Genome-Wide Association Study Reveals Candidate Genes for Control of Plant Height, Branch Initiation Height and Branch Number in Rapeseed (Brassica napus L.)

Plant architecture is crucial for rapeseed yield and is determined by plant height (PH), branch initiation height (BIH), branch number(BN)and leaf and inflorescence morphology. In this study, we measured three major factors (PH, BIH,and BN) in a panel of 333 rapeseed accessions across four years. A genome-wide association study (GWAS) was performed via Q+K model and the panel was genotyped using the 60k BrassicaInfinium SNP array. We identified seven loci for PH, four for BIH and five for BN. Subsequently, by determining linkage disequilibrium (LD) decay associated with 38 significant SNPs, we gained 31, 15 and 17 candidate genes for these traits, respectively. We also showed that PH is significantly correlated with BIH, while no other correlation was revealed. Notably, a GA signaling gene (BnRGA) and a flowering gene (BnFT) located on chromosome A02 were identified as the most likely candidate genes associated with PH regulation. Furthermore, a meristem initiation gene (BnLOF2) and a NAC domain transcriptional factor (BnCUC3) that may be associated with branch number were identified on the chromosome A07. This study reveals novel insight into the genetic control of plant architecture and may facilitate marker-based breeding for rapeseed.