A naturally occurring long insertion in the first intron in the Brassica rapaFLC2 gene causes delayed bolting

We investigated the molecular basis of an extremely late bolting, non-heading ‘Leafy Green Parental Line No. 2 (Tsukena No. 2)’, to obtain suitable DNA markers for breeding the late bolting trait in Chinese cabbage ( Brassica rapa L. ssp. pekinensis ). We found that Tsukena No. 2 contains a ~5 kbp large insertion near the 5′ end of the first intron of BrFLC2 , BrFLC3 and BrFLC3 ′, which are homologs of an Arabidopsis repressor gene for floral transition, FLOWERING LOCUS C ( FLC ). The transcript abundance of BrFLC1 in Tsukena No. 2 was repressed during cold exposure to the same level as found in a mid-season bolting commercial F 1 variety “Muso” (heading Chinese cabbage) and an early-bolting parent of commercial F 1 varieties, “Early” (Sakata Co.), whereas repression of BrFLC2 and BrFLC3 containing the large insertion was weak. Furthermore, QTL analysis of a F 2 population derived from the Tsukena No. 2 × “Early” revealed that polymorphisms at the BrFLC2 and BrFLC3 loci explained 46.0 and 9.9 % of the phenotypic variation in the bolting time of vernalized plants, respectively. In Arabidopsis , cold-induced repression of FLC and maintenance of that repression are associated with the first intron of FLC . Our study suggests that a naturally occurring large insertion in the first intron resulted in weak repression of BrFLC2 and BrFLC3 during cold exposure and therefore explains the extremely late bolting of the Tsukena No. 2 cultivar.