Korean Soybean Nested Association Mapping (K-SoyNAM) population: genetic linkage map, genetic mapping, and genotype imputation

BACKGROUND: The nested association mapping (NAM) population, first developed in maize, have been widely adopted across diverse crop species including barley, sorghum, rice, and soybean. These populations enable high-resolution mapping of complex traits and have been extensively utilized worldwide to dissect the genetic architecture of agronomically important traits such as yield, disease resistance, and seed composition. After quality control filtering, 2,669 RILs from 24 families were retained for downstream analyses. The parental lines were deeply sequenced using whole genome reference sequencing, and the RILs were genotyped using the Axiom 180 K SoyaSNP array. Genetic linkage maps were constructed for each family, and a composite linkage map was developed across families. Linkage analysis of three agronomic traits, flowering time, flower color, and seed protein content, the utility of the K-SoyNAM population for quantitative trait locus (QTL) mapping. Genotype imputation based on a composite genetic linkage map generated 4,057,789 high-confidence single nucleotide polymorphisms (SNPs) for the RILs. Comparison of genome-wide association study (GWAS) results before and after imputation demonstrated improved detection of small significant peaks in the imputed GWAS dataset. CONCLUSIONS: The genotypic datasets for the RILs and parents are publicly available and are expected to be helpful in dissecting the genetic architecture and mapping QTLs controlling important complex traits in soybean.