Harnessing heterogeneity within soybean cultivars to prioritize loci for quantitative trait improvement

Authors: MAHMOOD, ANSER - University Of Missouri; MEYER, ELIZABETH - University Of Missouri; USOVSKY, MARIOLA - University Of Missouri; MEINHARDT, CLINTON - University Of Missouri; DENNINGMANN, MICHAEL - University Of Missouri; SINGH, ASHEESH - Iowa State University; GRAEF, GEORGE - University Of Nebraska; DOMINGUEZ, ELIANA - University Of Illinois; Song, Qijian; JOSHI, TRUPTI - University Of Missouri; Washburn, Jacob; Bilyeu, Kristin; SCABOO, ANDREW - University Of Missouri

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/17/2026
Publication Date: 4/4/2026
Citation: Mahmood, A., Meyer, E.D., Usovsky, M., Meinhardt, C., Denningmann, M., Singh, A., Graef, G., Dominguez, E., Song, Q., Joshi, T., Washburn, J.D., Bilyeu, K.D., Scaboo, A. 2026. Harnessing heterogeneity within soybean cultivars to prioritize loci for quantitative trait improvement. Crop Science. 66(2). Article e70283. https://doi.org/10.1002/csc2.70283.
DOI: https://doi.org/10.1002/csc2.70283

Interpretive Summary: Most people think that modern soybean varieties are pretty much all the same—uniform. But this study shows that even within elite, high-yielding soybean cultivars, plants that are supposed to be “clones” of each other actually carry small genetic differences, and those differences can make some plants grow better, yield more, or have more protein and oil than others. By studying the DNA behind these differences, the team at University of Missouri, Iowa State University, University of Nebraska, University of Illinois, and USDA-ARS, Columbia, MO, and Beltsville, MD identified specific regions of the soybean genome that influence traits like protein, oil, and plant height. Importantly, they found that improvements in protein or oil didn’t come at the expense of yield, which is often the big tradeoff in crop breeding. One gene in particular stood out as a strong candidate affecting plant height. This study provided a framework for characterization of soybean genomic regions associated with important quantitative traits for soybean breeders and demonstrated the potential of exploiting intra-cultivar variation for trait improvement.

Technical Abstract: Soybean cultivars are presumed to be highly homogenous, however intra-cultivar variation has been reported in previous studies. The objective of this study was to characterize intra-cultivar variation and utilize it to identify sublines out-performing source cultivars for agronomic and seed composition traits. Additionally, we aimed to identify QTL and candidate genes underlying these traits. Multiple sublines derived from elite high-yielding soybean cultivars outperformed source cultivars for both agronomic and seed composition related traits. Across subline populations, protein content QTL were identified on soybean chromosomes 1, 10, 14, and 19 with the effect sizes ranging from 3 to 7 g kg-1. Additionally, two QTL on chromosomes 10 and 16 were identified for oil content with effect sizes of 5 and 4 g kg-1 respectively. These protein and oil QTL were non-pleiotropic for seed composition and yield, offering a valuable resource for soybean breeders to improve seed composition without negatively impacting grain yield. An additional QTL located on chromosome 13 was associated with plant height. Through investigating functional impacts of genetic variation, we were able to identify candidate genes for QTL from two subline populations. A strong candidate gene, Glyma.13G196000, for plant height was identified containing a ~ 40 bp deletion encompassing the stop codon. Overall, this study provides a framework for characterization of genomic regions associated with important quantitative traits in soybean. Furthermore, our results demonstrate the potential of exploiting intra-cultivar variation for trait improvement.