Abstract

Plant height (PH) and main stem node number (MSN) are core agronomic traits that jointly shape soybean plant architecture and determine yield potential. Here, a natural population of 264 soybean ( Glycine max (L.) Merr.) accessions was phenotyped for PH and MSN across two environments to dissect their genetic basis. Genome-wide association study (GWAS) revealed that both traits are quantitatively inherited with extensive phenotypic variation, identifying 73 significant single-nucleotide polymorphisms (SNPs) associated with PH (distributed on chromosomes 2, 6, 7, 9, 14, 16, and 19) and 572 SNPs associated with MSN. Notably, loci on chromosomes 6 and 19 were consistently detected across environments, exhibiting stable genetic effects on PH. Candidate gene analysis within the major locus on chromosome 6 identified six potential regulators, among which GmCESA7 ( Glyma.06G225500 ) — encoding a cellulose synthase involved in secondary cell wall biosynthesis — was prioritized. Functional validation using ethyl methyl sulfonate (EMS)-induced gmcesa7 mutants showed that mutants in GmCESA7 were associated with significantly reduced PH at both vegetative and mature stages, supporting a positive role for GmCESA7 in stem elongation. Additionally, the major locus on chromosome 19, which was also associated with MSN via 60 co-localized SNPs across environments, harbored the known plant architecture regulator GmDt1 . Collectively, these findings uncover GmCESA7 as a key genetic determinant of soybean PH and highlight conserved genetic pathways regulating PH and MSN, providing valuable genetic resources and a theoretical basis for optimizing plant architecture in soybean breeding.