Journal Article

Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses

Yan, Yueming, Liu, Nannan, Liu, Yue, Liu, Dongmiao, Deng, Xiong, Li, Mengfei, Cui, Dada, Hu, Yingkao

2020

Overview

Background DNA binding with one finger (Dof) transcription factors play important roles in plant growth and abiotic stress responses. Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat. The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family. Results Using the recently released wheat genome database (IWGSC RefSeq v1.0), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences. Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31 T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and qRT-PCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses. Conclusions The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Abiotic stress / Amino acids / Analysis / Animal Genetics and Genomics / Barley / Binding / Biological evolution / Biomedical and Life Sciences / Chromosomes / Comparative and evolutionary genomics / Deoxyribonucleic acid / Developmental stages / Divergence / DNA / DNA binding proteins / Dof transcription factors / Evolution / Gene duplication / Gene expression / Genes / Genetic aspects / Genomes / Genomics / Heavy metals / Kinases / Life Sciences / Localization / Maximum likelihood method / Microarrays / Microbial Genetics and Genomics / Organs / Phylogenetics / Phylogeny / Plant genetics / Plant Genetics and Genomics / Plant growth / Positive selection / Proteins / Proteomics / Reproduction (copying) / Research Article / Ribonucleic acid / RNA / RNA polymerase / Structural stability / Structure-function relationships / Transcript expression / Transcription factors / Wheat