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

Xueyin Li,Shiqing Gao,Zhaofeng Fang,Biane Feng,Lingjian Ma,Fengjie Zhang,Lei Li,Changping Zhao,Yimiao Tang

doi:10.1186/s12864-015-2196-7

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.

Highlights

Among the largest and most diverse transcription factor families in plants, basic leucine zipper family participate in regulating various processes, including floral induction and development, stress and hormone signaling, photomorphogenesis, seed maturation and germination, and pathogen defense
We have proposed the evolutionary relationship among wheat and its relatives based on the orthology analyses of basic leucine zipper (bZIP) family. bZIP transcription factors in wheat, T.urartu and Ae.tauschii have been classified on the basis of phylogenetic analyses. 23 anther development related bZIP genes are selected from differentially expressed genes by microarray data analyses
Evolutionary relationship of wheat, T. urartu, Ae. tauschii, barley and Brachypodium To further explore the evolutionary relationship of bZIP family genes among these five evolutionarily close species, we identified orthologs and in-paralogs between each pair of these five species (Fig. 2 and Additional file 1: Table S2) using InParanoid 7, which allowed us to define the evolutionary point of the orthology precisely

Summary

Introduction

Among 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. Among the largest and most diverse dimerizing transcription factor families, the basic leucine zipper (bZIP) family of proteins in plants participates in regulating various processes including floral induction and development, stress and hormone signaling, photomorphogenesis, seed maturation and germination, and pathogen defense [1, 2]. Plant bZIP proteins preferentially bind to DNA sequences contain an ACGT core, especially like G-box (CACGTG), C-box (GACGTC) and A-box (TACGTA) [4, 5]

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Conclusion