Development and implementation of nested single-nucleotide polymorphism (SNP) assays for breeding and genetic research applications.

SoySNP50K and SoySNP6K are commonly used for soybean (Glycine max) genotyping. The SoySNP50K assay has been used to genetically analyze the entire USDA Soybean Germplasm Collection, while the SoySNP6K assay, containing a subset of 6000 single-nucleotide polymorphisms (SNPs) from SoySNP50K, has been used for quantitative trait loci mapping of different traits. To meet the needs for genomic selection, selection of parents for crosses, and characterization of breeding populations, especially early selection of ideal offspring from thousands of lines, we developed two assays, SoySNP3K and SoySNP1K, containing 3072 and 1252 SNPs, respectively, based on SoySNP50K and SoySNP6K mark sets. These two assays also contained the trait markers reported or contributed by soybean breeders. The SNPs in the SoySNP3K are a subset from SoySNP6K, while the SNPs in the SoySNP1K are a subset from SoySNP3K. These SNPs were chosen to reduce the SNP number in the large linkage blocks while capturing as much of the haplotype diversity as possible. They are highly polymorphic and of high quality. The mean minor allele frequencies of the SNPs in the southern and northern US elites were 0.25 and 0.27 for SoySNP3K, respectively, and 0.29 and 0.33 for SoySNP1K. The selected SNPs are a valuable source for developing targeted amplicon sequencing assay or beadchip assay in soybean. SoySNP3K and SoySNP1K assays are commercialized by Illumina Inc. and AgriPlex Genomics, respectively. Together with SoySNP50K and SoySNP6K, a series of nested assays with different marker densities will serve as additional low-cost genomic tools for genetic, genomic, and breeding research.