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

Abstract

The TIFY family is a plant-specific group of proteins with a diversity of functions and includes four subfamilies, viz. 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 Arabidopsis, rice, chickpea, and grape. However, there is no information about this family in any Brassica crop. This study identifies 36 TIFY genes in Brassica rapa, an economically important crop species in the Brassicaceae. An extensive in silico analysis of phylogenetic grouping, protein motif organization and intron-exon distribution confirmed that there are four subfamilies of BrTIFY proteins. Out of 36 BrTIFY 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 BrTIFY JAZs in various tissues, especially in floral organs and at different flower growth stages revealed constitutive expression patterns, which suggest that BrTIFY JAZ genes are important during growth and development of B. rapa flowers. A protein interaction network analysis also pointed to association of these proteins with fertility and defense processes of B. rapa. Using a low temperature-treated whole-genome microarray data set, most of the JAZ genes were found to have variable transcript abundance between the contrasting inbred lines Chiifu and Kenshin of B. rapa. Subsequently, the expression of all 21 BrTIFY JAZs in response to cold stress was characterized in the same two lines via qPCR, demonstrating that nine genes were up-regulated. Importantly, the BrTIFY JAZs 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, BrTIFY JAZs were induced in response to salt, drought, Fusarium, ABA, and SA treatments, and six genes (BrTIFY3a, 3b, 6a, 9a, 9b, and 9c) 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 TIFY genes in stress resistance and different developmental functions, which ultimately provides the basis for functional characterization and exploitation of the candidate TIFY genes for genetic engineering of B. rapa.

Genome-Wide Identification, Expression Profile of the TIFY Gene Family in Brassica oleracea var. capitata, and Their Divergent Response to Various Pathogen Infections and Phytohormone Treatments

“…In this work, qRT-PCR was conducted to evaluate the responses of cabbage JAZ genes after different phytohormone (JA, SA, ET) treatments. After treatment with MeJA, the transcription of all JAZ genes in cabbage seedlings was induced compared to the control (Figure 7), which was consistent with the results in A. thaliana and B. rapa [21,26]. Among the JAZ genes, fifteen were significantly upregulated, and six (BoJAZ6, BoJAZ8, BoJAZ15, BoJAZ16, BoJAZ18, and BoJAZ20) were upregulated more than 10-fold, while BoJAZ11 was upregulated less than twofold and not significantly, showing the different responses of these JAZ genes to MeJA.…”

“…The first part of the candidate TIFY family proteins was obtained. In addition, BLAST analyses were conducted using 18 Arabidopsis [7] and 36 Brassica rapa [26] TIFY protein sequences as queries on the D134 genome by using the BLASTP program, thus obtaining the second part of the candidate TIFY proteins in B. oleracea. Subsequently, the two candidate sets were merged, the redundant proteins were removed, and their conserved domains were further identified by using NCBI-CDD (https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) [41].…”

“…Seven TIFY subfamily genes only contained the tify motif, while five ZML subfamily genes had the extra CCT and ZnF_GATA motifs, 2 PPD genes had the PPD motif, and the largest JAZ subfamily had 22 members with the C-terminal Jas motif. Based on the amino acid sequences of full-length TIFY proteins in A. thaliana (18) [7], B. oleracea (36) and B. rapa (36) [26], the phylogenetic tree was constructed using the neighbour-joining method in MEGA 6 software. The 91 TIFY proteins were grouped into ten clades (groups 1-10 with different background colours) ( Figure 4).…”

“…In addition to MYC transcription factors, MYB TFs (MYB21/MYB24/MYB75/GL1) targeted by JAZ repressors were identified by yeast two-hybrid screens and confirmed in vivo [24,25].Brassicaceae (alternative name Cruciferae) is a family with numerous economically valuable members, including vegetables, oil crops, medicinal plants, and ornamental plants. Among these species, genome-wide identification of the TIFY gene family has been carried out in Arabidopsis and Brassica rapa [7,26]. Cabbage (Brassica oleracea var.…”

“…Brassicaceae (alternative name Cruciferae) is a family with numerous economically valuable members, including vegetables, oil crops, medicinal plants, and ornamental plants. Among these species, genome-wide identification of the TIFY gene family has been carried out in Arabidopsis and Brassica rapa [7,26]. Cabbage (Brassica oleracea var.…”