Skip to main content
ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Publications at this Location » Publication #427185
Research Project: Redesigning Soybeans for a Resilient Future of Food, Feeds, and Bio-Industry

Location: Plant Genetics Research

Title: Dissecting seed composition QTL from wild soybean: fine-mapping, candidate gene identification, and evaluation of introgression effects on agronomic performance

Author
item DE MEYER, ELIZABETH - University Of Missouri
item MAHMOOD, ANSER - University Of Missouri
item USOVSKY, MARIOLA - University Of Missouri
item Gillman, Jason
item YANG, BING - University Of Missouri
item DECKER, JARED - University Of Missouri
item Song, Qijian
item MEINHARDT, CLINTON - University Of Missouri
item DENNIGMANN, MICHAEL - University Of Missouri
item SINGH, ASHEESH - Iowa State University
item GRAEF, GEORGE - University Of Nebraska
item MONTEVERDE, ELIANA - University Of Illinois
item SCABOO, ANDREW - University Of Missouri

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2025
Publication Date: 10/3/2025
Citation: De Meyer, E., Mahmood, A., Usovsky, M., Gillman, J.D., Yang, B., Decker, J., Song, Q., Meinhardt, C., Dennigmann, M., Singh, A., Graef, G., Monteverde, E., Scaboo, A. 2025. Dissecting seed composition QTL from wild soybean: fine-mapping, candidate gene identification, and evaluation of introgression effects on agronomic performance. Theoretical and Applied Genetics. 138. https://doi.org/10.1007/s00122-025-05048-x.
DOI: https://doi.org/10.1007/s00122-025-05048-x

Interpretive Summary: While soybean farmers are primary interested in how productive a variety will be in their fields (seed yield), the entire soybean value chain is dependent on seeds with high quality seed composition. Over time due to selection for high seed yield, breeders have historically reduced the average content of seed protein. If this trend continues, American soybeans may no longer be considered to be of premium quality. To address this problem, we have been evaluating exotic genetic material and in previous work reported the discovery of a highly valuable genomic region from wild soybean. This region has a gene (or genes) which was found to increase seed protein content, with no impact on seed oil content. In this current study, we confirmed the unique protein boosting effects of this genomic region (and lack of impact on seed oil) and also reported on the impacts of agronomic traits of interest to farmers (plant height, plant maturity, plant lodging and seed yield). We were also able to narrow the genomic region significantly and were able to identify a number of candidate genes which could be responsible for this valuable trait. We also identified linked genetic markers to assist and accelerate ongoing breeding efforts towards new, improved varieties with higher protein levels, for the eventual benefit of soybean farmers and the entire soybean value chain.

Technical Abstract: Through selection for soybean yield, breeders have inadvertently reduced seed protein content and increased oil due to phenotypic and genetic correlations between these three traits. Therefore, identifying alleles that increase protein without adversely affecting oil and yield is of interest for breeders and the entire soybean value chain. Previously, a G. max × G. soja population was used to fine-map a protein-associated region to ~4.6 Mbp on chromosome (Chr) 14. The G. soja allele significantly increased protein 6.5-7.2 g kg-1, without significantly decreasing oil. Additionally, two oil QTL were reported on Chrs 8 and 14. In this study, we aimed to confirm the Chr 14 protein QTL, evaluate QTL effects on seed composition and agronomic performance, and further fine-map to identify candidate genes. We confirmed and fine-mapped the Chr 14 protein QTL to a 0.6 Mbp region in a new genetic background, where the G. soja allele significantly increased protein by 9.3 g kg-1. Further, we confirmed the Chr 14 oil QTL linked to the protein QTL and the Chr 8 oil QTL. Chr 14 protein QTL effects on agronomic traits were evaluated in a backcross population across eight environments. The QTL significantly increased protein content, without significantly impacting oil, maturity, or plant height. While the QTL impacted yield and lodging, effect sizes and significance varied within environments. The candidate genes identified for these three validated seed composition QTL, along with additional molecular markers developed, offer valuable resources for understanding and improving seed composition in soybean breeding programs.