AUTHOR=Liu Xianjun , Lu Ying , Yan Mingli , Sun Donghong , Hu Xuefang , Liu Shuyan , Chen Sheyuan , Guan Chunyun , Liu Zhongsong 

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

JOURNAL=Frontiers in Plant Science

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2016.01831

DOI=10.3389/fpls.2016.01831

ISSN=1664-462X

ABSTRACT=<p>Proanthocyanidins (PA) is a type of prominent flavonoid compound deposited in seed coats which controls the pigmentation in all <italic>Brassica</italic> species. Annotation of <italic>Brassica juncea</italic> 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 <italic>B. juncea</italic>. A total of 284 BAC clones were identified and sequenced. Alignment of the sequences confirmed that 55 genes were cloned, with every <italic>Arabidopsis</italic> PA gene having 2–7 homologs in <italic>B. juncea</italic>. BLAST analysis using the recently released <italic>B. rapa</italic> or <italic>B. napus</italic> genome database identified 31 and 58 homologous genes, respectively. Mapping and phylogenetic analysis indicated that 30 <italic>B. juncea</italic> 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 <italic>B. juncea</italic> and <italic>B. napus</italic>, and that <italic>BjuTT3, BjuTT18, BjuANR, BjuTT4-2, BjuTT4-3, BjuTT19-1</italic>, and <italic>BjuTT19-3</italic> are transcriptionally regulated, and not expressed or downregulated in yellow-seeded testa. Importantly, our study facilitates in better understanding of the molecular mechanism underlying <italic>Brassica</italic> PA profiles and accumulation, as well as in further characterization of PA genes.</p>