Abstract Soybean Glycine max (L.) Merr. cultivars are presumed to be highly homogeneous; 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 that out‐perform source cultivars for agronomic and seed composition traits. Additionally, we aimed to identify quantitative trait loci (QTLs) and candidate genes underlying these traits. Multiple sublines derived from high‐yielding soybean cultivars outperformed source cultivars for both agronomic and seed composition‐related traits. Across subline populations, protein content QTLs were identified on soybean chromosomes 1, 10, 14, and 19, with the effect sizes ranging from 3 to 7 g kg −1 . Additionally, two QTLs 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 QTLs 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 underlying QTL. A 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 agronomic and seed quality trait improvement.
Mahmood et al. (2026) studied this question.