Genome-wide identification and evolutionary analyses of bZIP transcription factors in wheat and its relatives and expression profiles of anther development related TabZIP genes

Abstract

BackgroundAmong the largest and most diverse transcription factor families in plants, basic leucine zipper (bZIP) family participate in regulating various processes, including floral induction and development, stress and hormone signaling, photomorphogenesis, seed maturation and germination, and pathogen defense. Although common wheat (Triticum aestivum L.) is one of the most widely cultivated and consumed food crops in the world, there is no comprehensive analysis of bZIPs in wheat, especially those involved in anther development. Previous studies have demonstrated wheat, T. urartu, Ae. tauschii, barley and Brachypodium are evolutionarily close in Gramineae family, however, the real evolutionary relationship still remains mysterious.ResultsIn this study, 187 bZIP family genes were comprehensively identified from current wheat genome. 98, 96 and 107 members of bZIP family were also identified from the genomes of T.urartu, Ae.tauschii and barley, respectively. Orthology analyses suggested 69.4 % of TubZIPs were orthologous to 68.8 % of AetbZIPs and wheat had many more in-paralogs in the bZIP family than its relatives. It was deduced wheat had a closer phylogenetic relationship with barley and Brachypodium than T.urartu and Ae.tauschii. bZIP proteins in wheat, T.urartu and Ae.tauschii were divided into 14 subgroups based on phylogenetic analyses. Using Affymetrix microarray data, 48 differentially expressed TabZIP genes were identified to be related to anther development from comparison between the male sterility line and the restorer line. Genes with close evolutionary relationship tended to share similar gene structures. 15 of 23 selected TabZIP genes contained LTR elements in their promoter regions. Expression of 21 among these 23 TabZIP genes were obviously responsive to low temperature. These 23 TabZIP genes all exhibited distinct tissue-specific expression pattern. Among them, 11 TabZIP genes were predominantly expressed in anther and most of them showed over-dominance expression mode in the cross combination TY806 × BS366.ConclusionsThe genome-wide identification provided an overall insight of bZIP gene family in wheat and its relatives. The evolutionary relationship of wheat and its relatives was proposed based on orthology analyses. Microarray and expression analyses suggested the potential involvement of bZIP genes in anther development and facilitated selection of anther development related gene for further functional characterization.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2196-7) contains supplementary material, which is available to authorized users.

Bioinformatic Analyses of Subgroup-A Members of the Wheat bZIP Transcription Factor Family and Functional Identification of TabZIP174 Involved in Drought Stress Response

“…In our previous study, 187 bZIP transcription factor family members were identified from the wheat genome (Li X. et al, 2015). Among these, 35 novel TabZIP proteins belonged to Subgroup A of the wheat bZIP family.…”

“…Members of the bZIP family in wheat, including most of Subgroup-A members, were identified in our previous study (Li X. et al, 2015). In the present study, we first added a few more bZIP members to Subgroup A.…”

“…The basic region takes charge of sequence-specific DNA binding. By comparison, the leucine zipper is less conserved and comprises heptad repeats of leucine (Leu) or other bulky hydrophobic amino acid (such as Ile, Val, Phe, or Met) residues positioned accurately nine amino acid residues toward the C-terminus to create an amphipathic helix that confers homo- or hetero-dimerization specificity (Jakoby et al, 2002; Nijhawan et al, 2008; Li X. et al, 2015). …”

“…Members of the bZIP transcription factor family were comprehensively identified or predicted in some plant genomes, such as Arabidopsis , rice, soybean, sorghum, maize, cucumber, grapevine, castor bean, Brachypodium distachyon , tomato, wheat, Triticum urartu, Aegilops tauschii , barley, and apple (Jakoby et al, 2002; Liao et al, 2008; Nijhawan et al, 2008; Wang et al, 2011; Wei et al, 2012; Baloglu et al, 2014; Jin et al, 2014; Liu et al, 2014; Li D. et al, 2015; Li X. et al, 2015; Liu and Chu, 2015; Zhao et al, 2016). bZIP family members were classified into 14 subgroups (Jakoby et al, 2002; Li X. et al, 2015).…”

“…bZIP family members were classified into 14 subgroups (Jakoby et al, 2002; Li X. et al, 2015). Extensive studies in Arabidopsis and rice demonstrated that Subgroup-A proteins of the bZIP family participated in mediating abscisic acid (ABA) signaling and/or regulating abiotic stress responses in plants, and held great potential in enhancing the resistance of transgenic plants to multiple abiotic stresses.…”