ORIGINAL RESEARCH article
Front. Genet.
Sec. Evolutionary and Population Genetics
This article is part of the Research TopicBridging Genomic Technology and Traditional Wisdom for Sustainable Native Crop EnhancementView all articles
Identification of major QTLs for seed vigor and growth-related traits using a bi-parental population in soybean
Provisionally accepted
- 1Jamie Whitten Delta States Research Center, Agricultural Research Service (USDA), Stoneville, United States
- 2USDA-ARS Plant Genetics Research Unit, Columbia, United States
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Soybean [Glycine max (L.) Merr.] is one of the most widely cultivated crops globally and serves as a primary source of plant-based protein and oil for human consumption. Seed vigor is a critical trait for germination and rapid seedling establishment, especially under sub-optimal environmental conditions. Genetic control of seed vigor measured as accelerated aging (%) (AA) was investigated using a QTL mapping approach. Associations of AA with six other traits: pubescence color (PC), beginning bloom (R1), reproductive period (RP), maturity (R8), plant height (PH) and stem termination (ST) were examined. A recombinant inbred line (RIL) population (247 F6-derived RILs) from a cross between DS25-1 and DT97-4290 was developed and genotyped using genotyping-by-sequencing (GBS) which yielded a set of 8,445 curated single nucleotide polymorphism (SNP) markers from ~90,000 SNPs. A sub-set of 201 RILs was phenotyped in Stoneville, Mississippi over three years (2017-2019). A molecular linkage map was constructed using SNP marker dataset and composite interval mapping performed using the R/qtl package. In total, 33 QTLs associated with seven phenotypic traits were identified across 12 chromosomes, using means of individual environments and best linear unbiased prediction (BLUP). Phenotypic variation of individual QTLs ranged from 0.56 to 89.77%, and the additive effects varied from - 10.52% to 15.12%. Twelve QTLs detected across multiple environments on Gm03, Gm06, Gm07, and Gm19, were classified as stable. Notably, four genomic regions demonstrated QTL co-localization: Gm06 (all traits except ST), Gm07 (AA, R1, RP, and R8), Gm03 (AA and R1), and Gm19 (PH, R8, and ST). Major QTLs were in proximity to previously known genes: the T locus for pubescence color (Gm06), E1 (Gm06) and E11 (Gm07) loci for flowering and maturity, and Dt1 (Gm19) for stem termination. The closest SNPs associated with stable QTLs can be used to develop KASP markers for marker-assisted selection programs.
Keywords: Growth-related traits, High-density genetic map, QTL mapping, Seed vigor, Soybean
Received: 30 Aug 2025; Accepted: 08 Dec 2025.
Copyright: © 2025 Kumar, Smith, Ray, Gillman and Bellaloui. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Neeraj Kumar
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