Genome-Wide Identification, Localization, and Expression Analysis of Proanthocyanidin-Associated Genes in Brassica

Abstract

Proanthocyanidins (PA) is a type of prominent flavonoid compound deposited in seed coats which controls the pigmentation in all <i>Brassica</i> species. Annotation of <i>Brassica juncea</i> genome survey sequences showed 72 PA genes; however, a functional description of these genes, especially how their interactions regulate seed pigmentation, remains elusive. In the present study, we designed 19 primer pairs to screen a bacterial artificial chromosome (BAC) library of <i>B. juncea</i>. A total of 284 BAC clones were identified and sequenced. Alignment of the sequences confirmed that 55 genes were cloned, with every <i>Arabidopsis</i> PA gene having 2-7 homologs in <i>B. juncea</i>. BLAST analysis using the recently released <i>B. rapa</i> or <i>B. napus</i> genome database identified 31 and 58 homologous genes, respectively. Mapping and phylogenetic analysis indicated that 30 <i>B. juncea</i> PA genes are located in the A-genome chromosomes except A04, whereas the remaining 25 genes are mapped to the B-genome chromosomes except B05 and B07. RNA-seq data and Fragments Per Kilobase of a transcript per Million mapped reads (FPKM) analysis showed that most of the PA genes were expressed in the seed coat of <i>B. juncea</i> and <i>B. napus</i>, and that <i>BjuTT3, BjuTT18, BjuANR, BjuTT4-2, BjuTT4-3, BjuTT19-1</i>, and <i>BjuTT19-3</i> are transcriptionally regulated, and not expressed or downregulated in yellow-seeded testa. Importantly, our study facilitates in better understanding of the molecular mechanism underlying <i>Brassica</i> PA profiles and accumulation, as well as in further characterization of PA genes.