A naturally occurring InDel variation in BraA.FLC.b (BrFLC2) associated with flowering time variation in Brassica rapa

We analyzed the BrFLC2 sequence in nine B. rapa accessions, and identified a 57-bp insertion/deletion (InDel) across exon 4 and intron 4 resulting in a non-functional allele. In total, three types of transcripts were identified for this mutated BrFLC2 allele. The InDel was used to develop a PCR-based marker, which was used to screen a collection of 159 B. rapa accessions. The deletion genotype was present only in oil-type B. rapa, including ssp. oleifera and ssp. tricolaris, and not in other subspecies. The deletion genotype was significantly correlated with variation in flowering time. In contrast, the reported splicing site variation in BrFLC1, which also leads to a non-functional locus, was detected but not correlated with variation in flowering time in oil-type B. rapa, although it was correlated with variation in flowering time in vegetable-type B. rapa.Our results suggest that the naturally occurring deletion mutation across exon 4 and intron 4 in BrFLC2 gene contributes greatly to variation in flowering time in oil-type B. rapa. The observed different relationship between BrFLC1 or BrFLC2 and flowering time variation indicates that the control of flowering time has evolved separately between oil-type and vegetable-type B. rapa groups.Brassica rapa is a genus comprising a variety of vegetables such as Chinese cabbage (ssp. pekinensis), pak choi (ssp. chinensis), and turnip (ssp. rapa) as well as oil crops including turnip rape (ssp. oleifera) and sarson (ssp. tricolaris). Flowering time is an important trait in Brassica vegetables because early flowering often leads to low yield and low quality. It is also important for oilseed rape varieties as they are divided into “winter” and “spring” types according to their different flowering times and responsiveness to vernalization. Winter types must be exposed to cold to transition from the vegetative growth stage to the reproductive stage, while this is not necessary for the spring types, which are generally grown i