LAUSR

Abstract 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