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Integrating Genetics and Genomics to Advance Soybean Research

SoySNP50K iSelect BeadChip

An Illumina Infinium BeadChip containing over 50,000 SNPs from soybean (Glycine max L. Merr.) has been developed (Song et al. 2013). A total of 498,921,777 reads 35-45 bp in length were obtained from DNA sequence analysis of reduced representation libraries from several soybean accessions which included six cultivated and two wild soybean (G. soja Sieb. et Zucc.) genotypes. These reads were mapped to the soybean whole genome sequence and 209,903 SNPs were identified. After applying several filters, a total of 146,161 SNPs were determined to be candidates for Illumina Infinium II BeadChip design. To equalize the distance between selected SNPs, increase assay success rate, and minimize the number of SNPs with low minor allele frequency, an iteration algorithm based on a selection index was developed and used to select 60,800 SNPs for Infinium BeadChip design. Of the 60,800 SNPs, 50,701 were targeted to euchromatic regions and 10,000 to heterochromatic regions of the 20 soybean chromosomes. In addition, 99 SNPs were targeted to unanchored sequence scaffolds. Of the 60,800 SNPs, a total of 52,041 passed Illumina's manufacturing phase to produce the SoySNP50K iSelect BeadChip. Validation of the SoySNP50K chip with 96 landrace genotypes, 96 elite cultivars and 96 wild soybean accessions showed that 47,337 SNPs were polymorphic and generated successful SNP allele calls. In addition, 40,841 of the 47,337 SNPs (86%) had minor allele frequencies >10% among the landraces, elite cultivars and the wild soybean accessions.

Examples: ss715578909 or BARC_1.01_Gm01_29091115_A_G

Note: Searches covering the original BARC SNPs can be done on this page.

The dbSNP ID (e.g. ss715587030) is the official name of the SoySNP50K SNPs and should always be used in publications. The SoySNP50K Nomenclature Conversion Tool can be used to convert a list of deprecated names into their dbSNP IDs.


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. Haplotypes of individual PI lines can be downloaded using the download tool. Note that the download is limited to less than 1000 lines at a time. The complete data set for 20,087 G. max and G. soja accessions genotyped with 42,509 SNPs is available for Wm82.a1 and Wm82.a2 in either vcf, bcf or HapMap format. You can extract a large list of cultivars using BCFtools and a VCF file chosen below.

SNP50K Downloads
113.08 Megabytes

107.14 Megabytes

114.43 Megabytes
159.54 Megabytes

118.05 Megabytes

131.09 Megabytes

Download file of Minor Allele
Frequencies (MAF) of SNPs

20.24 Megabytes

Download allele counts for each accession in the dataset

Funded by the USDA-ARS. Developed by the USDA-ARS SoyBase and Legume Clade Database group at the Iowa State University, Ames, IA
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