Expansion and Molecular Characterization of AP2/ERF Gene Family in Wheat (Triticum aestivum L.).

Chuanxi Ma,Liu Xue,Xu Dong Mei,Muhammad Abdullah,Hongqi Si,Muhammad Waheed Riaz,Can Chen,Shamsur Rehman,Jie Lu,Muhammad Aamir Manzoor,Liu Yang,Liaqat Shah

doi:10.3389/fgene.2021.632155

Abstract

The AP2/ERF is a large protein family of transcription factors, playing an important role in signal transduction, plant growth, development, and response to various stresses. AP2/ERF super-family is identified and functionalized in a different plant but no comprehensive and systematic analysis in wheat (Triticum aestivum L.) has been reported. However, a genome-wide and functional analysis was performed and identified 322 TaAP2/ERF putative genes from the wheat genome. According to the phylogenetic and structural analysis, TaAP2/ERF genes were divided into 12 subfamilies (Ia, Ib, Ic, IIa, IIb, IIc, IIIa, IIIb, IIIc, IVa, IVb, and IVc). Furthermore, conserved motifs and introns/exons analysis revealed may lead to functional divergence within clades. Cis-Acting analysis indicated that many elements were involved in stress-related and plant development. Chromosomal location showed that 320 AP2/ERF genes were distributed among 21 chromosomes and 2 genes were present in a scaffold. Interspecies microsynteny analysis revealed that maximum orthologous between Arabidopsis, rice followed by wheat. Segment duplication events have contributed to the expansion of the AP2/ERF family and made this family larger than rice and Arabidopsis. Additionally, AP2/ERF genes were differentially expressed in wheat seedlings under the stress treatments of heat, salt, and drought, and expression profiles were verified by qRT-PCR. Remarkably, the RNA-seq data exposed that AP2/ERF gene family might play a vital role in stress-related. Taken together, our findings provided useful and helpful information to understand the molecular mechanism and evolution of the AP2/ERF gene family in wheat.

Highlights

Plants have a typical and complicated regulation process to defend their growth, productivity, and development
For searching the APETALA2/Ethylene Responsive Factor (AP2/ethylene response factors (ERF)) family genes in wheat genome, we used the HMM (Hidden Markov Model) search which uses HMM profiles with the AP2 domain of Arabidopsis (Pfam ID: PF00847) as a query to search for wheat AP2/ERF gene in the overall plant database
We used CDD3 model to confirm all genes with AP2/ERF domains listed in Supplementary Table 2

Summary

Introduction

Plants have a typical and complicated regulation process to defend their growth, productivity, and development. These plant parts are suffering from the adverse effects of many abiotic stresses such as drought, high temperature and salinity. Transcription factors, the regulators of gene expressions, play a key role in the signal transformation network. APETALA2/Ethylene Responsive Factor (AP2/ERF) gene family is the most extensive group of plant transcription factors (TFs) having a significant role in signal transduction, plant growth, and development, and participating in biotic/abiotic stress response (Licausi et al, 2013). According to the sequence similarity and number of AP2 domains, the AP2/ERF gene family is further divided into five main groups: AP2, DREB, ERF, RAV, and Soloist group. A small part of the transcription factor with a large deviation from an AP2 domain (similar to AP2 domain) and the gene structure is named as Soloist group (Sakuma et al, 2002)

Methods

Results

Conclusion