Journal Article

Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat

Xiao, Jie, He, Guangyuan, Su, Peipei, Chang, Junli, Hu, Rui, Qiu, Ding, Feng, Jialu, Yang, Guangxiao, Gu, Ting, Han, Jiapeng

2019

Overview

Background The trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization of the trihelix genes has yet been conducted in wheat and its close relatives. Results We identified a total of 94 trihelix genes in wheat, as well as 22 trihelix genes in Triticum urartu , 29 in Aegilops tauschii , and 31 in Brachypodium distachyon . We analyzed the chromosomal locations and orthology relations of the identified trihelix genes, and no trihelix gene was found to be located on chromosome 7A, 7B, or 7D of wheat, thereby reflecting the uneven distributions of wheat trihelix genes. Phylogenetic analysis indicated that the 186 identified trihelix proteins in wheat, rice, B. distachyon , and Arabidopsis were clustered into five major clades. The trihelix genes belonging to the same clades usually shared similar motif compositions and exon/intron structural patterns. Five pairs of tandem duplication genes and three pairs of segmental duplication genes were identified in the wheat trihelix gene family, thereby validating the supposition that more intrachromosomal gene duplication events occur in the genome of wheat than in that of other grass species. The tissue-specific expression and differential expression profiling of the identified genes under cold and drought stresses were analyzed by using RNA-seq data. qRT-PCR was also used to confirm the expression profiles of ten selected wheat trihelix genes under multiple abiotic stresses, and we found that these genes mainly responded to salt and cold stresses. Conclusions In this study, we identified trihelix genes in wheat and its close relatives and found that gene duplication events are the main driving force for trihelix gene evolution in wheat. Our expression profiling analysis demonstrated that wheat trihelix genes responded to multiple abiotic stresses, especially salt and cold stresses. The results of our study built a basis for further investigation of the functions of wheat trihelix genes and provided candidate genes for stress-resistant wheat breeding programs.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abiotic stress / Animal Genetics and Genomics / Arabidopsis / Arabidopsis thaliana / Biodiversity / Bioinformatics / Biological evolution / Biomedical and Life Sciences / Brachypodium distachyon / Chromosome 7 / Chromosomes / Chromosomes, Plant - genetics / Climate change / Criminal investigation / Deoxyribonucleic acid / DNA / Drought / Evolutionary genetics / Expression profile / Flowers & plants / Gene duplication / Gene expression / Gene Expression Profiling / Genes / Genome-wide association studies / Genomes / Genomics / Goat grass / Identification / Life Sciences / Localization / Microarrays / Microbial Genetics and Genomics / Organ Specificity / Orthology / Orthology relation / Phylogeny / Plant breeding / Plant Genetics and Genomics / Plant genomics / Plant growth / Plant Proteins - genetics / Proteins / Proteomics / Reproduction (copying) / Research Article / Ribonucleic acid / Rice / RNA / Sequence Homology, Nucleic Acid / Stress, Physiological - genetics / Stresses / Synteny / Transcription (Genetics) / Transcription factor / Transcription Factors - genetics / trihelix gene family / Triticum - genetics / Triticum - physiology / Wheat