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Zou JJ, Zhang J, Wang X, Xia H, Zeng X, Cai X, Yang J, Zeng J, Li Z, Zhang G, Chen H. Comprehensive transcriptome analysis of AP2/ERFs in Osmanthus fragrans reveals the role of OfERF017-mediated organic acid metabolism pathway in flower senescence. FRONTIERS IN PLANT SCIENCE 2024; 15:1467232. [PMID: 39391780 PMCID: PMC11464312 DOI: 10.3389/fpls.2024.1467232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 08/26/2024] [Indexed: 10/12/2024]
Abstract
Osmanthus fragrans is an ethylene-sensitive flower, and flower senescence was mediated by ethylene-responsive transcription factors (OfERFs). A total of 227 OfERFs were identified from O. fragrans, which were classified into five subfamilies: AP2 (35), DREB (57), ERF (125), RAV (6), and Soloist (4). Gene composition and structural analysis indicate that members of different subfamilies have different gene structures and conserved domains. Their gene promoter contains various functional responsive elements, including auxin, jasmonic acid, and other responsive elements. Among them, 124 OfAP2/ERF genes have expressed at any stage of flowering, and 10 of them may play roles in flowering or senescence. By comparative transcriptome analysis, OfAP2/ERFs affected by ethephon (ETH) and 5'-azacytidine (Aza) treatment were divided into three categories, which have various target gene sets. Importantly, these target gene sets participate in similar or different biological processes and metabolic pathways, suggesting that ethylene and DNA hypomethylation have crosstalk and a unique mechanism in regulating the flower senescence of O. fragrans. Co-expression analysis revealed that several key OfAP2/ERFs played a central role in organic acid metabolism and biosynthesis of branched-chain amino acids (BcAAs), among which OfERF017 was selected for further functional analysis. Overexpression of OfERF017 leads to significant enrichment of genes in organic acid metabolism pathways, which leads to a decrease in organic acid levels and promoting the flower senescence of O. fragrans. Together, these results give insights into the characteristics and functional analysis of OfAP2/ERF genes in O. fragrans.
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Affiliation(s)
- Jing-Jing Zou
- National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, China
- Osmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, China
- Research Center for Osmanthus fragrans, Xianning Research Academy of Industrial Technology of Osmanthus fragrans, Xianning, China
| | - Jun Zhang
- Science Division, IGENEBOOK Biotechnology Co., Ltd., Wuhan, China
| | - Xiaoqian Wang
- National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, China
- Osmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, China
- College of Pharmacy, Hubei Universily of Science and Technology, Xianning, China
| | - Hui Xia
- National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, China
- Osmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, China
| | - Xiangling Zeng
- National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, China
- Osmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, China
- Research Center for Osmanthus fragrans, Xianning Research Academy of Industrial Technology of Osmanthus fragrans, Xianning, China
| | - Xuan Cai
- National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, China
- Osmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, China
- Research Center for Osmanthus fragrans, Xianning Research Academy of Industrial Technology of Osmanthus fragrans, Xianning, China
| | - Jie Yang
- National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, China
- Osmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, China
- Research Center for Osmanthus fragrans, Xianning Research Academy of Industrial Technology of Osmanthus fragrans, Xianning, China
| | - Jin Zeng
- National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, China
- Osmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, China
| | - Zeqing Li
- National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, China
- Osmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, China
- Science Division, IGENEBOOK Biotechnology Co., Ltd., Wuhan, China
| | - Guifu Zhang
- National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, China
- Osmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, China
| | - Hongguo Chen
- National Forestry and Grassland Administration Engineering Research Center for Osmanthus fragrans, Hubei University of Science and Technology, Xianning, China
- Osmanthus Innovation Center of National Engineering Research Center for Floriculture, Hubei University of Science and Technology, Xianning, China
- Research Center for Osmanthus fragrans, Xianning Research Academy of Industrial Technology of Osmanthus fragrans, Xianning, China
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Liao Y, Liu X, Xu N, Chen G, Qiao X, Gu Q, Wang Y, Sun J. Fine mapping and identification of ERF transcription factor ERF017 as a candidate gene for cold tolerance in pumpkin. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:230. [PMID: 39320412 DOI: 10.1007/s00122-024-04720-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/16/2024] [Indexed: 09/26/2024]
Abstract
KEY MESSAGE Two major QTLs for cold tolerance in pumpkin were localised, and CmoERF017 was identified as a key candidate gene within these QTLs via RNA-seq. Functional analysis revealed that CmoERF017 was a positive regulator of pumpkin in response to low-temperature stress. Low temperature is a key environmental factor that affects the protected cultivation of cucumber (Cucumis sativus L.) in winter, and the cold tolerance of cucumber/pumpkin-grafted seedlings depends on the rootstock. Pumpkin (Cucurbita spp.) has a well-developed root system, high resistance and wide adaptation, commonly used as rootstock for cucumber to improve the cold tolerance of grafted seedlings. This study used two high-generation inbred lines of Cucurbita moschata with significant differences in cold tolerance. We identified key candidate genes within the major cold tolerance QTL of rootstocks using QTL-seq and RNA-seq and investigated the function and molecular mechanisms of these genes in response to low-temperature stress. Results showed that QTL-seq located two cold tolerance QTLs, qCII-1 and qCII-2, while RNA-seq located 28 differentially expressed genes within these QTLs. CmoERF017 was finally identified as a key candidate gene. Functional validation results indicated that CmoERF017 is a positive regulator of pumpkin in response to low-temperature stress and affected root ABA synthesis and signalling by directly regulating the expression of SDR7 and ABI5. This study identified a key gene for low-temperature stress tolerance in rootstock pumpkin and clarified its role in the molecular mechanism of hormone-mediated plant cold tolerance. The study findings enrich the theoretical understanding of low-temperature stress tolerance in pumpkin and are valuable for the selection and breeding of cold-tolerant varieties of pumpkin used for rootstocks.
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Affiliation(s)
- Yarong Liao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoying Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Na Xu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangling Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinhui Qiao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qinsheng Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yu Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jin Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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Ma L, Shi Q, Ma Q, Wang X, Chen X, Han P, Luo Y, Hu H, Fei X, Wei A. Genome-wide analysis of AP2/ERF transcription factors that regulate fruit development of Chinese prickly ash. BMC PLANT BIOLOGY 2024; 24:565. [PMID: 38879490 PMCID: PMC11179286 DOI: 10.1186/s12870-024-05244-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 06/04/2024] [Indexed: 06/19/2024]
Abstract
BACKGROUND AP2/ERF is a large family of plant transcription factor proteins that play essential roles in signal transduction, plant growth and development, and responses to various stresses. The AP2/ERF family has been identified and verified by functional analysis in various plants, but so far there has been no comprehensive study of these factors in Chinese prickly ash. Phylogenetic, motif, and functional analyses combined with transcriptome analysis of Chinese prickly ash fruits at different developmental stages (30, 60, and 90 days after anthesis) were conducted in this study. RESULTS The analysis identified 146 ZbAP2/ERF genes that could be classified into 15 subgroups. The motif analysis revealed the presence of different motifs or elements in each group that may explain the functional differences between the groups. ZbERF13.2, ZbRAP2-12, and ZbERF2.1 showed high levels of expression in the early stages of fruit development. ZbRAP2-4, and ZbERF3.1 were significantly expressed at the fruit coloring stage (R2 and G2). ZbERF16 were significantly expressed at fruit ripening and expression level increased as the fruit continued to develop. Relative gene expression levels of 6 representative ZbAP2/ERFs assessed by RT-qPCR agreed with transcriptome analysis results. CONCLUSIONS These genes identified by screening can be used as candidate genes that affect fruit development. The results of the analysis can help guide future genetic improvement of Chinese prickly ash and enrich our understanding of AP2/ERF transcription factors and their regulatory functions in plants.
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Affiliation(s)
- Lei Ma
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Qianqian Shi
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
| | - Qin Ma
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Xiaona Wang
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Xin Chen
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Peilin Han
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Yingli Luo
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Haichao Hu
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Xitong Fei
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China.
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China.
| | - Anzhi Wei
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Xianyang, 712100, China.
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China.
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Wang Z, Song G, Zhang F, Shu X, Wang N. Functional Characterization of AP2/ERF Transcription Factors during Flower Development and Anthocyanin Biosynthesis Related Candidate Genes in Lycoris. Int J Mol Sci 2023; 24:14464. [PMID: 37833913 PMCID: PMC10572147 DOI: 10.3390/ijms241914464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/16/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
The APETALA2/ethylene-responsive transcription factor (AP2/ERF) family has been extensively investigated because of its significant involvement in plant development, growth, fruit ripening, metabolism, and plant stress responses. To date, there has been little investigation into how the AP2/ERF genes influence flower formation and anthocyanin biosynthesis in Lycoris. Herein, 80 putative LrAP2/ERF transcription factors (TFs) with complete open reading frames (ORFs) were retrieved from the Lycoris transcriptome sequence data, which could be divided into five subfamilies dependent on their complete protein sequences. Furthermore, our findings demonstrated that genes belonging to the same subfamily had structural similarities and conserved motifs. LrAP2/ERF genes were analyzed for playing an important role in plant growth, water deprivation, and flower formation by means of gene ontology (GO) enrichment analysis. The expression pattern of the LrAP2/ERF genes differed across tissues and might be important for Lycoris growth and flower development. In response to methyl jasmonate (MeJA) exposure and drought stress, the expression of each LrAP2/ERF gene varied across tissues and time. Moreover, a total of 20 anthocyanin components were characterized using ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis, and pelargonidin-3-O-glucoside-5-O-arabinoside was identified as the major anthocyanin aglycone responsible for the coloration of the red petals in Lycoris. In addition, we mapped the relationships between genes and metabolites and found that LrAP2/ERF16 is strongly linked to pelargonidin accumulation in Lycoris petals. These findings provide the basic conceptual groundwork for future research into the molecular underpinnings and regulation mechanisms of AP2/ERF TFs in anthocyanin accumulation and Lycoris floral development.
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Affiliation(s)
- Zhong Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Guowei Song
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Xiaochun Shu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Ning Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (Z.W.); (G.S.); (F.Z.); (X.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybeans (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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Turek S, Skarzyńska A, Pląder W, Pawełkowicz M. Understanding Transcription Factors and How They Affect Processes in Cucumber Sex Determination. Metabolites 2023; 13:740. [PMID: 37367898 DOI: 10.3390/metabo13060740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
Plant reproduction is a fundamental process on Earth from the perspective of biodiversity, biomass gain, and crop productivity. It is therefore important to understand the sex determination process, and many researchers are investigating the molecular basis of this phenomenon. However, information on the influence of transcription factors (TFs), genes that encode DNA-binding proteins, on this process is limited, although cucumber is a model plant in this regard. In the present study, based on RNA-seq data for differentially expressed genes (DEGs), we aimed to investigate the regulatory TFs that may influence the metabolic processes in the shoot apex containing the forming flower buds. Therefore, the annotation of the genome of the B10 cucumber line was supplemented with the assigned families of transcription factors. By performing ontology analyses of the DEGs, the processes they participate in were identified, and TFs were located among the results. In addition, TFs that have significantly overrepresented targets among DEGs were detected, and sex-specific interactome network maps were generated, indicating the regulatory TFs based on their effects on DEGs and furthermore, on the processes leading to the formation of different-sex flowers. Among the most overrepresented TF families in the sex comparisons were the NAC, bHLH, MYB, and bZIP families. An interaction network analysis indicated the most abundant families among DEGs' regulatory TFs were MYB, AP2/ERF, NAC, and bZIP, and those with the most significant impact on developmental processes were identified, namely the AP/ERF family, followed by DOF, MYB, MADS, and others. Thus, the networks' central nodes and key regulators were identified with respect to male, female, and hermaphrodite forms. Here, we proposed the first model of the regulatory network of TFs that influences the metabolism of sex development in cucumber. These findings may help us to understand the molecular genetics and functional mechanisms underlying sex determination processes.
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Affiliation(s)
- Szymon Turek
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Agnieszka Skarzyńska
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
| | - Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, 02-776 Warsaw, Poland
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Liu Y, Chen S, Chen J, Wang J, Wei M, Tian X, Chen L, Ma J. Comprehensive analysis and expression profiles of the AP2/ERF gene family during spring bud break in tea plant (Camellia sinensis). BMC PLANT BIOLOGY 2023; 23:206. [PMID: 37081399 PMCID: PMC10116778 DOI: 10.1186/s12870-023-04221-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/10/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND AP2/ERF transcription factors (AP2/ERFs) are important regulators of plant physiological and biochemical metabolism. Evidence suggests that AP2/ERFs may be involved in the regulation of bud break in woody perennials. Green tea is economically vital in China, and its production value is significantly affected by the time of spring bud break of tea plant. However, the relationship between AP2/ERFs in tea plant and spring bud break remains largely unknown. RESULTS A total of 178 AP2/ERF genes (CsAP2/ERFs) were identified in the genome of tea plant. Based on the phylogenetic analysis, these genes could be classified into five subfamilies. The analysis of gene duplication events demonstrated that whole genome duplication (WGD) or segmental duplication was the primary way of CsAP2/ERFs amplification. According to the result of the Ka/Ks value calculation, purification selection dominated the evolution of CsAP2/ERFs. Furthermore, gene composition and structure analyses of CsAP2/ERFs indicated that different subfamilies contained a variety of gene structures and conserved motifs, potentially resulting in functional differences among five subfamilies. The promoters of CsAP2/ERFs also contained various signal-sensing elements, such as abscisic acid responsive elements, light responsive elements and low temperature responsive elements. The evidence presented here offers a theoretical foundation for the diverse functions of CsAP2/ERFs. Additionally, the expressions of CsAP2/ERFs during spring bud break of tea plant were analyzed by RNA-seq and grouped into clusters A-F according to their expression patterns. The gene expression changes in clusters A and B were more synchronized with the spring bud break of tea plant. Moreover, several potential correlation genes, such as D-type cyclin genes, were screened out through weighted correlation network analysis (WGCNA). Temperature and light treatment experiments individually identified nine candidate CsAP2/ERFs that may be related to the spring bud break of tea plant. CONCLUSIONS This study provides new evidence for role of the CsAP2/ERFs in the spring bud break of tea plant, establishes a theoretical foundation for analyzing the molecular mechanism of the spring bud break of tea plant, and contributes to the improvement of tea cultivars.
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Affiliation(s)
- Yujie Liu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Si Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Jiedan Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Junyu Wang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Mengyuan Wei
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Xiaomiao Tian
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Liang Chen
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
| | - Jianqiang Ma
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.
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Salih H, Bai W, Zhao M, Liang Y, Yang R, Zhang D, Li X. Genome-Wide Characterization and Expression Analysis of Transcription Factor Families in Desert Moss Syntrichia caninervis under Abiotic Stresses. Int J Mol Sci 2023; 24:ijms24076137. [PMID: 37047111 PMCID: PMC10094499 DOI: 10.3390/ijms24076137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/05/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Transcription factor (TF) families play important roles in plant stress responses. S. caninervis is a new model moss for plant desiccation tolerance studies. Here, we report a high-confidence identification and characterization of 591 TFs representing 52 families that covered all chromosomes in S. caninervis. GO term and KEGG pathway analysis showed that TFs were involved in the regulation of transcription, DNA-templated, gene expression, binding activities, plant hormone signal transduction, and circadian rhythm. A number of TF promoter regions have a mixture of various hormones-related cis-regulatory elements. AP2/ERF, bHLH, MYB, and C2H2-zinc finger TFs were the overrepresented TF families in S. caninervis, and the detailed classification of each family is performed based on structural features. Transcriptome analysis revealed the transcript abundances of some ScAP2/ERF, bHLH, MYB, and C2H2 genes were accumulated in the treated S. caninervis under cold, dehydration, and rehydration stresses. The RT-qPCR results strongly agreed with RNA-seq analysis, indicating these TFs might play a key role in S. caninervis response to abiotic stress. Our comparative TF characterization and classification provide the foundations for functional investigations of the dominant TF genes involved in S. caninervis stress response, as well as excellent stress tolerance gene resources for plant stress resistance breeding.
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Genome-Wide Identification of the ERF Transcription Factor Family for Structure Analysis, Expression Pattern, and Response to Drought Stress in Populus alba × Populus glandulosa. Int J Mol Sci 2023; 24:ijms24043697. [PMID: 36835107 PMCID: PMC9967527 DOI: 10.3390/ijms24043697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
The Ethylene Responsive Factor (ERF) transcription factor family is important for regulating plant growth and stress responses. Although the expression patterns of ERF family members have been reported in many plant species, their role in Populus alba × Populus glandulosa, an important model plant for forest research, remains unclear. In this study, we identified 209 PagERF transcription factors by analyzing the P. alba × P. glandulosa genome. We analyzed their amino acid sequences, molecular weight, theoretical pI (Isoelectric point), instability index, aliphatic index, grand average of hydropathicity, and subcellular localization. Most PagERFs were predicted to localize in the nucleus, with only a few PagERFs localized in the cytoplasm and nucleus. Phylogenetic analysis divided the PagERF proteins into ten groups, Class I to X, with those belonging to the same group containing similar motifs. Cis-acting elements associated with plant hormones, abiotic stress responses, and MYB binding sites were analyzed in the promoters of PagERF genes. We used transcriptome data to analyze the expression patterns of PagERF genes in different tissues of P. alba × P. glandulosa, including axillary buds, young leaves, functional leaves, cambium, xylem, and roots, and the results indicated that PagERF genes are expressed in all tissues of P. alba × P. glandulosa, especially in roots. Quantitative verification results were consistent with transcriptome data. When P. alba × P. glandulosa seedlings were treated with 6% polyethylene glycol 6000 (PEG6000), the results of RT-qRCR showed that nine PagERF genes responded to drought stress in various tissues. This study provides a new perspective on the roles of PagERF family members in regulating plant growth and development, and responses to stress in P. alba × P. glandulosa. Our study provides a theoretical basis for ERF family research in the future.
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Zhao M, Li Y, Zhang X, You X, Yu H, Guo R, Zhao X. Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress. Int J Mol Sci 2022; 23:ijms232315225. [PMID: 36499551 PMCID: PMC9736363 DOI: 10.3390/ijms232315225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/08/2022] Open
Abstract
Juglans mandshurica has strong freezing resistance, surviving temperatures as low as -40 °C, making it an important freeze tolerant germplasm resource of the genus Juglans. APETALA2/ethylene responsive factor (AP2/ERF) is a plant-specific superfamily of transcription factors that regulates plant development, growth, and the response to biotic and abiotic stress. In this study, phylogenetic analysis was used to identify 184 AP2/ERF genes in the J. mandshurica genome, which were classified into five subfamilies (JmAP2, JmRAV, JmSoloist, JmDREB, and JmERF). A significant amount of discordance was observed in the 184 AP2/ERF genes distribution of J. mandshurica throughout its 16 chromosomes. Duplication was found in 14 tandem and 122 segmental gene pairs, which indicated that duplications may be the main reason for JmAP2/ERF family expansion. Gene structural analysis revealed that 64 JmAP2/ERF genes contained introns. Gene evolution analysis among Juglandaceae revealed that J. mandshurica is separated by 14.23 and 15 Mya from Juglans regia and Carya cathayensis, respectively. Based on promoter analysis in J. mandshurica, many cis-acting elements were discovered that are related to light, hormones, tissues, and stress response processes. Proteins that may contribute to cold resistance were selected for further analysis and were used to construct a cold regulatory network based on GO annotation and JmAP2/ERF protein interaction network analysis. Expression profiling using qRT-PCR showed that 14 JmAP2/ERF genes were involved in cold resistance, and that seven and five genes were significantly upregulated under cold stress in female flower buds and phloem tissues, respectively. This study provides new light on the role of the JmAP2/ERF gene in cold stress response, paving the way for further functional validation of JmAP2/ERF TFs and their application in the genetic improvement of Juglans and other tree species.
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Affiliation(s)
- Minghui Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Yan Li
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Xinxin Zhang
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
| | - Xiangling You
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Haiyang Yu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Ruixue Guo
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (R.G.); (X.Z.)
| | - Xiyang Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (R.G.); (X.Z.)
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Maqsood H, Munir F, Amir R, Gul A. Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum. FRONTIERS IN PLANT SCIENCE 2022; 13:1031679. [PMID: 36507398 PMCID: PMC9731513 DOI: 10.3389/fpls.2022.1031679] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/25/2022] [Indexed: 06/12/2023]
Abstract
Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have a vital role in regulating plant abiotic stress tolerance by networking with DRE/CRT cis-regulatory elements in response to stresses. In this study, bioinformatics analysis was performed to conduct the genome-wide identification and characterization of DREB genes and promoter elements in Solanum lycopersicum. In genome-wide coverage, 58 SlDREB genes were discovered on 12 chromosomes that justified the criteria of the presence of AP2 domain as conserved motifs. Intron-exon organization and motif analysis showed consistency with phylogenetic analysis and confirmed the absence of the A3 class, thus dividing the SlDREB genes into five categories. Gene expansion was observed through tandem duplication and segmental duplication gene events in SlDREB genes. Ka/Ks values were calculated in ortholog pairs that indicated divergence time and occurrence of purification selection during the evolutionary period. Synteny analysis demonstrated that 32 out of 58 and 47 out of 58 SlDREB genes were orthologs to Arabidopsis and Solanum tuberosum, respectively. Subcellular localization predicted that SlDREB genes were present in the nucleus and performed primary functions in DNA binding to regulate the transcriptional processes according to gene ontology. Cis-acting regulatory element analysis revealed the presence of 103 motifs in 2.5-kbp upstream promoter sequences of 58 SlDREB genes. Five representative SlDREB proteins were selected from the resultant DREB subgroups for 3D protein modeling through the Phyre2 server. All models confirmed about 90% residues in the favorable region through Ramachandran plot analysis. Moreover, active catalytic sites and occurrence in disorder regions indicated the structural and functional flexibility of SlDREB proteins. Protein association networks through STRING software suggested the potential interactors that belong to different gene families and are involved in regulating similar functional and biological processes. Transcriptome data analysis has revealed that the SlDREB gene family is engaged in defense response against drought and heat stress conditions in tomato. Overall, this comprehensive research reveals the identification and characterization of SlDREB genes that provide potential knowledge for improving abiotic stress tolerance in tomato.
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Affiliation(s)
| | - Faiza Munir
- Department of Plant Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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GWAS Reveals a Novel Candidate Gene CmoAP2/ERF in Pumpkin ( Cucurbita moschata) Involved in Resistance to Powdery Mildew. Int J Mol Sci 2022; 23:ijms23126524. [PMID: 35742978 PMCID: PMC9223685 DOI: 10.3390/ijms23126524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
Pumpkin (Cucurbita moschata Duchesne ex Poir.) is a multipurpose cash crop rich in antioxidants, minerals, and vitamins; the seeds are also a good source of quality oils. However, pumpkin is susceptible to the fungus Podosphaera xanthii, an obligate biotrophic pathogen, which usually causes powdery mildew (PM) on both sides of the leaves and reduces photosynthesis. The fruits of infected plants are often smaller than usual and unpalatable. This study identified a novel gene that involves PM resistance in pumpkins through a genome-wide association study (GWAS). The allelic variation identified in the CmoCh3G009850 gene encoding for AP2-like ethylene-responsive transcription factor (CmoAP2/ERF) was proven to be involved in PM resistance. Validation of the GWAS data revealed six single nucleotide polymorphism (SNP) variations in the CmoAP2/ERF coding sequence between the resistant (IT 274039 [PMR]) and the susceptible (IT 278592 [PMS]). A polymorphic marker (dCAPS) was developed based on the allelic diversity to differentiate these two haplotypes. Genetic analysis in the segregating population derived from PMS and PMR parents provided evidence for an incomplete dominant gene-mediated PM resistance. Further, the qRT-PCR assay validated the elevated expression of CmoAP2/ERF during PM infection in the PMR compared with PMS. These results highlighted the pivotal role of CmoAP2/ERF in conferring resistance to PM and identifies it as a valuable molecular entity for breeding resistant pumpkin cultivars.
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