supplementary_tables-1.xlsx

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1	Table S1. Crop type datasets. The table provides a summary of the 14 crop type datasets included in the database. For each crop type dataset, shown are: the identifier of the original dataset, the species name, the sequencing strategy (WGS = whole genome sequencing, GBS = genotyping by sequencing, RAD-seq = restriction site-associated DNA sequencing), a link to the SNP matrix, a link to the reference genome used for SNP calling, the number of SNPs in the original dataset (before and after linkage disequilibrium (LD) filtering), the number of SNPs retained when focusing on the crop type of interest (before and after minor allele frequency filtering, and after retaining those located within orthogroups), the genotype imputation accuracy, the number of samples in the original dataset, the number of samples retained for the crop type of interest (after filtering out those without geographic data or with excessive missingness), the number of sampling locations, and the median distance between sampling sites.
2	Crop type dataset	Original dataset	Species name	Sequencing strategy	Link to SNP matrix	Link to reference genome	# SNPs original dataset	# SNPs original dataset (after LD filtering)	# SNPs	# SNPs (filter MAF)	# SNPs (in orthogenes)	genotype imputation accuracy	# samples original dataset	# samples	# samples (filter geographic data)	# samples (filter missingness)	# of sampling sites	median distance sam. sites [km]
3	Barley landraces	Chen et al., 2022	Hordeum vulgare	Exome sequencing	https://zenodo.org/records/6382440	https://doi.ipk-gatersleben.de/DOI/57ce5c4c-3584-48fe-a33f-2544a06e555f/a27d49c1-10a3-42ce-9d43-25cea920a5f4/2	609339	339388	236503	116499	46890	0.84	816	388	388	388	299	3087
4	Barley wild relatives	Chen et al., 2022	Hordeum vulgare	Exome sequencing	https://zenodo.org/records/6382440		609339	339388	318254	182856	72272	0.85	816	264	264	264	177	624
5	Common bean landraces	Wu et al., 2020	Phaseolus vulgaris	WGS	https://zenodo.org/records/3236786	https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000499845.1/	826481	57816	57447	35071	13164	0.87	629	484	476	476	238	1370
6	Common bean wild relatives	Lopez-Hernandez et al., 2019	Phaseolus vulgaris	GBS	https://datadryad.org/dataset/doi:10.5061/dryad.9k862c8	https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000499845.1/	19179	12608	10482	10289	7032	0.86	79	78	78	78	69	2159
7	Maize landraces	Aiyesa et al., 2025	Zea mays	GBS	https://figshare.com/authors/Leke_Victor_Aiyesa/19326223	https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_902167145.1/	90393	72710	72710	52568	34784	0.73	334	332	332	332	35	845
8	Maize wild relatives	Chen et al., 2022	Zea mays subsp. mexicana Zea mays subsp. parviglumis	WGS	https://ftp2.cngb.org/pub/CNSA/data3/CNP0001565/zeamap/02_Variants/PAN_Zea_Variants/Zea-vardb/	https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005005.2/	2033259	1108680	635350	434324	121116	0.76	745	151	151	151	84	187
9	Rice landraces	Gutaker et al., 2020 Wang et al., 2018	Oryza sativa	WGS	https://42basepairs.com/browse/s3/3kricegenome/reduced?file=NB-core_v4.map.gz	https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001433935.1/	137501	136618	92877	55835	14631	0.82	3024	1280	1280	1272	503	2207
10	Rice wild relatives	Bedford et al., 2023 Huang et al., 2012	Oryza rufipogon	WGS (low-coverage)	https://figshare.com/articles/journal_contribution/Island/21916038	https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_001433935.1/	574773	431837	377492	377282	91715	0.88	287	286	286	284	129	1273
11	Sorghum landraces	Lasky et al. 2015	Sorghum bicolor	GBS	https://datadryad.org/dataset/doi:10.5061/dryad.jc3ht	https://data.jgi.doe.gov/search?datasets=Phytozome-79	76682	52456	22039	13551	8449	0.89	2329	1943	1943	1676	1307	3884
12	Soybean landraces	Zhang et al., 2022	Glycine max	WGS	https://agdatacommons.nal.usda.gov/articles/dataset/Data_from_Development_of_a_versatile_resource_from_1500_diverse_genomes_for_post-genomics_research/24853704	https://data.jgi.doe.gov/search?datasets=Phytozome-275	1824205	915606	676822	366953	103101	0.80	1512	457	457	451	80	1141
13	Soybean wild relatives	Zhang et al., 2022	Glycine soja	WGS		https://data.jgi.doe.gov/search?datasets=Phytozome-275	1824205	915606	731008	583642	151898	0.75	1512	175	175	174	104	1080
14	Tepary bean landraces	Bornowski et al., 2023	Phaseolus acutifolius A. Gray	GBS	https://figshare.com/articles/journal_contribution/Genetic_variation_in_a_tepary_bean_Phaseolus_acutifolius_A_Gray_diversity_panel_reveals_loci_associated_with_biotic_stress_resistance/22557487	https://datadryad.org/dataset/doi:10.5061/dryad.6q573n5w2	67777	35424	9219	4346	2704	0.88	475	205	157	148	86	798
15	Tepary bean wild relatives	Bornowski et al., 2023	Phaseolus acutifolius A. Gray	GBS		https://datadryad.org/dataset/doi:10.5061/dryad.6q573n5w2	67777	35424	16640	13741	8816	0.86	475	186	162	154	90	551
16	Tomato wild relatives	Gibson et al., 2020	Solanum pimpinellifolium	RAD-seq	https://datadryad.org/dataset/doi:10.5061/dryad.8gtht76k4	https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000188115.3/	53666	21669	8950	5241	1403	0.83	161	149	149	139	120	535
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