Genome-Wide Identification and Transcriptional Analysis of Ap2/EREBP Transcription Factor Family in Rice Under Abiotic and Biotic Stress Conditions

Abstract

The AP2/EREBP (Ethylene Responsive Element Binding Protein) genes play various roles in developmental processes and in stress-related responses in plants. We identified 163 AP2/EREBP genes in rice. We analyzed gene structures, phylogenies, domain duplication, genome localizations, and expression profiles. Conserved amino acid residues and phylogeny construction using the AP2/ERF conserved domain sequence suggest that in rice the OsAP2/EREBP gene family can be classified broadly into four subfamilies (AP2, RAV, DREB, and ERF). The chromosomal localizations of the OsAP2/EREBP genes indicated 20 segmental duplication events involving 40 genes; 58 redundant OsAP2/EREBP genes were involved in tandem duplication events. There were fewer introns after segmental duplication. We investigated expression profiles of this gene family under biotic stresses (infection with rice viruses such as Rice stripe virus [RSV], Rice tungro spherical virus [RTSV], and Rice dwarf virus [RDV, three virus strains S, O and D84]), and various abiotic stresses. Symptoms of virus infection were severe in RSV infection than by RTSV and RDV. Biotic stresses are novel work and enhance ability to identify the best candidate genes for further functional analysis. The genes of subgroup B-5 were not induced under abiotic treatments whereas activated by three RDV strains. None of the genes of subgroups A-3 were differentially expressed by all biotic stresses. Our 44K- and 22K-microarray results suggest that 53 and 52 non-redundant genes in this family were upregulated in response to biotic and abiotic stresses, respectively. We further examined the stress responsiveness of most genes by RT-PCR. The study results should be useful in selecting candidate genes from specific subgroup for functional analysis. The AP2/EREBP genes play various roles in developmental processes and in stress-related responses in plants. Genome-wide microarrays based on the gene expression profiles of the AP2/EREBP family were analyzed under conditions of normal growth and drought stress. The preferential expression of fifteen genes was observed in specific tissues, suggesting that these genes may play important roles in vegetative and reproductive stages of growth. A large number of redundant genes were differentially expressed following phytohormone treatments (NAA, GA3, KT, SA, JA, and ABA). To investigate the gene expression responses in the root, leaf, and panicle of three rice genotypes, two drought stress conditions were applied using the fraction of transpirable soil water (FTSW) under severe (0.2 FTSW), mild (0.5 FTSW), and control (1.0 FTSW) conditions. Following treatment, transcriptomic analysis using a 44K oligoarray from Agilent was performed on all the tissue samples. We identified common and specific genes in all tissues from two near-isogenic lines, IR77298-14-1-2-B-10 (drought-tolerant) and IR77298-14-1-2-B-13 (drought-susceptible), under drought stress conditions. The majority of the genes that were activated in the IR77298-14-1-2-B-10 line were members of the AP2/EREBP gene family. Non-redundant genes (sixteen) were found in the drought-tolerant line, and four genes were selected as candidate novel reference genes because of their higher expression levels in IR77298-14-1-2-B-10. Most of the genes in the AP2, B3, and B5 subgroups were involved in the panicle under severe stress conditions, but genes from the B1 and B2 subgroups were down-regulated in the root. Of the four subfamilies, RAV exhibited the highest number of up-regulated genes (80%) in the panicle under severe stress conditions in the drought-tolerant line compared to Minghui 63 under normal conditions, and the gene structures of the RAV subfamily may be involved in the response to drought stress in the flowering stage. These results provide a useful reference for the cloning of candidate genes from the specific subgroup for further functional analysis.