AUTHOR=Saha Gopal , Park Jong-In , Kayum Md. Abdul , Nou Ill-Sup 

TITLE=A Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of TIFY Family Genes in Brassica rapa

JOURNAL=Frontiers in Plant Science

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2016.00936

DOI=10.3389/fpls.2016.00936

ISSN=1664-462X

ABSTRACT=<p>The TIFY family is a plant-specific group of proteins with a diversity of functions and includes four subfamilies, <italic>viz</italic>. ZML, TIFY, PPD, and JASMONATE ZIM-domain (JAZ) proteins. TIFY family members, particularly JAZ subfamily proteins, play roles in biological processes such as development and stress and hormone responses in <italic>Arabidopsis</italic>, rice, chickpea, and grape. However, there is no information about this family in any <italic>Brassica</italic> crop. This study identifies 36 <italic>TIFY</italic> genes in <italic>Brassica rapa</italic>, an economically important crop species in the <italic>Brassicaceae</italic>. An extensive <italic>in silico</italic> analysis of phylogenetic grouping, protein motif organization and intron-exon distribution confirmed that there are four subfamilies of BrTIFY proteins. Out of 36 <italic>BrTIFY</italic> genes, we identified 21 in the JAZ subfamily, seven in the TIFY subfamily, six in ZML and two in PPD. Extensive expression profiling of 21 <italic>BrTIFY JAZs</italic> in various tissues, especially in floral organs and at different flower growth stages revealed constitutive expression patterns, which suggest that <italic>BrTIFY JAZ</italic> genes are important during growth and development of <italic>B. rapa</italic> flowers. A protein interaction network analysis also pointed to association of these proteins with fertility and defense processes of <italic>B. rapa</italic>. Using a low temperature-treated whole-genome microarray data set, most of the <italic>JAZ</italic> genes were found to have variable transcript abundance between the contrasting inbred lines Chiifu and Kenshin of <italic>B. rapa</italic>. Subsequently, the expression of all 21 <italic>BrTIFY JAZs</italic> in response to cold stress was characterized in the same two lines via qPCR, demonstrating that nine genes were up-regulated. Importantly, the <italic>BrTIFY JAZs</italic> showed strong and differential expression upon JA treatment, pointing to their probable involvement in JA-mediated growth regulatory functions, especially during flower development and stress responses. Additionally, <italic>BrTIFY JAZs</italic> were induced in response to salt, drought, <italic>Fusarium</italic>, ABA, and SA treatments, and six genes (<italic>BrTIFY3a, 3b, 6a, 9a, 9b</italic>, and <italic>9c</italic>) were identified to have co-responsive expression patterns. The extensive annotation and transcriptome profiling reported in this study will be useful for understanding the involvement of <italic>TIFY</italic> genes in stress resistance and different developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate <italic>TIFY</italic> genes for genetic engineering of <italic>B. rapa</italic>.</p>