Genome-Wide Identification, Phylogeny, Evolution and Expression Patterns of AP2/ERF Genes and Cytokinin Response Factors in Brassica rapa ssp. pekinensis

Zhenning Liu,Xiaolin Yu,Mei Zhang,Gang Lu,Minghau Zou,Yapei Liu,Jiashu Cao,Yanxia Lv,Lijun Kong,Shu-Biao Wu

doi:10.1371/journal.pone.0083444

Zhenning Liu, Xiaolin Yu + Show 8 more

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https://doi.org/10.1371/journal.pone.0083444

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Abstract

The AP2/ERF transcription factor family is one of the largest families involved in growth and development, hormone responses, and biotic or abiotic stress responses in plants. In this study, 281 AP2/ERF transcription factor unigenes were identified in Chinese cabbage. These superfamily members were classified into three families (AP2, ERF, and RAV). The ERF family was subdivided into the DREB subfamily and the ERF subfamily with 13 groups (I– XI) based on sequence similarity. Duplication, evolution and divergence of the AP2/ERF genes in B. rapa and Arabidopsis thaliana were investigated and estimated. Cytokinin response factors (CRFs), as a subclade of the AP2/ERF family, are important transcription factors that define a branch point in the cytokinin two-component signal (TCS) transduction pathway. Up to 21 CRFs with a conserved CRF domain were retrieved and designated as BrCRFs. The amino acid sequences, conserved regions and motifs, phylogenetic relationships, and promoter regions of the 21 BrCRFs were analyzed in detail. The BrCRFs broadly expressed in various tissues and organs. The transcripts of BrCRFs were regulated by factors such as drought, high salinity, and exogenous 6-BA, NAA, and ABA, suggesting their involvement in abiotic stress conditions and regulatory mechanisms of plant hormone homeostasis. These results provide new insight into the divergence, variation, and evolution of AP2/ERF genes at the genome-level in Chinese cabbage.

Highlights

Abiotic stress conditions such as drought and high salinity are the most common stress factors that adversely affect plant growth and yield
The ethylene responsive factor (ERF) family was subdivided into 13 groups (I– XI), with 21 BrCRFs classified in groups VI and VI-L
The remaining 236 genes assigned to the ERF family were further subclassified into two groups based on the similarity of the amino acid sequences of the AP2/ERF domains: 105 genes that encode a dehydration-responsive element-binding protein (DREB)-like protein were assigned to the DREB subfamily, and 131 genes that encode an ERF-like protein were assigned to ERF subfamily

Summary

Introduction

Abiotic stress conditions such as drought and high salinity are the most common stress factors that adversely affect plant growth and yield. The AP2/ERF superfamily, one of the largest groups of TFs in plants, is characterized by the presence of AP2/ERF-type DNA-binding domains that consist of 60–70 highly conserved amino acids and plays significant roles in regulating abiotic stress-responsive genes expression in plants [5,6]. Previous research showed that CRF domain proteins alone could form both homodimers and heterodimers with each other and interact directly with most Arabidopsis histidine phosphotransfer proteins (AHP1– AHP5). This is the first described ability of the CRF domain in plants. Information on the CRF genes in other species remains limited and their biological functions still need further research

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