Characterization of a G. max × G. soja nested association mapping population and identification of loci controlling seed composition traits from wild soybean

Wild soybean (Glycine soja Siebold & Zucc.) has valuable genetic diversity for improved disease resistance, stress tolerance, seed protein content and seed sulfur-containing amino acid concentrations. Many studies have reported loci controlling seed composition traits based on cultivated soybean populations, but wild soybean has been largely overlooked. In this study, a nested association mapping (NAM) population consisting of 10 families and 1107 recombinant inbred lines was developed by crossing 10 wild accessions with the common cultivar NC-Raleigh. Seed composition of the F6 generation grown at two locations was phenotyped, and genetic markers were identified for each line. The average number of recombination events in the wild soybean-derived population was significantly higher than that in the cultivated soybean-derived population, which resulted in a higher resolution for QTL mapping. Segregation bias in almost all NAM families was significantly biased toward the alleles of the wild soybean parent. Through single-family linkage mapping and association analysis of the entire NAM population, new QTLs with positive allele effects were identified from wild parents, including 5, 6, 18, 9, 16, 17 and 20 for protein content, oil content, total protein and oil content, methionine content, cysteine content, lysine content and threonine content, respectively. Candidate genes associated with these traits were identified based on gene annotations and gene expression levels in different tissues. This is the first study to reveal the genetic characteristics of wild soybean-derived populations, landscapes and the extent of effects of QTLs and candidate genes controlling traits from different wild soybean parents.