Precise mapping and candidate gene identification of the qSBD-6 locus controlling stem basal diameter in soybean

Stem basal diameter (SBD) is a critical determinant of soybean lodging resistance, nutrient transport efficiency and yield potential, yet its genetic regulatory mechanism remains largely unclear. Using a 194-line recombinant inbred line (RIL) population derived from parents with distinct SBD phenotypes, combined with high-density bin maps, the genetic architecture of stem basal diameter was analyzed under two environments. A total of five quantitative trait loci (QTLs) were identified, among which two were stably detected across environments. Of these stable loci, qSBD-6 on chromosome 6 spanned a 611.25 kb physical interval, explained 9.54%–10.42% of the phenotypic variation, showed the highest phenotypic contribution and exhibited positive additive effects from the thick-stem parent QH34. The broad-sense heritability of SBD reached 0.73. Through co-localization analysis, parental sequence variation comparison, haplotype effect evaluation and gene expression profiling, Glyma.06G263500 was identified as the key candidate gene for this locus. Glyma.06G263500 encodes an NPR1-interacting protein. Haplotype analysis demonstrated that the superior haplotype Hap1 G markedly increases stem basal diameter of 241 soybean germplasms. qSBD-6 may regulate stem diameter by affecting cambial development, cell wall formation, and microtubule development, thereby further influencing soybean quality and yield. Overall, this study elucidates the genetic determinants of soybean SBD, provides stable loci and elite haplotypes for marker-assisted selection, and supports molecular breeding for lodging-resistant and high-yielding soybean cultivars.