Fine mapping and identification of candidate Br-or gene controlling orange head of Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Orange head Chinese cabbage accumulates significant amounts of carotenoids with enhanced nutritional quality. To develop molecular markers for breeding of Chinese cabbage lines with high carotenoid content and to isolate the candidate gene underlying carotenoid synthesis, we performed fine mapping of the orange locus in a F2S4 mapping population. Genetic analysis revealed that the phenotype of the orange head trait was controlled by a single recessive gene, Br-or. The F2S4 mapping population consisting of 1,724 individuals was developed from the cross between parental lines 11J16 and 11S39-2 by continuous selfing of a single heterozygous individual. Twenty-one tightly linked simple sequence repeat (SSR) and insertion/deletion polymorphism (InDel) markers were obtained. High-resolution genetic mapping of these markers in the F2S4 mapping population placed Br-InDel2 and Br-InDel1 at genetic distances of 0.1 and 0.2 cM, respectively, on either side of the Br-or locus. Based on comparison of these two marker sequences with the fully sequenced Brassica rapa genome, the Br-or locus was delimited to a 16.7 kb genomic region. Three open reading frames (ORFs) were predicted in the target region. ORF1 encoded carotenoid isomerase, which is involved in the isomerization of carotenoids. ORF1 was found to be co-segregated with the Br-or locus and was thus the most likely candidate gene for Br-or. The information obtained here will facilitate the breeding of nutrient-enriched Chinese cabbage through marker-assisted selection and provide a platform for gaining a better understanding of the regulation of carotenoid biosynthesis in these plants.