Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean

“…LD decay was higher in group II compared to group I, indicating greater homozygosity in group II and highlighting diversity as a key factor distinguishing Brazilian soybean cultivars. The LD decay distance observed in this study was higher than the results reported by [ 20 ], who studied 70% of the USDA Soybean Germplasm core collection and found that LD fell below 0.2 at approximately 250 kb. [ 45 , 46 ] observed that LD reached r² = 0.1 after 574 kb among North American elite cultivars.…”

“…SNPs with MAF < 0.10 in the North American elites were also eliminated in the 1K assay. The density of selected SNPs in the euchromatin region versus the heterochromatin region is approximately 5:1 for both 3K and 1K, which is consistent with the 5:1 ratio of recombination rate/Mb in the two regions of the soybean genome (Song et al., 2013).…”

“…This, in turn, could enable breeders to identify individual accessions of a crop wild relative that may have alleles associated with abiotic stress tolerance. The nonreference variant detected in association with “Mean Temperature Wettest Quarter” on chromosome 8, which is associated with higher temperature, is found in ∼90% of our G. soja samples, while a previous study found this variant in 3.6% of elite soybean lines ( Song et al 2013 ). Another locus with potential effect on temperature response was detected on chromosome 16, this variant was present in accessions sampled from the Korean Peninsula north into Russia, corresponding to cooler growing season temperatures.…”