Genetic Mapping Using a Large Axiom® Soybean SNP Genotyping Array

Soybean is an important worldwide plant source of dietary protein and oil. Modern breeding and improvement of soybean has experienced challenges by a narrow improved or domesticated germplasm relative to other crop species. This is likely due to the underuse of wild soybeans as breeding resources. SNP genotyping arrays are regarded as promising tools to identify agronomically important genes by high-density genetic mapping and genome-wide association studies (GWAS) with the eventual purpose of dissecting wild and cultivated gerrmplasms. Here, we present the establishment of a large soybean SNP array and its use for diversity analysis and high density linkage mapping. More than 4 million high-quality SNPs were identified from 16 high-depth and 31 low-depth soybean genome resequencing data. From this list, 180,961 SNPs were selected for inclusion on the Axiom_SoyaSNP custom myDesign® genotyping array that was manufactured by Affymetrix®, Santa Clara, CA. The number of SNPs is estimated to provide ~ 1 SNP every 6.1 kb along the 20 chromosomes of soybean. However, the selected SNPs are not evenly distributed across the genome as SNPs from genic regions were preferentially selected. Our current analysis for more than hundreds of wild and cultivated soybean accessions showed >97% call rate, >98% pair-wise concordance, and >80% successful SNP allele calls. This array is being used to construct high-density genetic maps in populations generated from intermatings of two cultivated and two wild soybeans.