Genome-wide identification of the AP2/ERF transcription factor family in pepper (<i>Capsicum annuum</i>L.)

Jin, Jing-Hao; Wang, Min; Zhang, Huai-Xia; Khan, Abid; Wei, Aimin; Luo, Da; Gong, Zhen-Hui

doi:10.1139/gen-2018-0036

Cited by 68 publications

(53 citation statements)

References 75 publications

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“…The classification of the tree was defined and annotated based on the proposed by Nakano et al [15], and it ultimately defined 11 groups. This result was similar to that of Jin's study in peppers [50], no matter the topology or classification of the tree. However, in this study, both groups X and IX were subdivided, and a new group XI was identified.…”

Section: Discussionsupporting

confidence: 90%

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Systematic analysis of the Capsicum ERF transcription factor family uncovers new insights into the regulation of species-specific metabolites

Song

Chen

Zhang

et al. 2020

Preprint

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Background: ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relatively high economic and nutritional value, and they are specifically found in Capsicum. However, there is little understanding of how ERFs participate in the regulatory networks of capsorubin and capsaicinoids biosynthesis. Results: In this study, a total of 142 ERFs were identified in the Capsicum annuum genome. Subsequent phylogenetic analysis allowed us to divide ERFs into DREB (dehydration responsive element binding proteins) and ERF subfamilies, and further classify them into 11 groups with several subgroups. Expression analysis of biosynthetic pathway genes and CaERFs facilitated the identification of candidate genes related to the regulation of capsorubin and capsaicinoids biosynthesis; the candidates were focused in cluster C9 and cluster C10, as well as cluster L3 and cluster L4, respectively. The expression patterns of CaERF82, CaERF97, CaERF66, CaERF107 and CaERF101, which were found in cluster C9 and cluster C10, were consistent with those of accumulating of carotenoids (β-carotene, zeaxanthin and capsorubin) in the pericarp. In cluster L3 and cluster L4, the expression patterns of CaERF102, CaERF53, CaERF111 and CaERF92 were similar to those of the accumulating capsaicinoids. Furthermore, CaERF92, CaERF102 and CaERF111 were found to be potentially involved in temperature-mediated capsaicinoids biosynthesis. Conclusion: This study will provide an extremely useful foundation for the study of candidate ERFs in the regulation of carotenoids and capsaicinoids biosynthesis in peppers.

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Section: Discussionsupporting

confidence: 90%

“…Although the AP2/ERF superfamily in peppers was reported by Jin et al [50], they indicated that CaAP2/ERFs might be involved in the response to P. capsici in peppers. Capsorubin and capsaicinoids are unique to Capsicum spp., and they possess high economic and nutritional values.…”

Section: Discussionmentioning

confidence: 90%

Systematic analysis of the Capsicum ERF transcription factor family uncovers new insights into the regulation of species-specific metabolites

Song

Chen

Zhang

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The classi cation of the tree was de ned and annotated based on the proposed by Nakano et al [15], and it ultimately de ned 11 groups. This result was similar to that of Jin's study in peppers [50], no matter the topology or classi cation of the tree. However, in this study, both groups X and IX were subdivided, and a new group XI was identi ed.…”

Section: Discussionsupporting

confidence: 90%

“…The AP2/ERF superfamily is one of the largest TF families in the plant kingdom, and it has been successfully identi ed and investigated in many plant species of sequenced genomes [47][48][49]. Although the AP2/ERF superfamily in peppers was reported by Jin et al [50], they indicated that CaAP2/ERFs might be involved in the response to P. capsici in peppers. Capsorubin and capsaicinoids are unique to Capsicum spp., and they possess high economic and nutritional values.…”

Section: Discussionmentioning

confidence: 99%

Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites

Song

Chen

Zhang

et al. 2020

Preprint

View full text Add to dashboard Cite

Abstract Background: ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relatively high economic and nutritional value, and they are specifically found in Capsicum. However, there is little understanding of how ERFs participate in the regulatory networks of capsorubin and capsaicinoids biosynthesis. Results: In this study, a total of 142 ERFs were identified in the Capsicum annuum genome. Subsequent phylogenetic analysis allowed us to divide ERFs into DREB (dehydration responsive element binding proteins) and ERF subfamilies, and further classify them into 11 groups with several subgroups. Expression analysis of biosynthetic pathway genes and CaERFs facilitated the identification of candidate genes related to the regulation of capsorubin and capsaicinoids biosynthesis; the candidates were focused in cluster C9 and cluster C10, as well as cluster L3 and cluster L4, respectively. The expression patterns of CaERF82, CaERF97, CaERF66, CaERF107 and CaERF101, which were found in cluster C9 and cluster C10, were consistent with those of accumulating of carotenoids (β-carotene, zeaxanthin and capsorubin) in the pericarp. In cluster L3 and cluster L4, the expression patterns of CaERF102, CaERF53, CaERF111 and CaERF92 were similar to those of the accumulating capsaicinoids. Furthermore, CaERF92, CaERF102 and CaERF111 were found to be potentially involved in temperature-mediated capsaicinoids biosynthesis. Conclusion: This study will provide an extremely useful foundation for the study of candidate ERFs in the regulation of carotenoids and capsaicinoids biosynthesis in peppers.

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“…The genome wide analyses of each transcription factor have been completed and "-"indicates the genome wide analysis was not done yet. Potato's WRKY [63] Dof [58], NAC [145]; ARF [192]; ERF [181] Pepper WRKY [193] ERF [194]; Dof [51] MYB [103]; ARF [190]; NAC [195] Tomato WRKY [62] Dof [53] MYB [88] HSF [120] ARF [196] ERF [171]; Eggplant's WRKY [197] Dof [52] MYB [84].…”

Section: List Of Major Transcription Factors In Major Solanaceous Foomentioning

confidence: 99%

The Role of Major Transcription Factors in Solanaceous Food Crops under Different Stress Conditions: Current and Future Perspectives

Tolosa

Zhengbin

2020

Plants

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Plant growth, development, and productivity are adversely affected by environmental stresses such as drought (osmotic stress), soil salinity, cold, oxidative stress, irradiation, and diverse diseases. These impacts are of increasing concern in light of climate change. Noticeably, plants have developed their adaptive mechanism to respond to environmental stresses by transcriptional activation of stress-responsive genes. Among the known transcription factors, DoF, WRKY, MYB, NAC, bZIP, ERF, ARF and HSF are those widely associated with abiotic and biotic stress response in plants. Genome-wide identification and characterization analyses of these transcription factors have been almost completed in major solanaceous food crops, emphasizing these transcription factor families which have much potential for the improvement of yield, stress tolerance, reducing marginal land and increase the water use efficiency of solanaceous crops in arid and semi-arid areas where plant demand more water. Most importantly, transcription factors are proteins that play a key role in improving crop yield under water-deficient areas and a place where the severity of pathogen is very high to withstand the ongoing climate change. Therefore, this review highlights the role of major transcription factors in solanaceous crops, current and future perspectives in improving the crop traits towards abiotic and biotic stress tolerance and beyond. We have tried to accentuate the importance of using genome editing molecular technologies like CRISPR/Cas9, Virus-induced gene silencing and some other methods to improve the plant potential in giving yield under unfavorable environmental conditions.

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Genome-wide identification of the AP2/ERF transcription factor family in pepper (Capsicum annuumL.)

Cited by 68 publications

References 75 publications

Systematic analysis of the Capsicum ERF transcription factor family uncovers new insights into the regulation of species-specific metabolites

Systematic analysis of the Capsicum ERF transcription factor family uncovers new insights into the regulation of species-specific metabolites

Systematic analysis of the Capsicum ERF transcription factor family: identification of regulatory factors involved in the regulation of species-specific metabolites

The Role of Major Transcription Factors in Solanaceous Food Crops under Different Stress Conditions: Current and Future Perspectives

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