticated | Linkage Mapping | Ala23Pro | Coding | No | Nonsynonymous | Wimmer | GCN | CCN | 1 | transition | Ala | 23 | Pro | SNP | Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. | Understanding the molecular basis of phenotypic diversity is a critical challenge in biology; yet we know little about the mechanistic effects of different mutations and epistatic relationships among loci that contribute to complex traits. Pigmentation genetics offers a powerful model for identifying mutations underlying diversity and for determining how additional complexity emerges from interactions among loci. Centuries of artificial selection in domestic rock pigeons (Columba livia) have cultivated tremendous variation in plumage pigmentation through the combined effects of dozens of loci. The dominance and epistatic hierarchies of key loci governing this diversity are known through classical genetic studies; but their molecular identities and the mechanisms of their genetic interactions remain unknown. Here we identify protein-coding and cis-regulatory mutations in Tyrp1; Sox10; and Slc45a2 that underlie classical color phenotypes of pigeons and present a mechanistic explanation of their dominance and epistatic relationships. We also find unanticipated allelic heterogeneity at Tyrp1 and Sox10; indicating that color variants evolved repeatedly though mutations in the same genes. These results demonstrate how a spectrum of coding and regulatory mutations in a small number of genes can interact to generate substantial phenotypic diversity in a classic Darwinian model of evolution. Copyright © 2014 Elsevier Ltd. All rights reserved. | 2014 | 24508169,1 | https://sci-hub.tw/10.1016/j.cub.2014.01.020 | @Epistasis - the ash-red mutation occurred only once and spread species-wide through selective breeding (as the EphB2 mutation for head crest phenotypes) | ||||||
13 | GP00001149 | tyrosinase-related protein 1 (TYRP1) | Martin | Tyrp1 | P07147 | Mus musculus | 10090.ENSMUSP00000006151 | Belongs to the tyrosinase family. | b;isa;Oca3;TRP1;Tyrp;TRP-1;brown;Tyrp-1 | GO:0042803;GO:0046982;GO:0046872;GO:0004497 | GO:0016021;GO:0030669;GO:0010008;GO:0042470;GO:0033162 | GO:0032438;GO:0043473;GO:0048023;GO:0006583;GO:0030318;GO:0043438;GO:0006582 | NP_001302454 | Morphology | Coloration (coat) | Columba livia - blue/black | Columba livia - brown b1 allele | 8932 | Columba livia | rock pigeon | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba | 0 | 8932 | Columba livia | rock pigeon | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba | 0 | Taxon A | Domesticated | Linkage Mapping | Ala23Pro | Coding | No | Nonsynonymous | Wimmer | GCN | CCN | 1 | transition | Ala | 23 | Pro | SNP | Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. | Understanding the molecular basis of phenotypic diversity is a critical challenge in biology; yet we know little about the mechanistic effects of different mutations and epistatic relationships among loci that contribute to complex traits. Pigmentation genetics offers a powerful model for identifying mutations underlying diversity and for determining how additional complexity emerges from interactions among loci. Centuries of artificial selection in domestic rock pigeons (Columba livia) have cultivated tremendous variation in plumage pigmentation through the combined effects of dozens of loci. The dominance and epistatic hierarchies of key loci governing this diversity are known through classical genetic studies; but their molecular identities and the mechanisms of their genetic interactions remain unknown. Here we identify protein-coding and cis-regulatory mutations in Tyrp1; Sox10; and Slc45a2 that underlie classical color phenotypes of pigeons and present a mechanistic explanation of their dominance and epistatic relationships. We also find unanticipated allelic heterogeneity at Tyrp1 and Sox10; indicating that color variants evolved repeatedly though mutations in the same genes. These results demonstrate how a spectrum of coding and regulatory mutations in a small number of genes can interact to generate substantial phenotypic diversity in a classic Darwinian model of evolution. Copyright © 2014 Elsevier Ltd. All rights reserved. | 2014 | 24508169,1 | https://sci-hub.tw/10.1016/j.cub.2014.01.020 | @Epistasis Multiple alleles | ||||||
14 | GP00001150 | tyrosinase-related protein 1 (TYRP1) | Martin | Tyrp1 | P07147 | Mus musculus | 10090.ENSMUSP00000006151 | Belongs to the tyrosinase family. | b;isa;Oca3;TRP1;Tyrp;TRP-1;brown;Tyrp-1 | GO:0042803;GO:0046982;GO:0046872;GO:0004497 | GO:0016021;GO:0030669;GO:0010008;GO:0042470;GO:0033162 | GO:0032438;GO:0043473;GO:0048023;GO:0006583;GO:0030318;GO:0043438;GO:0006582 | NP_001302454 | Morphology | Coloration (coat) | Columba livia - blue/black | Columba livia - brown b2 allele | 8932 | Columba livia | rock pigeon | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba | 0 | 8932 | Columba livia | rock pigeon | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Columbiformes; Columbidae; Columba | 0 | Taxon A | Domesticated | Linkage Mapping | Arg72* | Coding | Yes | Nonsense | Wimmer | MGA | TGA | 1 | transition | Arg | 72 | STP | SNP | Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. | Understanding the molecular basis of phenotypic diversity is a critical challenge in biology; yet we know little about the mechanistic effects of different mutations and epistatic relationships among loci that contribute to complex traits. Pigmentation genetics offers a powerful model for identifying mutations underlying diversity and for determining how additional complexity emerges from interactions among loci. Centuries of artificial selection in domestic rock pigeons (Columba livia) have cultivated tremendous variation in plumage pigmentation through the combined effects of dozens of loci. The dominance and epistatic hierarchies of key loci governing this diversity are known through classical genetic studies; but their molecular identities and the mechanisms of their genetic interactions remain unknown. Here we identify protein-coding and cis-regulatory mutations in Tyrp1; Sox10; and Slc45a2 that underlie classical color phenotypes of pigeons and present a mechanistic explanation of their dominance and epistatic relationships. We also find unanticipated allelic heterogeneity at Tyrp1 and Sox10; indicating that color variants evolved repeatedly though mutations in the same genes. These results demonstrate how a spectrum of coding and regulatory mutations in a small number of genes can interact to generate substantial phenotypic diversity in a classic Darwinian model of evolution. Copyright © 2014 Elsevier Ltd. All rights reserved. | 2014 | 24508169,1 | https://sci-hub.tw/10.1016/j.cub.2014.01.020 | @Epistasis Multiple alleles | ||||||
15 | GP00000897 | plep-1 | Martin | KPt.1 | GO:0043531 | GO:0005623 | GO:0045454 | CTQ86544 | Behavior | Male-male copulatory behavior | Caenorhabditis elegans - CB4856 (no plug behavior) | Caenorhabditis elegans - CB4856 (no plug behavior) | 6239 | Caenorhabditis elegans | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis | 1 | 6239 | Caenorhabditis elegans | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis | 1 | Taxon A | Intraspecific | Linkage Mapping | V278D | Coding | No | Nonsynonymous | Rym | GTN | GAN | 2 | transvertion | valine | 287 | Asp | SNP | Natural Variation in plep-1 Causes Male-Male Copulatory Behavior in C. elegans. | In sexual species; gametes have to find and recognize one another. Signaling is thus central to sexual reproduction and involves a rapidly evolving interplay of shared and divergent interests [1-4]. Among Caenorhabditis nematodes; three species have evolved self-fertilization; changing the balance of intersexual relations [5]. Males in these androdioecious species are rare; and the evolutionary interests of hermaphrodites dominate. Signaling has shifted accordingly; with females losing behavioral responses to males [6; 7] and males losing competitive abilities [8; 9]. Males in these species also show variable same-sex and autocopulatory mating behaviors [6; 10]. These behaviors could have evolved by relaxed selection on male function; accumulation of sexually antagonistic alleles that benefit hermaphrodites and harm males [5; 11]; or neither of these; because androdioecy also reduces the ability of populations to respond to selection [12-14]. We have identified the genetic cause of a male-male mating behavior exhibited by geographically dispersed C. elegans isolates; wherein males mate with and deposit copulatory plugs on one another's excretory pores. We find a single locus of major effect that is explained by segregation of a loss-of-function mutation in an uncharacterized gene; plep-1; expressed in the excretory cell in both sexes. Males homozygous for the plep-1 mutation have excretory pores that are attractive or receptive to copulatory behavior of other males. Excretory pore plugs are injurious and hermaphrodite activity is compromised in plep-1 mutants; so the allele might be unconditionally deleterious; persisting in the population because the species' androdioecious mating system limits the reach of selection. Copyright © 2015 Elsevier Ltd. All rights reserved. | 2015 | 26455306,1 | https://sci-hub.tw/10.1016/j.cub.2015.09.019 | @SexualDimorphism | |||||||||||||
16 | GP00001602 | Chitin synthase 1 (CHS1) | Prigent | chs1 | H9U0G2 | Tetranychus urticae | chs1;107359084 | GO:0004100 | GO:0016021 | GO:0007166 | Physiology | Xenobiotic resistance (insecticide; etoxazole acaricide) | spider mite Tetranychus urticae susceptible | spider mite Tetranychus urticae strain HexR and strain005 hexythiazox clofentezine and etoxazole-resistant | 32264 | Tetranychus urticae | two-spotted spider mite | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Trombidiformes; Prostigmata; Eleutherengona; Raphignathae; Tetranychoidea; Tetranychidae; Tetranychus | 1 | 32264 | Tetranychus urticae | two-spotted spider mite | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Chelicerata; Arachnida; Acari; Acariformes; Trombidiformes; Prostigmata; Eleutherengona; Raphignathae; Tetranychoidea; Tetranychidae; Tetranychus | 1 | Unknown | Intraspecific | Linkage Mapping | A>T p.I1017F (I1056 in D. melanogaster) located in the C-terminal transmembrane domain | Coding | No | Nonsynonymous | Wimmer | TTA | TTT | 3 | transversion | Leu | 1017 | Phe | SNP | High resolution genetic mapping uncovers chitin synthase-1 as the target-site of the structurally diverse mite growth inhibitors clofentezine; hexythiazox and etoxazole in Tetranychus urticae. | The acaricides clofentezine; hexythiazox and etoxazole are commonly referred to as 'mite growth inhibitors'; and clofentezine and hexythiazox have been used successfully for the integrated control of plant mite pests for decades. Although they are still important today; their mode of action has remained elusive. Recently; a mutation in chitin synthase 1 (CHS1) was linked to etoxazole resistance. In this study; we identified and investigated a Tetranychus urticae strain (HexR) harboring recessive; monogenic resistance to each of hexythiazox; clofentezine; and etoxazole. To elucidate if there is a common genetic basis for the observed cross-resistance; we adapted a previously developed bulk segregant analysis method to map with high resolution a single; shared resistance locus for all three compounds. This finding indicates that the underlying molecular basis for resistance to all three compounds is identical. This locus is centered on the CHS1 gene; and as supported by additional genetic and biochemical studies; a non-synonymous variant (I1017F) in CHS1 associates with resistance to each of the tested acaricides in HexR. Our findings thus demonstrate a shared molecular mode of action for the chemically diverse mite growth inhibitors clofentezine; hexythiazox and etoxazole as inhibitors of an essential; non-catalytic activity of CHS1. Given the previously documented cross-resistance between clofentezine; hexythiazox and the benzyolphenylurea (BPU) compounds flufenoxuron and cycloxuron; CHS1 should be also considered as a potential target-site of insecticidal BPUs. Copyright © 2014 Elsevier Ltd. All rights reserved. | 2014 | 24859419,1 | https://sci-hub.tw/10.1016/j.ibmb.2014.05.004 | 22393009,1 | Observed pattern is indicative of recurrent mutation and selection in EtoxR and Strain005. Transgenic flies with the same mutation is highly resistant to etoxazole and all tested benzoylureas as well as buprofezin | ||||||||
17 | GP00000841 | para (kdr) | Martin | para | P35500 | Drosophila melanogaster | 7227.FBpp0303597 | Belongs to the sodium channel (TC 1.A.1.10) family. Para subfamily. | bas;bss;CG9907;Dmel\CG9907;DmNav;DmNav1;DmNa[[v]];DmNa[[V]];DmNa[[v]]1;l(1)14Da;l(1)ESHS48;lincRNA.S9469;Nav1;Ocd;olfD;par;sbl;sbl-1;Shu;Shudderer | GO:0005509;GO:0005244;GO:0005248;GO:0005272 | GO:0005887;GO:0001518 | GO:0019228;GO:0045433;GO:0001666;GO:0009612;GO:0034765;GO:0086010;GO:0035725;GO:0007638;GO:0060078 | Physiology | Xenobiotic resistance (insecticide) | Leptinotarsa decemlineata | Leptinotarsa decemlineata - resistant | 7539 | Leptinotarsa decemlineata | Colorado potato beetle | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Coleoptera; Polyphaga; Cucujiformia; Chrysomeloidea; Chrysomelidae; Chrysomelinae; Doryphorini; Leptinotarsa | 0 | 7539 | Leptinotarsa decemlineata | Colorado potato beetle | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Coleoptera; Polyphaga; Cucujiformia; Chrysomeloidea; Chrysomelidae; Chrysomelinae; Doryphorini; Leptinotarsa | 0 | Taxon A | Intraspecific | Candidate Gene | L1014H | Coding | No | Nonsynonymous | Wimmer | CTY | CAY | 2 | transversion | Leu | 1014 | His | SNP | Diversity and Convergence of Sodium Channel Mutations Involved in Resistance to Pyrethroids. | Pyrethroid insecticides target voltage-gated sodium channels; which are critical for electrical signaling in the nervous system. The intensive use of pyrethroids in controlling arthropod pests and disease vectors has led to many instances of pyrethroid resistance around the globe. In the past two decades; studies have identified a large number of sodium channel mutations that are associated with resistance to pyrethroids. The purpose of this review is to summarize both common and unique sodium channel mutations that have been identified in arthropod pests of importance to agriculture or human health. Identification of these mutations provides valuable molecular markers for resistance monitoring in the field and helped the discovery of the elusive pyrethroid receptor site(s) on the sodium channel. | 2013 | 24019556,1 | https://sci-hub.tw/10.1016/j.pestbp.2013.02.007 | ||||||||
18 | GP00001118 | teosinte glume architecture (tga1) | Martin | TGA1 | Q39237 | Arabidopsis thaliana | 3702.AT5G65210.1 | Belongs to the bZIP family. | MQN23.15;MQN23_15;TGACG sequence-specific binding protein 1;BZIP47;At5g65210 | GO:0003700;GO:0043565;GO:0044212 | GO:0005634 | GO:0006351;GO:0042742 | AEP96351 | Morphology | Cupule retraction | Zea mays ssp. parviglumis and mexicana (teosinthe) | Zea mays ssp. mays | 4577 | Zea mays | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea | 1 | 4577 | Zea mays | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea | 1 | Data not curated | Domesticated | Linkage Mapping | K6N; the lysine residue being conserved in rice and wheat | Coding | No | Nonsynonymous | Wimmer | AAR | AAY | 3 | transversion | Lys | 6 | Asn | SNP | The origin of the naked grains of maize. | The most critical step in maize (Zea mays ssp. mays) domestication was the liberation of the kernel from the hardened; protective casing that envelops the kernel in the maize progenitor; teosinte. This evolutionary step exposed the kernel on the surface of the ear; such that it could readily be used by humans as a food source. Here we show that this key event in maize domestication is controlled by a single gene (teosinte glume architecture or tga1); belonging to the SBP-domain family of transcriptional regulators. The factor controlling the phenotypic difference between maize and teosinte maps to a 1-kilobase region; within which maize and teosinte show only seven fixed differences in their DNA sequences. One of these differences encodes a non-conservative amino acid substitution and may affect protein function; and the other six differences potentially affect gene regulation. Molecular evolution analyses show that this region was the target of selection during maize domestication. Our results demonstrate that modest genetic changes in single genes can induce dramatic changes in phenotype during domestication and evolution. | 2005 | 16079849,1 | https://sci-hub.tw/10.1038/nature03863 | |||||||||
19 | GP00001047 | SHELL | Martin | AGL11 | Q38836 | Arabidopsis thaliana | 3702.AT4G09960.3 | AGAMOUS-like 11;AGL11;SEEDSTICK;T5L19.90;T5L19_90;STK;At4g09960 | GO:0046983;GO:0003700;GO:0000977 | GO:0005634 | GO:0007275;GO:0045944;GO:0006351 | Morphology | Fruit shell thickness | Elaeis guineensis; thick shelled | Elaeis guineensis; thin shelled (Nigeria) | 51953 | Elaeis guineensis | African oil palm | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Arecales; Arecaceae; Arecoideae; Cocoseae; Elaeidinae; Elaeis | 0 | 51953 | Elaeis guineensis | African oil palm | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Arecales; Arecaceae; Arecoideae; Cocoseae; Elaeidinae; Elaeis | 1 | Data not curated | Domesticated | Linkage Mapping | 1a.a substitution in DNA binding domain | Coding | No | Nonsynonymous | Wimmer | AAR | AAY | 3 | transversion | Lys | 128 | Asn | SNP | The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK. | A key event in the domestication and breeding of the oil palm Elaeis guineensis was loss of the thick coconut-like shell surrounding the kernel. Modern E. guineensis has three fruit forms; dura (thick-shelled); pisifera (shell-less) and tenera (thin-shelled); a hybrid between dura and pisifera. The pisifera palm is usually female-sterile. The tenera palm yields far more oil than dura; and is the basis for commercial palm oil production in all of southeast Asia. Here we describe the mapping and identification of the SHELL gene responsible for the different fruit forms. Using homozygosity mapping by sequencing; we found two independent mutations in the DNA-binding domain of a homologue of the MADS-box gene SEEDSTICK (STK; also known as AGAMOUS-LIKE 11); which controls ovule identity and seed development in Arabidopsis. The SHELL gene is responsible for the tenera phenotype in both cultivated and wild palms from sub-Saharan Africa; and our findings provide a genetic explanation for the single gene hybrid vigour (or heterosis) attributed to SHELL; via heterodimerization. This gene mutation explains the single most important economic trait in oil palm; and has implications for the competing interests of global edible oil production; biofuels and rainforest conservation. | 2013 | 23883930,1 | https://sci-hub.tw/10.1038/nature12356 | |||||||||
20 | GP00001048 | SHELL | Martin | AGL11 | Q38836 | Arabidopsis thaliana | 3702.AT4G09960.3 | AGAMOUS-like 11;AGL11;SEEDSTICK;T5L19.90;T5L19_90;STK;At4g09960 | GO:0046983;GO:0003700;GO:0000977 | GO:0005634 | GO:0007275;GO:0045944;GO:0006351 | Morphology | Fruit shell thickness | Elaeis guineensis; thick shelled | Elaeis guineensis; thin shelled (Congo) | 51953 | Elaeis guineensis | African oil palm | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Arecales; Arecaceae; Arecoideae; Cocoseae; Elaeidinae; Elaeis | 0 | 51953 | Elaeis guineensis | African oil palm | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Arecales; Arecaceae; Arecoideae; Cocoseae; Elaeidinae; Elaeis | 1 | Data not curated | Domesticated | Candidate Gene | 1a.a substitution in DNA binding domain | Coding | No | Nonsynonymous | Wimmer | CTN | CCN | 2 | transition | Leu | 128 | Pro | SNP | The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK. | A key event in the domestication and breeding of the oil palm Elaeis guineensis was loss of the thick coconut-like shell surrounding the kernel. Modern E. guineensis has three fruit forms; dura (thick-shelled); pisifera (shell-less) and tenera (thin-shelled); a hybrid between dura and pisifera. The pisifera palm is usually female-sterile. The tenera palm yields far more oil than dura; and is the basis for commercial palm oil production in all of southeast Asia. Here we describe the mapping and identification of the SHELL gene responsible for the different fruit forms. Using homozygosity mapping by sequencing; we found two independent mutations in the DNA-binding domain of a homologue of the MADS-box gene SEEDSTICK (STK; also known as AGAMOUS-LIKE 11); which controls ovule identity and seed development in Arabidopsis. The SHELL gene is responsible for the tenera phenotype in both cultivated and wild palms from sub-Saharan Africa; and our findings provide a genetic explanation for the single gene hybrid vigour (or heterosis) attributed to SHELL; via heterodimerization. This gene mutation explains the single most important economic trait in oil palm; and has implications for the competing interests of global edible oil production; biofuels and rainforest conservation. | 2013 | 23883930,1 | https://sci-hub.tw/10.1038/nature12356 | |||||||||
21 | GP00000099 | APOE (apolipoprotein E) | Martin | APOE | P02649 | Homo sapiens | 9606.ENSP00000252486 | Belongs to the apolipoprotein A1/A4/E family. | AD2;LPG;APO-E;ApoE4;LDLCQ5 | GO:0042802;GO:0046983;GO:0042803;GO:0001540;GO:0016209;GO:0015485;GO:0017127;GO:0008201;GO:0008289;GO:0005319;GO:0071813;GO:0050750;GO:0046911;GO:0060228;GO:0005543;GO:0044877;GO:0005198;GO:0048156;GO:0070326 | GO:0005886;GO:0005737;GO:0016020;GO:0070062;GO:0005634;GO:0005576;GO:0005794;GO:0043083;GO:0031012;GO:0062023;GO:0005615;GO:0072562;GO:0042627;GO:0030669;GO:0030425;GO:0034365;GO:0005769;GO:0071682;GO:0005783;GO:0005788;GO:1903561;GO:0034364;GO:0034363;GO:1990777;GO:0034362;GO:0043025;GO:0034361;GO:0098978 | GO:0033344;GO:0097113;GO:0042982;GO:0048844;GO:0006874;GO:0044267;GO:0019934;GO:0006707;GO:0042632;GO:0008203;GO:0034378;GO:0034382;GO:0034371;GO:0007010;GO:0055089;GO:0007186;GO:0034380;GO:0034384;GO:0034375;GO:0046907;GO:0010877;GO:0042158;GO:0042159;GO:0035641;GO:0015909;GO:0007616;GO:0034374;GO:0051651;GO:1902430;GO:0030195;GO:0043537;GO:0090090;GO:0032269;GO:0045541;GO:0090370;GO:0061000;GO:1902951;GO:0001937;GO:0010629;GO:0050728;GO:0051055;GO:1903001;GO:1900272;GO:0043407;GO:0043524;GO:1901215;GO:0010977;GO:1902999;GO:0010544;GO:1901627;GO:1901630;GO:0090209;GO:0031102;GO:0007263;GO:0097114;GO:0033700;GO:0044794;GO:1905908;GO:1902004;GO:0010875;GO:0010873;GO:0060999;GO:1902952;GO:0045807;GO:1905855;GO:1905860;GO:0046889;GO:1903002;GO:0032805;GO:0051044;GO:1902998;GO:1901216;GO:0010976;GO:0051000;GO:1902995;GO:1901628;GO:1901631;GO:0043687;GO:0017038;GO:0006898;GO:1905906;GO:1900221;GO:0030516;GO:2000822;GO:0032489;GO:1905890;GO:0090181;GO:1901214;GO:0048168;GO:0032462;GO:0051246;GO:1902947;GO:0006357;GO:0061771;GO:0002021;GO:0000302;GO:0001523;GO:0043691;GO:0007271;GO:0019433;GO:0070328;GO:0006641;GO:0042311;GO:0034447;GO:0034372;GO:0019068 | NP_001289617 | Physiology | Aging | Homo sapiens | Homo sapiens | 9606 | Homo sapiens | human | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo | 0 | 9606 | Homo sapiens | human | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo | 0 | Data not curated | Intraspecific | Association Mapping | Cys112Arg | Coding | No | Nonsynonymous | Dupuis | TGY | CGY | transition | Cys | 112 | Arg | SNP | Variants near CHRNA3/5 and APOE have age- and sex-related effects on human lifespan. | Lifespan is a trait of enormous personal interest. Research into the biological basis of human lifespan; however; is hampered by the long time to death. Using a novel approach of regressing (272;081) parental lifespans beyond age 40 years on participant genotype in a new large data set (UK Biobank); we here show that common variants near the apolipoprotein E and nicotinic acetylcholine receptor subunit alpha 5 genes are associated with lifespan. The effects are strongly sex and age dependent; with APOE ɛ4 differentially influencing maternal lifespan (P=4.2 × 10(-15); effect -1.24 years of maternal life per imputed risk allele in parent; sex difference; P=0.011); and a locus near CHRNA3/5 differentially affecting paternal lifespan (P=4.8 × 10(-11); effect -0.86 years per allele; sex difference P=0.075). Rare homozygous carriers of the risk alleles at both loci are predicted to have 3.3-3.7 years shorter lives. | 2016 | 27029810,1 | https://sci-hub.tw/10.1038/ncomms11174 | LD with SNP previously associated to other age-related conditions and traits including Alzheimer | |||||||
22 | GP00001346 | tyrosinase (TYR) | Prigent | Tyr | P11344 | Mus musculus | 10090.ENSMUSP00000004770 | Belongs to the tyrosinase family. | c;Oca1;skc35;albino | GO:0042803;GO:0046982;GO:0005507;GO:0004503 | GO:0016021;GO:0005737;GO:0005829;GO:0005634;GO:0043231;GO:0048471;GO:0042470;GO:0033162 | GO:0042438;GO:0043473;GO:0008283;GO:0033280;GO:0051591;GO:0009411;GO:0048538 | Morphology | Coloration (skin) | Lion-Wild type | Lion-white coat | 9689 | Panthera leo | lion | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae; Panthera | 0 | 9689 | Panthera leo | lion | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae; Panthera | 0 | Taxon A | Intraspecific | Association Mapping | c.260G>A p.Arg87Gln | Coding | No | Nonsynonymous | Wimmer | CGN | CAR | 2 | transition | Arg | 87 | Gln | SNP | The tiger genome and comparative analysis with lion and snow leopard genomes. | Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger; African lion; white African lion and snow leopard. Through comparative genetic analyses of these genomes; we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39); which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close; but distinct; species. | 2013 | 24045858,1 | https://sci-hub.tw/10.1038/ncomms3433 | ||||||||
23 | GP00001357 | EPAS1 | Prigent | EPAS1 | Q99814 | Homo sapiens | 9606.ENSP00000263734 | HLF;MOP2;ECYT4;HIF2A;PASD2;bHLHe73;BHLHE73 | GO:0046982;GO:0043565;GO:0008134;GO:0003677;GO:0000981;GO:0001077;GO:0035035 | GO:0005829;GO:0005654;GO:0005634;GO:0005667;GO:0016607 | GO:0045944;GO:0043687;GO:0007165;GO:0030324;GO:0071456;GO:0061418;GO:0001666;GO:0001525;GO:0001974;GO:0048469;GO:0001892;GO:0030218;GO:0055072;GO:0007005;GO:0048625;GO:0042415;GO:0120162;GO:0002027;GO:0043619;GO:0043129;GO:0006366;GO:0007601 | Physiology | Hypoxia response | Panthera spp + Neofilis clouded leopard | snow leopard | 9688 | Panthera | genus | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae | 0 | 29064 | Panthera uncia | snow leopard | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae; Panthera | 0 | Taxon A | Interspecific | Association Mapping | Ile663 and Arg794 | Coding | No | Nonsynonymous | SNP | The tiger genome and comparative analysis with lion and snow leopard genomes. | Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger; African lion; white African lion and snow leopard. Through comparative genetic analyses of these genomes; we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39); which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close; but distinct; species. | 2013 | 24045858,1 | https://sci-hub.tw/10.1038/ncomms3433 | putative candidate | |||||||||||||||||
24 | GP00001358 | EGLN1 | Prigent | EGLN1 | Q9GZT9 | Homo sapiens | 9606.ENSP00000355601 | HPH2;PHD2;SM20;ECYT3;HALAH;HPH-2;HIFPH2;ZMYND6;C1orf12;HIF-PH2;PNAS-118;PNAS-137 | GO:0016706;GO:0019899;GO:0008198;GO:0031418;GO:0031545;GO:0031543 | GO:0005737;GO:0005829;GO:0005634;GO:0014069;GO:0098978 | GO:0045944;GO:1901214;GO:0006879;GO:0055008;GO:0060347;GO:0060711;GO:0051344;GO:0043433;GO:0032364;GO:0018401;GO:0045765;GO:0061418;GO:0001666;GO:0071731;GO:0060412;GO:0099175;GO:0099576 | Physiology | Hypoxia response | Panthera spp + Neofilis clouded leopard | snow leopard | 9688 | Panthera | genus | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae | 0 | 29064 | Panthera uncia | snow leopard | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Carnivora; Feliformia; Felidae; Pantherinae; Panthera | 0 | Taxon A | Interspecific | Association Mapping | p.Met39Lys | Coding | No | Nonsynonymous | Dupuis | ATG | AAG | transversion | Met | Lys | SNP | The tiger genome and comparative analysis with lion and snow leopard genomes. | Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger; African lion; white African lion and snow leopard. Through comparative genetic analyses of these genomes; we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39); which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close; but distinct; species. | 2013 | 24045858,1 | https://sci-hub.tw/10.1038/ncomms3433 | putative candidate | |||||||||||
25 | GP00001421 | Aquaporin | Prigent | AQP1 | P29972 | Homo sapiens | 9606.ENSP00000311165 | Belongs to the MIP/aquaporin (TC 1.A.8) family. | CO;CHIP28;AQP-CHIP | GO:0042802;GO:0015079;GO:0015250;GO:0008519;GO:0022857;GO:0035379;GO:0015168;GO:0005223;GO:0030184;GO:0005267;GO:0005372 | GO:0005886;GO:0016324;GO:0005737;GO:0070062;GO:0005887;GO:0005634;GO:0016323;GO:0031965;GO:0045177;GO:0005903;GO:0042383;GO:0031526;GO:0009925;GO:0020003 | GO:0043066;GO:0019934;GO:0006813;GO:0071260;GO:0042493;GO:0071280;GO:0003091;GO:0071456;GO:0006833;GO:0071300;GO:0042476;GO:0070301;GO:0071732;GO:0015701;GO:0030185;GO:0045766;GO:0043154;GO:0048146;GO:0071320;GO:0015696;GO:0071549;GO:0034644;GO:0030157;GO:0035378;GO:0015670;GO:0006884;GO:0019725;GO:0071474;GO:0071241;GO:0071288;GO:0071472;GO:0033326;GO:0030950;GO:0015793;GO:0021670;GO:0085018;GO:0050891;GO:0046878;GO:0003097;GO:0035377 | AB281620 | Physiology | Water transport (selective accumulation of water or glycerol) | BgAqp Aquaporin water selective channel | PvAqp2 aquaglyceroporin glycerol transporter | 6973 | Blattella germanica | German cockroach | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Polyneoptera; Dictyoptera; Blattodea; Blaberoidea; Ectobiidae; Blattellinae; Blattella | 0 | 319348 | Polypedilum vanderplanki | sleeping chironomid | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Nematocera; Culicomorpha; Chironomoidea; Chironomidae; Chironominae; Chironomini; Polypedilum; Polypedilum | 0 | Unknown | Interspecific | Candidate Gene | p.His174Ala | Coding | No | Nonsynonymous | Dupuis | CAY | GCN | ??? | His | Ala | SNP | Insect glycerol transporters evolved by functional co-option and gene replacement. | Transmembrane glycerol transport is typically facilitated by aquaglyceroporins in Prokaryota and Eukaryota. In holometabolan insects however; aquaglyceroporins are absent; yet several species possess polyol permeable aquaporins. It thus remains unknown how glycerol transport evolved in the Holometabola. By combining phylogenetic and functional studies; here we show that a more efficient form of glycerol transporter related to the water-selective channel AQP4 specifically evolved and multiplied in the insect lineage; resulting in the replacement of the ancestral branch of aquaglyceroporins in holometabolan insects. To recapitulate this evolutionary process; we generate specific mutants in distantly related insect aquaporins and human AQP4 and show that a single mutation in the selectivity filter converted a water-selective channel into a glycerol transporter at the root of the crown clade of hexapod insects. Integration of phanerozoic climate models suggests that these events were associated with the emergence of complete metamorphosis and the unparalleled radiation of insects. | 2015 | 26183829,1 | https://sci-hub.tw/10.1038/ncomms8814 | ancestry is difficult to understand because phylogenetic tree seems to show the opposite of the article's conclusion | ||||||||
26 | GP00001023 | SBNO1 | Martin | SBNO1 | A3KN83 | Homo sapiens | 9606.ENSP00000387361 | Belongs to the SBNO family. | Sno;MOP3 | GO:0046872;GO:0009055;GO:0051537;GO:0015035 | GO:0005737;GO:0005634 | GO:0006355 | BC133704 | Morphology | Head size | Homo sapiens - European ancestry | Homo sapiens - European ancestry | 9606 | Homo sapiens | human | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo | 0 | 9606 | Homo sapiens | human | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo | 0 | Data not curated | Intraspecific | Association Mapping | Ser729Asn | Coding | No | Nonsynonymous | Pinton | AGY | AAY | 2 | transition | Ser | 729 | Asn | SNP | Common variants at 12q15 and 12q24 are associated with infant head circumference. | To identify genetic variants associated with head circumference in infancy; we performed a meta-analysis of seven genome-wide association studies (GWAS) (N = 10;768 individuals of European ancestry enrolled in pregnancy and/or birth cohorts) and followed up three lead signals in six replication studies (combined N = 19;089). rs7980687 on chromosome 12q24 (P = 8.1 × 10(-9)) and rs1042725 on chromosome 12q15 (P = 2.8 × 10(-10)) were robustly associated with head circumference in infancy. Although these loci have previously been associated with adult height; their effects on infant head circumference were largely independent of height (P = 3.8 × 10(-7) for rs7980687 and P = 1.3 × 10(-7) for rs1042725 after adjustment for infant height). A third signal; rs11655470 on chromosome 17q21; showed suggestive evidence of association with head circumference (P = 3.9 × 10(-6)). SNPs correlated to the 17q21 signal have shown genome-wide association with adult intracranial volume; Parkinson's disease and other neurodegenerative diseases; indicating that a common genetic variant in this region might link early brain growth with neurological disease in later life. | 2012 | 22504419,1 | https://sci-hub.tw/10.1038/ng.2238 | |||||||
27 | GP00001042 | Shattering1 - Sh1 | Martin | YAB2 | Q10FZ7 | Oryza sativa subsp. japonica | 39947.LOC_Os03g44710.1 | Belongs to the YABBY family. | FIL2;YAB2;YABBY;OsYAB2;OsYABBY2;Os03g0650000;LOC_Os03g44710 | GO:0046872 | GO:0005634 | GO:0007275 | Physiology | Seed shattering | Sorghum virgatum - shattering | Sorghum bicolor; SC265-like non-shattering | 1428165 | Sorghum virgatum | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum | 0 | 4113 | Solanum tuberosum | potato | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum | 1 | Data not curated | Domesticated | Linkage Mapping | GT-to-GG splice-site variant | Coding | No | SNP | Parallel domestication of the Shattering1 genes in cereals. | A key step during crop domestication is the loss of seed shattering. Here; we show that seed shattering in sorghum is controlled by a single gene; Shattering1 (Sh1); which encodes a YABBY transcription factor. Domesticated sorghums harbor three different mutations at the Sh1 locus. Variants at regulatory sites in the promoter and intronic regions lead to a low level of expression; a 2.2-kb deletion causes a truncated transcript that lacks exons 2 and 3; and a GT-to-GG splice-site variant in the intron 4 results in removal of the exon 4. The distributions of these non-shattering haplotypes among sorghum landraces suggest three independent origins. The function of the rice ortholog (OsSh1) was subsequently validated with a shattering-resistant mutant; and two maize orthologs (ZmSh1-1 and ZmSh1-5.1+ZmSh1-5.2) were verified with a large mapping population. Our results indicate that Sh1 genes for seed shattering were under parallel selection during sorghum; rice and maize domestication. | 2012 | 22581231,1 | https://sci-hub.tw/10.1038/ng.2281 | @Splicing Verify Orthology | |||||||||||||||||
28 | GP00000679 | MTH1 | Martin | CUP1-1 | P0CX80 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) | 4932.YHR055C | Belongs to the metallothionein superfamily. Type 12 family. | CUP1;MTH1;YHR053C | GO:0016209;GO:0005507;GO:0046870;GO:0004784 | GO:0005829 | GO:0071585;GO:0010273;GO:0046688;GO:0019430 | K02204 | Physiology | Low-glucose adaptation (experimental evolution) | Saccharomyces cerevisiae | Saccharomyces cerevisiae | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | 4932 | Saccharomyces cerevisiae | baker's yeast | species | cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces | 0 | Data not curated | Experimental Evolution | Association Mapping | 1bp substitution resulting in premature stop codon | Coding | Yes | Nonsense | Wimmer | TCR | TAR | 2 | transversion | Ser | 441 | STP | SNP | Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. | The classical model of adaptive evolution in an asexual population postulates that each adaptive clone is derived from the one preceding it. However; experimental evidence has suggested more complex dynamics; with theory predicting the fixation probability of a beneficial mutation as dependent on the mutation rate; population size and the mutation's selection coefficient. Clonal interference has been demonstrated in viruses and bacteria but not in a eukaryote; and a detailed molecular characterization is lacking. Here we use three different fluorescent markers to visualize the dynamics of asexually evolving yeast populations. For each adaptive clone within one of our evolving populations; we identified the underlying mutations; monitored their population frequencies and used microarrays to characterize changes in the transcriptome. These results represent the most detailed molecular characterization of experimental evolution to date and provide direct experimental evidence supporting both the clonal interference and the multiple mutation models. | 2008 | 19029899,1 | https://sci-hub.tw/10.1038/ng.280 | 21552329,1 | ||||||
29 | GP00001510 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 7.70 hours from Vietnam (5 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | D353Y affecting the BTB/POZ domain | Coding | No | Nonsynonymous | Pinton | GAY | TAY | 1 | transversion | Asp | 353 | Tyr | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
30 | GP00001511 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.34 hours from Myanmar (5 samples) and Thailand (6 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | P441L affecting the BTB/POZ domain | Coding | No | Nonsynonymous | Barthome | CCN | CTN | 2 | transition | Pro | 441 | Leu | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
31 | GP00001512 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.02 hours from Myanmar (3 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | F446I affecting the encoded propeller and BTB/POZ domains | Coding | No | Nonsynonymous | Barthome | TTY | ATY | 1 | transversion | Phe | 446 | Ile | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
32 | GP00001513 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.55 hours from Myanmar (2 samples) Thailand (3 samples) and Cambodia (2 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | G449A affecting the encoded propeller and BTB/POZ domains | Coding | No | Nonsynonymous | Barthome | GGN | GCN | 3 | transversion | Gly | 449 | Ala | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
33 | GP00001514 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 8.38 hours from Thailand (6 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | N458Y affecting the encoded propeller and BTB/POZ domains | Coding | No | Nonsynonymous | Barthome | AAY | TAY | 1 | transversion | Asn | 458 | Tyr | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
34 | GP00001515 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.13 hours from Thailand (1 sample) and Cambodia (2 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | A481V affecting the encoded propeller domain | Coding | No | Nonsynonymous | Barthome | GCN | GTN | 2 | transition | Ala | 481 | Val | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
35 | GP00001516 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.76 hours from Cambodia (45 samples) and Vietnam (4 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | p.Tyr493His affecting the encoded propeller domain | Coding | No | Nonsynonymous | Barthome | TAY | CAY | 1 | transition | Tyr | 493 | His | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
36 | GP00001517 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 4.68 hours from Thailand (1 sample) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | N525D affecting the encoded propeller domain | Coding | No | Nonsynonymous | Barthome | AAY | GAY | 1 | transition | Asn | 525 | Asp | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
37 | GP00001518 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.02 hours from Thailand (1 sample) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | N537I affecting the encoded propeller domain | Coding | No | Nonsynonymous | Barthome | AAY | ATH | 2 | transversion | Asn | 537 | Ile | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
38 | GP00001519 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.70 hours from Thailand (13 samples) Laos (2 samples) Cambodia (25 samples) and Vietnam (4 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | p.Arg539Thr affecting the encoded propeller domain | Coding | No | Nonsynonymous | Barthome | AGN | ACN | 2 | transversion | Arg | 539 | Thr | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
39 | GP00001520 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 7.07 hours from Cambodia (2 samples) and Vietnam (22 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | p.Ile543Thr affecting the encoded propeller domain | Coding | No | Nonsynonymous | Barthome | ATH | ACH | 2 | transition | Ile | 543 | Thr | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
40 | GP00001521 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.03 hours from Thailand (2 samples) and Vietnam (9 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | p.Pro553Leu affecting the encoded propeller domain | Coding | No | Nonsynonymous | Cortier | CCY | nd | CTY | 2 | transition | Pro | 553 | Leu | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | ||||||||
41 | GP00001522 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.93 hours from Myanmar (2 samples) and Thailande (5 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | R561H affecting the encoded propeller domain | Coding | No | Nonsynonymous | Cortier | CGY | nd | CAY | 2 | transition | Arg | 561 | Hist | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | ||||||||
42 | GP00001523 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.67 hours from Vietnam (5 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | V568G affecting the encoded propeller domain | Coding | No | Nonsynonymous | Cortier | GTY | nd | GGY | 2 | transversion | Val | 568 | Gly | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | ||||||||
43 | GP00001524 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.85 hours from Myanmar (6 samples) and Thailand (1 sample) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | P574L affecting the encoded propeller domain | Coding | No | Nonsynonymous | Cortier | CTY | nd | CCY | 2 | tranition | Pro | 574 | Leu | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | ||||||||
44 | GP00001525 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.72 hours from Myanmar (11 samples) Thailand (21 samples) Cambodia (241 samples) and Vietnam (9 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | p.Cys580Tyr affecting the encoded propeller domain | Coding | No | Nonsynonymous | Cortier | TGY | nd | TAY | 2 | transversion | Cys | 580 | Tyr | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | k13-C580Y the most widespread resistance allele has originated independently in multiple locations | |||||||
45 | GP00001526 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.41 hours from Cambodia (2 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | D584V affecting the encoded propeller domain | Coding | No | Nonsynonymous | Cortier | GAY | nd | GTY | 2 | tranversion | Asp | 584 | Val | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | ||||||||
46 | GP00001527 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 6.32 hours from Myanmar (2 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | F673I affecting the encoded propeller domain | Coding | No | Nonsynonymous | Cortier | TTY | nd | ATY | 1 | transversion | Phe | 678 | Ile | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | ||||||||
47 | GP00001528 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.60 hours from Myanmar (2 samples) and Thailand (11 samples) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | A675V affecting the encoded propeller domain | Coding | No | Nonsynonymous | Cortier | GCY | nd | GTY | 2 | transition | Ala | 675 | Val | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | ||||||||
48 | GP00001529 | kelch 13 | Prigent | PF3D7_1343700 | Q8IDQ2 | Plasmodium falciparum (isolate 3D7) | PF3D7_1343700 | GO:0003677;GO:0003682 | GO:0031463 | GO:0016567;GO:0042493;GO:0051260 | KM187892.1 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with mean parasite clearance half-life of 5.80 hours from Cambodia (1 sample) | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | H719N affecting the encoded propeller domain | Coding | No | Nonsynonymous | Cortier | CAY | nd | AAY | 1 | transversion | His | 719 | Asn | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | ||||||||
49 | GP00001530 | ferredoxin | Prigent | PF3D7_1318100 | Q8IED5 | Plasmodium falciparum (isolate 3D7) | Belongs to the 2Fe2S plant-type ferredoxin family. | PF3D7_1318100 | GO:0046872;GO:0009055;GO:0051537 | GO:0020011 | GO:0055114 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with parasite clearance half-life estimated prolongation of 0.53 h | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | p.Asp193Tyr | Coding | No | Nonsynonymous | Mous | GAY | TAY | 1 | transversion | Asp | 193 | Tyr | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
50 | GP00001531 | apicoplast ribosomal protein S10 | Prigent | PF3D7_1460900.1 | Q8IKM3 | Plasmodium falciparum (isolate 3D7) | PF3D7_1460900.1 | GO:0003735 | GO:0005739;GO:0015935 | GO:0006412 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with parasite clearance half-life estimated prolongation of 0.58 h | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | p.Val127Met | Coding | No | Nonsynonymous | Mous | GTG | ATG | 1 | transition | Val | 127 | Met | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | ||||||||||
51 | GP00001532 | multidrug resistance protein 2 | Prigent | PF3D7_1447900 | Q8IKZ6 | Plasmodium falciparum (isolate 3D7) | PF3D7_1447900 | GO:0005524;GO:0042626;GO:0008559;GO:0046872;GO:0046873 | GO:0016021;GO:0005773 | GO:0006855 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with parasite clearance half-life estimated prolongation of 0.54 h | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | p.Thr484Ile | Coding | No | Nonsynonymous | Mous | ACH | ATH | 2 | transition | Thr | 484 | Ile | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | ||||||||||
52 | GP00001533 | chloroquine resistance transporter | Prigent | CRT | Q9N623 | Plasmodium falciparum | Belongs to the CRT-like transporter family. | PF3D7_1447900 | GO:0015238 | GO:0016021;GO:0005774 | GO:0006855 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with parasite clearance half-life estimated prolongation of 0.47 h | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | p.Ile356Thr | Coding | No | Nonsynonymous | Mous | ATH | ACH | 2 | transition | Ile | 356 | Thr | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
53 | GP00001534 | protein phosphatase | Prigent | PF3D7_1012700 | Q8IJR8 | Plasmodium falciparum (isolate 3D7) | PF3D7_1012700 | GO:0008420 | GO:0016591 | GO:0070940 | Physiology | Xenobiotic resistance (artemisinin) | Artemisinin-sensitive Plasmodium with mean parasite clearance half-life of 2.6 hours | Artemisinin-resistant Plasmodium with parasite clearance half-life estimated prolongation of 0.52 h | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | 5833 | Plasmodium falciparum | malaria parasite P. falciparum | species | cellular organisms; Eukaryota; Alveolata; Apicomplexa; Aconoidasida; Haemosporida; Plasmodiidae; Plasmodium; Plasmodium (Laverania) | 0 | Taxon A | Intraspecific | Association Mapping | p.Val1157Leu | Coding | No | Nonsynonymous | Mous | GTN | 490720 | YTR, CTN | 1 | transversion | Val | 1157 | Leu | SNP | Genetic architecture of artemisinin-resistant Plasmodium falciparum. | We report a large multicenter genome-wide association study of Plasmodium falciparum resistance to artemisinin; the frontline antimalarial drug. Across 15 locations in Southeast Asia; we identified at least 20 mutations in kelch13 (PF3D7_1343700) affecting the encoded propeller and BTB/POZ domains; which were associated with a slow parasite clearance rate after treatment with artemisinin derivatives. Nonsynonymous polymorphisms in fd (ferredoxin); arps10 (apicoplast ribosomal protein S10); mdr2 (multidrug resistance protein 2) and crt (chloroquine resistance transporter) also showed strong associations with artemisinin resistance. Analysis of the fine structure of the parasite population showed that the fd; arps10; mdr2 and crt polymorphisms are markers of a genetic background on which kelch13 mutations are particularly likely to arise and that they correlate with the contemporary geographical boundaries and population frequencies of artemisinin resistance. These findings indicate that the risk of new resistance-causing mutations emerging is determined by specific predisposing genetic factors in the underlying parasite population. | 2015 | 25599401,1 | https://sci-hub.tw/10.1038/ng.3189 | |||||||||
54 | GP00001444 | CREBRF | Prigent | CREBRF | Q8IUR6 | Homo sapiens | 9606.ENSP00000296953 | Belongs to the bZIP family. CREBRF subfamily. | LRF;C5orf41 | GO:0000977;GO:0001228;GO:0000981 | GO:0005737;GO:0005654;GO:0005634;GO:0016604 | GO:0045944;GO:0000122;GO:0042711;GO:0030968;GO:0034976;GO:0045732;GO:1900102;GO:1900170;GO:0032388;GO:1902213;GO:0051222 | NM_153607 | Morphology | Body size (obesity) | human Samoan not associated with higher BMI | human Samoan associated with higher BMI | 9606 | Homo sapiens | human | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo | 0 | 9606 | Homo sapiens | human | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo | 0 | Taxon A | Intraspecific | Association Mapping | c.1370G>A p.Arg457Gln | Coding | No | Nonsynonymous | Mous | SNP | A thrifty variant in CREBRF strongly influences body mass index in Samoans. | Samoans are a unique founder population with a high prevalence of obesity; making them well suited for identifying new genetic contributors to obesity. We conducted a genome-wide association study (GWAS) in 3;072 Samoans; discovered a variant; rs12513649; strongly associated with body mass index (BMI) (P = 5.3 × 10(-14)); and replicated the association in 2;102 additional Samoans (P = 1.2 × 10(-9)). Targeted sequencing identified a strongly associated missense variant; rs373863828 (p.Arg457Gln); in CREBRF (meta P = 1.4 × 10(-20)). Although this variant is extremely rare in other populations; it is common in Samoans (frequency of 0.259); with an effect size much larger than that of any other known common BMI risk variant (1.36-1.45 kg/m(2) per copy of the risk-associated allele). In comparison to wild-type CREBRF; the Arg457Gln variant when overexpressed selectively decreased energy use and increased fat storage in an adipocyte cell model. These data; in combination with evidence of positive selection of the allele encoding p.Arg457Gln; support a 'thrifty' variant hypothesis as a factor in human obesity. | 2016 | 27455349,1 | https://sci-hub.tw/10.1038/ng.3620 | ||||||||||||||
55 | GP00000873 | phytochrome C (PHYC) | Martin | PHYC | P14714 | Arabidopsis thaliana | 3702.AT5G35840.1 | Belongs to the phytochrome family. | MIK22.15;MIK22_15;phytochrome C;PHYTOCHROME C;At5g35840 | GO:0042803;GO:0009881 | GO:0005829;GO:0005634;GO:0016604;GO:0016607 | GO:0006355;GO:0006351;GO:0018298;GO:0009585;GO:0009584;GO:0017006 | X17343 | Physiology | Light sensitivity | Arabidopsis thaliana- Col0 | Arabidopsis thaliana- Fr-2 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Intraspecific | Linkage Mapping | K299*; the predicted Fr-2 PHYC protein therefore lacks half of the GAF domain; and the entire PHY; PAS and histidine kinase domains; all of which are typically required for phytochrome function | Coding | Yes | Nonsense | Mous | SNP | The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. | Light has an important role in modulating seedling growth and flowering time. We show that allelic variation at the PHYTOCHROME C (PHYC) photoreceptor locus affects both traits in natural populations of A. thaliana. Two functionally distinct PHYC haplotype groups are distributed in a latitudinal cline dependent on FRIGIDA; a locus that together with FLOWERING LOCUS C explains a large portion of the variation in A. thaliana flowering time. In a genome-wide scan for association of 65 loci with latitude; there was an excess of significant P values; indicative of population structure. Nevertheless; PHYC was the most strongly associated locus across 163 strains; suggesting that PHYC alleles are under diversifying selection in A. thaliana. Our work; together with previous findings; suggests that photoreceptor genes are major agents of natural variation in plant flowering and growth response. | 2006 | 16732287,1 | https://sci-hub.tw/10.1038/ng1818 | ||||||||||||||
56 | GP00000786 | opsin - rhodopsin1 (RH1) | Martin | RHO | P08100 | Homo sapiens | 9606.ENSP00000296271 | Belongs to the G-protein coupled receptor 1 family. Opsin subfamily. | RP4;OPN2;CSNBAD1 | GO:0046872;GO:0004930;GO:0008020;GO:0005502 | GO:0016021;GO:0005886;GO:0000139;GO:0005887;GO:0005794;GO:0005911;GO:0001750;GO:0097381;GO:0060170;GO:0030660;GO:0001917;GO:0060342;GO:0042622 | GO:0007186;GO:0001523;GO:0018298;GO:0006468;GO:0007601;GO:0016038;GO:0045494;GO:0007603;GO:0022400;GO:0060041;GO:0016056 | Physiology | Color vision (blue-shift) | Cichlid fishes; shallow waters | Cichlid fishes; deep waters | 319095 | African cichlids | no rank | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea; Percomorphaceae; Ovalentaria; Cichlomorphae; Cichliformes; Cichlidae | 0 | 319095 | African cichlids | no rank | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea; Percomorphaceae; Ovalentaria; Cichlomorphae; Cichliformes; Cichlidae | 0 | Data not curated | Interspecific | Candidate Gene | A292S and reversals; many independent cases | Coding | No | Nonsynonymous | Auguste | GCN | 874 | TCN | 1 | transversion | Ala | 292 | Ser | SNP | Parallelism of amino acid changes at the RH1 affecting spectral sensitivity among deep-water cichlids from Lakes Tanganyika and Malawi. | Many examples of the appearance of similar traits in different lineages are known during the evolution of organisms. However; the underlying genetic mechanisms have been elucidated in very few cases. Here; we provide a clear example of evolutionary parallelism; involving changes in the same genetic pathway; providing functional adaptation of RH1 pigments to deep-water habitats during the adaptive radiation of East African cichlid fishes. We determined the RH1 sequences from 233 individual cichlids. The reconstruction of cichlid RH1 pigments with 11-cis-retinal from 28 sequences showed that the absorption spectra of the pigments of nine species were shifted toward blue; tuned by two particular amino acid replacements. These blue-shifted RH1 pigments might have evolved as adaptations to the deep-water photic environment. Phylogenetic evidence indicates that one of the replacements; A292S; has evolved several times independently; inducing similar functional change. The parallel evolution of the same mutation at the same amino acid position suggests that the number of genetic changes underlying the appearance of similar traits in cichlid diversification may be fewer than previously expected. | 2005 | 15809435,1 | https://sci-hub.tw/10.1073/pnas.0405302102 | 21172834,1 | ||||||||
57 | GP00000576 | MC1R | Martin | MC1R | Q01726 | Homo sapiens | 9606.ENSP00000451605 | Belongs to the G-protein coupled receptor 1 family. | CMM5;MSH-R;SHEP2;MSHR | GO:0008528;GO:0004977;GO:0004980;GO:0031625 | GO:0005886;GO:0005887;GO:0005622 | GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914 | AAP03515 | Morphology | Coloration (coat) | Chaetodipus intermedius | Chaetodipus intermedius | 38666 | Chaetodipus intermedius | rock pocket mouse | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus | 0 | 38666 | Chaetodipus intermedius | rock pocket mouse | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus | 0 | Taxon A | Intraspecific | Candidate Gene | R18C | Coding | No | Nonsynonymous | Auguste | CGC | 52 | TGC | 1 | transition | Arg | 18 | Cys | SNP | The genetic basis of adaptive melanism in pocket mice. | Identifying the genes underlying adaptation is a major challenge in evolutionary biology. Here; we describe the molecular changes underlying adaptive coat color variation in a natural population of rock pocket mice; Chaetodipus intermedius. Rock pocket mice are generally light-colored and live on light-colored rocks. However; populations of dark (melanic) mice are found on dark lava; and this concealing coloration provides protection from avian and mammalian predators. We conducted association studies by using markers in candidate pigmentation genes and discovered four mutations in the melanocortin-1-receptor gene; Mc1r; that seem to be responsible for adaptive melanism in one population of lava-dwelling pocket mice. Interestingly; another melanic population of these mice on a different lava flow shows no association with Mc1r mutations; indicating that adaptive dark color has evolved independently in this species through changes at different genes. | 2003 | 12704245,1 | https://sci-hub.tw/10.1073/pnas.0431157100 | ||||||
58 | GP00000577 | MC1R | Martin | MC1R | Q01726 | Homo sapiens | 9606.ENSP00000451605 | Belongs to the G-protein coupled receptor 1 family. | CMM5;MSH-R;SHEP2;MSHR | GO:0008528;GO:0004977;GO:0004980;GO:0031625 | GO:0005886;GO:0005887;GO:0005622 | GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914 | AAP03515 | Morphology | Coloration (coat) | Chaetodipus intermedius | Chaetodipus intermedius | 38666 | Chaetodipus intermedius | rock pocket mouse | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus | 0 | 38666 | Chaetodipus intermedius | rock pocket mouse | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus | 0 | Taxon A | Intraspecific | Candidate Gene | R109W | Coding | No | Nonsynonymous | Auguste | CGG | 325 | TGG | 1 | transition | Arg | 109 | Trip | SNP | The genetic basis of adaptive melanism in pocket mice. | Identifying the genes underlying adaptation is a major challenge in evolutionary biology. Here; we describe the molecular changes underlying adaptive coat color variation in a natural population of rock pocket mice; Chaetodipus intermedius. Rock pocket mice are generally light-colored and live on light-colored rocks. However; populations of dark (melanic) mice are found on dark lava; and this concealing coloration provides protection from avian and mammalian predators. We conducted association studies by using markers in candidate pigmentation genes and discovered four mutations in the melanocortin-1-receptor gene; Mc1r; that seem to be responsible for adaptive melanism in one population of lava-dwelling pocket mice. Interestingly; another melanic population of these mice on a different lava flow shows no association with Mc1r mutations; indicating that adaptive dark color has evolved independently in this species through changes at different genes. | 2003 | 12704245,1 | https://sci-hub.tw/10.1073/pnas.0431157100 | ||||||
59 | GP00000578 | MC1R | Martin | MC1R | Q01726 | Homo sapiens | 9606.ENSP00000451605 | Belongs to the G-protein coupled receptor 1 family. | CMM5;MSH-R;SHEP2;MSHR | GO:0008528;GO:0004977;GO:0004980;GO:0031625 | GO:0005886;GO:0005887;GO:0005622 | GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914 | AAP03515 | Morphology | Coloration (coat) | Chaetodipus intermedius | Chaetodipus intermedius | 38666 | Chaetodipus intermedius | rock pocket mouse | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus | 0 | 38666 | Chaetodipus intermedius | rock pocket mouse | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus | 0 | Taxon A | Intraspecific | Candidate Gene | R160W | Coding | No | Nonsynonymous | Auguste | CGG | 478 | TGG | 1 | transition | Arg | 160 | Trip | SNP | The genetic basis of adaptive melanism in pocket mice. | Identifying the genes underlying adaptation is a major challenge in evolutionary biology. Here; we describe the molecular changes underlying adaptive coat color variation in a natural population of rock pocket mice; Chaetodipus intermedius. Rock pocket mice are generally light-colored and live on light-colored rocks. However; populations of dark (melanic) mice are found on dark lava; and this concealing coloration provides protection from avian and mammalian predators. We conducted association studies by using markers in candidate pigmentation genes and discovered four mutations in the melanocortin-1-receptor gene; Mc1r; that seem to be responsible for adaptive melanism in one population of lava-dwelling pocket mice. Interestingly; another melanic population of these mice on a different lava flow shows no association with Mc1r mutations; indicating that adaptive dark color has evolved independently in this species through changes at different genes. | 2003 | 12704245,1 | https://sci-hub.tw/10.1073/pnas.0431157100 | ||||||
60 | GP00000579 | MC1R | Martin | MC1R | Q01726 | Homo sapiens | 9606.ENSP00000451605 | Belongs to the G-protein coupled receptor 1 family. | CMM5;MSH-R;SHEP2;MSHR | GO:0008528;GO:0004977;GO:0004980;GO:0031625 | GO:0005886;GO:0005887;GO:0005622 | GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914 | AAP03515 | Morphology | Coloration (coat) | Chaetodipus intermedius | Chaetodipus intermedius | 38666 | Chaetodipus intermedius | rock pocket mouse | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus | 0 | 38666 | Chaetodipus intermedius | rock pocket mouse | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Glires; Rodentia; Castorimorpha; Heteromyidae; Perognathinae; Chaetodipus | 0 | Taxon A | Intraspecific | Candidate Gene | Q233H | Coding | No | Nonsynonymous | Auguste | CAA | 699 | CAC | 3 | transversion | Gin | 233 | His | SNP | The genetic basis of adaptive melanism in pocket mice. | Identifying the genes underlying adaptation is a major challenge in evolutionary biology. Here; we describe the molecular changes underlying adaptive coat color variation in a natural population of rock pocket mice; Chaetodipus intermedius. Rock pocket mice are generally light-colored and live on light-colored rocks. However; populations of dark (melanic) mice are found on dark lava; and this concealing coloration provides protection from avian and mammalian predators. We conducted association studies by using markers in candidate pigmentation genes and discovered four mutations in the melanocortin-1-receptor gene; Mc1r; that seem to be responsible for adaptive melanism in one population of lava-dwelling pocket mice. Interestingly; another melanic population of these mice on a different lava flow shows no association with Mc1r mutations; indicating that adaptive dark color has evolved independently in this species through changes at different genes. | 2003 | 12704245,1 | https://sci-hub.tw/10.1073/pnas.0431157100 | ||||||
61 | GP00001135 | TRIM5alpha | Martin | TRIM5 | Q9C035 | Homo sapiens | 9606.ENSP00000369373 | Belongs to the TRIM/RBCC family. | RNF88;TRIM5alpha | GO:0042802;GO:0042803;GO:0008270;GO:0019901;GO:0030674;GO:0008329;GO:0004842 | GO:0005737;GO:0005829;GO:0005634;GO:0000932 | GO:0045087;GO:0043410;GO:0051092;GO:0051607;GO:0043123;GO:0032880;GO:0060333;GO:0016032;GO:0051091;GO:0002218;GO:0006914;GO:0046597;GO:1902187;GO:0070534;GO:0070206;GO:0031664 | AEO45780 | Physiology | Pathogen resistance (retroviruses) | Old World Monkeys | Old World Monkeys | 9527 | Cercopithecidae | Old World monkeys | family | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Cercopithecoidea | 0 | 9527 | Cercopithecidae | Old World monkeys | family | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Cercopithecoidea | 0 | Data not curated | Intraspecific | Candidate Gene | Complex a.a. substtutions with retrovirus-specific activities; under balancing selection in several species | Coding | No | Nonsynonymous | SNP | Balancing selection and the evolution of functional polymorphism in Old World monkey TRIM5alpha. | Retroviral restriction factor TRIM5alpha exhibits a high degree of sequence variation among primate species. It has been proposed that this diversity is the cumulative result of ancient; lineage-specific episodes of positive selection. Here; we describe the contribution of within-species variation to the evolution of TRIM5alpha. Sampling within two geographically distinct Old World monkey species revealed extensive polymorphism; including individual polymorphisms that predate speciation (shared polymorphism). In some instances; alleles were more closely related to orthologues of other species than to one another. Both silent and nonsynonymous changes clustered in two domains. Functional assays revealed consequences of polymorphism; including differential restriction of a small panel of retroviruses by very similar alleles. Together; these features indicate that the primate TRIM5alpha locus has evolved under balancing selection. Except for the MHC there are few; if any; examples of long-term balancing selection in primates. Our results suggest a complex evolutionary scenario; in which fixation of lineage-specific adaptations is superimposed on a subset of critical polymorphisms that predate speciation events and have been maintained by balancing selection for millions of years. | 2006 | 17142324,1 | https://sci-hub.tw/10.1073/pnas.0605838103 | @& @BalancingSelection | ||||||||||||||
62 | GP00001191 | VRS1 = SIX-ROWED SPIKE 1 | Martin | Vrs1 | A1IHK8 | Hordeum vulgare subsp. vulgare | Hox1 | GO:0043565 | GO:0005634 | GO:0006355 | Morphology &2 Morphology | Plant architecture &2 Inflorescence architecture | Hordeum vulgare &2 | Hordeum vulgare &2 | 4513 | Hordeum vulgare | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Triticodae; Triticeae; Hordeinae; Hordeum | 0 | 4513 | Hordeum vulgare | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Triticodae; Triticeae; Hordeinae; Hordeum | 0 | Data not curated | Domesticated | Linkage Mapping | Phe75Leu | Coding | No | Nonsynonymous | Mariam | TTY | nd | YTR,CTN | SNP | Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. | Increased seed production has been a common goal during the domestication of cereal crops; and early cultivators of barley (Hordeum vulgare ssp. vulgare) selected a phenotype with a six-rowed spike that stably produced three times the usual grain number. This improved yield established barley as a founder crop for the Near Eastern Neolithic civilization. The barley spike has one central and two lateral spikelets at each rachis node. The wild-type progenitor (H. vulgare ssp. spontaneum) has a two-rowed phenotype; with additional; strictly rudimentary; lateral rows; this natural adaptation is advantageous for seed dispersal after shattering. Until recently; the origin of the six-rowed phenotype remained unknown. In the present study; we isolated vrs1 (six-rowed spike 1); the gene responsible for the six-rowed spike in barley; by means of positional cloning. The wild-type Vrs1 allele (for two-rowed barley) encodes a transcription factor that includes a homeodomain with a closely linked leucine zipper motif. Expression of Vrs1 was strictly localized in the lateral-spikelet primordia of immature spikes; suggesting that the VRS1 protein suppresses development of the lateral rows. Loss of function of Vrs1 resulted in complete conversion of the rudimentary lateral spikelets in two-rowed barley into fully developed fertile spikelets in the six-rowed phenotype. Phylogenetic analysis demonstrated that the six-rowed phenotype originated repeatedly; at different times and in different regions; through independent mutations of Vrs1. | 2007 | 17220272,1 | https://sci-hub.tw/10.1073/pnas.0608580104 | 21217754,1 | |||||||||||||||
63 | GP00000769 | opsin - rhodopsin (LWRh) | Martin | LWRh | E2DZP1 | Heliconius melpomene | Belongs to the G-protein coupled receptor 1 family. Opsin subfamily. | BCP;BOP;CBT | GO:0004930;GO:0009881 | GO:0016021 | GO:0018298;GO:0007601;GO:0007602 | AF385332 | Physiology | Color vision (blue shift) | Limenitis astyanax; other butterflies | Limenitis weidemeyerii; L. archippus; L. lorquini | 124411 | Limenitis arthemis | white admiral | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea; Nymphalidae; Limenitidinae; Limenitidini; Limenitis | 0 | 42270 | Limenitis archippus | viceroy | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea; Nymphalidae; Limenitidinae; Limenitidini; Limenitis | 0 | Data not curated | Intergeneric or Higher | Candidate Gene | I17M; S137A=S180A in human LWS/MWS numbering system | Coding | No | Nonsynonymous | SNP | Adaptive evolution of color vision as seen through the eyes of butterflies. | Butterflies and primates are interesting for comparative color vision studies; because both have evolved middle- (M) and long-wavelength- (L) sensitive photopigments with overlapping absorbance spectrum maxima (lambda(max) values). Although positive selection is important for the maintenance of spectral variation within the primate pigments; it remains an open question whether it contributes similarly to the diversification of butterfly pigments. To examine this issue; we performed epimicrospectrophotometry on the eyes of five Limenitis butterfly species and found a 31-nm range of variation in the lambda(max) values of the L-sensitive photopigments (514-545 nm). We cloned partial Limenitis L opsin gene sequences and found a significant excess of replacement substitutions relative to polymorphisms among species. Mapping of these L photopigment lambda(max) values onto a phylogeny revealed two instances within Lepidoptera of convergently evolved L photopigment lineages whose lambda(max) values were blue-shifted. A codon-based maximum-likelihood analysis indicated that; associated with the two blue spectral shifts; four amino acid sites (Ile17Met; Ala64Ser; Asn70Ser; and Ser137Ala) have evolved substitutions in parallel and exhibit significant d(N)/d(S) >1. Homology modeling of the full-length Limenitis arthemis astyanax L opsin placed all four substitutions within the chromophore-binding pocket. Strikingly; the Ser137Ala substitution is in the same position as a site that in primates is responsible for a 5- to 7-nm blue spectral shift. Our data show that some of the same amino acid sites are under positive selection in the photopigments of both butterflies and primates; spanning an evolutionary distance >500 million years. | 2007 | 17494749,1 | https://sci-hub.tw/10.1073/pnas.0701447104 | ||||||||||||||||
64 | GP00000770 | opsin - rhodopsin (LWRh) | Martin | LWRh | E2DZP1 | Heliconius melpomene | Belongs to the G-protein coupled receptor 1 family. Opsin subfamily. | BCP;BOP;CBT | GO:0004930;GO:0009881 | GO:0016021 | GO:0018298;GO:0007601;GO:0007602 | AF385332 | Physiology | Color vision (blue shift) | Other butterflies | Junonia coenia; Siproeta steneles | 33415 | Nymphalidae | brushfoots | family | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea | 0 | 39707 | Junonia | buckeyes | genus | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea; Nymphalidae; Nymphalinae; Junoniini | 0 | Data not curated | Intergeneric or Higher | Candidate Gene | I17M; S137A=S180A in human LWS/MWS numbering system | Coding | No | Nonsynonymous | SNP | Adaptive evolution of color vision as seen through the eyes of butterflies. | Butterflies and primates are interesting for comparative color vision studies; because both have evolved middle- (M) and long-wavelength- (L) sensitive photopigments with overlapping absorbance spectrum maxima (lambda(max) values). Although positive selection is important for the maintenance of spectral variation within the primate pigments; it remains an open question whether it contributes similarly to the diversification of butterfly pigments. To examine this issue; we performed epimicrospectrophotometry on the eyes of five Limenitis butterfly species and found a 31-nm range of variation in the lambda(max) values of the L-sensitive photopigments (514-545 nm). We cloned partial Limenitis L opsin gene sequences and found a significant excess of replacement substitutions relative to polymorphisms among species. Mapping of these L photopigment lambda(max) values onto a phylogeny revealed two instances within Lepidoptera of convergently evolved L photopigment lineages whose lambda(max) values were blue-shifted. A codon-based maximum-likelihood analysis indicated that; associated with the two blue spectral shifts; four amino acid sites (Ile17Met; Ala64Ser; Asn70Ser; and Ser137Ala) have evolved substitutions in parallel and exhibit significant d(N)/d(S) >1. Homology modeling of the full-length Limenitis arthemis astyanax L opsin placed all four substitutions within the chromophore-binding pocket. Strikingly; the Ser137Ala substitution is in the same position as a site that in primates is responsible for a 5- to 7-nm blue spectral shift. Our data show that some of the same amino acid sites are under positive selection in the photopigments of both butterflies and primates; spanning an evolutionary distance >500 million years. | 2007 | 17494749,1 | https://sci-hub.tw/10.1073/pnas.0701447104 | ||||||||||||||||
65 | GP00000871 | phytochrome B (PHYB) | Martin | PHYB | P14713 | Arabidopsis thaliana | 3702.AT2G18790.1 | Belongs to the phytochrome family. | HY3;MSF3.17;MSF3_17;OOP1;OUT OF PHASE 1;phytochrome B;PHYTOCHROME B;At2g18790 | GO:0042802;GO:0042803;GO:0043565;GO:0000155;GO:0031516;GO:0009883;GO:1990841;GO:0031517 | GO:0005829;GO:0005634;GO:0016604;GO:0016607 | GO:0009640;GO:0006351;GO:0045892;GO:0009409;GO:0006325;GO:0010617;GO:0009638;GO:0018298;GO:2000028;GO:0010244;GO:0010148;GO:0009266;GO:0010218;GO:0009867;GO:0009649;GO:0009584;GO:0009630;GO:0010161;GO:0009687;GO:0015979;GO:0017012;GO:0031347;GO:0010029;GO:0010202;GO:0010374 | CP002685 | Physiology | Light sensitivity | Arabidopsis thaliana- Ler0 | Arabidopsis thaliana - Cvi | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Intraspecific | Linkage Mapping | I143L | Coding | No | Nonsynonymous | Pinton | ATH | CTH | 1 | transversion | Ile | 143 | Leu | SNP | Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. | Plants have a sophisticated system for sensing and responding to their light environment. The light responses of populations and species native to different habitats show adaptive variation; understanding the mechanisms underlying photomorphogenic variation is therefore of significant interest. In Arabidopsis thaliana; phytochrome B (PHYB) is the dominant photoreceptor for red light and plays a major role in white light. Because PHYB has been proposed as a candidate gene for several quantitative trait loci (QTLs) affecting light response; we have investigated sequence and functional variation in Arabidopsis PHYB. We examined PHYB sequences in 33 A. thaliana individuals and in the close relative Arabidopsis lyrata. From 14 nonsynonymous polymorphisms; we chose 5 for further study based on previous QTL studies. In a larger collection of A. thaliana accessions; one of these five polymorphisms; I143L; was associated with variation in red light response. We used transgenic analysis to test this association and confirmed experimentally that natural PHYB polymorphisms cause differential plant responses to light. Furthermore; our results show that allelic variation of PHYB activity is due to amino acid rather than regulatory changes. Together with earlier studies linking variation in light sensitivity to photoreceptor genes; our work suggests that photoreceptors may be a common target of natural selection. | 2008 | 18287016,1 | https://sci-hub.tw/10.1073/pnas.0712174105 | @GxE | ||||||
66 | GP00001020 | S5 | Martin | GRXS5 | Q5QLR2 | Oryza sativa subsp. japonica | 39947.LOC_Os01g47760.1 | Belongs to the glutaredoxin family. CC-type subfamily. | GRXS5;P0014E08.2;Os01g0667900;LOC_Os01g47760;OSJNBb0063G05.32 | GO:0046872;GO:0009055;GO:0051537;GO:0015035 | GO:0005737;GO:0005634 | GO:0045454 | ACG76112 | Physiology | Hybrid incompatibility (F1 female sterility) | Oryza sativa japonica | Oryza sativa indica | 4530 | Oryza sativa | rice | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza | 1 | 4530 | Oryza sativa | rice | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza | 1 | Data not curated | Domesticated | Linkage Mapping | 6 non-synonymous changes | Coding | No | Nonsynonymous | SNP | A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice. | Hybrid sterility is a major form of postzygotic reproductive isolation. Although reproductive isolation has been a key issue in evolutionary biology for many decades in a wide range of organisms; only very recently a few genes for reproductive isolation were identified. The Asian cultivated rice (Oryza sativa L.) is divided into two subspecies; indica and japonica. Hybrids between indica and japonica varieties are usually highly sterile. A special group of rice germplasm; referred to as wide-compatibility varieties; is able to produce highly fertile hybrids when crossed to both indica and japonica. In this study; we cloned S5; a major locus for indica-japonica hybrid sterility and wide compatibility; using a map-based cloning approach. We show that S5 encodes an aspartic protease conditioning embryo-sac fertility. The indica (S5-i) and japonica (S5-j) alleles differ by two nucleotides. The wide compatibility gene (S5-n) has a large deletion in the N terminus of the predicted S5 protein; causing subcellular mislocalization of the protein; and thus is presumably nonfunctional. This triallelic system has a profound implication in the evolution and artificial breeding of cultivated rice. Genetic differentiation between indica and japonica would have been enforced because of the reproductive barrier caused by S5-i and S5-j; and species coherence would have been maintained by gene flow enabled by the wide compatibility gene. | 2008 | 18678896,1 | https://sci-hub.tw/10.1073/pnas.0804761105 | @& | ||||||||||||||
67 | GP00000804 | OR7D4 | Martin | OR7D4 | Q8NG98 | Homo sapiens | 9606.ENSP00000310488 | Belongs to the G-protein coupled receptor 1 family. | OR19B;hg105;OR19-7;OR19-B;OR7D4P | GO:0004930;GO:0004984 | GO:0016021;GO:0005886 | GO:0007186;GO:0050911 | ALI87882 | Physiology | Olfaction | Human/Chimpanzee ancestor | Homo sapiens | 207598 | Homininae | subfamily | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae | 0 | 9606 | Homo sapiens | human | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo | 0 | Data not curated | Interspecific | Candidate Gene | M273T | Coding | No | Nonsynonymous | Pinton | ATG | ACG | 2 | transition | Met | 273 | Thr | SNP | Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates. | Odorant receptors are among the fastest evolving genes in animals. However; little is known about the functional changes of individual odorant receptors during evolution. We have recently demonstrated a link between the in vitro function of a human odorant receptor; OR7D4; and in vivo olfactory perception of 2 steroidal ligands--androstenone and androstadienone--chemicals that are shown to affect physiological responses in humans. In this study; we analyzed the in vitro function of OR7D4 in primate evolution. Orthologs of OR7D4 were cloned from different primate species. Ancestral reconstruction allowed us to reconstitute additional putative OR7D4 orthologs in hypothetical ancestral species. Functional analysis of these orthologs showed an extremely diverse range of OR7D4 responses to the ligands in various primate species. Functional analysis of the nonsynonymous changes in the Old World Monkey and Great Ape lineages revealed a number of sites causing increases or decreases in sensitivity. We found that the majority of the functionally important residues in OR7D4 were not predicted by the maximum likelihood analysis detecting positive Darwinian selection. | 2009 | 19955411,1 | https://sci-hub.tw/10.1073/pnas.0808378106 | ||||||||
68 | GP00000779 | opsin - rhodopsin (UVRh2) | Martin | UVRh2 | E2DZL8 | Heliconius melpomene | Belongs to the G-protein coupled receptor 1 family. | GCP;GOP;OPN1MW | GO:0004930 | GO:0016021 | GO:0007601;GO:0007602 | Physiology | Color vision (UV-shift) | Other butterflies | Heliconius spp. | 33415 | Nymphalidae | brushfoots | family | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea | 0 | 33428 | Heliconius pachinus | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Papilionoidea; Nymphalidae; Heliconiinae; Heliconiini; Heliconius | 0 | Data not curated | Intergeneric or Higher | Candidate Gene | T180A; Y277F (human LWS/MWS numbering system) | Coding | No | Nonsynonymous | Cortier | Met | SNP | Positive selection of a duplicated UV-sensitive visual pigment coincides with wing pigment evolution in Heliconius butterflies. | The butterfly Heliconius erato can see from the UV to the red part of the light spectrum with color vision proven from 440 to 640 nm. Its eye is known to contain three visual pigments; rhodopsins; produced by an 11-cis-3-hydroxyretinal chromophore together with long wavelength (LWRh); blue (BRh) and UV (UVRh1) opsins. We now find that H. erato has a second UV opsin mRNA (UVRh2)-a previously undescribed duplication of this gene among Lepidoptera. To investigate its evolutionary origin; we screened eye cDNAs from 14 butterfly species in the subfamily Heliconiinae and found both copies only among Heliconius. Phylogeny-based tests of selection indicate positive selection of UVRh2 following duplication; and some of the positively selected sites correspond to vertebrate visual pigment spectral tuning residues. Epi-microspectrophotometry reveals two UV-absorbing rhodopsins in the H. erato eye with lambda(max) = 355 nm and 398 nm. Along with the additional UV opsin; Heliconius have also evolved 3-hydroxy-DL-kynurenine (3-OHK)-based yellow wing pigments not found in close relatives. Visual models of how butterflies perceive wing color variation indicate this has resulted in an expansion of the number of distinguishable yellow colors on Heliconius wings. Functional diversification of the UV-sensitive visual pigments may help explain why the yellow wing pigments of Heliconius are so colorful in the UV range compared to the yellow pigments of close relatives lacking the UV opsin duplicate. | 2010 | 20133601,1 | https://sci-hub.tw/10.1073/pnas.0910085107 | 20478921,1 | @& | ||||||||||||||
69 | GP00000953 | RAS1 | Martin | RAS1 | O04515 | Arabidopsis thaliana | 3702.AT1G09950.1 | F21M12.34;F21M12_34;RESPONSE TO ABA AND SALT 1;At1g09950 | GO:0043565 | GO:0005886;GO:0005634;GO:0005739;GO:0005789 | GO:0006351 | CP002684 | Physiology &2 Physiology | Salt tolerance &2 Abscisic acid sensitivity | Arabidopsis thaliana - Sha &2 | Arabidopsis thaliana- Ler0 &2 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Intraspecific | Linkage Mapping | Premature stop codon; Lys>STOP | Coding | Yes | Nonsense | Pinton | TTA | TAA | 2 | transversion | Leu | STP | SNP | RAS1; a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis. | Soil salinity limits agricultural production and is a major obstacle for feeding the growing world population. We used natural genetic variation in salt tolerance among different Arabidopsis accessions to map a major quantitative trait locus (QTL) for salt tolerance and abscisic acid (ABA) sensitivity during seed germination and early seedling growth. A recombinant inbred population derived from Landsberg erecta (Ler; salt and ABA sensitive) x Shakdara (Sha; salt and ABA resistant) was used for QTL mapping. High-resolution mapping and cloning of this QTL; Response to ABA and Salt 1 (RAS1); revealed that it is an ABA- and salt stress-inducible gene and encodes a previously undescribed plant-specific protein. A premature stop codon results in a truncated RAS1 protein in Sha. Reducing the expression of RAS1 by transfer-DNA insertion in Col or RNA interference in Ler leads to decreased salt and ABA sensitivity; whereas overexpression of the Ler allele but not the Sha allele causes increased salt and ABA sensitivity. Our results suggest that RAS1 functions as a negative regulator of salt tolerance during seed germination and early seedling growth by enhancing ABA sensitivity and that its loss of function contributes to the increased salt tolerance of Sha. | 2010 | 20212128,1 | https://sci-hub.tw/10.1073/pnas.0910798107 | |||||||||
70 | GP00000629 | MC1R | Martin | MC1R | Q01726 | Homo sapiens | 9606.ENSP00000451605 | Belongs to the G-protein coupled receptor 1 family. | CMM5;MSH-R;SHEP2;MSHR | GO:0008528;GO:0004977;GO:0004980;GO:0031625 | GO:0005886;GO:0005887;GO:0005622 | GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914 | AAT90269 | Morphology | Coloration (scales) | Scleropus undulatus | Scleropus undulatus | 8520 | Sceloporus undulatus | fence lizard | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera; Iguania; Phrynosomatidae; Phrynosomatinae; Sceloporus | 0 | 8520 | Sceloporus undulatus | fence lizard | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera; Iguania; Phrynosomatidae; Phrynosomatinae; Sceloporus | 0 | Data not curated | Intraspecific | Candidate Gene | H208Y | Coding | No | Nonsynonymous | PInton | CAY | TAY | 1 | transition | His | 208 | Tyr | SNP | Molecular and functional basis of phenotypic convergence in white lizards at White Sands. | There are many striking examples of phenotypic convergence in nature; in some cases associated with changes in the same genes. But even mutations in the same gene may have different biochemical properties and thus different evolutionary consequences. Here we dissect the molecular mechanism of convergent evolution in three lizard species with blanched coloration on the gypsum dunes of White Sands; New Mexico. These White Sands forms have rapidly evolved cryptic coloration in the last few thousand years; presumably to avoid predation. We use cell-based assays to demonstrate that independent mutations in the same gene underlie the convergent blanched phenotypes in two of the three species. Although the same gene contributes to light phenotypes in these White Sands populations; the specific molecular mechanisms leading to reduced melanin production are different. In one case; mutations affect receptor signaling and in the other; the ability of the receptor to integrate into the melanocyte membrane. These functional differences have important ramifications at the organismal level. Derived alleles in the two species show opposite dominance patterns; which in turn affect their visibility to selection and the spatial distribution of alleles across habitats. Our results demonstrate that even when the same gene is responsible for phenotypic convergence; differences in molecular mechanism can have dramatic consequences on trait expression and ultimately the adaptive trajectory. | 2010 | 20080544,1 | https://sci-hub.tw/10.1073/pnas.0911042107 | |||||||
71 | GP00001121 | TFL1/GmTFL1 | Martin | TFL1 | P93003 | Arabidopsis thaliana | 3702.AT5G03840.1 | Belongs to the phosphatidylethanolamine-binding protein family. | MED24.6;TERMINAL FLOWER 1;TFL-1;At5g03840;F8F6_50 | GO:0003712 | GO:0005886;GO:0005737;GO:0005634;GO:0031982;GO:0005773 | GO:0030154;GO:0009908;GO:0009910;GO:0009744;GO:0090344;GO:0006623 | ABS57463 | Physiology | Growth determination habit | Glycine max; Glycine soja | Glycine max (determinate growth habit) | 3847 | Glycine max | soybean | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja | 0 | 3847 | Glycine max | soybean | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja | 0 | Data not curated | Domesticated | Linkage Mapping | R62S | Coding | No | Nonsynonymous | Santana | AGG | AGT | 3 | transversion | Arg | 62 | Ser | SNP | Artificial selection for determinate growth habit in soybean. | Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit; whereas Glycine soja; the wild progenitor of soybean; is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes; when mated; produce progeny that segregate in a monogenic pattern. Here; we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1); a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene; each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype; but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However; the GmTfl1 homeolog; despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1; appears to be sub- or neo-functionalized; as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci. | 2010 | 20421496,1 | https://sci-hub.tw/10.1073/pnas.1000088107 | Information was double checked with Supp Table 1. | ||||||
72 | GP00001122 | TFL1/GmTFL1 | Martin | TFL1 | P93003 | Arabidopsis thaliana | 3702.AT5G03840.1 | Belongs to the phosphatidylethanolamine-binding protein family. | MED24.6;TERMINAL FLOWER 1;TFL-1;At5g03840;F8F6_50 | GO:0003712 | GO:0005886;GO:0005737;GO:0005634;GO:0031982;GO:0005773 | GO:0030154;GO:0009908;GO:0009910;GO:0009744;GO:0090344;GO:0006623 | ABS57463 | Physiology | Growth determination habit | Glycine max; Glycine soja | Glycine max (determinate growth habit) | 3847 | Glycine max | soybean | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja | 0 | 3847 | Glycine max | soybean | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja | 0 | Data not curated | Domesticated | Candidate Gene | P113L | Coding | No | Nonsynonymous | PInton | CCT | CTT | 2 | transition | Pro | 113 | Leu | SNP | Artificial selection for determinate growth habit in soybean. | Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit; whereas Glycine soja; the wild progenitor of soybean; is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes; when mated; produce progeny that segregate in a monogenic pattern. Here; we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1); a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene; each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype; but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However; the GmTfl1 homeolog; despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1; appears to be sub- or neo-functionalized; as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci. | 2010 | 20421496,1 | https://sci-hub.tw/10.1073/pnas.1000088107 | Information was double checked with Supp Table 1. | ||||||
73 | GP00001123 | TFL1/GmTFL1 | Martin | TFL1 | P93003 | Arabidopsis thaliana | 3702.AT5G03840.1 | Belongs to the phosphatidylethanolamine-binding protein family. | MED24.6;TERMINAL FLOWER 1;TFL-1;At5g03840;F8F6_50 | GO:0003712 | GO:0005886;GO:0005737;GO:0005634;GO:0031982;GO:0005773 | GO:0030154;GO:0009908;GO:0009910;GO:0009744;GO:0090344;GO:0006623 | ABS57463 | Physiology | Growth determination habit | Glycine max; Glycine soja | Glycine max (determinate growth habit) | 3847 | Glycine max | soybean | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja | 0 | 3847 | Glycine max | soybean | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja | 0 | Data not curated | Domesticated | Candidate Gene | R130K | Coding | No | Nonsynonymous | Pinton | AGA | AAA | 2 | transition | Arg | 130 | Lys | SNP | Artificial selection for determinate growth habit in soybean. | Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit; whereas Glycine soja; the wild progenitor of soybean; is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes; when mated; produce progeny that segregate in a monogenic pattern. Here; we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1); a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene; each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype; but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However; the GmTfl1 homeolog; despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1; appears to be sub- or neo-functionalized; as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci. | 2010 | 20421496,1 | https://sci-hub.tw/10.1073/pnas.1000088107 | Information was double checked with Supp Table 1. | ||||||
74 | GP00001124 | TFL1/GmTFL1 | Martin | TFL1 | P93003 | Arabidopsis thaliana | 3702.AT5G03840.1 | Belongs to the phosphatidylethanolamine-binding protein family. | MED24.6;TERMINAL FLOWER 1;TFL-1;At5g03840;F8F6_50 | GO:0003712 | GO:0005886;GO:0005737;GO:0005634;GO:0031982;GO:0005773 | GO:0030154;GO:0009908;GO:0009910;GO:0009744;GO:0090344;GO:0006623 | ABS57463 | Physiology | Growth determination habit | Glycine max; Glycine soja | Glycine max (determinate growth habit) | 3847 | Glycine max | soybean | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja | 0 | 3847 | Glycine max | soybean | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine; Soja | 0 | Data not curated | Domesticated | Candidate Gene | R166W | Coding | No | Nonsynonymous | Midoun | AGG | TGG | 1 | transversion | Arg | 166 | Trp | SNP | Artificial selection for determinate growth habit in soybean. | Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit; whereas Glycine soja; the wild progenitor of soybean; is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes; when mated; produce progeny that segregate in a monogenic pattern. Here; we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1); a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene; each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype; but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However; the GmTfl1 homeolog; despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1; appears to be sub- or neo-functionalized; as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci. | 2010 | 20421496,1 | https://sci-hub.tw/10.1073/pnas.1000088107 | Information was double checked with Supp Table 1. | ||||||
75 | GP00000103 | ARHGAP15 | Martin | Arhgap15 | Q811M1 | Mus musculus | 10090.ENSMUSP00000056461 | 5830480G12Rik | GO:0005096 | GO:0005737;GO:0016020 | GO:0007165;GO:0008360 | AAI34461 | Physiology | Pathogen resistance (Trypanosoma) | Bos indicus (zebu) ; other breeds | Bos taurus (N'dama breed) | 9903 | Bos | oxen; cattle | genus | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Bovinae | 0 | 9913 | Bos taurus | cattle | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bos | 1 | Data not curated | Intraspecific | Linkage Mapping | H282P | Coding | No | Nonsynonymous | Midoun | CAY | CCN | His | 282 | Pro | SNP | Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection. | African bovine trypanosomiasis caused by Trypanosoma sp.; is a major constraint on cattle productivity in sub-Saharan Africa. Some African Bos taurus breeds are highly tolerant of infection; but the potentially more productive Bos indicus zebu breeds are much more susceptible. Zebu cattle are well adapted for plowing and haulage; and increasing their tolerance of trypanosomiasis could have a major impact on crop cultivation as well as dairy and beef production. We used three strategies to obtain short lists of candidate genes within QTL that were previously shown to regulate response to infection. We analyzed the transcriptomes of trypanotolerant N'Dama and susceptible Boran cattle after infection with Trypanosoma congolense. We sequenced EST libraries from these two breeds to identify polymorphisms that might underlie previously identified quantitative trait loci (QTL); and we assessed QTL regions and candidate loci for evidence of selective sweeps. The scan of the EST sequences identified a previously undescribed polymorphism in ARHGAP15 in the Bta2 trypanotolerance QTL. The polymorphism affects gene function in vitro and could contribute to the observed differences in expression of the MAPK pathway in vivo. The expression data showed that TLR and MAPK pathways responded to infection; and the former contained TICAM1; which is within a QTL on Bta7. Genetic analyses showed that selective sweeps had occurred at TICAM1 and ARHGAP15 loci in African taurine cattle; making them strong candidates for the genes underlying the QTL. Candidate QTL genes were identified in other QTL by their expression profile and the pathways in which they participate. | 2011 | 21593421,1 | https://sci-hub.tw/10.1073/pnas.1013486108 | ||||||||||
76 | GP00001027 | Sd1 (=GA20ox-2) | Martin | 20ox2 | Q0JH50 | Oryza sativa subsp. japonica | 39947.LOC_Os01g66100.1 | Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily. | sd1;GA20;Sd-1;20ox2;C20ox2;SD1-2E;Os20ox2;osGA20ox2;Os01g0883800;LOC_Os01g66100;B1065E10.46 | GO:0046872;GO:0016491 | GO:0016021;GO:0005886 | GO:0006935;GO:0040024;GO:0007606;GO:0050893 | AER45908 | Morphology | Plant size (height) | Oryza indica - Kasalath | Oryza sativa japonica - Nipponbare | 4530 | Oryza sativa | rice | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza | 1 | 4530 | Oryza sativa | rice | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza | 1 | Data not curated | Domesticated | Linkage Mapping | G100E + R340Q | Coding | No | Nonsynonymous | Codon-Taxon-A | Codon-Position | Codon-TaxonB | Codon-Site | transition-transversion | AminoAcid-Taxon A | AA-Position | AminoAcid-Taxon B | SNP | Artificial selection for a green revolution gene during japonica rice domestication. | The semidwarf phenotype has been extensively selected during modern crop breeding as an agronomically important trait. Introduction of the semidwarf gene; semi-dwarf1 (sd1); which encodes a gibberellin biosynthesis enzyme; made significant contributions to the "green revolution" in rice (Oryza sativa L.). Here we report that SD1 was involved not only in modern breeding including the green revolution; but also in early steps of rice domestication. We identified two SNPs in O. sativa subspecies (ssp.) japonica SD1 as functional nucleotide polymorphisms (FNPs) responsible for shorter culm length and low gibberellin biosynthetic activity. Genetic diversity analysis among O. sativa ssp. japonica and indica; along with their wild ancestor O. rufipogon Griff; revealed that these FNPs clearly differentiate the japonica landrace and O. rufipogon. We also found a dramatic reduction in nucleotide diversity around SD1 only in the japonica landrace; not in the indica landrace or O. rufipogon. These findings indicate that SD1 has been subjected to artificial selection in rice evolution and that the FNPs participated in japonica domestication; suggesting that ancient humans already used the green revolution gene. | 2011 | 21646530,1 | https://sci-hub.tw/10.1073/pnas.1019490108 | @& | ||||||
77 | GP00000931 | PRR37 pseudoresponse regulator protein 37 (SbPRR37) | Martin | PRR37 | Q0D3B6 | Oryza sativa subsp. japonica | 39947.LOC_Os07g49460.1 | Belongs to the ARR-like family. | PRR37;OsPRR37;DTH7;HD2;Os07g0695100;LOC_Os07g49460;P0627E10.21 | GO:0042803;GO:0046872;GO:0017046;GO:0042978;GO:0004925 | GO:0005634 | GO:0006355;GO:0006351;GO:0009908;GO:0000160;GO:0009585;GO:0048579;GO:0048511 | AGN92469 | Physiology | Flowering time | Sorghum bicolor | Sorghum bicolor- ATx623 | 4558 | Sorghum bicolor | sorghum | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum | 0 | 4113 | Solanum tuberosum | potato | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum | 1 | Data not curated | Domesticated | Linkage Mapping | K162N + G270* | Coding | Yes | Nonsense | Fayollas | SNP | Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum. | Optimal flowering time is critical to the success of modern agriculture. Sorghum is a short-day tropical species that exhibits substantial photoperiod sensitivity and delayed flowering in long days. Genotypes with reduced photoperiod sensitivity enabled sorghum's utilization as a grain crop in temperate zones worldwide. In the present study; Ma(1); the major repressor of sorghum flowering in long days; was identified as the pseudoresponse regulator protein 37 (PRR37) through positional cloning and analysis of SbPRR37 alleles that modulate flowering time in grain and energy sorghum. Several allelic variants of SbPRR37 were identified in early flowering grain sorghum germplasm that contain unique loss-of-function mutations. We show that in long days SbPRR37 activates expression of the floral inhibitor CONSTANS and represses expression of the floral activators Early Heading Date 1; FLOWERING LOCUS T; Zea mays CENTRORADIALIS 8; and floral induction. Expression of SbPRR37 is light dependent and regulated by the circadian clock; with peaks of RNA abundance in the morning and evening in long days. In short days; the evening-phase expression of SbPRR37 does not occur due to darkness; allowing sorghum to flower in this photoperiod. This study provides insight into an external coincidence mechanism of photoperiodic regulation of flowering time mediated by PRR37 in the short-day grass sorghum and identifies important alleles of SbPRR37 that are critical for the utilization of this tropical grass in temperate zone grain and bioenergy production. | 2011 | 21930910,1 | https://sci-hub.tw/10.1073/pnas.1106212108 | ||||||||||||||
78 | GP00000932 | PRR37 pseudoresponse regulator protein 37 (SbPRR37) | Martin | PRR37 | Q0D3B6 | Oryza sativa subsp. japonica | 39947.LOC_Os07g49460.1 | Belongs to the ARR-like family. | PRR37;OsPRR37;DTH7;HD2;Os07g0695100;LOC_Os07g49460;P0627E10.21 | GO:0042803;GO:0046872;GO:0017046;GO:0042978;GO:0004925 | GO:0005634 | GO:0006355;GO:0006351;GO:0009908;GO:0000160;GO:0009585;GO:0048579;GO:0048511 | AGN92469 | Physiology | Flowering time | Sorghum bicolor | Sorghum bicolor- Blackhull Kafir | 4558 | Sorghum bicolor | sorghum | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum | 0 | 4113 | Solanum tuberosum | potato | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum | 1 | Data not curated | Domesticated | Linkage Mapping | K162N | Coding | No | Nonsynonymous | Fayollas | AAR | 162 | AAY | 3 | transversion | Lys | 162 | Asn | SNP | Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum. | Optimal flowering time is critical to the success of modern agriculture. Sorghum is a short-day tropical species that exhibits substantial photoperiod sensitivity and delayed flowering in long days. Genotypes with reduced photoperiod sensitivity enabled sorghum's utilization as a grain crop in temperate zones worldwide. In the present study; Ma(1); the major repressor of sorghum flowering in long days; was identified as the pseudoresponse regulator protein 37 (PRR37) through positional cloning and analysis of SbPRR37 alleles that modulate flowering time in grain and energy sorghum. Several allelic variants of SbPRR37 were identified in early flowering grain sorghum germplasm that contain unique loss-of-function mutations. We show that in long days SbPRR37 activates expression of the floral inhibitor CONSTANS and represses expression of the floral activators Early Heading Date 1; FLOWERING LOCUS T; Zea mays CENTRORADIALIS 8; and floral induction. Expression of SbPRR37 is light dependent and regulated by the circadian clock; with peaks of RNA abundance in the morning and evening in long days. In short days; the evening-phase expression of SbPRR37 does not occur due to darkness; allowing sorghum to flower in this photoperiod. This study provides insight into an external coincidence mechanism of photoperiodic regulation of flowering time mediated by PRR37 in the short-day grass sorghum and identifies important alleles of SbPRR37 that are critical for the utilization of this tropical grass in temperate zone grain and bioenergy production. | 2011 | 21930910,1 | https://sci-hub.tw/10.1073/pnas.1106212108 | ||||||
79 | GP00000729 | SCN4A (Nav1.4) | Martin | SCN4A | P35499 | Homo sapiens | 9606.ENSP00000396320 | Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.4/SCN4A subfamily. | HYPP;SkM1;CMS16;HYKPP;NAC1A;HOKPP2;Nav1.4;Na(V)1.4 | GO:0005244;GO:0005248 | GO:0005887;GO:0001518 | GO:0006814;GO:0019228;GO:0034765;GO:0086010;GO:0006936 | AFD23228 | Physiology | Xenobiotic resistance (TTX) | Amphiesma vibakari | Amphiesma pryeri | 1159329 | Hebius vibakari | Japanese keelback | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera; Serpentes; Colubroidea; Colubridae; Natricinae; Hebius | 0 | 1159330 | Hebius pryeri | Pryer's keelback | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Sauropsida; Sauria; Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera; Serpentes; Colubroidea; Colubridae; Natricinae; Hebius | 0 | Taxon A | Interspecific | Candidate Gene | D1227E = D945E in DIII domain | Coding | No | Nonsynonymous | SNP | Constraint shapes convergence in tetrodotoxin-resistant sodium channels of snakes. | Natural selection often produces convergent changes in unrelated lineages; but the degree to which such adaptations occur via predictable genetic paths is unknown. If only a limited subset of possible mutations is fixed in independent lineages; then it is clear that constraint in the production or function of molecular variants is an important determinant of adaptation. We demonstrate remarkably constrained convergence during the evolution of resistance to the lethal poison; tetrodotoxin; in six snake species representing three distinct lineages from around the globe. Resistance-conferring amino acid substitutions in a voltage-gated sodium channel; Na(v)1.4; are clustered in only two regions of the protein; and a majority of the replacements are confined to the same three positions. The observed changes represent only a small fraction of the experimentally validated mutations known to increase Na(v)1.4 resistance to tetrodotoxin. These results suggest that constraints resulting from functional tradeoffs between ion channel function and toxin resistance led to predictable patterns of evolutionary convergence at the molecular level. Our data are consistent with theoretical predictions and recent microcosm work that suggest a predictable path is followed during an adaptive walk along a mutational landscape; and that natural selection may be frequently constrained to produce similar genetic outcomes even when operating on independent lineages. | 2012 | 22392995,1 | https://sci-hub.tw/10.1073/pnas.1113468109 | 27291053,1 | Non-null mutation. Extreme TTX resistance evolved 5 times in Nav1.4 channel; but only in lineages that had previously evolved resistance in paralogous NaV channels | |||||||||||||
80 | GP00000982 | resistant to methyl viologen 1 (RMV1) | Martin | RMV1 | Q9FFL1 | Arabidopsis thaliana | 3702.AT5G05630.1 | Belongs to the amino acid-polyamine-organocation (APC) superfamily. Polyamine:cation symporter (PHS) (TC 2.A.3.12) family. | MJJ3.2;MJJ3_2;POLYAMINE UPTAKE TRANSPORTER 3;PUT3;resistant to methyl viologen 1;At5g05630 | GO:0015297;GO:0015293;GO:0015179;GO:0015203 | GO:0005886;GO:0005887 | GO:0009408;GO:0015839;GO:0015846 | BT008298 | Physiology | Polyamine uptake | Arabidopsis thaliana- Col0 | Arabidopsis thaliana- Nos-d | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Intraspecific | Linkage Mapping | Ile377Phe | Coding | Yes | Nonsense | Mariam | ATH | nd | TTY | 1 | transversions | Ile | 377 | Phe | SNP | Natural variation in a polyamine transporter determines paraquat tolerance in Arabidopsis. | Polyamines (PAs) are ubiquitous; polycationic compounds that are essential for the growth and survival of all organisms. Although the PA-uptake system plays a key role in mammalian cancer and in plant survival; the underlying molecular mechanisms are not well understood. Here; we identified an Arabidopsis L-type amino acid transporter (LAT) family transporter; named RMV1 (resistant to methyl viologen 1); responsible for uptake of PA and its analog paraquat (PQ). The natural variation in PQ tolerance was determined in 22 Arabidopsis thaliana accessions based on the polymorphic variation of RMV1. An RMV1-GFP fusion protein localized to the plasma membrane in transformed cells. The Arabidopsis rmv1 mutant was highly resistant to PQ because of the reduction of PQ uptake activity. Uptake studies indicated that RMV1 mediates proton gradient-driven PQ transport. RMV1 overexpressing plants were hypersensitive to PA and PQ and showed elevated PA/PQ uptake activity; supporting the notion that PQ enters plant cells via a carrier system that inherently functions in PA transport. Furthermore; we demonstrated that polymorphic variation in RMV1 controls PA/PQ uptake activity. Our identification of a molecular entity for PA/PQ uptake and sensitivity provides an important clue for our understanding of the mechanism and biological significance of PA uptake. | 2012 | 22492932,1 | https://sci-hub.tw/10.1073/pnas.1121406109 | ||||||
81 | GP00000820 | para (kdr) | Martin | para | P35500 | Drosophila melanogaster | 7227.FBpp0303597 | Belongs to the sodium channel (TC 1.A.1.10) family. Para subfamily. | bas;bss;CG9907;Dmel\CG9907;DmNav;DmNav1;DmNa[[v]];DmNa[[V]];DmNa[[v]]1;l(1)14Da;l(1)ESHS48;lincRNA.S9469;Nav1;Ocd;olfD;par;sbl;sbl-1;Shu;Shudderer | GO:0005509;GO:0005244;GO:0005248;GO:0005272 | GO:0005887;GO:0001518 | GO:0019228;GO:0045433;GO:0001666;GO:0009612;GO:0034765;GO:0086010;GO:0035725;GO:0007638;GO:0060078 | Physiology | Xenobiotic resistance (insecticide) | Anopheles gambiae | Anopheles gambiae - resistant from Kenya | 7165 | Anopheles gambiae | African malaria mosquito | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Nematocera; Culicomorpha; Culicoidea; Culicidae; Anophelinae; Anopheles; Cellia; Pyretophorus; gambiae species complex | 0 | 7165 | Anopheles gambiae | African malaria mosquito | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Nematocera; Culicomorpha; Culicoidea; Culicidae; Anophelinae; Anopheles; Cellia; Pyretophorus; gambiae species complex | 0 | Taxon A | Intraspecific | Candidate Gene | N1575Y | Coding | No | Nonsynonymous | Midoun | AAY | TAY | Asn | 1575 | Tyr | SNP | Footprints of positive selection associated with a mutation (N1575Y) in the voltage-gated sodium channel of Anopheles gambiae. | Insecticide resistance is an ideal model to study the emergence and spread of adaptative variants. In the African malaria mosquito; Anopheles gambiae; this is complemented by a strong public health rationale. In this insect; resistance to pyrethroid and DDT insecticides is strongly associated with the mutations L1014F and L1014S within the para voltage-gated sodium channel (VGSC). Across much of West Africa; 1014F frequency approaches fixation. Here; we document the emergence of a mutation; N1575Y; within the linker between domains III-IV of the VGSC. In data extending over 40 kbp of the VGSC 1575Y occurs on only a single long-range haplotype; also bearing 1014F. The 1014F-1575Y haplotype was found in both M and S molecular forms of An. gambiae in West/Central African sample sites separated by up to 2;000 km. In Burkina Faso M form; 1575Y allele frequency rose significantly from 0.053 to 0.172 between 2008 and 2010. Extended haplotype homozygosity analysis of the wild-type 1575N allele showed rapid decay of linkage disequilibrium (LD); in sharp contrast to the extended LD exhibited by 1575Y. A haplotype with long-range LD and high/increasing frequency is a classical sign of strong positive selection acting on a recent mutant. 1575Y occurs ubiquitously on a 1014F haplotypic background; suggesting that the N1575Y mutation compensates for deleterious fitness effects of 1014F and/or confers additional resistance to insecticides. Haplotypic tests of association suggest the latter: The 1014F-1575Y haplotype confers a significant additive benefit above 1014F-1575N for survival to DDT (M form P = 0.03) and permethrin (S form P = 0.003). | 2012 | 22493253,1 | https://sci-hub.tw/10.1073/pnas.1201475109 | ||||||||||
82 | GP00000709 | Na/K-ATPase alpha-subunit | Martin | K+ ATPase alpha subunit | R4ZHW8 | Danaus plexippus | Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIC subfamily. | Na+ | GO:0005524;GO:0046872;GO:0005391 | GO:0016021 | GO:0071383;GO:0006813;GO:0006814;GO:0071260;GO:0042493;GO:0008217;GO:0090662;GO:0030007;GO:0006883;GO:0060081;GO:0086009;GO:0031947;GO:0045822;GO:0045823;GO:0045989;GO:0010107;GO:1990573;GO:0086004;GO:0002028;GO:0002026;GO:0036376 | Physiology | Xenobiotic resistance (cardiac glucosides) | Other insects | Oncopeltus fasciatus and Lygaeus kalmii | 50557 | Insecta | true insects | class | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda | 0 | 7536 | Oncopeltus fasciatus | milkweed bug | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Paraneoptera; Hemiptera; Prosorrhyncha; Heteroptera; Euheteroptera; Neoheteroptera; Panheteroptera; Pentatomomorpha; Lygaeoidea; Lygaeidae; Lygaeinae; Oncopeltus | 0 | Data not curated | Intergeneric or Higher | Candidate Gene | Q111T + D121N + N122H +F786N + T797A on one gene copy | Coding | No | Nonsynonymous | SNP | Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na;K-ATPase. | The extent of convergent molecular evolution is largely unknown; yet is critical to understanding the genetics of adaptation. Target site insensitivity to cardenolides is a prime candidate for studying molecular convergence because herbivores in six orders of insects have specialized on these plant poisons; which gain their toxicity by blocking an essential transmembrane carrier; the sodium pump (Na;K-ATPase). We investigated gene sequences of the Na;K-ATPase α-subunit in 18 insects feeding on cardenolide-containing plants (spanning 15 genera and four orders) to screen for amino acid substitutions that might lower sensitivity to cardenolides. The replacement N122H that was previously shown to confer resistance in the monarch butterfly (Danaus plexippus) and Chrysochus leaf beetles was found in four additional species; Oncopeltus fasciatus and Lygaeus kalmii (Heteroptera; Lygaeidae); Labidomera clivicollis (Coleoptera; Chrysomelidae); and Liriomyza asclepiadis (Diptera; Agromyzidae). Thus; across 300 Myr of insect divergence; specialization on cardenolide-containing plants resulted in molecular convergence for an adaptation likely involved in coevolution. Our screen revealed a number of other substitutions connected to cardenolide binding in mammals. We confirmed that some of the particular substitutions provide resistance to cardenolides by introducing five distinct constructs of the Drosophila melanogaster gene into susceptible eucaryotic cells under an ouabain selection regime. These functional assays demonstrate that combined substitutions of Q(111) and N(122) are synergistic; with greater than twofold higher resistance than either substitution alone and >12-fold resistance over the wild type. Thus; even across deep phylogenetic branches; evolutionary degrees of freedom seem to be limited by physiological constraints; such that the same molecular substitutions confer adaptation. | 2012 | 22826239,1 | https://sci-hub.tw/10.1073/pnas.1202111109 | 23019645,1 | @& | |||||||||||||||
83 | GP00000710 | Na/K-ATPase alpha-subunit | Martin | K+ ATPase alpha subunit | R4ZHW8 | Danaus plexippus | Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIC subfamily. | Na+ | GO:0005524;GO:0046872;GO:0005391 | GO:0016021 | GO:0071383;GO:0006813;GO:0006814;GO:0071260;GO:0042493;GO:0008217;GO:0090662;GO:0030007;GO:0006883;GO:0060081;GO:0086009;GO:0031947;GO:0045822;GO:0045823;GO:0045989;GO:0010107;GO:1990573;GO:0086004;GO:0002028;GO:0002026;GO:0036376 | Physiology | Xenobiotic resistance (cardiac glucosides) | Other insects | Labidomera clivicollis | 50557 | Insecta | true insects | class | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda | 0 | 131652 | Labidomera clivicollis | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Coleoptera; Polyphaga; Cucujiformia; Chrysomeloidea; Chrysomelidae; Chrysomelinae; Doryphorini; Labidomera | 0 | Data not curated | Interspecific | Candidate Gene | Q111V + N122H | Coding | No | Nonsynonymous | SNP | Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na;K-ATPase. | The extent of convergent molecular evolution is largely unknown; yet is critical to understanding the genetics of adaptation. Target site insensitivity to cardenolides is a prime candidate for studying molecular convergence because herbivores in six orders of insects have specialized on these plant poisons; which gain their toxicity by blocking an essential transmembrane carrier; the sodium pump (Na;K-ATPase). We investigated gene sequences of the Na;K-ATPase α-subunit in 18 insects feeding on cardenolide-containing plants (spanning 15 genera and four orders) to screen for amino acid substitutions that might lower sensitivity to cardenolides. The replacement N122H that was previously shown to confer resistance in the monarch butterfly (Danaus plexippus) and Chrysochus leaf beetles was found in four additional species; Oncopeltus fasciatus and Lygaeus kalmii (Heteroptera; Lygaeidae); Labidomera clivicollis (Coleoptera; Chrysomelidae); and Liriomyza asclepiadis (Diptera; Agromyzidae). Thus; across 300 Myr of insect divergence; specialization on cardenolide-containing plants resulted in molecular convergence for an adaptation likely involved in coevolution. Our screen revealed a number of other substitutions connected to cardenolide binding in mammals. We confirmed that some of the particular substitutions provide resistance to cardenolides by introducing five distinct constructs of the Drosophila melanogaster gene into susceptible eucaryotic cells under an ouabain selection regime. These functional assays demonstrate that combined substitutions of Q(111) and N(122) are synergistic; with greater than twofold higher resistance than either substitution alone and >12-fold resistance over the wild type. Thus; even across deep phylogenetic branches; evolutionary degrees of freedom seem to be limited by physiological constraints; such that the same molecular substitutions confer adaptation. | 2012 | 22826239,1 | https://sci-hub.tw/10.1073/pnas.1202111109 | 23019645,1 | @& | ||||||||||||||||
84 | GP00000711 | Na/K-ATPase alpha-subunit | Martin | K+ ATPase alpha subunit | R4ZHW8 | Danaus plexippus | Belongs to the cation transport ATPase (P-type) (TC 3.A.3) family. Type IIC subfamily. | Na+ | GO:0005524;GO:0046872;GO:0005391 | GO:0016021 | GO:0071383;GO:0006813;GO:0006814;GO:0071260;GO:0042493;GO:0008217;GO:0090662;GO:0030007;GO:0006883;GO:0060081;GO:0086009;GO:0031947;GO:0045822;GO:0045823;GO:0045989;GO:0010107;GO:1990573;GO:0086004;GO:0002028;GO:0002026;GO:0036376 | Physiology | Xenobiotic resistance (cardiac glucosides) | Other insects | Liriomyza asclepiadis | 50557 | Insecta | true insects | class | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda | 0 | 1200980 | Liriomyza asclepiadis | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha; Eremoneura; Cyclorrhapha; Schizophora; Acalyptratae; Opomyzoidea; Agromyzidae; Phytomyzinae; Liriomyza | 0 | Data not curated | Interspecific | Candidate Gene | N122H | Coding | No | Nonsynonymous | Midoun | AAY | CAY | Asn | 122 | His | SNP | Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na;K-ATPase. | The extent of convergent molecular evolution is largely unknown; yet is critical to understanding the genetics of adaptation. Target site insensitivity to cardenolides is a prime candidate for studying molecular convergence because herbivores in six orders of insects have specialized on these plant poisons; which gain their toxicity by blocking an essential transmembrane carrier; the sodium pump (Na;K-ATPase). We investigated gene sequences of the Na;K-ATPase α-subunit in 18 insects feeding on cardenolide-containing plants (spanning 15 genera and four orders) to screen for amino acid substitutions that might lower sensitivity to cardenolides. The replacement N122H that was previously shown to confer resistance in the monarch butterfly (Danaus plexippus) and Chrysochus leaf beetles was found in four additional species; Oncopeltus fasciatus and Lygaeus kalmii (Heteroptera; Lygaeidae); Labidomera clivicollis (Coleoptera; Chrysomelidae); and Liriomyza asclepiadis (Diptera; Agromyzidae). Thus; across 300 Myr of insect divergence; specialization on cardenolide-containing plants resulted in molecular convergence for an adaptation likely involved in coevolution. Our screen revealed a number of other substitutions connected to cardenolide binding in mammals. We confirmed that some of the particular substitutions provide resistance to cardenolides by introducing five distinct constructs of the Drosophila melanogaster gene into susceptible eucaryotic cells under an ouabain selection regime. These functional assays demonstrate that combined substitutions of Q(111) and N(122) are synergistic; with greater than twofold higher resistance than either substitution alone and >12-fold resistance over the wild type. Thus; even across deep phylogenetic branches; evolutionary degrees of freedom seem to be limited by physiological constraints; such that the same molecular substitutions confer adaptation. | 2012 | 22826239,1 | https://sci-hub.tw/10.1073/pnas.1202111109 | ||||||||||||
85 | GP00000749 | Odorant receptor 3 (OR3) | Martin | OR3 | D3J5H6 | Ostrinia nubilalis | Belongs to the insect chemoreceptor superfamily. Heteromeric odorant receptor channel (TC 1.A.69) family. | p;D7Nic1;p<cas>;D7H15S12;D7Icr28RN;P | GO:0005549;GO:0004984 | GO:0016021;GO:0005886 | GO:0007165 | AFK30395 | Behavior | Olfactory behavior (pheromone) | Ostrinia nubilalis | Ostrinia furnacalis | 29057 | Ostrinia nubilalis | European corn borer | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Pyraloidea; Crambidae; Pyraustinae; Ostrinia | 0 | 93504 | Ostrinia furnacalis | Asian corn borer | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Holometabola; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Pyraloidea; Crambidae; Pyraustinae; Ostrinia | 0 | Data not curated | Interspecific | Candidate Gene | A148T | Coding | No | Nonsynonymous | Pinton | GCN | ACN | 1 | transition | Ala | 148 | Thr | SNP | Single mutation to a sex pheromone receptor provides adaptive specificity between closely related moth species. | Sex pheromone communication; acting as a prezygotic barrier to mating; is believed to have contributed to the speciation of moths and butterflies in the order Lepidoptera. Five decades after the discovery of the first moth sex pheromone; little is known about the molecular mechanisms that underlie the evolution of pheromone communication between closely related species. Although Asian and European corn borers (ACB and ECB) can be interbred in the laboratory; they are behaviorally isolated from mating naturally by their responses to subtly different sex pheromone isomers; (E)-12- and (Z)-12-tetradecenyl acetate and (E)-11- and (Z)-11-tetradecenyl acetate (ACB: E12; Z12; ECB; E11; Z11). Male moth olfactory systems respond specifically to the pheromone blend produced by their conspecific females. In vitro; ECB(Z) odorant receptor 3 (OR3); a sex pheromone receptor expressed in male antennae; responds strongly to E11 but also generally to the Z11; E12; and Z12 pheromones. In contrast; we show that ACB OR3; a gene that has been subjected to positive selection (ω = 2.9); responds preferentially to the ACB E12 and Z12 pheromones. In Ostrinia species the amino acid residue corresponding to position 148 in transmembrane domain 3 of OR3 is alanine (A); except for ACB OR3 that has a threonine (T) in this position. Mutation of this residue from A to T alters the pheromone recognition pattern by selectively reducing the E11 response ∼14-fold. These results suggest that discrete mutations that narrow the specificity of more broadly responsive sex pheromone receptors may provide a mechanism that contributes to speciation. | 2012 | 22891317,1 | https://sci-hub.tw/10.1073/pnas.1204661109 | @SexualDimorphism | |||||||
86 | GP00001337 | MC1R | Prigent | MC1R | Q01726 | Homo sapiens | 9606.ENSP00000451605 | Belongs to the G-protein coupled receptor 1 family. | CMM5;MSH-R;SHEP2;MSHR | GO:0008528;GO:0004977;GO:0004980;GO:0031625 | GO:0005886;GO:0005887;GO:0005622 | GO:0007275;GO:0045944;GO:0043473;GO:0007186;GO:0051897;GO:0007189;GO:0035556;GO:0007187;GO:0032720;GO:0010739;GO:0090037;GO:0009650;GO:0070914 | Morphology | Coloration (coat) | Hawaiian feral pig | Hawaiian feral pig-black | 9823 | Sus scrofa | pig | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus | 1 | 9825 | Sus scrofa domesticus | domestic pig | subspecies | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus; Sus scrofa | 1 | Taxon A | Intraspecific | Candidate Gene | c.G>A p.Asp124Asn | Coding | No | Nonsynonymous | Pinton | GAY | AAY | 1 | transition | Asp | 124 | Asn | SNP | Strong signatures of selection in the domestic pig genome. | Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits; including behavior; body composition; reproduction; and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig--the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1; PLAG1; and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other domestic animals and in humans. Most European domestic pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in domestic pigs; most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted pigs; carrying the Dominant white; Patch; or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals and how alleles in domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection. | 2012 | 23151514,1 | https://sci-hub.tw/10.1073/pnas.1217149109 | 26431999,1 | the same mutation is known in European domestic pigs but happens independently in Hawaii | ||||||
87 | GP00000812 | OsPPKL1/qGL3 | Martin | qLTG-3-1 | B3IWI0 | Oryza sativa subsp. japonica | qGL3-1;qLTG3-1 | GO:0004930;GO:0004984 | GO:0016021;GO:0005886 | GO:0007186;GO:0050911 | AAD27631 | Morphology | Grain size | Oryza sativa L. ssp. indica - N643 | Oryza sativa L. ssp. Japonica N411 | 4530 | Oryza sativa | rice | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza | 1 | 4530 | Oryza sativa | rice | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza | 1 | Data not curated | Domesticated | Linkage Mapping | Asp364Glu | Coding | No | Nonsynonymous | Pinton | GAY | GAR | 3 | transversion | Asp | 364 | Glu | SNP | Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. | Grain size and shape are important components determining rice grain yield; and they are controlled by quantitative trait loci (QTLs). Here; we report the cloning and functional characterization of a major grain length QTL; qGL3; which encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1). We found a rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1. The rice genome has other two OsPPKL1 homologs; OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length; whereas OsPPKL2 as a positive regulator. The Kelch domains are essential for the OsPPKL1 biological function. Field trials showed that the application of the qgl3 allele could significantly increase grain yield in both inbred and hybrid rice varieties; due to its favorable effect on grain length; filling; and weight. | 2012 | 23236132,1 | https://sci-hub.tw/10.1073/pnas.1219776110 | |||||||||
88 | GP00000839 | para (kdr) | Martin | para | P35500 | Drosophila melanogaster | 7227.FBpp0303597 | Belongs to the sodium channel (TC 1.A.1.10) family. Para subfamily. | bas;bss;CG9907;Dmel\CG9907;DmNav;DmNav1;DmNa[[v]];DmNa[[V]];DmNa[[v]]1;l(1)14Da;l(1)ESHS48;lincRNA.S9469;Nav1;Ocd;olfD;par;sbl;sbl-1;Shu;Shudderer | GO:0005509;GO:0005244;GO:0005248;GO:0005272 | GO:0005887;GO:0001518 | GO:0019228;GO:0045433;GO:0001666;GO:0009612;GO:0034765;GO:0086010;GO:0035725;GO:0007638;GO:0060078 | Physiology | Xenobiotic resistance (insecticide) | Hyalella azteca -sensitive to pyrethroids | Hyalella azteca - resistant to pyrethroids | 294128 | Hyalella azteca | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Crustacea; Multicrustacea; Malacostraca; Eumalacostraca; Peracarida; Amphipoda; Senticaudata; Talitrida; Talitroidea; Hyalellidae; Hyalella | 0 | 294128 | Hyalella azteca | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Crustacea; Multicrustacea; Malacostraca; Eumalacostraca; Peracarida; Amphipoda; Senticaudata; Talitrida; Talitroidea; Hyalellidae; Hyalella | 0 | Taxon A | Intraspecific | Candidate Gene | L925I | Coding | No | Nonsynonymous | Pinton | ATR | ATY | 3 | transversion | Leu | 925 | Ile | SNP | Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean; Hyalella azteca. | Use of pesticides can have substantial nonlethal impacts on nontarget species; including driving evolutionary change; often with unknown consequences for species; ecosystems; and society. Hyalella azteca; a species complex of North American freshwater amphipods; is widely used for toxicity testing of water and sediment and has frequently shown toxicity due to pyrethroid pesticides. We demonstrate that 10 populations; 3 from laboratory cultures and 7 from California water bodies; differed by at least 550-fold in sensitivity to pyrethroids. The populations sorted into four phylogenetic groups consistent with species-level divergence. By sequencing the primary pyrethroid target site; the voltage-gated sodium channel; we show that point mutations and their spread in natural populations were responsible for differences in pyrethroid sensitivity. At least one population had both mutant and WT alleles; suggesting ongoing evolution of resistance. Although nonresistant H. azteca were susceptible to the typical neurotoxic effects of pyrethroids; gene expression analysis suggests the mode of action in resistant H. azteca was not neurotoxicity but was oxidative stress sustained only at considerably higher pyrethroid concentrations. The finding that a nontarget aquatic species has acquired resistance to pesticides used only on terrestrial pests is troubling evidence of the impact of chronic pesticide transport from land-based applications into aquatic systems. Our findings have far-reaching implications for continued uncritical use of H. azteca as a principal species for monitoring and environmental policy decisions. | 2013 | 24065824,1 | https://sci-hub.tw/10.1073/pnas.1302023110 | ||||||||||
89 | GP00000840 | para (kdr) | Martin | para | P35500 | Drosophila melanogaster | 7227.FBpp0303597 | Belongs to the sodium channel (TC 1.A.1.10) family. Para subfamily. | bas;bss;CG9907;Dmel\CG9907;DmNav;DmNav1;DmNa[[v]];DmNa[[V]];DmNa[[v]]1;l(1)14Da;l(1)ESHS48;lincRNA.S9469;Nav1;Ocd;olfD;par;sbl;sbl-1;Shu;Shudderer | GO:0005509;GO:0005244;GO:0005248;GO:0005272 | GO:0005887;GO:0001518 | GO:0019228;GO:0045433;GO:0001666;GO:0009612;GO:0034765;GO:0086010;GO:0035725;GO:0007638;GO:0060078 | Physiology | Xenobiotic resistance (insecticide) | Hyalella azteca -sensitive to pyrethroids | Hyalella azteca - resistant to pyrethroids | 294128 | Hyalella azteca | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Crustacea; Multicrustacea; Malacostraca; Eumalacostraca; Peracarida; Amphipoda; Senticaudata; Talitrida; Talitroidea; Hyalellidae; Hyalella | 0 | 294128 | Hyalella azteca | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Crustacea; Multicrustacea; Malacostraca; Eumalacostraca; Peracarida; Amphipoda; Senticaudata; Talitrida; Talitroidea; Hyalellidae; Hyalella | 0 | Taxon A | Intraspecific | Candidate Gene | M918L | Coding | No | Nonsynonymous | Pinton | ATG | YTG | 1 | transversion | Met | 918 | Leu | SNP | Multiple origins of pyrethroid insecticide resistance across the species complex of a nontarget aquatic crustacean; Hyalella azteca. | Use of pesticides can have substantial nonlethal impacts on nontarget species; including driving evolutionary change; often with unknown consequences for species; ecosystems; and society. Hyalella azteca; a species complex of North American freshwater amphipods; is widely used for toxicity testing of water and sediment and has frequently shown toxicity due to pyrethroid pesticides. We demonstrate that 10 populations; 3 from laboratory cultures and 7 from California water bodies; differed by at least 550-fold in sensitivity to pyrethroids. The populations sorted into four phylogenetic groups consistent with species-level divergence. By sequencing the primary pyrethroid target site; the voltage-gated sodium channel; we show that point mutations and their spread in natural populations were responsible for differences in pyrethroid sensitivity. At least one population had both mutant and WT alleles; suggesting ongoing evolution of resistance. Although nonresistant H. azteca were susceptible to the typical neurotoxic effects of pyrethroids; gene expression analysis suggests the mode of action in resistant H. azteca was not neurotoxicity but was oxidative stress sustained only at considerably higher pyrethroid concentrations. The finding that a nontarget aquatic species has acquired resistance to pesticides used only on terrestrial pests is troubling evidence of the impact of chronic pesticide transport from land-based applications into aquatic systems. Our findings have far-reaching implications for continued uncritical use of H. azteca as a principal species for monitoring and environmental policy decisions. | 2013 | 24065824,1 | https://sci-hub.tw/10.1073/pnas.1302023110 | ||||||||||
90 | GP00001468 | Rhodopsin (RH1) | Prigent | rho | P35359 | Danio rerio | 7955.ENSDARP00000011562 | Belongs to the G-protein coupled receptor 1 family. Opsin subfamily. | Rh;RH1;zfo2;rh1.1;zfrho;wu:fi06d11 | GO:0008020;GO:0009881;GO:0005502;GO:0016918 | GO:0016021;GO:0001750;GO:0097381 | GO:0018298;GO:0007601;GO:0016038;GO:0016056;GO:0009583 | AB290449 | Physiology | Color vision (blue shift) | other teleost Percomorphaceae fishes (fugu & stickleback & medaka) | Pacific bluefin tuna | 1489872 | Percomorphaceae | no rank | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea | 0 | 8238 | Thunnus orientalis | Pacific bluefin tuna | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea; Percomorphaceae; Pelagiaria; Scombriformes; Scombridae; Scombrinae; Thunnini; Thunnus | 0 | Taxon A | Intergeneric or Higher | Candidate Gene | p.E122Q (G>C) | Coding | No | Nonsynonymous | Pinton | GAR | GGR | 2 | transition | Glu | 122 | Gln | SNP | Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. | Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values; the open-ocean lifestyle of tuna; in which effective sensing systems such as color vision are required for capture of prey; has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna; we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis); using next-generation sequencing technology. A total of 26;433 protein-coding genes were predicted from 16;802 assembled scaffolds. From these; we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS); UV-sensitive (short-wavelength sensitive 1; SWS1); blue-sensitive (SWS2); rhodopsin (RH1); and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e.; blue shift). Pacific bluefin tuna has at least five RH2 paralogs; the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover; phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus; Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1; RH2; and SWS2); which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and; thereby; could help to improve the technology to culture such fish in captivity for resource management. | 2013 | 23781100,1 | https://sci-hub.tw/10.1073/pnas.1302051110 | Effect of the mutation demonstrated in a previous study in coelacanth | |||||||
91 | GP00001469 | Green-sensitive opsin (RH2) | Prigent | opn1mw1 | Q9W6A5 | Danio rerio | 7955.ENSDARP00000001158 | Belongs to the G-protein coupled receptor 1 family. Opsin subfamily. | RH2-1;rh2.1;zfgr1;grops1;rh21 | GO:0008020;GO:0009881 | GO:0016021;GO:0001750 | GO:0018298;GO:0007601;GO:0007602 | AB290451 | Physiology | Color vision (blue shift) | other teleost Percomorphaceae fishes (fugu & stickleback) | Pacific bluefin tuna | 1489872 | Percomorphaceae | no rank | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea | 0 | 8238 | Thunnus orientalis | Pacific bluefin tuna | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea; Percomorphaceae; Pelagiaria; Scombriformes; Scombridae; Scombrinae; Thunnini; Thunnus | 0 | Taxon A | Intergeneric or Higher | Candidate Gene | p.E122Q (G>C) in four of five genes | Coding | No | Nonsynonymous | PInton | GAR | GGR | 2 | transition | Glu | 122 | Gln | SNP | Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. | Tunas are migratory fishes in offshore habitats and top predators with unique features. Despite their ecological importance and high market values; the open-ocean lifestyle of tuna; in which effective sensing systems such as color vision are required for capture of prey; has been poorly understood. To elucidate the genetic and evolutionary basis of optic adaptation of tuna; we determined the genome sequence of the Pacific bluefin tuna (Thunnus orientalis); using next-generation sequencing technology. A total of 26;433 protein-coding genes were predicted from 16;802 assembled scaffolds. From these; we identified five common fish visual pigment genes: red-sensitive (middle/long-wavelength sensitive; M/LWS); UV-sensitive (short-wavelength sensitive 1; SWS1); blue-sensitive (SWS2); rhodopsin (RH1); and green-sensitive (RH2) opsin genes. Sequence comparison revealed that tuna's RH1 gene has an amino acid substitution that causes a short-wave shift in the absorption spectrum (i.e.; blue shift). Pacific bluefin tuna has at least five RH2 paralogs; the most among studied fishes; four of the proteins encoded may be tuned to blue light at the amino acid level. Moreover; phylogenetic analysis suggested that gene conversions have occurred in each of the SWS2 and RH2 loci in a short period. Thus; Pacific bluefin tuna has undergone evolutionary changes in three genes (RH1; RH2; and SWS2); which may have contributed to detecting blue-green contrast and measuring the distance to prey in the blue-pelagic ocean. These findings provide basic information on behavioral traits of predatory fish and; thereby; could help to improve the technology to culture such fish in captivity for resource management. | 2013 | 23781100,1 | https://sci-hub.tw/10.1073/pnas.1302051110 | by gene duplication and conversion there are 5 RH2 genes in tuna and four of which have the same substitution | |||||||
92 | GP00001284 | Phosphate transporter PHO1 | Arnoult | PHO1 | Q8S403 | Arabidopsis thaliana | 3702.AT3G23430.1 | Belongs to the SYG1 (TC 2.A.94) family. | ARABIDOPSIS PHOSPHATE 1;ATPHO1;phosphate 1;At3g23430;MLM24.26 | GO:0000822;GO:0015114 | GO:0016021;GO:0005886;GO:0000139;GO:0005794;GO:0005789;GO:0005802 | GO:0016036;GO:0048016;GO:0006799 | 821924 | Morphology | Root growth (allometry of lateral roots) | Arabidopsis thaliana- 69 accessions | Arabidopsis thaliana- 69 accessions | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 0 | Unknown | Intraspecific | Association Mapping | histidine to tyrosine @position 8388425 in chromosome III | Coding | No | Nonsynonymous | Pinton | CAY | 8388425 | TAY | 1 | transition | His | Tyr | SNP | Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. | Phenotypic plasticity is presumed to be involved in adaptive change toward species diversification. We thus examined how candidate genes underlying natural variation across populations might also mediate plasticity within an individual. Our implementation of an integrative "plasticity space" approach revealed that the root plasticity of a single Arabidopsis accession exposed to distinct environments broadly recapitulates the natural variation "space." Genome-wide association mapping identified the known gene PHOSPHATE 1 (PHO1) and other genes such as Root System Architecture 1 (RSA1) associated with differences in root allometry; a highly plastic trait capturing the distribution of lateral roots along the primary axis. The response of mutants in the Columbia-0 background suggests their involvement in signaling key modulators of root development including auxin; abscisic acid; and nitrate. Moreover; genotype-by-environment interactions for the PHO1 and RSA1 genes in Columbia-0 phenocopy the root allometry of other natural variants. This finding supports a role for plasticity responses in phenotypic evolution in natural environments. | 2013 | 23980140,1 | https://sci-hub.tw/10.1073/pnas.1305883110 | @GxE - no strong demonstration of the putative causal SNP; natural variation between accessions recapitulates phenotypic plasticity in Col-0 | ||||||
93 | GP00000117 | AtGA20ox1 (=GA5=Sd1) | Martin | GA20OX1 | Q39110 | Arabidopsis thaliana | 3702.AT4G25420.1 | Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily. | ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420 | GO:0046872;GO:0045544 | GO:0005737 | GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826 | U20872 | Morphology | Plant size (dwarfism) | Arabidopsis thaliana - Col | Arabidopsis thaliana - dwarf accession (see manuscript) | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Domesticated | Linkage Mapping | W46* | Coding | Yes | Nonsense | Courtier | TGG | nd | TGA | 3 | transition | Trp | 46 | STP | SNP | Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley. | Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants. | 2013 | 24023067,1 | https://sci-hub.tw/10.1073/pnas.1314979110 | ||||||
94 | GP00000118 | AtGA20ox1 (=GA5=Sd1) | Martin | GA20OX1 | Q39110 | Arabidopsis thaliana | 3702.AT4G25420.1 | Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily. | ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420 | GO:0046872;GO:0045544 | GO:0005737 | GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826 | U20872 | Morphology | Plant size (dwarfism) | Arabidopsis thaliana - Col | Arabidopsis thaliana - dwarf accession (see manuscript) | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Domesticated | Linkage Mapping | W271* | Coding | Yes | Nonsense | Courtier | TGG | nd | TGA | 3 | transition | Trp | 271 | STP | SNP | Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley. | Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants. | 2013 | 24023067,1 | https://sci-hub.tw/10.1073/pnas.1314979110 | ||||||
95 | GP00000119 | AtGA20ox1 (=GA5=Sd1) | Martin | GA20OX1 | Q39110 | Arabidopsis thaliana | 3702.AT4G25420.1 | Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily. | ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420 | GO:0046872;GO:0045544 | GO:0005737 | GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826 | U20872 | Morphology | Plant size (dwarfism) | Arabidopsis thaliana - Col | Arabidopsis thaliana - dwarf accession (see manuscript) | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Domesticated | Linkage Mapping | E312* | Coding | Yes | Nonsense | Courtier | GAR | nd | TAR | 1 | transversion | Glu | 312 | STP | SNP | Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley. | Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants. | 2013 | 24023067,1 | https://sci-hub.tw/10.1073/pnas.1314979110 | ||||||
96 | GP00000120 | AtGA20ox1 (=GA5=Sd1) | Martin | GA20OX1 | Q39110 | Arabidopsis thaliana | 3702.AT4G25420.1 | Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily. | ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420 | GO:0046872;GO:0045544 | GO:0005737 | GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826 | U20872 | Morphology | Plant size (dwarfism) | Arabidopsis thaliana - Col | Arabidopsis thaliana - dwarf accession (see manuscript) | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Domesticated | Linkage Mapping | G919A | Coding | No | Nonsynonymous | Karla | GGN | GCN | 2 | transversion | Gly | 919 | Ala | SNP | Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley. | Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants. | 2013 | 24023067,1 | https://sci-hub.tw/10.1073/pnas.1314979110 | |||||||
97 | GP00000121 | AtGA20ox1 (=GA5=Sd1) | Martin | GA20OX1 | Q39110 | Arabidopsis thaliana | 3702.AT4G25420.1 | Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily. | ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420 | GO:0046872;GO:0045544 | GO:0005737 | GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826 | U20872 | Morphology | Plant size (dwarfism) | Arabidopsis thaliana - Col | Arabidopsis thaliana - dwarf accession (see manuscript) | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Domesticated | Linkage Mapping | G940G | Coding | No | Nonsynonymous | SNP | Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley. | Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants. | 2013 | 24023067,1 | https://sci-hub.tw/10.1073/pnas.1314979110 | |||||||||||||||
98 | GP00000122 | AtGA20ox1 (=GA5=Sd1) | Martin | GA20OX1 | Q39110 | Arabidopsis thaliana | 3702.AT4G25420.1 | Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily. | ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420 | GO:0046872;GO:0045544 | GO:0005737 | GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826 | U20872 | Morphology | Plant size (dwarfism) | Arabidopsis thaliana - Col | Arabidopsis thaliana - dwarf accession (see manuscript) | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Domesticated | Linkage Mapping | C1334G | Coding | No | Nonsynonymous | Karla | TGY | GGN | 1 | transversion | Cys | 1334 | Gly | SNP | Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley. | Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants. | 2013 | 24023067,1 | https://sci-hub.tw/10.1073/pnas.1314979110 | |||||||
99 | GP00000123 | AtGA20ox1 (=GA5=Sd1) | Martin | GA20OX1 | Q39110 | Arabidopsis thaliana | 3702.AT4G25420.1 | Belongs to the iron/ascorbate-dependent oxidoreductase family. GA20OX subfamily. | ARABIDOPSIS THALIANA GIBBERELLIN 20-OXIDASE 1;AT2301;ATGA20OX1;GA REQUIRING 5;GA5;GIBBERELLIN 20-OXIDASE;T30C3.90;T30C3_90;20ox1;At2301;At4g25420 | GO:0046872;GO:0045544 | GO:0005737 | GO:0009908;GO:0009740;GO:0009686;GO:0048366;GO:0009739;GO:0048575;GO:0009826 | U20872 | Morphology | Plant size (dwarfism) | Arabidopsis thaliana - Col | Arabidopsis thaliana - dwarf accession (see manuscript) | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | 3702 | Arabidopsis thaliana | thale cress | species | cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis | 1 | Data not curated | Domesticated | Linkage Mapping | Splice Site mutation G742A | Coding | No | Nonsynonymous | Karla | GGN | GCN | 2 | transversion | Gly | 742 | Ala | SNP | Arabidopsis semidwarfs evolved from independent mutations in GA20ox1; ortholog to green revolution dwarf alleles in rice and barley. | Understanding the genetic bases of natural variation for developmental and stress-related traits is a major goal of current plant biology. Variation in plant hormone levels and signaling might underlie such phenotypic variation occurring even within the same species. Here we report the genetic and molecular basis of semidwarf individuals found in natural Arabidopsis thaliana populations. Allelism tests demonstrate that independent loss-of-function mutations at GA locus 5 (GA5); which encodes gibberellin 20-oxidase 1 (GA20ox1) involved in the last steps of gibberellin biosynthesis; are found in different populations from southern; western; and northern Europe; central Asia; and Japan. Sequencing of GA5 identified 21 different loss-of-function alleles causing semidwarfness without any obvious general tradeoff affecting plant performance traits. GA5 shows signatures of purifying selection; whereas GA5 loss-of-function alleles can also exhibit patterns of positive selection in specific populations as shown by Fay and Wu's H statistics. These results suggest that antagonistic pleiotropy might underlie the occurrence of GA5 loss-of-function mutations in nature. Furthermore; because GA5 is the ortholog of rice SD1 and barley Sdw1/Denso green revolution genes; this study illustrates the occurrence of conserved adaptive evolution between wild A.thaliana and domesticated plants. | 2013 | 24023067,1 | https://sci-hub.tw/10.1073/pnas.1314979110 | @Splicing | ||||||
100 | GP00001348 | tyrosinase (TYR) | Prigent | Tyr | P11344 | Mus musculus | 10090.ENSMUSP00000004770 | Belongs to the tyrosinase family. | c;Oca1;skc35;albino | GO:0042803;GO:0046982;GO:0005507;GO:0004503 | GO:0016021;GO:0005737;GO:0005829;GO:0005634;GO:0043231;GO:0048471;GO:0042470;GO:0033162 | GO:0042438;GO:0043473;GO:0008283;GO:0033280;GO:0051591;GO:0009411;GO:0048538 | Morphology | Coloration (skin; eye; freckles) | Human-dark pigmentation | human-light pigmentation | 9606 | Homo sapiens | human | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo | 0 | 9606 | Homo sapiens | human | species | cellular organisms; Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo | 0 | Taxon A | Intraspecific | Association Mapping | c. C>A p.Ser192Tyr | Coding | No | Nonsynonymous | Karla | TCN | TAY | 2 | transversion | Ser | 192 | Tyr | SNP | Direct evidence for positive selection of skin; hair; and eye pigmentation in Europeans during the last 5;000 y. | Pigmentation is a polygenic trait encompassing some of the most visible phenotypic variation observed in humans. Here we present direct estimates of selection acting on functional alleles in three key genes known to be involved in human pigmentation pathways--HERC2; SLC45A2; and TYR--using allele frequency estimates from Eneolithic; Bronze Age; and modern Eastern European samples and forward simulations. Neutrality was overwhelmingly rejected for all alleles studied; with point estimates of selection ranging from around 2-10% per generation. Our results provide direct evidence that strong selection favoring lighter skin; hair; and eye pigmentation has been operating in European populations over the last 5;000 y. | 2014 | 24616518,1 | https://sci-hub.tw/10.1073/pnas.1316513111 | codominance is assumed- under positive selection in European populations |