Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut (Arachis hypogaea L.)

Mengjie Cui,Lei Shi,Hongyan Li,Junjia Guo,Pengpei Chai,Zheng Zheng,Suoyi Han,Bingyan Huang,Muhammad Salman Haider,Pei Du,Wenzhao Dong,Xinyou Zhang

doi:10.3389/fgene.2021.750761

Mengjie Cui, Lei Shi + Show 10 more

Open Access

https://doi.org/10.3389/fgene.2021.750761

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Abstract

APETALA2/ethylene response element-binding factor (AP2/ERF) transcription factors (TFs) have been found to regulate plant growth and development and response to various abiotic stresses. However, detailed information of AP2/ERF genes in peanut against drought has not yet been performed. Herein, 185 AP2/ERF TF members were identified from the cultivated peanut (A. hypogaea cv. Tifrunner) genome, clustered into five subfamilies: AP2 (APETALA2), ERF (ethylene-responsive-element-binding), DREB (dehydration-responsive-element-binding), RAV (related to ABI3/VP), and Soloist (few unclassified factors)). Subsequently, the phylogenetic relationship, intron–exon structure, and chromosomal location of AhAP2/ERF were further characterized. All of these AhAP2/ERF genes were distributed unevenly across the 20 chromosomes, and 14 tandem and 85 segmental duplicated gene pairs were identified which originated from ancient duplication events. Gene evolution analysis showed that A. hypogaea cv. Tifrunner were separated 64.07 and 66.44 Mya from Medicago truncatula L. and Glycine max L., respectively. Promoter analysis discovered many cis-acting elements related to light, hormones, tissues, and stress responsiveness process. The protein interaction network predicted the exitance of functional interaction among families or subgroups. Expression profiles showed that genes from AP2, ERF, and dehydration-responsive-element-binding subfamilies were significantly upregulated under drought stress conditions. Our study laid a foundation and provided a panel of candidate AP2/ERF TFs for further functional validation to uplift breeding programs of drought-resistant peanut cultivars.

Highlights

Transcription factors (TFs) are the main class of regulatory proteins that can combine with DNA-binding domains and perform a key role by regulating the expression of downstream genes (Singh et al, 2002; Licausi et al, 2013)
A total of 185 unigenes with the AP2 domain were characterized as APETALA2/ethyleneresponsive element-binding factor (AP2/ERF) TFs in A. hypogaea cv
Depending on the sequence characteristics, the AP2 domains, phylogenetic tree analysis, and the classification system established by the group of Yamaguchi-Shinozaki (Tamura et al, 2011) and Shinshi (Nakano et al, 2006), the AP2/ERF superfamily genes are mainly classified into AP2 (APETALA2), ERF (VI-X, ethylene-responsive-elementbinding), DREB (I-V, dehydration-responsive-elementbinding), RAV, and Soloist subfamilies (Figure 1 and Supplementary Figure S1)

Summary

Introduction

Transcription factors (TFs) (or trans-acting factors) are the main class of regulatory proteins that can combine with DNA-binding domains and perform a key role by regulating the expression of downstream genes (Singh et al, 2002; Licausi et al, 2013). 60 different TF families have been found in higher plants, such as AP2/ERF (Gutterson and Reuber, 2004; Xu et al, 2011; Li M.-Y. et al, 2015), ARF (Finet et al, 2010; Rademacher et al, 2011), bHLH (Li et al, 2006), bZIP (Ulm et al, 2004; Liu et al, 2012), C2H2 (Tsutsui et al, 2011), MADS (Trevaskis et al, 2003; Terol et al, 2019), MYB (Dubos et al, 2010; Feller et al, 2011), NAC (Mao et al, 2012; Nakashima et al, 2012), SBP (Kandori et al, 2006; Ferreira et al, 2014), and WRKY (Rushton et al, 2010) Among these TFs, the APETALA2/ethyleneresponsive element-binding factor (AP2/ERF) superfamily contains the largest group of TFs in plant, which are reportedly involved in plant growth progress and abiotic stress responsiveness according to relevant reports (Licausi et al, 2013; Feng et al, 2020). In plants, related AP2/ERF superfamily proteins are found in ciliates and protists that may be associated with the His- and Asn-rich HNH class of homing endonucleases (Magnani et al, 2004; Wuitschick et al, 2004)

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