Tools

SoySNP50K iSelect BeadChip

An Illumina Infinium BeadChip containing over 50,000 SNPs from soybean is widely used by researchers and breeders. (Song et al. 2013; Song et al. 2015). This chip has been used to genotype more than 20,000 accessions in the USDA soybean germplasm collection, as well as other populations and collections.

View the SoySNP50K with DivBrowse

View variants for all cultivars in the USDA soybean collection using the DivBrowse application from the links below.

Wm82.a4 Wm82.gnm4.div.Song_Hyten_2015
Wm82.a5 Wm82.gnm5.div.Song_Hyten_2015
Wm82.a6 Wm82.gnm6.div.Song_Hyten_2015

View SoySNP50K in the SoyBase Genome Browser

Assembly Chromosome
Wm82.a1 Gm01 Gm02 Gm03 Gm04 Gm05 Gm06 Gm07 Gm08 Gm09 Gm10 Gm11 Gm12 Gm13 Gm14 Gm15 Gm16 Gm17 Gm18 Gm19 Gm20
Wm82.a2 Gm01 Gm02 Gm03 Gm04 Gm05 Gm06 Gm07 Gm08 Gm09 Gm10 Gm11 Gm12 Gm13 Gm14 Gm15 Gm16 Gm17 Gm18 Gm19 Gm20
Wm82.a4 Gm01 Gm02 Gm03 Gm04 Gm05 Gm06 Gm07 Gm08 Gm09 Gm10 Gm11 Gm12 Gm13 Gm14 Gm15 Gm16 Gm17 Gm18 Gm19 Gm20
Wm82.a5 Chr01 Chr02 Chr03 Chr04 Chr05 Chr06 Chr07 Chr08 Chr09 Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 Chr20
Wm82.a6 Gm01 Gm02 Gm03 Gm04 Gm05 Gm06 Gm07 Gm08 Gm09 Gm10 Gm11 Gm12 Gm13 Gm14 Gm15 Gm16 Gm17 Gm18 Gm19 Gm20

Bulk Downloads

The complete data set for 20,087 G. max and G. soja accessions genotyped with 42,509 SNPs is available in either vcf or HapMap format. You can extract the list of cultivars from the "#CHROM" line of VCF files from any of the collections below.

Wm82.a1 Wm82.gnm1.div.Song_Hyten_2015
Wm82.a2 Wm82.gnm2.div.Song_Hyten_2015
Wm82.a4 Wm82.gnm4.div.Song_Hyten_2015
Wm82.a5 Wm82.gnm5.div.Song_Hyten_2015
Wm82.a6 Wm82.gnm6.div.Song_Hyten_2015

SNP Data Sources

The SoySNP50K iSelect BeadChip has been used to genotype the USDA Soybean Germplasm Collection ( Song, Qijian, David L. Hyten, Gaofeng Jia, Charles V. Quigley, Edward W. Fickus, Randall L. Nelson, and Perry B. Cregan. 2015. Fingerprinting soybean germplasm and its utility in genomic research, G3: Genes| Genomes| Genetics 50(10):1999-2006.) and the data generously provided by the authors.

SoySNP50K SNP positional information in relationship to the Wm82.a2 and Wm82.a1 assemblies can be found in Construction of high resolution genetic linkage maps to improve the soybean genome sequence assembly Glyma1.01, Song et al. 2016 BMC Genomics 17:33 in Supplemental table S1.

A subset of the SoySNP50K dataset was produced by Song et al. called the BARCSoySNP6K SNP set described in Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research, Plant Journal (2020) 104(3):800-811 . The SNP set assembled can be found in Supplemental Table S1.