Characterization and expression profiling of the ICE-CBF-COR genes in wheat

Jie Guo,Yongkang Ren,Weiping Shi,Zhaohui Tang,Meixue Zhou

doi:10.7717/peerj.8190

Abstract

Cold stress is one of the major abiotic stresses that limit crop production. The ICE-CBF-COR pathway is associated with cold stress response in a wide variety of crop species. However, the ICE-CBF-COR genes has not been well characterized in wheat (Triticum aestivum). This study identified, characterized and examined the expression profiles of the ICE, CBF and COR genes for cold defense in wheat. Five ICE (inducer of CBF expression) genes, 37 CBF (C-repeat binding factor) genes and 11 COR (cold-responsive or cold-regulated) genes were discovered in the wheat genome database. Phylogenetic trees based on all 53 genes revealed that CBF genes were more diverse than ICE and COR genes. Twenty-two of the 53 genes appeared to include 11 duplicated pairs. Twenty rice (Oryza sativa) genes and 21 sorghum (Sorghum bicolor) and maize (Zea mays) genes showed collinearity with the wheat ICE, CBF and COR genes. Transcriptome data and qRT-PCR analyses revealed tissue-specific expression patterns of the ICE, CBF and COR genes, and identified similarities in the expression pattern of genes from the same family when subjected to drought, heat, drought plus heat, and cold stress. These results provide information for better understanding the biological roles of ICE, CBF, COR genes in wheat.

Highlights

Low-temperature damage in crops is a global problem for production and security with global economic losses estimated to be as high as hundreds of millions of dollars annually
A Hidden Markov Model (HMM) was established using 10 CBF protein sequences from rice (Oryza sativa) and 17 CBF protein sequences from barley (Hordeum vulgare) for sequence alignment against the protein sequences of other crop genomes (Badawi et al, 2007; Skinner et al, 2005)
Alignment results from 42 species indicated that the numbers of ICE, CBF and COR genes were 274, 131 and 188, respectively

Summary

Introduction

Low-temperature damage in crops is a global problem for production and security with global economic losses estimated to be as high as hundreds of millions of dollars annually. Low temperatures throughout the winter are a frequent occurrence in the winter wheat (Triticum aestivum) production regions of northern China (Li et al, 2013). The ICE-CBF-COR pathway is a universal pathway related to cold stress tolerance in crop species (Wang et al, 2017a; Jin et al, 2018). ICE (inducer of CBF expression) genes are members of the MYC family of transcription factors, and MYC is a subfamily of bHLH. The main structural feature of ICE is that it shares highly conserved regions in the bHLH domain and their C-terminal regions (Chinnusamy et al, 2003; Badawi et al, 2008; Peng et al, 2014; Lee, Henderson & Zhu, 2015; Lu et al, 2017; Jin et al, 2018). ICE factors are positive regulators of CBF expression in the upstream region of the low-temperature

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Conclusion