Genome-Wide Identification and Characterization of AP2/ERF Transcription Factor Family Genes in Oil Palm under Abiotic Stress Conditions

Zhou, Lixia; Yarra, Rajesh

doi:10.3390/ijms22062821

Cited by 21 publications

(19 citation statements)

References 54 publications

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“…The pecan AP2/ERF gene structural analysis revealed that a higher number of AP2 subfamily members contained more introns (4–10) compared to ERF, RAV , or Soloist subfamily members. This was consistent with the results observed in other plants [ 11 , 15 , 41 , 42 ]. It suggested that the AP2/ERF superfamily members of pecan were functionally diverse, but the functions of members of the same subfamily were similar, which further proved the accuracy of AP2/ERF genes evolution and classification.…”

Section: Discussionsupporting

confidence: 93%

“…With more extensive genome sequences, the AP2/ERF superfamily has been identified in various plant species, such as Arabidopsis [ 6 , 8 ], rice [ 8 ], poplar [ 10 ], oil palm [ 11 ], dark jute [ 12 ], cucumber [ 13 ], wheat [ 14 ], and sunflower [ 15 ]. These studies have shown that AP2/ERF superfamily members are involved in abiotic and biotic stress responses in plants.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification, Characterization, and Expression Profiling of AP2/ERF Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (Carya illinoinensis)

Yang

Yao

Zeng

et al. 2022

IJMS

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The ethylene-responsive element (AP2/ERF) is one of the keys and conserved transcription factors (TFs) in plants that play a vital role in regulating plant growth, development, and stress response. A total of 202 AP2/ERF genes were identified from the pecan genome and renamed according to the chromosomal distribution of the CiAP2/ERF genes. They were divided into four subfamilies according to the domain and phylogenetic analysis, including 26 AP2, 168 ERF, six RAV, and two Soloist gene family members. These genes were distributed randomly across the 16 chromosomes, and we found 19 tandem and 146 segmental duplications which arose from ancient duplication events. The gene structure and conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the AP2/ERF genes. Several cis-regulatory elements, which were related to light responsiveness, stress, and defense responses, were identified in the promoter regions of AP2/ERFs. The expression profiling of 202 CiAP2/ERF genes was assessed by using RNA-Seq data and qRT-PCR during development (pistillate flowering development, graft union development, and kernel development) and under abiotic stresses (waterlogging, drought). Moreover, the results suggested that the ERF-VII members may play a critical role in waterlogging stress. These findings provided new insights into AP2/ERF gene evolution and divergence in pecan and can be considered a valuable resource for further functional validation, as well as for utilization in a stress-resistance-variety development program.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification, Characterization, and Expression Profiling of AP2/ERF Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (Carya illinoinensis)

Yang

Yao

Zeng

et al. 2022

IJMS

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“…The AP2/ERF family of TFs is the largest and unique TF family in plants, the members of which play important roles in regulating diverse processes of plant growth, development, and response to hormone and environmental stress ( Riechmann and Meyerowitz, 1998 ). The AP2/ERF family has been identified in many plants, such as Arabidopsis, rice ( Nakano et al, 2006 ), maize ( Zhuang et al, 2010 ), wheat ( Zhuang et al, 2011 ), radish ( Karanja et al, 2019 ), cucumber ( Hu and Liu, 2011 ), mung bean ( Labbo et al, 2018 ), sugarcane ( Li et al, 2020 ), durum wheat ( Faraji et al, 2020 ), eggplant ( Li D. et al, 2021 ), banana ( Lakhwani et al, 2016 ), and oil palm ( Zhou and Yarra, 2021 ). This family contains at least one highly conserved AP2/ERF DNA binding domain, which consists of 60–70 amino acids.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of APETALA2/ETHYLENE RESPONSIVE FACTOR Transcription Factors in Cucurbita moschata and Their Involvement in Ethylene Response

Zhang

Chen

et al. 2022

Front. Plant Sci.

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APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF), a plant-specific transcription factor (TF) family, plays an essential role in the growth and development of plants, and in their response to biotic and abiotic stresses. However, information on AP2/ERF in Cucurbita moschata (pumpkin), an edible and medicinal vegetable used worldwide, is scarce. A total of 212 AP2/ERF genes were identified in the C. moschata genome (CmoAP2/ERFs). Based on phylogenetic analysis, they were divided into four groups—28 AP2s, 92 ERFs, 86 dehydration-responsive element-binding (DREB) factors, and 6 ABI3/VPs (RAV). The 212 AP2/ERF genes were unevenly distributed on the 20 chromosomes of C. moschata. The results of structural analysis showed the absence of introns on 132 CmoAP2/ERFs. Four pairs of tandem duplication and 155 pairs of segmental duplication events were identified, which indicated that segmental duplications might be the main reason for the expansion of the CmoAP2/ERF family. The analysis of cis-regulatory elements (CREs) showed that most of the CmoAP2/ERFs contained hormone response elements (ABREs, EREs) in their promoters, suggesting that AP2/ERFs could contribute to the processes regulated by ethylene and abscisic acid. By comparing the transcriptome of ethephon-treated and control plants, we found that 16 CmoAP2/ERFs were significantly upregulated after ethephon treatment. Furthermore, we determined the expression patterns of these genes at different developmental stages of female and male flowers. This study provides insights into the identification, classification, physicochemical property, phylogenetic analysis, chromosomal location, gene structure, motif identification, and CRE prediction of the AP2/ERF superfamily in C. moschata. Sixteen CmoAP2/ERF genes were identified as ethylene-inducible genes. The results of this study will be valuable for understanding the roles of CmoAP2/ERFs in ethylene response and should provide a foundation for elucidating the function of AP2/ERF TFs in C. moschata.

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“…Eggplant RNA-seq data on anthocyanin biosynthesis were combined with yeast single-hybridization and double-luciferase analysis to determine that smap2/ERF genes ( Smechr0902114.1 and Smechr1102075.1 ) were involved in regulation of anthocyanin biosynthesis ( Li et al, 2021 ). Zhou and Yarra (2021) used genome-wide analysis to identify 172 EgAP2/ERF s (AP2, ERF, RAV, and Soloist subfamily members) in oil palm. Quantitative PCR analysis validated abiotic stress (salinity, cold, and drought)-responsive AP2/ERFs in the oil palm genome ( Zhou and Yarra, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

“… Zhou and Yarra (2021) used genome-wide analysis to identify 172 EgAP2/ERF s (AP2, ERF, RAV, and Soloist subfamily members) in oil palm. Quantitative PCR analysis validated abiotic stress (salinity, cold, and drought)-responsive AP2/ERFs in the oil palm genome ( Zhou and Yarra, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of the AP2/ERF Gene Family and Functional Analysis of GmAP2/ERF144 for Drought Tolerance in Soybean

Wang

Shen

et al. 2022

Front. Plant Sci.

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Drought is a major environmental constraint that causes substantial reductions in plant growth and yield. Expression of stress-related genes is largely regulated by transcription factors (TFs), including in soybean [Glycine max (L.) Merr.]. In this study, 301 GmAP2/ERF genes that encode TFs were identified in the soybean genome. The TFs were divided into five categories according to their homology. Results of previous studies were then used to select the target gene GmAP2/ERF144 from among those up-regulated by drought and salt stress in the transcriptome. According to respective tissue expression analysis and subcellular determination, the gene was highly expressed in leaves and encoded a nuclear-localized protein. To validate the function of GmAP2/ERF144, the gene was overexpressed in soybean using Agrobacterium-mediated transformation. Compared with wild-type soybean, drought resistance of overexpression lines increased significantly. Under drought treatment, leaf relative water content was significantly higher in overexpressed lines than in the wild-type genotype, whereas malondialdehyde content and electrical conductivity were significantly lower than those in the wild type. Thus, drought resistance of transgenic soybean increased with overexpression of GmAP2/ERF144. To understand overall function of the gene, network analysis was used to predict the genes that interacted with GmAP2/ERF144. Reverse-transcription quantitative PCR showed that expression of those interacting genes in two transgenic lines was 3 to 30 times higher than that in the wild type. Therefore, GmAP2/ERF144 likely interacted with those genes; however, that conclusion needs to be verified in further specific experiments.

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Genome-Wide Identification and Characterization of AP2/ERF Transcription Factor Family Genes in Oil Palm under Abiotic Stress Conditions

Cited by 21 publications

References 54 publications

Genome-Wide Identification, Characterization, and Expression Profiling of AP2/ERF Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (Carya illinoinensis)

Genome-Wide Identification, Characterization, and Expression Profiling of AP2/ERF Superfamily Genes under Different Development and Abiotic Stress Conditions in Pecan (Carya illinoinensis)

Genome-Wide Identification of APETALA2/ETHYLENE RESPONSIVE FACTOR Transcription Factors in Cucurbita moschata and Their Involvement in Ethylene Response

Genome-Wide Identification of the AP2/ERF Gene Family and Functional Analysis of GmAP2/ERF144 for Drought Tolerance in Soybean

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