Genetic mapping and regional association analysis revealed a CYTOKININ RESPONSE FACTOR 10 gene controlling flowering time in Brassica napus L.

Oilseed rape (Brassica napus L.), as an important source of renewable energy and an industrial crop, has received extensive attention. Breeding cultivars with appropriate flowering time (FT) is of high significance for crop yields, but it is currently impeded by incomplete understanding of genetic control for flowering time in B. napus. In this study, ebm, an ethyl methanesulfonate mutagenesis (EMS) mutant with early blooming, was derived from B. napus cv. Zhongshuang9 (ZS9). Genetic analysis showed that the early blooming of ebm was controlled by a dominant nuclear gene. The Ebm locus was delimitated in a 905-kb region on chromosome A02 by bulked segregant analysis sequencing and fine mapping. Based on the expression and variation analysis of the genes in the candidate region, and gene conservation analysis in pan-genome, a potential gene BnaA02.CRF10 was pinpointed, which encodes a cytokinin response factor involved in the cytokinin signaling pathway. Regional association and haplotype analyses of the initial and blooming FT in a worldwide bio-panel of 263 re-sequenced B. napus accessions further confirmed the candidate gene and mined favorable allelic variations. Additionally, differentially expressed genes (DEGs) related to ethylene and cytokinin genetic factors were significantly induced in the ebm mutant by comparative transcriptome analysis. Moreover, phylogenetic and synteny network analyses provided strong evidence for the phylogenetic conservation of the CRF subfamily during the evolutionary history from Chlorophyta to dicotyledonous plants. Taken together, a novel conserved gene with favorable alleles conferring early flowering trait in B. napus was identified, which lays a foundation for the genetic improvement and cultivar breeding of this important crop with shortened growth periods in the future.