SNP-Based Genetic Linkage Map of Soybean Using the SoySNP6K Illumina Infinium BeadChip Genotyping Array

This study reports a high density genetic linkage map based on the ‘Maryland 96-5722’ by ‘Spencer’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.] and constructed exclusively with single nucleotide polymorphism (SNP) markers. The Illumina Infinium SoySNP6K BeadChip genotyping array produced 5,376 SNPs in the mapping population, with a 96.75% success rate. Significant level of goodness-of-fit for each locus was tested based on the observed vs. expected ratio (1:1). Out of 5,376 markers, 1,465 SNPs fit the 1:1 segregation rate having ≤20% missing data plus heterozygosity among the RILs. Among this 1,456 just 657 were polymorphic between the parents DNAs tested. These 657 SNPs were mapped using the JoinMap 4.0 software and 550 SNPs were distributed on 16 linkage groups (LGs) among the 20 chromosomes of the soybean genome. The total map length was just 201.57 centiMorgans (cM) with an average marker density of 0.37 cM. This is one of the high density SNP-based genetic linkage maps of soybean that will be used by the scientific community to map quantitative trait loci (QTL) and identify candidate genes for important agronomic traits in soybean