Enhanced soybean salt tolerance and oil content via marker-assisted pyramiding of GmSALT3 and high-oil QTLs

Soil salinity and demand for edible oil are two major challenges facing global soybean production. Traditional breeding approaches often encounter negative correlations between salinity tolerance and seed-quality traits. This study aimed to overcome this trade-off by pyramiding the salt tolerance gene GmSALT3 with multiple oil content quantitative trait loci (QTL) through marker-assisted selection. Using a cross between the salt-tolerant line, 2125, and high-oil cultivar Neiminda 3, we developed backcross (BC₃F₅) populations and employed kompetitive allele-specific polymerase chain reaction genotyping for five markers linked to GmSALT3 and three major oil QTL (qOil-5-1, qOil-10-1, qOil-15). A total of 892 BC₃F₂ plants were screened, with 3.8% carrying the complete pyramided genotype. Phenotypic evaluation revealed successful improvement in both traits: pyramided lines showed a 42.3% reduction in salt injury index under 150-mM NaCl hydroponic stress (F₅,₂₁₀ = 87.3, P < 0.001) and a 2.8% increase in seed oil content compared with the recurrent parent (t₆₈ = 6.84, P < 0.001). Multi-environment trials across two locations (Nanjing: 32°03’N, 118°46’E, pH: 6.8, electrical conductivity [EC]: 1.3 dS/m; Yancheng: 33°23’N, 120°08’E, pH: 7.2, EC: 2.8 dS/m) over 2 years demonstrated stable performance with no yield penalty under non-saline conditions. Trade-off analysis indicated modest positive synergy between traits (r = 0.31, P < 0.05, n = 70), suggesting the potential to mitigate expected negative correlations. Best linear unbiased prediction analysis confirmed genotype stability with minimal genotype–environment interaction (17.5% of total variation, indicating robust performance). This study demonstrates the feasibility of simultaneously improving stress tolerance and quality traits through strategic gene pyramiding, although the relatively low recovery frequency (3.8%) of fully pyramided genotypes highlights technical challenges. The pyramided lines provide valuable germplasm for sustainable soybean production in marginal lands, acknowledging limitations in QTL coverage and the need for broader validation across additional environments.