QTL-seq analysis of seed protein quantity and quality traits in two soybean recombinant inbred line populations

Soybean [Glycine max (L.) Merr.] is an important source of plant-based dietary protein, yet its nutritional quality is frequently constrained by deficiencies in the concentrations of amino acids cysteine (Cys), methionine (Met), threonine (Thr), and lysine (Lys). The identification of quantitative trait loci (QTL) associated with seed protein quantity and quality traits are essential for assisting breeders in the development of improved cultivars. This study aimed to identify and validate QTL associated with these five seed traits using novel genetic backgrounds.

Two recombinant inbred line (RIL) populations, POP179 and POP180, were derived from crosses between unique high-protein fast neutron-induced mutants. Phenotypic evaluations were conducted across four site-year environments in southern Ontario, Canada. A modified QTL-sequencing (QTL-seq) method was implemented to detect genomic regions with unequal parental contributions that likely harbour putative QTL.

All five seed traits exhibited high broad-sense heritability (0.81 to 0.90) and significant positive correlations. Three stable putative QTL were identified and validated on chromosomes 1 (27.1-32.3 Mbp), 2 (8.6-10.8 Mbp), and 15 (16.7-20.8 Mbp) in both populations.

The co-localization of genomic regions associated with multiple traits suggests a shared genetic architecture governing seed composition. Identified candidate genes, such as glutamine synthase and peptide transporters, are likely involved in nitrogen assimilation and nutrient loading during seed development. These findings provide additional resources for marker-assisted selection and genomic prediction that can support the development of soybean cultivars with superior nutritional profiles.