Phenotypic characterization and genetic dissection of nine agronomic traits in Tokachi nagaha and its derived cultivars in soybean (Glycine max (L.) Merr.)

•Phenotypic characters of nine traits in soybean cultivars across three locations and three consecutive years.•The genetic architecture for nine traits under two planting densities by genome-wide association mapping.•Stable and novel QTL controlling traits related to soybean quality and yield.

By using the soybean founder parent Tokachi nagaha and its 137 derived cultivars as materials, a genome-wide association analysis was performed to identify the single nucleotide polymorphisms (SNPs) underlying soybean yield and quality related traits at two planting densities. Results of ANOVA showed that genotype, environment, and genotype by environment interaction effects were all significant for each trait. The Tokachi nagaha-derived soybean population could be divided into two subpopulations based on molecular data, and accessions in each subpopulation were almost all from the same Chinese province. Relatedness was detected between pair-wise accessions within the population. Linkage disequilibrium was obvious and the level of intra-chromosome linkage disequilibrium was about 8370 kb. A total of 40 SNPs with significant signal were detected and distributed across 18 chromosomes. Some SNP markers were located in or near regions where QTLs have been previously mapped by linkage analysis. Nineteen SNPs were identified both in low- and high- density planting treatments, indicating those loci were common and sTable Sixteen SNPs were co-associated with two or more different traits, suggesting that some of the QTLs/genes underlying those identified SNPs were likely to be pleiotropic.