Soybean BARCSoySNP6K Beadchip - a Tool for Soybean Genetics Research

The USDA-ARS, Beltsville, Maryland has completed the analysis of the entire USDA Soybean Germplasm Collection with the SoySNP50K Illumina iSelect BeadChip.  High quality data were obtained for >42,000 SNPs on >19,000 soybean landraces, N. American cultivars and wild soybeans.  The analysis of these data has allowed the assessment of minor allele frequencies (MAF) and a definition of haplotype blocks that cover 50.7% and 46.7% of the genomes of the landrace and N. Am. Elite cultivars, respectively.  The 5,403 SNPs that are included in the new BARCSoySNP6K Illumina iSelect BeadChip were selected to reduce the number of SNPs in the large linkage blocks while still capturing as much of the haplotype diversity as possible.  In addition, MAF, the quality of the genotyping data associated with SNP loci among G. max genotypes, and regions of the genome (euchromatic vs. heterochromatic) in which the SNP resided were also important criteria in the SNP selection process.  In the segments of the genome not present in haplotype blocks, SNP selection was based upon the even spacing between SNPs as well as MAF.  Approximately five-sixths of theSNPs are from euchromatic and theremainer from heterochromatic regions.  The average MAF of the SNPs was 0.34 in the euchromatic and 0.30 in the heterochromatic regions.  The percentage of SNPs with MAF >0.10 were 95% and 91% in the euchromatic and heterochromatic regions, respectively.  The BARCSoySNP6K beadchip will be an excellent tool for the detection of quantitative trait loci and for assessing genetic diversity.