Identification of candidate genes involved in the biosynthesis of carotenoids in Brassica rapa

To better understand carotenoid biosynthesis in Brassica rapa, a genome-wide investigation was performed using the EST/mRNA sequences and the draft genome of B. rapa. We have identified 46 full-length coding sequences in the B. rapa genome by comparing with the Arabidopsis thaliana genes that were involved in carotenoid biosynthesis. The identified genes were categorized to belong to 11 protein families encoding various enzymes involving the biosynthesis. A detailed domain structural analysis of the enzymes showed that these were highly conserved and overlapping. The genes were localized to all 10 chromosomes of the plant, six of which were single-copy genes; whereas others had more than one paralogue. Phylogenetic analysis of A. thaliana and B. rapa sequences revealed sequence identities ranging from 70–90%, indicating the conservation of genes among the species. Approximately 185 single nucleotide polymorphisms (SNPs) were annotated at the exonic and intronic regions of these genes, while comparing the resequenced parental lines RcBr and Kenshin against Chiifu as reference genome. Expression profiling was done for all the identified genes with the available microarray data of inbred lines, Chiifu and RcBr. Finally, a knowledge-based carotenoid biosynthesis pathway was proposed for B. rapa using details retrieved from the comparative study.