Phenotypic Defect

Protein class/Molecular function

Alternate names

Medicago Gene ID

Soybean Gene ID

Phaseolus Gene ID

Myc Phenotype

Nodule Organogenesis

Medtr7g080390

Mtr.48571.1.S1_at

Glyma.18G244300

Phvul.008G052400

Wang, J., Tóth, K., Tanaka, K., Nguyen, C.T., Yan, Z., Brechenmacher, L., Dahmen, J., Chen, M., Thelen, J.J., and Qiu, L. (2014). A soybean acyl carrier protein, GmACP, is important for root nodule symbiosis. Molecular Plant-Microbe Interactions 27, 415-423.

PvAGO5, GmAGO5

Nod+/-, White++

Multidomain protein (RNA silencing)

Medtr4g056430, Medtr4g056470

Mtr.45521.1.S1_at

Lj0g3v0169039.1

Glyma.12G083500

Phvul.011G088200

Reyero-Saavedra, M., Qiao, Z., Sánchez-Correa, M., Díaz-Pineda, M., Reyes, J., Covarrubias, A., Libault, M., and Valdés-López, O. (2017). Gene silencing of ARGONAUTE5 negatively affects the establishment of the legume-rhizobia symbiosis. Genes 8, 352.

Enzyme (Metalloprotease; Deubiquitinating)

ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM (AMSH)

Medtr6g083940

Mtr.21924.1.S1_at; Mtr.21925.1.S1_s_at

Glyma.07G093100

Phvul.003G094300

Małolepszy, A., Urbański, D.F., James, E.K., Sandal, N., Isono, E., Stougaard, J., and Andersen, S.U. (2015). The deubiquitinating enzyme AMSH 1 is required for rhizobial infection and nodule organogenesis in Lotus japonicus. The Plant Journal 83, 719-731.

Transporter (Ammonium)

AMMONIUM TRANSPORTER 1.1 (AMT1.1)

Medtr1g045550

Mtr.10556.1.S1_at

Lj5g3v1314550, Lj0g3v0302059

Glyma.10G132300

Phvul.007G231700

Rogato, A., D’Apuzzo, E., Barbulova, A., Omrane, S., Stedel, C., Simon-Rosin, U., Katinakis, P., Flemetakis, M., Udvardi, M., and Chiurazzi, M. (2008). Tissue-specific down-regulation of LjAMT1; 1 compromises nodule function and enhances nodulation in Lotus japonicus. Plant molecular biology 68, 585.

Membrane binding protein

Medtr8g038210

Mtr.14183.1.S1_at

Glyma.13G199800

Phvul.011G209300

Carrasco-Castilla, J., Ortega-Ortega, Y., Jáuregui-Zúñiga, D., Juárez-Verdayes, M.A., Arthikala, M.-K., Monroy-Morales, E., Nava, N., Santana, O., Sánchez-López, R., and Quinto, C. (2018). Down-regulation of a Phaseolus vulgaris annexin impairs rhizobial infection and nodulation. Environmental and Experimental Botany 153, 108-119.

Enzyme (Aspartyl protease)

ASPARTIC PEPTIDASE NODULE-INDUCED 1 (APN1)

Somaclonal mutagenesis

Medtr0036s0070

Mtr.8869.1.S1_at

Lotus Chromosome 3 LC279017.1

Glyma.08G166200

Phvul.005G050500

Yamaya‐Ito, H., Shimoda, Y., Hakoyama, T., Sato, S., Kaneko, T., Hossain, M.S., Shibata, S., Kawaguchi, M., Hayashi, M., and Kouchi, H. (2018). Loss‐of‐function of ASPARTIC PEPTIDASE NODULE‐INDUCED 1 (APN 1) in Lotus japonicus restricts efficient nitrogen‐fixing symbiosis with specific Mesorhizobium loti strains. The Plant Journal 93, 5-16.

TF (Auxin responsive)

AUXIN RESPONSE FACTOR 16a (ARF16a)

Medtr1g094960

Mtr.39233.1.S1_at

Glyma.10G210600

Phvul.007G095000

Breakspear, A., Liu, C., Roy, S., Stacey, N., Rogers, C., Trick, M., Morieri, G., Mysore, K.S., Wen, J., and Oldroyd, G.E. (2014). The root hair “infectome” of Medicago truncatula uncovers changes in cell cycle genes and reveals a requirement for auxin signaling in rhizobial infection. The Plant Cell 26, 4680-4701.

GmARF8a/GmARF8b

TF (Auxin responsive)

AUXIN RESPONSE FACTOR 16a (ARF8a/ARF8b)

Medtr5g076270, Medtr5g076270

Mtr.5139.1.S1_at, Mtr.5198.1.S1_at

Glyma.14G208500, Glyma.02G239600

Phvul.008G242400

Wang, Y., Li, K., Chen, L., Zou, Y., Liu, H., Tian, Y., Li, D., Wang, R., Zhao, F., and Ferguson, B.J. (2015). MicroRNA167-directed regulation of the auxin response factors GmARF8a and GmARF8b is required for soybean nodulation and lateral root development. Plant physiology 168, 984-999.

TF (Auxin responsive)

Medtr8g089630

Mtr.13778.1.S1_at

Glyma.05G172600

Phvul.002G253600

Gavrin, A., Jansen, V., Ivanov, S., Bisseling, T., and Fedorova, E. (2015). ARP2/3-Mediated Actin Nucleation Associated With Symbiosome Membrane Is Essential for the Development of Symbiosomes in Infected Cells of Medicago truncatula Root Nodules. Mol Plant Microbe Interact 28, 605-614.

Nod++, White++

Multiprotein complex subunit (Actin nucleator)

ACTIN-RELATED PROTEIN COMPONENT1 (ARPC1)

Medtr3g049070

Mtr.37170.1.S1_at

Glyma.10G216300

Phvul.005G127400

Hossain, M.S., Liao, J., James, E.K., Sato, S., Tabata, S., Jurkiewicz, A., Madsen, L.H., Stougaard, J., Ross, L., and Szczyglowski, K. (2012). Lotus japonicus ARPC1 is required for rhizobial infection. Plant physiology 160, 917-928.

Multiprotein complex subunit (Autophagy related)

Mtr.9470.1.S1_at

Glyma.11G153900

Phvul.005G029900

Estrada-Navarrete, G., Cruz-Mireles, N., Lascano, R., Alvarado-Affantranger, X., Hernández-Barrera, A., Barraza, A., Olivares, J.E., Arthikala, M.-K., Cárdenas, L., and Quinto, C. (2016). An autophagy-related kinase is essential for the symbiotic relationship between Phaseolus vulgaris and both rhizobia and arbuscular mycorrhizal fungi. The Plant Cell 28, 2326-2341.

GmBCH1/GmBCH2

Enzyme (Hydroxylase)

β-CAROTENE HYDROXYLASE (BCH1/BCH2)

Medtr6g048440, Medtr7g085180

Mtr.33915.1.S1_at, Mtr.50032.1.S1_at

Lj5g3v1988680, Lj0g3v0299729, Lj1g3v3948070 (BCH2), Lj1g3v3948060 (BCH2)

Glyma.10G231200, Glyma.16G043300

Phvul.004G108900, Phvul.001G099900, Phvul.001G100100

Kim, Y.-K., Kim, S., Um, J.-H., Kim, K., Choi, S.-K., Um, B.-H., Kang, S.-W., Kim, J.-W., Takaichi, S., and Song, S.-B. (2013). Functional implication of β-carotene hydroxylases in soybean nodulation. Plant physiology 162, 1420-1433.

TF (Brassinosteroid pathway)

Medtr5g019550

Mtr.43192.1.S1_at

Glyma.01G178000

Phvul.002G026700, Phvul.002G026800

Yan, Q., Wang, L., and Li, X. (2018). GmBEHL1, a BES1/BZR1 family protein, negatively regulates soybean nodulation. Scientific reports 8, 7614.

Enzyme (Glucanase)

Medtr3g083580

Mtr.20928.1.S1_at

Glyma.17G202900

Phvul.001G056400

Gaudioso-Pedraza, R., Beck, M., Frances, L., Kirk, P., Ripodas, C., Niebel, A., Oldroyd, G.E., Benitez-Alfonso, Y., and de Carvalho-Niebel, F. (2018). Callose-regulated symplastic communication coordinates symbiotic root nodule development. Current Biology 28, 3562-3577. e3566

TF (bHLH motif containing)

Medtr3g099620

Mtr.10993.1.S1_at

Glyma.04G098400

Phvul.009G033800

Godiard, L., Lepage, A., Moreau, S., Laporte, D., Verdenaud, M., Timmers, T., and Gamas, P. (2011). MtbHLH1, a bHLH transcription factor involved in Medicago truncatula nodule vascular patterning and nodule to plant metabolic exchanges. New Phytologist 191, 391-404.

TF (bHLH motif containing)

BASIC HELIX–LOOP–HELIX 476 (BHLH476)

Medtr5g014520

Glyma.01G198100

Phvul.002G007400

Ariel, F., Brault-Hernandez, M., Laffont, C., Huault, E., Brault, M., Plet, J., Moison, M., Blanchet, S., Ichanté, J.L., and Chabaud, M. (2012). Two direct targets of cytokinin signaling regulate symbiotic nodulation in Medicago truncatula. The Plant Cell 24, 3838-3852.

Msa.1056.1.S1_at

Glyma.18G237000

Phvul.008G059600

Arthikala, M.-K., Nanjareddy, K., and Lara, M. (2018). In BPS1 Downregulated Roots, the BYPASS1 Signal Disrupts the Induction of Cortical Cell Divisions in Bean-Rhizobium Symbiosis. Genes 9, 11.

Kinase (LRR-RLK)

Medtr3g095100

Mtr.45830.1.S1_at

Glyma.04G218300, Glyma.06G147600

Phvul.005G005900

Cheng, X., Gou, X., Yin, H., Mysore, K.S., Li, J., and Wen, J. (2017). Functional characterisation of brassinosteroid receptor MtBRI1 in Medicago truncatula. Scientific reports 7, 9327.

Channel (Cations)

Medtr5g007630

Glyma.09G168500

Phvul.004G143800

Chiasson, D.M., Haage, K., Sollweck, K., Brachmann, A., Dietrich, P., and Parniske, M. (2017). A quantitative hypermorphic CNGC allele confers ectopic calcium flux and impairs cellular development. Elife 6, e25012.

TF (bZIP domain containing)

BASIC LEUCINE ZIPPER FAMILY PROTEIN (BZF)

Medtr3g436010

Mtr.9651.1.S1_at

Glyma.18G117100, Glyma.08G302500

Phvul.006G029200

Nishimura, R., Ohmori, M., Fujita, H., and Kawaguchi, M. (2002). A Lotus basic leucine zipper protein with a RING-finger motif negatively regulates the developmental program of nodulation. Proceedings of the National Academy of Sciences 99, 15206-15210.

Nod+, Pink +/- (C)

Medtr6g084640

Mtr.8651.1.S1_a_at

Glyma.09G185500

Li, X., Feng, H., Wen, J., Dong, J., and Wang, T. (2018). MtCAS31 Aids Symbiotic Nitrogen Fixation by Protecting the Leghemoglobin MtLb120-1 Under Drought Stress in Medicago truncatula. Front Plant Sci 9, 633.

Enzyme (Synthase)

CYSTATHIONE BETASYNTHASE 1 (CBS1)

Medtr6g052300

Mtr.23516.1.S1_at

Glyma.09G129700, Glyma.16G177500

Phvul.004G106300

Sinharoy, S., Torres-Jerez, I., Bandyopadhyay, K., Kereszt, A., Pislariu, C.I., Nakashima, J., Benedito, V.A., Kondorosi, E., and Udvardi, M.K. (2013). The C2H2 transcription factor regulator of symbiosome differentiation represses transcription of the secretory pathway gene VAMP721a and promotes symbiosome development in Medicago truncatula. Plant Cell 25, 3584-3601.

Enzyme (Oxidoreductase)

CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7)

Mtr.32038.1.S1_at

Glyma.01G073200

Phvul.008G152801

Liu, J., Novero, M., Charnikhova, T., Ferrandino, A., Schubert, A., Ruyter-Spira, C., Bonfante, P., Lovisolo, C., Bouwmeester, H.J., and Cardinale, F. (2013). Carotenoid cleavage dioxygenase 7 modulates plant growth, reproduction, senescence, and determinate nodulation in the model legume Lotus japonicus. Journal of experimental botany 64, 1967-1981.

Anaphase-promoting complex activator

CELL CYCLE SWITCH GENE encoding a 52 kDa protein (CCS 52a)

Medtr4g102510

Msa.3010.1.S1_at; Mtr.12852.1.S1_at; Mtr.4030.1.S1_at

Glyma.7G133000

Phvul.003G213700

Vinardell, J.M., Fedorova, E., Cebolla, A., Kevei, Z., Horvath, G., Kelemen, Z., Tarayre, S., Roudier, F., Mergaert, P., Kondorosi, A., and Kondorosi, E. (2003). Endoreduplication mediated by the anaphase-promoting complex activator CCS52A is required for symbiotic cell differentiation in Medicago truncatula nodules. The Plant cell 15, 2093-2105.

Anaphase-promoting complex component

Medtr8g058380

Mtr.51354.1.S1_at

Glyma.06G228700

Phvul.011G165500

Kuppusamy, K.T., Ivashuta, S., Bucciarelli, B., Vance, C.P., Gantt, J.S., and VandenBosch, K.A. (2009). Knockdown of CELL DIVISION CYCLE16 reveals an inverse relationship between lateral root and nodule numbers and a link to auxin in Medicago truncatula. Plant physiology 151, 1155-1166.

Enzyme (Calcium dependent Kinase)

CALCIUM DEPENDANT PROTEIN KINASE 1 (CDPK1)

Mtr.249.1.S1_s_at

Glyma.01G166100, Glyma.11G077300

Phvul.002G108700

Ivashuta, S., Liu, J., Liu, J., Lohar, D.P., Haridas, S., Bucciarelli, B., VandenBosch, K.A., Vance, C.P., Harrison, M.J., and Gantt, J.S. (2005). RNA interference identifies a calcium-dependent protein kinase involved in Medicago truncatula root development. The Plant Cell 17, 2911-2921.

Enzyme (Glycosyl hydrolase)

Medtr1g013150

Mtr.42876.1.S1_at

Glyma.17G217000, Glyma.14G110700

Phvul.001G046400

Malolepszy, A., Kelly, S., Sørensen, K.K., James, E.K., Kalisch, C., Bozsoki, Z., Panting, M., Andersen, S.U., Sato, S., and Tao, K. (2018). A plant chitinase controls cortical infection thread progression and nitrogen-fixing symbiosis. Elife 7, e38874.

Enzyme (Oxidoreductase)

Medtr5g097910

Mtr.15678.1.S1_s_at

Lj2g3v3339170, Lj0g3v0328269, 8 other homologs

Glyma.02G307300

Phvul.008G287200

Wasson, A.P., Pellerone, F.I., and Mathesius, U. (2006). Silencing the flavonoid pathway in Medicago truncatula inhibits root nodule formation and prevents auxin transport regulation by rhizobia. The Plant Cell 18, 1617-1629.

Enzyme (Synthase)

Medtr7g084300

Msa.3134.1.S1_at

Glyma.19G105100

Phvul.001G083000

Zhang, J., Subramanian, S., Stacey, G., and Yu, O. (2009). Flavones and flavonols play distinct critical roles during nodulation of Medicago truncatula by Sinorhizobium meliloti. The Plant Journal 57, 171-183.

Unknown (Scythe_N Ubiquitin-like domain containing)

CCAMK INTERACTING PROTEIN OF APPROXIMATELY 73 KDa (CIP73)

Medtr4g116370

Mtr.7126.1.S1_at

Glyma.17G106000

Phvul.003G173700

Kang, H., Zhu, H., Chu, X., Yang, Z., Yuan, S., Yu, D., Wang, C., Hong, Z., and Zhang, Z. (2011). A novel interaction between CCaMK and a protein containing the Scythe_N ubiquitin-like domain in Lotus japonicus. Plant physiology 155, 1312-1324.

Enzyme (Oxidoreductase)

CYTOKININ OXIDASE/DEHYDROGENASE 3 (CKX3)

Medtr2g039410

Mtr.14413.1.S1_at

Glyma.09G063900, Glyma.15G140000

Phvul.009G231700

Reid, D.E., Heckmann, A.B., Novák, O., Kelly, S., and Stougaard, J. (2016). CYTOKININ OXIDASE/DEHYDROGENASE3 maintains cytokinin homeostasis during root and nodule development in Lotus japonicus. Plant physiology 170, 1060-1074.

Protein (Endocytosis)

Medtr3g070940

Mtr.41546.1.S1_at

Glyma.02G258200, Glyma.14G058300

Phvul.008G222800

Wang, C., Zhu, M., Duan, L., Yu, H., Chang, X., Li, L., Kang, H., Feng, Y., Zhu, H., Hong, Z., and Zhang, Z. (2015). Lotus japonicus Clathrin Heavy Chain1 Is Associated with Rho-Like GTPase ROP6 and Involved in Nodule Formation. Plant Physiology 167, 1497-1510.

Peptide (Signaling)

CLAVATA3/ENDOSPERM SURROUNDING REGION12 (CLE12/CLE13)

CLE-RS1/CLE-RS2 (root signal), RIC1/RIC2 (rhizobium induced CLE)

Medtr4g079630

Mtr.19172.1.S1_at

Lj0g3v0000559.1

Glyma.13G368300

Phvul.011G135900

Nishida, H., Tanaka, S., Handa, Y., Ito, M., Sakamoto, Y., Matsunaga, S., Betsuyaku, S., Miura, K., Soyano, T., and Kawaguchi, M. (2018). A NIN-LIKE PROTEIN mediates nitrate-induced control of root nodule symbiosis in Lotus japonicus. Nature communications 9, 499.

Peptide (Signaling)

CLAVATA3/ENDOSPERM SURROUNDING REGION12 (CLE12/CLE13)

Medtr4g079610

Mtr.19174.1.S1_at

Glyma.06G284100

Phvul.011G135900

Nishida, H., Tanaka, S., Handa, Y., Ito, M., Sakamoto, Y., Matsunaga, S., Betsuyaku, S., Miura, K., Soyano, T., and Kawaguchi, M. (2018). A NIN-LIKE PROTEIN mediates nitrate-induced control of root nodule symbiosis in Lotus japonicus. Nature communications 9, 499.

Receptor-like protein (LRR-RLP)

Medtr7g079550

Mtr.34002.1.S1_s_at

Glyma.09G251800

Phvul.008G055400

Krusell, L., Sato, N., Fukuhara, I., Koch, B.E., Grossmann, C., Okamoto, S., Oka‐Kira, E., Otsubo, Y., Aubert, G., and Nakagawa, T. (2011). The Clavata2 genes of pea and Lotus japonicus affect autoregulation of nodulation. The Plant Journal 65, 861-871.

Channel (Cations)

CYCLIC NUCLEOTIDE GATED CHANNELS 15A (CNGC15a)

Medtr1g064240

Mtr.50460.1.S1_at

Glyma.13G141000, Glyma.10G053900

Phvul.007G148700

Charpentier, M., Sun, J., Martins, T.V., Radhakrishnan, G.V., Findlay, K., Soumpourou, E., Thouin, J., Véry, A.-A., Sanders, D., and Morris, R.J. (2016). Nuclear-localized cyclic nucleotide–gated channels mediate symbiotic calcium oscillations. Science 352, 1102-1105.

Channel (Cations)

CYCLIC NUCLEOTIDE GATED CHANNELS 15B (CNGC 15b)

Medtr4g058730

Glyma.12G076800

Phvul.011G080800

Charpentier, M., Sun, J., Martins, T.V., Radhakrishnan, G.V., Findlay, K., Soumpourou, E., Thouin, J., Véry, A.-A., Sanders, D., and Morris, R.J. (2016). Nuclear-localized cyclic nucleotide–gated channels mediate symbiotic calcium oscillations. Science 352, 1102-1105.

Channel (Cations)

CYCLIC NUCLEOTIDE GATED CHANNELS 15C (CNGC 15c)

Medtr2g094860

Mtr.32319.1.S1_at

Lj3g3v1089390, Lj3g3v1089380

Glyma.12G175000

Phvul.005G133900

Charpentier, M., Sun, J., Martins, T.V., Radhakrishnan, G.V., Findlay, K., Soumpourou, E., Thouin, J., Véry, A.-A., Sanders, D., and Morris, R.J. (2016). Nuclear-localized cyclic nucleotide–gated channels mediate symbiotic calcium oscillations. Science 352, 1102-1105.

Transporter (Copper)

Medtr4g019870

Mtr.42937.1.S1_s_at

Lj0g3v0091689.1

Glyma.18G191300

Phvul.008G113200

Senovilla, M., Castro‐Rodríguez, R., Abreu, I., Escudero, V., Kryvoruchko, I., Udvardi, M.K., Imperial, J., and González‐Guerrero, M. (2018). Medicago truncatula COPPER TRANSPORTER 1 (Mt COPT 1) delivers copper for symbiotic nitrogen fixation. New Phytologist 218, 696-709.

Enzyme (Cysteine protease)

Medtr4g079800

Mtr.45750.1.S1_at

Glyma.12G127200

Phvul.011G132100

Pierre, O., Hopkins, J., Combier, M., Baldacci, F., Engler, G., Brouquisse, R., Hérouart, D., and Boncompagni, E. (2014). Involvement of papain and legumain proteinase in the senescence process of Medicago truncatula nodules. New Phytologist 202, 849-863.

Enzyme (Calcium dependent Kinase)

CALCIUM DEPENDANT PROTEIN KINASE 3 (CPK3)

Mtr.37994.1.S1_at

Glyma.08G316500

Phvul.006G043700

Gargantini, P.R., Gonzalez‐Rizzo, S., Chinchilla, D., Raices, M., Giammaria, V., Ulloa, R.M., Frugier, F., and Crespi, M.D. (2006). A CDPK isoform participates in the regulation of nodule number in Medicago truncatula. The Plant Journal 48, 843-856.

Enzyme (Kinase; LRR-RLK)

COMPACT ROOT ARCHITECTURE 2 (CRA2)

Medtr3g110840

Mtr.38398.1.S1_at

Glyma.06G090700, Glyma.04G088700

Phvul.009G114400

Huault, E., Laffont, C., Wen, J., Mysore, K.S., Ratet, P., Duc, G., and Frugier, F. (2014). Local and systemic regulation of plant root system architecture and symbiotic nodulation by a receptor-like kinase. PLoS Genetics 10, e1004891.

Enzyme (Histidine kinase)

Ljlhk1 (lotus histidine kinase), Ljlhk1 (lotus histidine kinase), spontaneous nodule formation (Ljsnf2) gof

Medtr8g106150

Mtr.45840.1.S1_at

Glyma.05G241600

Phvul.002G324900

Gonzalez-Rizzo, S., Crespi, M., and Frugier, F. (2006). The Medicago truncatula CRE1 cytokinin receptor regulates lateral root development and early symbiotic interaction with Sinorhizobium meliloti. The Plant Cell 18, 2680-2693.

White++ (spontaneous)

Enzyme (Histidine kinase)

hit1 (hyperinfected1)

Medtr8g106150

Mtr.45840.1.S1_at

Glyma.05G241600

Phvul.002G324900

Tirichine, L., Sandal, N., Madsen, L.H., Radutoiu, S., Albrektsen, A.S., Sato, S., Asamizu, E., Tabata, S., and Stougaard, J. (2007). A gain-of-function mutation in a cytokinin receptor triggers spontaneous root nodule organogenesis. Science 315, 104-107.

Medtr7g020850

Mtr.35355.1.S1_at

Glyma.08G257700, Glyma.18G282100

Phvul.008G019200

Crook, A.D., Schnabel, E.L., and Frugoli, J.A. (2016). The systemic nodule number regulation kinase SUNN in Medicago truncatula interacts with MtCLV2 and MtCRN. The Plant Journal 88, 108-119.

LjCYCLOPS (MtIPD3)

Transcriptional activator

Medtr5g026850

Mtr.42174.1.S1_at, Mtr.29567.1.S1_at, Mtr.3453.1.S1_s_at

Glyma.01G149500

Phvul.002G128600

Yano, K., Yoshida, S., Müller, J., Singh, S., Banba, M., Vickers, K., Markmann, K., White, C., Schuller, B., and Sato, S. (2008). CYCLOPS, a mediator of symbiotic intracellular accommodation. Proceedings of the National Academy of Sciences 105, 20540-20545.

Transcriptional activator

INTERACTING PROTEIN DMI 3 LIKE(IPD3/IPD3L)

MT35v5_contig_51603_1

Jin, Y., Liu, H., Luo, D., Yu, N., Dong, W., Wang, C., Zhang, X., Dai, H., Yang, J., and Wang, E. (2016). DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways. Nature Communications 7, 12433.

Enzyme (Cysteine protease)

Mtr.12217.1.S1_at

Glyma.17G254900

Phvul.001G009900

Sheokand, S., Dahiya, P., Vincent, J., and Brewin, N. (2005). Modified expression of cysteine protease affects seed germination, vegetative growth and nodule development in transgenic lines of Medicago truncatula. Plant Science 169, 966-975.

Transcriptional regulator (D-E-L-L-A motif)

Medtr3g065980

Mtr.31658.1.S1_s_at

Lj6g3v0433880.1

Glyma.11G216500, Glyma.18G040000

Phvul.001G230500

n/a (Myc+/- della1 della 2)

Fonouni-Farde, C., Tan, S., Baudin, M., Brault, M., Wen, J., Mysore, K.S., Niebel, A., Frugier, F., and Diet, A. (2016). DELLA-mediated gibberellin signalling regulates Nod factor signalling and rhizobial infection. Nature communications 7, 12636.; Jin, Y., Liu, H., Luo, D., Yu, N., Dong, W., Wang, C., Zhang, X., Dai, H., Yang, J., and Wang, E. (2016). DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways. Nature Communications 7, 12433.

Transcriptional regulator (D-E-L-L-A motif)

MT35v5_contig_52215_1

Lj4g3v2436020.1

Glyma.05G140400, Glyma.08G095800

Phvul.003G291500

n/a (Myc+/- della1 della 2)

Fonouni-Farde, C., Tan, S., Baudin, M., Brault, M., Wen, J., Mysore, K.S., Niebel, A., Frugier, F., and Diet, A. (2016). DELLA-mediated gibberellin signalling regulates Nod factor signalling and rhizobial infection. Nature communications 7, 12636.; Jin, Y., Liu, H., Luo, D., Yu, N., Dong, W., Wang, C., Zhang, X., Dai, H., Yang, J., and Wang, E. (2016). DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways. Nature Communications 7, 12433.

Transcriptional regulator (D-E-L-L-A motif)

MT35v5_contig_55897_1

Lj6g3v0959470.1

Glyma.04G150500, Glyma.06G213100, Glyma.10G190200, Glyma.20G200500

Phvul.007G131200

Fonouni-Farde, C., Tan, S., Baudin, M., Brault, M., Wen, J., Mysore, K.S., Niebel, A., Frugier, F., and Diet, A. (2016). DELLA-mediated gibberellin signalling regulates Nod factor signalling and rhizobial infection. Nature communications 7, 12636.; Jin, Y., Liu, H., Luo, D., Yu, N., Dong, W., Wang, C., Zhang, X., Dai, H., Yang, J., and Wang, E. (2016). DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways. Nature Communications 7, 12433.

Nod+, Nod*, White++

Enzyme (DNA glycosylase)

Medtr1g492760

Glyma.20G188300

Phvul.007G223600

Satge, C., Moreau, S., Sallet, E., Lefort, G., Auriac, M.-C., Rembliere, C., Cottret, L., Gallardo, K., Noirot, C., and Jardinaud, M.-F. (2016). Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula. Nature plants 2, 16166.

MtDMI1(LjPOLLUX)

Channel (Cations)

Ljcastor, Ljpollux, Pssym8

EMS mutagenesis, Tnt1 (Peiter et al., 2007)

Medtr2g005870

Mtr.124.1.S1_s_at; Mtr.19417.1.S1_at

Lj6g3v2275020, Lj6g3v2275010

Glyma.12G167300

Phvul.006G218700

Ané, J.-M., Kiss, G.B., Riely, B.K., Penmetsa, R.V., Oldroyd, G.E., Ayax, C., Lévy, J., Debellé, F., Baek, J.-M., and Kalo, P. (2004). Medicago truncatula DMI1 required for bacterial and fungal symbioses in legumes. Science 303, 1364-1367.

Channel (Cations)

Lj6g3v2275020, Lj6g3v2275010

Glyma.12G167300

Phvul.006G218700

Imaizumi-Anraku, H., Takeda, N., Charpentier, M., Perry, J., Miwa, H., Umehara, Y., Kouchi, H., Murakami, Y., Mulder, L., and Vickers, K. (2005). Plastid proteins crucial for symbiotic fungal and bacterial entry into plant roots. Nature 433, 527.

Enzyme (Kinase; LRR-RLK)

SYMBIOTIC RECEPTOR KINASE (SYMRK)/DOES NOT MAKE Infections 2 (DMI2)

Ljsymrk (symbiotic receptor kinase), Msnork (nodulation receptor kinase; Pssym19

EMS mutagenesis, LATER: y ray, Tnt1

Medtr5g030920

Mtr.51192.1.S1_at

Glyma.01G020100, Glyma.09G202300

Phvul.002G143400, Phvul.002G116200

Stracke, S., Kistner, C., Yoshida, S., Mulder, L., Sato, S., Kaneko, T., Tabata, S., Sandal, N., Stougaard, J., and Szczyglowski, K. (2002). A plant receptor-like kinase required for both bacterial and fungal symbiosis. Nature 417, 959.

MtCCaMK (L.O.F)

Kinase (Calcium/Calmodulin dependent)

CALCIUM CALMODULIN KINASE (CCaMK)/DOES NOT MAKE Infections 3 (DMI3)

EMS mutagenesis

Medtr8g043970

Mtr.8930.1.S1_at

Glyma.15G222300

Phvul.011G186900

Lévy, J., Bres, C., Geurts, R., Chalhoub, B., Kulikova, O., Duc, G., Journet, E.-P., Ané, J.-M., Lauber, E., and Bisseling, T. (2004). A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science 303, 1361-1364.; Mitra, R.M., Gleason, C.A., Edwards, A., Hadfield, J., Downie, J.A., Oldroyd, G.E., and Long, S.R. (2004). A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: gene identification by transcript-based cloning. Proceedings of the National Academy of Sciences 101, 4701-4705.

White++ (spontaneous)

Kinase (Calcium/Calmodulin dependent)

CALCIUM CALMODULIN KINASE (CCaMK)/DOES NOT MAKE Infections 3 (DMI3)

Lsnf1 (spontaneous nodule formation1)

EMS mutagenesis

Medtr8g043970

Mtr.8930.1.S1_at

Glyma.15G222300

Phvul.011G186900

Tirichine, L., Imaizumi-Anraku, H., Yoshida, S., Murakami, Y., Madsen, L.H., Miwa, H., Nakagawa, T., Sandal, N., Albrektsen, A.S., and Kawaguchi, M. (2006). Deregulation of a Ca 2+/calmodulin-dependent kinase leads to spontaneous nodule development. Nature 441, 1153.

Signal peptidase complex subunit

Mtr.43876.1.S1_at

Glyma.10G156000

Phvul.001G228900

Wang, D., Griffitts, J., Starker, C., Fedorova, E., Limpens, E., Ivanov, S., Bisseling, T., and Long, S. (2010). A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis. Science 327, 1126-1129., Van de Velde, W., Zehirov, G., Szatmari, A., Debreczeny, M., Ishihara, H., Kevei, Z., Farkas, A., Mikulass, K., Nagy, A., and Tiricz, H. (2010). Plant peptides govern terminal differentiation of bacteria in symbiosis. Science 327, 1122-1126.

Nod++, White++

Enzyme (Phosphatidylinositol phospholipase C‐like)

Medtr4g085800

Glyma.02G102700

Phvul.003G048300

Bourcy, M., Brocard, L., Pislariu, C.I., Cosson, V., Mergaert, P., Tadege, M., Mysore, K.S., Udvardi, M.K., Gourion, B., and Ratet, P. (2013). Medicago truncatula DNF2 is a PI‐PLC‐XD‐containing protein required for bacteroid persistence and prevention of nodule early senescence and defense‐like reactions. New Phytologist 197, 1250-1261.

Peptide (Cysteine-rich)

Medtr4g035705

Kim, M., Chen, Y., Xi, J., Waters, C., Chen, R., and Wang, D. (2015). An antimicrobial peptide essential for bacterial survival in the nitrogen-fixing symbiosis. Proceedings of the National Academy of Sciences 112, 15238-15243.

Peptide (Cysteine-rich)

Mtr.3210.1.S1_at

Horváth, B., Domonkos, Á., Kereszt, A., Szűcs, A., Ábrahám, E., Ayaydin, F., Bóka, K., Chen, Y., Chen, R., and Murray, J.D. (2015). Loss of the nodule-specific cysteine rich peptide, NCR169, abolishes symbiotic nitrogen fixation in the Medicago truncatula dnf7 mutant. Proceedings of the National Academy of Sciences 112, 15232-15237.

TF (Ethylene response factor)

ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (EFD)

Deletion TILLING

Medtr4g008860

Mtr.41581.1.S1_at

Glyma.08G216600, Glyma.07G025800

Phvul.010G159500

Vernié, T., Moreau, S., De Billy, F., Plet, J., Combier, J.-P., Rogers, C., Oldroyd, G., Frugier, F., Niebel, A., and Gamas, P. (2008). EFD is an ERF transcription factor involved in the control of nodule number and differentiation in Medicago truncatula. The Plant Cell 20, 2696-2713.

Medtr0041s0030

Mtr.9302.1.S1_at

Glyma.03G181400

Phvul.001G177500

Varma Penmetsa, R., Uribe, P., Anderson, J., Lichtenzveig, J., Gish, J.C., Nam, Y.W., Engstrom, E., Xu, K., Sckisel, G., and Pereira, M. (2008). The Medicago truncatula ortholog of Arabidopsis EIN2, sickle, is a negative regulator of symbiotic and pathogenic microbial associations. The Plant Journal 55, 580-595.

Glyma.13G145100, Glyma.10G058300

Phvul.007G150600

Reid, D., Liu, H., Kelly, S., Kawaharada, Y., Mun, T., Andersen, S.U., Desbrosses, G., and Stougaard, J. (2018). Dynamics of ethylene production in response to compatible Nod factor. Plant physiology 176, 1764-1772.

LjENOD40-1/ENOD40-2

MT4Noble_057132, Medtr8g069785

Glyma.01G028500

Phvul.002G064232

Kumagai, H., Kouchi, H., Kinoshita, E., and Ridge, R.W. (2006). RNAi Knock-Down of ENOD40 s Leads to Significant Suppression of Nodule Formation in Lotus japonicus. Plant and Cell Physiology 47, 1102-1111.

Membrane protein

Glyma.06G247600

Yan, Z., Hossain, M.S., Arikit, S., Valdés‐López, O., Zhai, J., Wang, J., Libault, M., Ji, T., Qiu, L., and Meyers, B.C. (2015). Identification of microRNAs and their mRNA targets during soybean nodule development: functional analysis of the role of miR393j‐3p in soybean nodulation. New Phytologist 207, 748-759.

Enzyme (Kinase; LysM-RLK)

EXOPOLYSACCHARIDE RECEPTOR (EPR3)

Ljlys3, Ljexo277,MtLYK10

Medtr5g033490

Mtr.25148.1.S1_at

Glyma.08G283300

Phvul.002G059500, Pv03g003063700

Kawaharada, Y., Kelly, S., Nielsen, M.W., Hjuler, C.T., Gysel, K., Muszyński, A., Carlson, R., Thygesen, M.B., Sandal, N., and Asmussen, M. (2015). Receptor-mediated exopolysaccharide perception controls bacterial infection. Nature 523, 308.

TF (Ethylene responsive)

Mtr.39861.1.S1_at

Glyma.20G203700

Phvul.007G127800

Asamizu, E., Shimoda, Y., Kouchi, H., Tabata, S., and Sato, S. (2008). A positive regulatory role for LjERF1 in the nodulation process is revealed by systematic analysis of nodule-associated transcription factors of Lotus japonicus. Plant physiology 147, 2030-2040.

TF (Ethylene responsive)

ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULATION1 (ERN1)

Mtbit1 (branched Infection thread, poodle

Fast Neutron mutagenesis

Medtr7g085810

Mtr.7556.1.S1_at

Glyma.19G113100

Phvul.001G111800

Middleton, P.H., Jakab, J., Penmetsa, R.V., Starker, C.G., Doll, J., Kaló, P., Prabhu, R., Marsh, J.F., Mitra, R.M., and Kereszt, A. (2007). An ERF transcription factor in Medicago truncatula that is essential for Nod factor signal transduction. The Plant Cell 19, 1221-1234.

TF (Ethylene responsive)

ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULATION2 (ERN2)

Medtr6g029180

Mtr.43947.1.S1_at

Glyma.16G154100, Glyma.02G072800

Phvul.001G160100

Cerri, M.R., Frances, L., Kelner, A., Fournier, J., Middleton, P.H., Auriac, M.-C., Mysore, K.S., Wen, J., Erard, M., and Barker, D.G. (2016). The symbiosis-related ERN transcription factors act in concert to coordinate rhizobial host root infection. Plant physiology 171, 1037-1054.

Membrane protein (Exocyst complex subunit)

Mtr.21216.1.S1_at

Glyma.11G144600, Glyma.12G075200

Phvul.011G068800, Phvul.L003900

Liu, C.W, Breakspear, A., Stacey, N., Findlay, K., Nakashima A., Ramakrishnan, K., Endre, A., de Carvalho-Niebel, F., Oldroyd, G.E.D, Udvardi, M.K., Fournier, J., Murray, J.D The infectosome is required for polar growth of rhizobial infection threads Nature Comms. 2019

Medtr0118s0070

Mtr.33549.1.S1_at

Lj5g3v0642670.1

Glyma.10G122300

Phvul.008G144100

Li, X., Zhao, J., Tan, Z., Zeng, R., and Liao, H. (2015). GmEXPB2, a cell wall β-expansin, affects soybean nodulation through modifying root architecture and promoting nodule formation and development. Plant Physiology 169, 2640-2653.

Enzyme (Homocitrate Synthase)

FAIL IN ENLARGEMENT of infection CELLS (FEN1)

EMS mutagenesis

Lj1g3v3690180, Lj1g3v3690020

Glyma.19g120400, Glyma.19g120600, Glyma.03g005700

Phvul.007G004600

Hakoyama, T., Niimi, K., Watanabe, H., Tabata, R., Matsubara, J., Sato, S., Nakamura, Y., Tabata, S., Jichun, L., and Matsumoto, T. (2009). Host plant genome overcomes the lack of a bacterial gene for symbiotic nitrogen fixation. Nature 462, 514.

Protein complex (Iron scavenging)

Medtr5g083170

Mtr.12355.1.S1_at

Glyma.02G262500

Phvul.001G245700

Dhanushkodi, R., Matthew, C., McManus, M.T., and Dijkwel, P.P. (2018). Drought-induced senescence of Medicago truncatula nodules involves serpin and ferritin to control proteolytic activity and iron levels. New Phytol 220, 196-208.

Protein complex (Iron scavenging)

Medtr4g014540

Msa.1670.1.S1_at

Glyma.03G050100

Phvul.010G065600

Dhanushkodi, R., Matthew, C., McManus, M.T., and Dijkwel, P.P. (2018). Drought-induced senescence of Medicago truncatula nodules involves serpin and ferritin to control proteolytic activity and iron levels. New Phytol 220, 196-208.

Membrane protein

Medtr3g106420

Glyma.06G065600

Phvul.009G090700

Haney, C.H., and Long, S.R. (2010). Plant flotillins are required for infection by nitrogen-fixing bacteria. Proc Natl Acad Sci U S A 107, 478-483.

Membrane protein

Medtr3g106430

Mtr.11786.S1_at

Lj0g3v0315989,

Glyma.06G065600

Phvul.009G090700

Haney, C.H., and Long, S.R. (2010). Plant flotillins are required for infection by nitrogen-fixing bacteria. Proc Natl Acad Sci U S A 107, 478-483.

Enzyme (Synthase)

Mtr.1299.1.S1_s_at

Glyma.13G173500

Phvul.003G074000

Zhang, J., Subramanian, S., Stacey, G., and Yu, O. (2009). Flavones and flavonols play distinct critical roles during nodulation of Medicago truncatula by Sinorhizobium meliloti. The Plant Journal 57, 171-183.

Unknown (PLAC8 domain containing)

Medtr6g084940

Chromosome location AP004536.1

Glyma.09G187000

Phvul.003G292900

Libault, M., Zhang, X.C., Govindarajulu, M., Qiu, J., Ong, Y.T., Brechenmacher, L., Berg, R.H., Hurley‐Sommer, A., Taylor, C.G., and Stacey, G. (2010). A member of the highly conserved FWL (tomato FW2. 2‐like) gene family is essential for soybean nodule organogenesis. The Plant Journal 62, 852-864.

Enzyme (Oxidase)

Medtr4g074130

Glyma.11G104800, Glyma.12G029800

Phvul.011G032800

Kim, G.-B., Son, S.-U., Yu, H.-J., and Mun, J.-H. (2019). MtGA2ox10 encoding C20-GA2-oxidase regulates rhizobial infection and nodule development in Medicago truncatula. Scientific Reports 9, 5952.

Heterotrimeric G-protein complex subunit

Soybean heterotrimeric G PROTEINS (Ga)

Medtr1g015750

Mtr.5675.1.S1_s_at

Glyma.17G226700

Phvul.001G092700

Choudhury, S.R., and Pandey, S. (2015). Phosphorylation-dependent regulation of G-protein cycle during nodule formation in soybean. The Plant Cell 27, 3260-3276.

Oxygen carrier hemoprotein

non-symbiotic Class 1 HAEMOGLOBIN 1 (GLB1)

Medtr4g068860

Msa.878.1.S1_at

Glyma.11G121800

Phvul.011G048700

Fukudome, M., Calvo-Begueria, L., Kado, T., Osuki, K.-i., Rubio, M.C., Murakami, E.-i., Nagata, M., Kucho, K.-i., Sandal, N., and Stougaard, J. (2016). Hemoglobin LjGlb1-1 is involved in nodulation and regulates the level of nitric oxide in the Lotus japonicus–Mesorhizobium loti symbiosis. Journal of experimental botany 67, 5275-5283.

GmGβ1/GmGβ2/GmGβ3/GmGβ4

Heterotrimeric G-protein complex subunit

Soybean heterotrimeric G PROTEINS (GmGβ1/GmGβ2/GmGβ3/GmGβ4)

Medtr3g116500

Mtr.10712.1.S1_at

Lj1g3v3407660(GmGβ3); Lj1g3v3407660 (GmGβ2)

GmGβ1 (Glyma.12G043900), GmGβ2 (Glyma.11G118500), GmGβ3 (Glyma.06G013000), GmGβ4 (Glyma.04G013100)

Phvul.011G045900

Choudhury, S.R., and Pandey, S. (2013). Specific subunits of heterotrimeric G proteins play important roles during nodulation in soybean. Plant physiology 162, 522-533.

GmGγ1/GmGγ2/GmGγ3/GmGγ4/GmGγ5/GmGγ6/GmGγ7/GmGγ8/GmGγ9,GmGγ10

Heterotrimeric G-protein complex subunit

Soybean heterotrimeric G PROTEINS (GmGγ1/GmGγ2/GmGγ3/GmGγ4/GmGγ5/GmGγ6/GmGγ7/GmGγ8/GmGγ9,GmGγ10)

Medtr1g071100

Mtr.7374.1.S1_at

Lj5g3v1014880 (GmGy1)

GmGγ1 (Glyma.10G03610), GmGγ2 (Glyma.02G16190), GmGγ3 (Glyma.20G33390), GmGγ4 (Glyma.10G32215), GmGγ5 (Glyma.11G18050), GmGγ6 (Glyma.14G17060), GmGγ7 (Glyma.17G29590), GmGγ8 (Glyma.15G19630), GmGγ9 (Glyma.17G05640), and GmGγ10 (Glyma.07G04510)

Phvul.007G175700

Choudhury, S.R., and Pandey, S. (2013). Specific subunits of heterotrimeric G proteins play important roles during nodulation in soybean. Plant physiology 162, 522-533.

Molecular chaperone protein

HSC/HSP70 INTERACTING PROTEIN (HIP)

Medtr4g102390

Mtr.40545.1.S1_a_at

Glyma.05G051600, Glyma.17G133600

Phvul.003G214200

Kang, H., Xiao, A., Huang, X., Gao, X., Yu, H., He, X., Zhu, H., Hong, Z., and Zhang, Z. (2015). A Lotus japonicus cochaperone protein interacts with the ubiquitin-like domain protein CIP73 and plays a negative regulatory role in nodulation. Molecular Plant-Microbe Interactions 28, 534-545.

Enzyme (Oxidoreductase)

3-HYDROXY-3-METHYLGLUTARYL COENZYME A REDUCTASE 1 (HMGR1)

Medtr5g026460

Mtr.40156.1.S1_at

Lj2g3v1574250.1

Glyma.01G156700

Phvul.006G008200

Kevei, Z., Lougnon, G., Mergaert, P., Horváth, G.V., Kereszt, A., Jayaraman, D., Zaman, N., Marcel, F., Regulski, K., and Kiss, G.B. (2007). 3-Hydroxy-3-methylglutaryl coenzyme A reductase1 interacts with NORK and is crucial for nodulation in Medicago truncatula. The Plant Cell 19, 3974-3989.

Enzyme (Synthase)

Medtr4g088160, Medtr4g088170, Medtr4g088195

Mtr.10492.1.S1_x_at, Mtr.40276.1.S1_at, Mtr.30765.1.S1_at

Lj4g3v0486150, Lj4g3v0485100, Lj4g3v0485090

Glyma.07G202300, Glyma.13G173500

Phvul.003G051700, Phvul.003G051800, Phvul.003G074000

Subramanian, S., Stacey, G., and Yu, O. (2006). Endogenous isoflavones are essential for the establishment of symbiosis between soybean and Bradyrhizobium japonicum. The Plant Journal 48, 261-273.

Membrane protein (Ankyrin-repeat domain)

INEFFECTIVE GREENISH NODULE 1 (IGN1)

Somatic mutation

Medtr7g100430

Mtr.11594.1.S1_at

Glyma.20G241200, Glyma.10G291900

Phvul.007G008900

Kumagai, H., Hakoyama, T., Umehara, Y., Sato, S., Kaneko, T., Tabata, S., and Kouchi, H. (2007). A novel ankyrin-repeat membrane protein, IGN1, is required for persistence of nitrogen-fixing symbiosis in root nodules of Lotus japonicus. Plant Physiology 143, 1293-1305.

Cell wall component (b-expansin)

Mtr.32987.1.S1_at

Glyma.07G172000

Phvul.003G016300

Li, X., Zheng, J., Yang, Y., and Liao, H. (2018a). INCREASING NODULE SIZE1 expression is required for normal rhizobial symbiosis and nodule development. Plant physiology 178, 1233-1248.

Enzyme (Transferase)

Medtr1g072540

Mtr.12113.1.S1_at

Lj5g3v0962690.1

Glyma.10G025300

Phvul.007G170100

Sasaki, T., Suzaki, T., Soyano, T., Kojima, M., Sakakibara, H., and Kawaguchi, M. (2014). Shoot-derived cytokinins systemically regulate root nodulation. Nature Communications 5, 4983.

Enzyme (Kinase; LRR-RLK)

Ion Beam Mutagenesis

Medtr6g015265, Medtr6g015190

Mtr.43460.1.S1_at, Mtr.9737.1.S1_at

Glyma.18G267000, Glyma.13G056200

Phvul.004G037600

Miyazawa, H., Oka-Kira, E., Sato, N., Takahashi, H., Wu, G.-J., Sato, S., Hayashi, M., Betsuyaku, S., Nakazono, M., and Tabata, S. (2010). The receptor-like kinase KLAVIER mediates systemic regulation of nodulation and non-symbiotic shoot development in Lotus japonicus. Development 137, 4317-4325.

MtKNAT3/MtKNAT5/MtKNAT9/MtKNAT10

TF (KNOX Homeodomain)

KNOTTED-1 LIKE TAKE HOMEDOMAIN proteins (KNAT3/KNAT5/KNAT9/KNAT10)

Medtr1g012960, Medtr3g106400, Medtr4g116545, Medtr2g461240

Lj1g3v1853300, Lj0g3v0268639, Lj6g3v1088990

Glyma.14G112400 (KNAT3), Glyma.04G064100 (KNAT5), Glyma.06G065200 (KNAT5), Glyma.17G104800 (KNAT9), Glyma.15G202200 (KNAT10)

Phvul.009G090500, Phvul.003G174900, Phvul.009G209500

Di Giacomo, E., Laffont, C., Sciarra, F., Iannelli, M.A., Frugier, F., and Frugis, G. (2017). KNAT3/4/5‐like class 2 KNOX transcription factors are involved in Medicago truncatula symbiotic nodule organ development. New Phytologist 213, 822-837.

Multiprotein complex

LACK OF SYMBIONT ACCOMMODATION (LAN)

EMS, LORE1, CRISPR/Cas9

Medtr3g116260

Mtr.51430.1.S1_at

Glyma.04G123300

Phvul.002G127500

Suzaki, T., Takeda, N., Nishida, H., Hoshino, M., Ito, M., Misawa, F., Handa, Y., Miura, K., and Kawaguchi, M. (2019). LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonius. PLoS genetics 15, e1007865.

Transporter (Auxin influx)

Medtr7g067450

Mtr.41246.1.S1_at

Glyma.07G147000

Phvul.008G106300

Roy, S., Robson, F., Lilley, J., Liu, C.-W., Cheng, X., Wen, J., Walker, S., Sun, J., Cousins, D., and Bone, C. (2017). MtLAX2, a functional homologue of the Arabidopsis auxin influx transporter AUX1, is required for nodule organogenesis. Plant Physiology 174, 326-338.

LjLB1/LjLB2/LjLB3

Oxygen carrier hemoprotein

Lj5g3v0035290, Lj5g3v0035290, Lj5g3v0465970

Ott, T., van Dongen, J.T., Gu, C., Krusell, L., Desbrosses, G., Vigeolas, H., Bock, V., Czechowski, T., Geigenberger, P., and Udvardi, M.K. (2005). Symbiotic leghemoglobins are crucial for nitrogen fixation in legume root nodules but not for general plant growth and development. Current biology 15, 531-535.

Enzyme (Ligase)

Medtr1g090320

Glyma.10G194500

Phvul.007G136300

Yano, K., Yoshida, S., Müller, J., Singh, S., Banba, M., Vickers, K., Markmann, K., White, C., Schuller, B., and Sato, S. (2008). CYCLOPS, a mediator of symbiotic intracellular accommodation. Proceedings of the National Academy of Sciences 105, 20540-20545., Kiss, E., Oláh, B., Kaló, P., Morales, M., Heckmann, A.B., Borbola, A., Lózsa, A., Kontár, K., Middleton, P., and Downie, J.A. (2009). LIN, a novel type of U-box/WD40 protein, controls early infection by rhizobia in legumes. Plant physiology 151, 1239-1249.

Enzyme (Hydrolase)

LECTIN NUCLEOTIDE PHOSPHOHYDROLASE (LNP)

Medtr7g085150

Mtr.14668.1.S1_at

Glyma.16G043300

Phvul.001G099900

Roberts, N.J., Morieri, G., Kalsi, G., Rose, A., Stiller, J., Edwards, A., Xie, F., Gresshoff, P.M., Oldroyd, G.E., and Downie, J.A. (2013). Rhizobial and mycorrhizal symbioses in Lotus japonicus require lectin nucleotide phosphohydrolase, which acts upstream of calcium signaling. Plant physiology 161, 556-567.

Enzyme (Hydrolase), cytokinin riboside 5′‐monophosphate phosphoribohydrolases

Medtr0041s0100

Mtr.39530.1.S1_s_at

Glyma.03G181300

Phvul.001G177400

Mortier, V., Wasson, A., Jaworek, P., De Keyser, A., Decroos, M., Holsters, M., Tarkowski, P., Mathesius, U., and Goormachtig, S. (2014). Role of LONELY GUY genes in indeterminate nodulation on Medicago truncatula. New Phytologist 202, 582-593.