Identification of major QTLs for seed vigor and growth-related traits using a bi-parental population in soybean

Authors: Kumar, Neeraj; Smith, James; Ray, Jeffery; Gillman, Jason; Bellaloui, Nacer

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/8/2025
Publication Date: 1/14/2026
Citation: Kumar, N.N., Smith, J.R., Ray, J.D., Gillman, J.D., Bellaloui, N. 2026. Identification of major QTLs for seed vigor and growth-related traits using a bi-parental population in soybean. Frontiers in Genetics. 16:1-15. https://doi.org/10.3389/fgene.2025.1695593.
DOI: https://doi.org/10.3389/fgene.2025.1695593

Interpretive Summary: Soybean is one of the most widely cultivated crops used for seed protein and oil for human consumption. For farmers, it is very important that soybean seeds are strong and can grow well, even in unfavorable weather conditions (high temperatures and inadequate water in the soil). This early growing strength of seeds is called seed vigor. If seeds are weak, fewer plants will grow, and that means a lower harvest. Seed vigor is a complex trait controlled by many genes with small effects. This study looked at the genetic control of seed vigor in soybean, using a test called accelerated aging (AA), and examined how it relates to other traits like pubescence color (PC), beginning flower(R1), reproductive period (RP), full maturity (R8), plant height (PH) and stem termination (ST). We used 247 lines developed from the cross between two parental lines (DS25-1 and DT97-4290). These lines were tested in the field for three years (2017, 2018, and 2019) in Stoneville, Mississippi, and were also analyzed at molecular levels using over 90,000 DNA markers. A genetic map was built using the high-quality DNA markers. Combined analysis of DNA markers along with three years field data identified 33 genetic regions (called QTLs) linked to seed vigor and other traits across 12 chromosomes of soybean. Some QTLs appeared in all years and locations, showing they are stable and reliable. Several QTLs were found close to known genes that control traits like plant maturity and stem growth. The most important markers found in this study can be turned into easy-to-use DNA markers to help breeders select better soybean varieties with strong seed vigor and improved yield.

Technical Abstract: 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) estimates. Phenotypic variation of individual QTLs ranged from 0.56 and 90.6%, 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.