Genome-Wide Association Study Reveals Candidate Genes Regulating Plant Height and First-Branch Height in Brassica napus

Rapeseed (<i>Brassica napus</i> L., 2<i>n</i> = 38) is an important oil crop worldwide, providing vegetable oil and biofuel. Despite improvements in breeding, rapeseed's harvest index and yield remain lower than other major crops. Plant height (PH) and first-branch height (FBH) are crucial plant architecture traits affecting yield, lodging resistance and efficiency of mechanical harvesting. Phenotypic analysis of 125 rapeseed accessions across four environments revealed wide variation in PH (100-198 cm) and FBH (15.56-112.4 cm), with high broad-sense heritability (<i>H</i>² = 81.59% for PH, 77.69% for FBH), and significant positive correlations between traits. To understand the genetic control of PH and FBH, a genome-wide association study (GWAS) of a natural population was conducted, covering 2,131,705 genome variants across four environments. The 13 QTLs for PH and 15 for FBH were identified. Meta-analysis revealed that 28.57% of these loci overlapped with previously reported QTLs. Haplotype analysis confirmed significant effects of these loci on the traits. Candidate genes for PH and FBH, respectively, were identified based on linkage disequilibrium and functional predictions. However, five novel loci lacked nearby annotated genes. The candidate genes are linked to traits in <i>Arabidopsis</i> and other species, as well as to phytohormone response and cell development, and cell development. Notably, <i>MOS1</i> gene copies (<i>BnaA03G0481200ZS</i> and <i>BnaC07G0459400ZS</i>) were associated with PH and FBH, indicating their multifunctional potential. Additionally, <i>BnaA05G0163200ZS</i>, with no functional annotation, emerged as a crucial gene for plant architecture. This study provides new genetic insights and may enhance marker-based breeding for ideotypes in rapeseed.