Genetic mapping of novel QTL for seed protein stability in food-grade soybean (Glycine max)

Andrew A. Mitchell, Feng Lin, Heng Ye, Tri Vuong, Zixiang Wen, Biructawit Tessema, Randall Laurenz, Raju Thada Magar, Henry T. Nguyen & Dechun Wang

Theoretical and Applied Genetics; 14 November 2025; vol. 138; article 304

Key message

Two novel quantitative trait loci associated with soybean protein content stability were identified on chromosomes 10 and 18. Haplotype analysis showed these to significantly improve stability without protein content penalty.

Abstract

Soybean seed protein content is a complex physiological trait under polygenic control and significant genotype by environment interaction. Protein content is largely influenced by ambient atmospheric temperature at pod-filling, with increased temperatures enhancing seed protein accumulation. The identification of genomic regions associated with protein content stability will facilitate an increased understanding of seed development physiology and assist in the development of more broadly adapted food-grade soybean cultivars. In this work, 210 recombinant inbred lines were derived from the intraspecific cross of the high protein accession BARC_-6 (PI 555396), and the low protein MSU breeding accession E14077 for the investigation of quantitative trait loci associated with protein content and protein content stability across multiple years and test locations. Indices for static protein content stability were used to estimate genome by environment interactions across Northern and Southern soybean production regions. Composite interval mapping returned one stable major effect QTL associated with protein content on chromosome 20 explaining approximately 20.7% of phenotypic variation. Two novel QTLs associated with absolute protein stability were detected on chromosomes 10 and 18, explaining approximately 8.6% and 7.6% of phenotypic variation, respectively. SNP-based haplotype analysis showed simultaneous favorable effects on protein content and stability when desirable alleles for these QTL were pyramided. These results will serve as a valuable tool for the molecular breeding of food-grade soybean cultivars harboring elevated protein content coupled with improved stability across varied environments, thus addressing a key challenge in meeting the global rise in soybean protein demand for both livestock feed and human consumption.

See https://link.springer.com/article/10.1007/s00122-025-05089-2

Figure 3: From: Genetic mapping of novel QTL for seed protein stability in food-grade soybean (Glycine max)

QTL cartographer results depicting significant peaks for stability and protein content metrics. a QTL Peaks obtained using CIM on for unadjusted absolute stability across all year/location environments; b QTL Peaks obtained using CIM on for BLUP- and Means-adjusted absolute stability across all year/location environments; c QTL peaks obtained using CIM on chromosome 20 for BLUP predicted protein content across individual year/location environments and pooled environment data; d QTL peaks obtained using CIM on chromosome 14 for BLUP predicted protein content across all year/location environments. Significant peak obtained from 2020 Michigan trial