High-throughput SNP Genotyping in Soybean

Genomic DNA was extracted from soybean seedling leaves according to the methods used by Kisha et al. [31 (link)], and DNA quality was detected by 1% agarose gel electrophoresis and a spectrophotometer. A genome-wide genotyping array containing 158,327 SNPs was applied to genotype the 410 accessions using the Illumina Infinium platform, according to the manufacturer’s protocol (Illumina) [32 (link),33 (link)]. All SNP genotype data were treated with raw data normalization, clustering, and genotype calling using Illumina Genome Studio Genotyping Module (Illumina). The SNPs with a minor allele frequency (MAF) < 0.05 and missing rates < 0.25 were removed to avoid problems of spurious LD and false positive associations. Finally, 117,811 high-quality SNPs were used for GWAS analysis. The SNPs were distributed relatively evenly across the 20 soybean chromosomes (Figure S1).