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

Authors: CHEN, LINFENG - Henan University Of Science And Technology; Taliercio, Earl; LI, ZENGLU - University Of Georgia; Mian, Rouf; Carter Jr, Thomas; WEI, HE - Henan Academy Of Agricultural Science; Quigley, Charles; ARAYA, SUSAN - Oak Ridge Institute For Science And Education (ORISE); He, Ruifeng; Song, Qijian

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2025
Publication Date: 3/7/2025
Citation: Chen, L., Taliercio, E.W., Li, Z., Mian, R.M., Carter Jr, T.E., Wei, H., Quigley, C.V., Araya, S., He, R., Song, Q. 2025. Characterization of a G. max × G. soja nested association mapping population and identification of loci controlling seed composition traits from wild soybean. Theoretical and Applied Genetics. 138. Article e65. https://doi.org/10.1007/s00122-025-04848-5.
DOI: https://doi.org/10.1007/s00122-025-04848-5

Interpretive Summary: Wild soybean is a valuable source for improving disease resistance, stress tolerance, seed protein content, and seed sulfur amino acid concentrations. Many past studies have focused on seed composition traits based on cultivated soybean populations, but wild soybean has been largely overlooked. In this study, USDA researchers and collaborators explored the genetic potential of wild soybean in improving seed composition traits in cultivated soybean. They developed a population of 10 wild accessions crossed with the cultivated variety NC-Raleigh. After genotyping more than 1,100 progenies and measuring seed composition of the progeny planted at two locations and over two years, the researchers revealed the genetic characteristics of wild soybean-derived populations, landscapes, and the extent of influence of QTLs and candidate genes controlling traits from different wild soybean parents. They also identified several genomic regions and candidate genes from wild soybean that could be used to improve the composition of cultivated soybean seeds. This is the first report to show the genetic characteristics of wild soybean population and its potential to improve seed composition in cultivated varieties based on progeny from many wild soybean germplasms. The findings highlight the importance of using wild soybean as a genetic resource to enhance seed composition traits in breeding programs.

Technical Abstract: 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 (RILs) was developed by crossing 10 wild accessions with the common cultivar NC-Raleigh. Seed composition of the F6 generation grown at 2 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.