Genome-wide association studies in the genetic dissection of ovule number, seed number, and seed weight in Brassica napus L

•Three yield-related traits were studied by six ML-GWAS and four SL-GWAS methods.•A total of 310 QTNs were identified for ovule number, seed number and seed weight.•94 novel QTNs were detected for the three traits.•Detection of 42 candidate genes and 74 superior alleles governing the three traits.•First attempt for QTNs detection controlling ovule number in Brassica napus. Ovule number (ON), seed per silique (SS), and thousand seed weight (TSW) are the most important but complex traits affecting yield. This study undertook genome-wide association studies (GWAS) on 521 accessions of rapeseed genotyped with the Brassica 60 K SNP array by six multi-locus GWAS (ML-GWAS) and four single-locus GWAS (SL-GWAS) methods. The findings of our study showed that 280 and 31 significant quantitative trait nucleotides/loci (QTNs/QTLs) were detected above six multi-locus and four single-locus models, respectively. Among these sequences, 74 common significant QTNs were repeatedly detected by more than three ML-GWAS models and in multiple environments. Among the QTNs, 26 were detected via multiple environments, while 13 were detected via multiple methods and environments. Interestingly, 119 QTNs were detected by a single model (pLARmEB), demonstrating that this model is largely reliable and stable. However, in SL-GWAS, the GLM model detected the highest number of QTNs. The distribution of the superior allele results showed that, among 74 common significant QTNs, 28 QTNs were >50%, while 45 QTNs were