The SNP genotypes of 1,007 soybean germplasms were determined using an Illumina Infinium SoySNP50K BeadChip at USDA-ARS, Beltsville, MD, USA. The dataset was obtained from the Soybean Genetics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA. The chip contained 52,041 SNPs from the euchromatic and heterochromatic regions of the soybean genome. Single nucleotide polymorphism genotyping was conducted on the Illumina platform by following the InfiniumH HD Assay Ultra Protocol (Illumina, Inc.). The SNPs were scored using the GenomeStudio Genotyping Module v1.8.4 (Illumina, Inc.).