Identification of a novel gene GmCESA7 encoding cellulose synthase controlling plant height in soybean

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.