Genetic dissection of flowering time and fine mapping of qFT.A02-1 in rapeseed (Brassica napus L.).

qFT.A02-1, a major quantitative trait locus controlling flowering time in Brassica napus, was mapped to a 104.8-kb region on chromosome A02, and BnaA02G0156900ZS is the candidate gene in response for flowering time. Flowering time is a key agronomic trait that determines the adaptability of crops to the environment and thus affects yields. The mechanism underlying flowering time is still far from clear in Brassica napus. In this study, a recombinant inbred line population composed of 215 lines was constructed and 35 flowering time QTLs were identified. One major QTL, qFT.A02-1 (explaining 16.40-17.80% of phenotypic variation), was detected in two environments, which was confirmed by QTL-seq. A residual heterozygous line containing qFT.A02-1 for flowering time was further constructed, and qFT.A02-1 was subsequently fine-mapped to a 104.8-kb interval, wherein a total of 11 genes were predicted. Candidate gene functional annotation implied that BnaA02G0156900ZS, a homologous gene of FLOWERING LOCUS T in B. napus, was likely the candidate gene for qFT.A02-1. HiFi sequencing of the two parents was subsequently conducted, and a 1,079-bp insertion in the promoter of BnaA02. FT was confirmed. The allelic variation analysis in a diversity of accessions identified another 6 SNPs existing in the non-coding region of BnaA02. FT and the 1,079-bp insertion in promoter region are closely associated with the flowering time in B. napus. Haplotype analysis indicated that the flowering time of Hap02 is significantly earlier than Hap01 and Hap04, and Hap05 is significantly earlier than Hap04. Yield-related trait analysis revealed that there are no significant differences in yield-related traits between the two near-isogenic lines based on the target locus. These results may advance our understanding of the mechanism underlying flowering time in B. napus.