Identification of Major QTLs and Candidate Genes Determining Stem Strength in Soybean

Stem strength is a key factor influencing lodging resistance in soybeans and other crops. To identify quantitative trait loci (QTLs) associated with stem strength in soybean, we assessed the peak forces required to break a 20 cm stem base segment for each individual within a collection of 2138 plants from eight F2 and F3 segregating populations in 2023 and 2024. These populations were derived from four crosses between soybean varieties with contrasting stem strength. Most populations exhibited an approximately normal distribution of stem strength. Using BSA-seq, we identified 17 QTLs associated with stem strength from four populations. Among these, one QTL overlapped with a previously reported locus, while the remaining 16 represented novel loci. Notably, nine loci overlapped with known lodging QTLs, suggesting a genetic relationship between stem strength and lodging. Three QTLs were repeatedly detected in multiple populations, indicating their stability. Further linkage mapping with molecular markers confirmed these three stable QTLs. Among them, qSS10 and qSS19-2 were identified as major QTLs, refined to 1.06 Mb and 1.54 Mb intervals, with phenotypic variation explained (PVE) 23.31–25.15% and 14.21–19.93%, respectively. Within these stable QTL regions, we identified 13 candidate genes and analyzed their sequence variation and expression profiles. Collectively, our findings provide a valuable foundation for future research on stem strength in soybeans and reveal novel genetic loci and candidate genes that may be utilized for the genetic improvement of soybean lodging resistance and yield stability.