Fine mapping via QTL-seq, Target-seq and RNA-seq of a novel QTL controlling early flowering time in spring B.napus

Abstract Days to flowering (DTF) is a very important trait of rapeseed, but the molecular mechanism in spring B. napus is unknown. We previously located a novel candidate QTL for the early-flowering trait in spring B. naopus, which was named BnaC08cqDTF. Here, DNA pools of extreme early-flowering and late-flowering BC3F2 plants from crosses between spring-type B. napus No. 4512 (early flowering parent) and No. 5246 (late flowering parent) were bulked for QTL sequencing (QTL-seq) and initial mapping. Target sequencing (Target-seq) and fine mapping were performed using the BC3F2 and BC4F2 population plants. BnaC08cqDTF was narrowed to the 86 kb region of chromosome C08. RNA-seq and qRT‒PCR analyses indicated that the expressing levels of two candidate genes (BnaC08G0010400ZS and BnaC08G0011200ZS) in No. 4512 were significantly higher than those in No. 5246. Furthermore, we cloned the genes of BnaC08G0010400ZS and BnaC08G0011200ZS from parents and NILs. An A/G nonsynonymous mutation was identified in the 1,259 bp locus of exon 3 in the CDS of BnaC08G00101400ZS, causing a 374 E to K amino acid substitution. This SNP haplotype also exists in a natural population. BnaC08G0010400ZS may be the candidate gene of BnaC08cqDTF, and this gene is homologous to the AT1G04400 gene (CRY2) in Arabidopsis. Our results may contribute to a better understanding of the molecular mechanism of early flowering regulation and promote the breeding program for prematurity in spring B. napus.