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Xu X, Zhang X, Fan Y, Zhou H, Pu X. Genome-wide identification and expression analysis of the TCP transcription factor family and its response to abiotic stress in rapeseed ( Brassica napus L.). 3 Biotech 2025; 15:119. [PMID: 40201755 PMCID: PMC11977093 DOI: 10.1007/s13205-025-04273-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Accepted: 03/10/2025] [Indexed: 04/10/2025] Open
Abstract
The study used 80 BnTCP genes (Brassica napus TCP genes) in rapeseed, which were identified and designated with nomenclature based on their chromosomal locations. A systematic analysis encompassed the evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events within these BnTCP genes. These 80 BnTCP proteins were categorized into three subfamilies, with the PCF subfamily showing significant expansion during evolution. Segmental duplications were identified as a major driver of TCP family amplification. To comprehensively assess the evolutionary relationships of the TCP family across diverse plant species, nine comparative genomic maps were constructed, elucidating homologous genes between B. napus and representative monocotyledonous and dicotyledonous plants. In the final phase of the study, the gene expression response characteristics of 15 selected BnTCP genes across various biological processes and stress responses were examined. Noteworthy candidates, including BnTCP28, BnTCP30, and BnTCP76, were identified as potentially crucial in tissue development and environmental stress responses. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-025-04273-x.
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Affiliation(s)
- Xinrui Xu
- Crop Research Institute of Sichuan Academy of Agricultural Sciences/Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
| | - Xin Zhang
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106 China
| | - Yu Fan
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106 China
| | - Hui Zhou
- Sichuan Province Seed Station, Chengdu, 610041 China
| | - Xiaobin Pu
- Crop Research Institute of Sichuan Academy of Agricultural Sciences/Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066 China
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Guo S, Xu Y, Zhou Y, Liu R, Wang Y, Yao L, Azam SM, Ma H, Liu X, Cao S, Wang K. Systematic Analysis of the Betula platyphylla TCP Gene Family and Its Expression Profile Identifies Potential Key Candidate Genes Involved in Abiotic Stress Responses. PLANTS (BASEL, SWITZERLAND) 2025; 14:880. [PMID: 40265781 PMCID: PMC11944959 DOI: 10.3390/plants14060880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2025] [Revised: 03/07/2025] [Accepted: 03/10/2025] [Indexed: 04/24/2025]
Abstract
The TCP transcription factor (TF) family is a vital set of plant-specific regulators involved in plant growth, development, and responses to environmental stresses. Despite the extensive research on TCP transcription factors in numerous plant species, the functions they fulfill in Betula platyphylla are still not well understood. In this study, 21 BpTCP genes were identified via genome-wide analysis. Bioinformatics analysis was used to examine the physicochemical properties of these transcription factors, including molecular weight, isoelectric point, chromosomal distribution, and predicted subcellular localization. We expected that most BpTCP transcription factors would be located in the nucleus. Collinearity analysis revealed that gene fragment duplication events played a major role in the evolutionary expansion and diversification of the BpTCP gene family. Promoter analysis identified diverse cis-acting elements in BpTCP, suggesting that they play a role in stress responses, hormonal regulation, and plant growth and development. qRT-PCR analysis showed that BpTCP genes displayed tissue-specific expression patterns in the roots, stems, and leaves, displaying remarkable differences in expression levels when subjected to abiotic stresses, including drought and high- and low-temperature conditions. Notably, BpTCP17 and BpTCP18 showed markedly higher expression levels under multiple stress conditions. Subcellular localization experiments confirmed that both BpTCP17 and BpTCP18 localize in the nucleus, consistent with bioinformatic predictions. These findings emphasize the potential roles of BpTCP17 and BpTCP18 in mediating abiotic stress responses, highlighting their potential as candidate genes for improving stress tolerance in B. platyphylla.
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Affiliation(s)
- Shengzhou Guo
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.G.); (Y.X.); (R.L.); (Y.W.)
| | - Yuan Xu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.G.); (Y.X.); (R.L.); (Y.W.)
| | - Yi Zhou
- College of Forestry, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China;
| | - Ronglin Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.G.); (Y.X.); (R.L.); (Y.W.)
| | - Yongkang Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.G.); (Y.X.); (R.L.); (Y.W.)
| | - Ling Yao
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Syed Muhammad Azam
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Huanhuan Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (H.M.); (X.L.)
| | - Xiaomin Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (H.M.); (X.L.)
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.G.); (Y.X.); (R.L.); (Y.W.)
| | - Kang Wang
- College of Forestry, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China;
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Zhu Y, Niu S, Lin J, Yang H, Zhou X, Wang S, Liu X, Yang Q, Zhang C, Zhuang Y, Cai T, Zhuang W, Chen H. Genome-Wide Identification and Expression Analysis of TCP Transcription Factors Responding to Multiple Stresses in Arachis hypogaea L. Int J Mol Sci 2025; 26:1069. [PMID: 39940846 PMCID: PMC11816611 DOI: 10.3390/ijms26031069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 01/20/2025] [Accepted: 01/24/2025] [Indexed: 02/16/2025] Open
Abstract
The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING-CELL-FACTOR (TCP) gene family, a plant-specific transcription factor family, plays pivotal roles in various processes such as plant growth and development regulation, hormone crosstalk, and stress responses. However, a comprehensive genome-wide identification and characterization of the TCP gene family in peanut has yet to be fully elucidated. In this study, we conducted a genome-wide search and identified 51 TCP genes (designated as AhTCPs) in peanut, unevenly distributed across 17 chromosomes. These AhTCPs were phylogenetically classified into three subclasses: PCF, CIN, and CYC/TB1. Gene structure analysis of the AhTCPs revealed that most AhTCPs within the same subclade exhibited conserved motifs and domains, as well as similar gene structures. Cis-acting element analysis demonstrated that the AhTCP genes harbored numerous cis-acting elements associated with stress response, plant growth and development, plant hormone response, and light response. Intraspecific collinearity analysis unveiled significant collinear relationships among 32 pairs of these genes. Further collinear evolutionary analysis found that peanuts share 30 pairs, 24 pairs, 33 pairs, and 100 pairs of homologous genes with A. duranensis, A. ipaensis, Arabidopsis thaliana, and Glycine max, respectively. Moreover, we conducted a thorough analysis of the transcriptome expression profiles in peanuts across various tissues, under different hormone treatment conditions, in response to low- and high-calcium treatments, and under low-temperature and drought stress scenarios. The qRT-PCR results were in accordance with the transcriptome expression data. Collectively, these studies have established a solid theoretical foundation for further exploring the biological functions of the TCP gene family in peanuts, providing valuable insights into the regulatory mechanisms of plant growth, development, and stress responses.
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Affiliation(s)
- Yanting Zhu
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Sijie Niu
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Jingyi Lin
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Hua Yang
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Xun Zhou
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Siwei Wang
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Xiaoyan Liu
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Qiang Yang
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Chong Zhang
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Yuhui Zhuang
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Tiecheng Cai
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Weijian Zhuang
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
| | - Hua Chen
- Research Center of Leguminous Oil Plant Genetics and Systems Biology, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (S.N.); (J.L.); (H.Y.); (X.Z.); (S.W.); (X.L.); (Q.Y.); (C.Z.); (Y.Z.); (T.C.); (W.Z.)
- Key Laboratory of Fujian-Taiwan Crop Biological Breeding and Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Genetics and Comprehensive Utilization, Ministry of Education, Fuzhou 350002, China
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Li C, Dong S, Beckles DM, Liu X, Guan J, Wang Z, Gu X, Miao H, Zhang S. Candidate genes associated with low temperature tolerance in cucumber adult plants identified by combining GWAS & QTL mapping. STRESS BIOLOGY 2024; 4:53. [PMID: 39658697 PMCID: PMC11631831 DOI: 10.1007/s44154-024-00191-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 09/25/2024] [Indexed: 12/12/2024]
Abstract
Fruit quality and yield are reduced when cucumber (Cucumis sativus L.) plants are exposed to low temperature (LT) stress, yet, the inheritance and genes linked to cold tolerance in adult plants have not been reported yet. Here, the LT-tolerance of 120 cucumber accessions representing four ecotypes were evaluated by GWAS, and also, in 140 recombinant inbred lines (RILs) derived from a biparental cross. Plants were exposed to naturally occurring LT environments in a plastic greenhouse, in winter 2022, and 2023, and a low temperature injury index (LTII) was employed to evaluate plant performance. Genetic analysis revealed that the LT-tolerance evaluated in the adult cucumber plants was a multigenic quantitative trait, and that 18 of the 120 accessions were highly LT tolerant by our LTII assessment. Two loci (gLTT1.1 and gLTT3.1) exhibited strong signals that were consistent and stable in two environments. In addition, two QTLs-qLTT1.2 on chromosome (Chr.) 1, and qLTT3.1 on Chr. 3, were discovered in all tests using RIL population derived from a cross between LT-sensitive 'CsIVF0106', and LT-tolerant 'CsIVF0168'. qLTT1.2 was delimited to a 1.24-Mb region and qLTT3.1 was narrowed to a 1.43-Mb region. Interestingly, a peak single nucleotide polymorphism (SNP) at gLTT1.1 and gLTT3.1 was also found in qLTT1.2 and qLTT3.1, respectively. These loci were thus renamed as gLTT1.1 and gLTT3.1. In these regions, 25 genes were associated with the LT response. By identifying differences in haplotypes and transcript profiles among these genes, we identified four candidates: CsaV3_1G012520 (an ethylene-responsive transcription factor) and CsaV3_1G013060 (a RING/U-box superfamily protein) in gLTT1.1, and two RING-type E3 ubiquitin transferases at CsaV3_3G018440 and CsaV3_3G017700 in gLTT3.1 that may regulate LT-tolerance in adult cucumber. Interestingly, the accessions in which the LT-tolerant haplotypes for two loci were pyramided, displayed maximally high tolerance for LT. These findings therefore provide a solid foundation for the identification of LT-tolerant genes and the molecular breeding of cucumber with LT-tolerance.
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Affiliation(s)
- Caixia Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shaoyun Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Diane M Beckles
- Department of Plant Sciences, University of California, One Shield Avenue, Davis, CA, 95616, USA
| | - Xiaoping Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zaizhan Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Han Miao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Shengping Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Han T, Khan MA, Wang Y, Tan W, Li C, Ai P, Zhao W, Li Z, Wang Z. Identification of SDG gene family members and exploration of flowering related genes in different cultivars of chrysanthemums and their wild ancestors. BMC PLANT BIOLOGY 2024; 24:813. [PMID: 39210253 PMCID: PMC11360836 DOI: 10.1186/s12870-024-05465-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
The SET domain genes (SDGs) are significant contributors to various aspects of plant growth and development, mainly includes flowering, pollen development, root growth, regulation of the biological clock and branching patterns. To clarify the biological functions of the chrysanthemum SDG family, the SDG family members of four chrysanthemum cultivars and three related wild species were identified; their physical and chemical properties, protein domains and conserved motifs were predicted and analyzed. The results showed that 59, 67, 67, 102, 106, 114, and 123 SDGs were identified from Chrysanthemum nankingense, Chrysanthemum lavandulifolium, Chrysanthemum seticuspe, Chrysanthemum × morifolium cv. 'Hechengxinghuo', 'Zhongshanzigui', 'Quanxiangshuichang' and 'Jinbeidahong', respectively. The SDGs were divided into 5-7 subfamilies by cluster analysis; different conserved motifs were observed in particular families. The SDGs of C. lavandulifolium and C. seticuspe were distributed unevenly on 9 chromosomes. SDG promoters of different species include growth and development, photo-response, stress response and hormone responsive elements, among them, the cis-acting elements related to MeJA response had the largest proportion. The expression of chrysanthemum SDG genes was observed for most variable selected genes which has close association with important Arabidopsis thaliana genes related to flowering regulation. The qPCR results showed that the expression trend of SDG genes varied in different tissues at different growth stages with high expression in the flowering period. The ClSDG29 showed higher expression in the flower and bud tissues, which indicate that ClSDG29 might be associated with flowering regulation in chrysanthemum. In summary, the results of this study can provide a basis for subsequent research on chrysanthemum flowering time regulation.
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Affiliation(s)
- Ting Han
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Muhammad Ayoub Khan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Yiming Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Wenchao Tan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Chenran Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Penghui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Wenqian Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Zhongai Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Zicheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China.
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Li Y, Liu X, Xu X, Zhu G, Xiang D, Liu P. Identification and characterization of the RcTCP gene family and its expression in response to abiotic stresses in castor bean. BMC Genomics 2024; 25:670. [PMID: 38965476 PMCID: PMC11223397 DOI: 10.1186/s12864-024-10347-6] [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: 11/28/2023] [Accepted: 04/25/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND The TCP (teosinte branched1/cincinnata/proliferating cell factor) family plays a prominent role in plant development and stress responses. However, TCP family genes have thus far not been identified in castor bean, and therefore an understanding of the expression and functional aspects of castor bean TCP genes is lacking. To identify the potential biological functions of castor bean (RcTCP) TCP members, the composition of RcTCP family members, their basic physicochemical properties, subcellular localizations, interacting proteins, miRNA target sites, and gene expression patterns under stress were assessed. RESULTS The presence of 20 RcTCP genes on the nine chromosomes of castor bean was identified, all of which possess TCP domains. Phylogenetic analysis indicated a close relationship between RcTCP genes and Arabidopsis AtTCP genes, suggesting potential functional similarity. Subcellular localization experiments confirmed that RcTC01/02/03/10/16/18 are all localized in the nucleus. Protein interaction analysis revealed that the interaction quantity of RcTCP03/06/11 proteins is the highest, indicating a cascade response in the functional genes. Furthermore, it was found that the promoter region of RcTCP genes contains a large number of stress-responsive elements and hormone-induced elements, indicating a potential link between RcTCP genes and stress response functions. qRT-PCR showed that all RcTCP genes exhibit a distinct tissue-specific expression pattern and their expression is induced by abiotic stress (including low temperature, abscisic acid, drought, and high salt). Among them, RcTCP01/03/04/08/09/10/14/15/18/19 genes may be excellent stress-responsive genes. CONCLUSION We discovered that RcTCP genes play a crucial role in various activities, including growth and development, the stress response, and transcription. This study provides a basis for studying the function of RcTCP gene in castor.
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Affiliation(s)
- Yanxiao Li
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Xingyang Liu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Xingyuan Xu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Guishuang Zhu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China
| | - Dianjun Xiang
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China.
| | - Peng Liu
- College of Agriculture Life Science, Inner Mongolia Minzu University, Tongliao, 028000, China.
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Wu X, Li J, Wen X, Zhang Q, Dai S. Genome-wide identification of the TCP gene family in Chrysanthemum lavandulifolium and its homologs expression patterns during flower development in different Chrysanthemum species. FRONTIERS IN PLANT SCIENCE 2023; 14:1276123. [PMID: 37841609 PMCID: PMC10570465 DOI: 10.3389/fpls.2023.1276123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023]
Abstract
TCP proteins, part of the transcription factors specific to plants, are recognized for their involvement in various aspects of plant growth and development. Nevertheless, a thorough investigation of TCPs in Chrysanthemum lavandulifolium, a prominent ancestral species of cultivated chrysanthemum and an excellent model material for investigating ray floret (RF) and disc floret (DF) development in Chrysanthemum, remains unexplored yet. Herein, a comprehensive study was performed to analyze the genome-wide distribution of TCPs in C. lavandulifolium. In total, 39 TCPs in C. lavandulifolium were identified, showing uneven distribution on 8 chromosomes. Phylogenetic and gene structural analyses revealed that ClTCPs were grouped into classes I and II. The class II genes were subdivided into two subclades, the CIN and CYC/TB1 subclades, with members of each clade having similar conserved motifs and gene structures. Four CIN subclade genes (ClTCP24, ClTCP25, ClTCP26, and ClTCP27) contained the potential miR319 target sites. Promoter analysis revealed that ClTCPs had numerous cis-regulatory elements associated with phytohormone responses, stress responses, and plant growth/development. The expression patterns of ClTCPs during capitulum development and in two different florets were determined using RNA-seq and qRT-PCR. The expression levels of TCPs varied in six development stages of capitula; 25 out of the 36 TCPs genes were specifically expressed in flowers. Additionally, we identified six key ClCYC2 genes, which belong to the class II TCP subclade, with markedly upregulated expression in RFs compared with DFs, and these genes exhibited similar expression patterns in the two florets of Chrysanthemum species. It is speculated that they may be responsible for RFs and DFs development. Subcellular localization and transactivation activity analyses of six candidate genes demonstrated that all of them were localized in the nucleus, while three exhibited self-activation activities. This research provided a better understanding of TCPs in C. lavandulifolium and laid a foundation for unraveling the mechanism by which important TCPs involved in the capitulum development.
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Affiliation(s)
- Xiaoyun Wu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Junzhuo Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xiaohui Wen
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qiuling Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Silan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
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Zhou H, Hwarari D, Ma H, Xu H, Yang L, Luo Y. Genomic survey of TCP transcription factors in plants: Phylogenomics, evolution and their biology. Front Genet 2022; 13:1060546. [PMID: 36437962 PMCID: PMC9682074 DOI: 10.3389/fgene.2022.1060546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/27/2022] [Indexed: 09/29/2023] Open
Abstract
The TEOSINTE BRANCHED1 (TBI1), CYCLOIDEA (CYC), and PROLIFERATING CELL NUCLEAR ANTIGEN FACTORS (PCF1 and PCF2) proteins truncated as TCP transcription factors carry conserved basic-helix-loop-helix (bHLH) structure, related to DNA binding functions. Evolutionary history of the TCP genes has shown their presence in early land plants. In this paper, we performed a comparative discussion on the current knowledge of the TCP Transcription Factors in lower and higher plants: their evolutionary history based on the phylogenetics of 849 TCP proteins from 37 plant species, duplication events, and biochemical roles in some of the plants species. Phylogenetics investigations confirmed the classification of TCP TFs into Class I (the PCF1/2), and Class II (the C- clade) factors; the Class II factors were further divided into the CIN- and CYC/TB1- subclade. A trace in the evolution of the TCP Factors revealed an absence of the CYC/TB1subclade in lower plants, and an independent evolution of the CYC/TB1subclade in both eudicot and monocot species. 54% of the total duplication events analyzed were biased towards the dispersed duplication, and we concluded that dispersed duplication events contributed to the expansion of the TCP gene family. Analysis in the TCP factors functional roles confirmed their involvement in various biochemical processes which mainly included promoting cell proliferation in leaves in Class I TCPs, and cell division during plant development in Class II TCP Factors. Apart from growth and development, the TCP Factors were also shown to regulate hormonal and stress response pathways. Although this paper does not exhaust the present knowledge of the TCP Transcription Factors, it provides a base for further exploration of the gene family.
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Affiliation(s)
- Haiying Zhou
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative In-novation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Delight Hwarari
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hongyu Ma
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Haibin Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Jiangsu Collaborative In-novation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai’an, China
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Mekapogu M, Kwon OK, Song HY, Jung JA. Towards the Improvement of Ornamental Attributes in Chrysanthemum: Recent Progress in Biotechnological Advances. Int J Mol Sci 2022; 23:ijms232012284. [PMID: 36293140 PMCID: PMC9603847 DOI: 10.3390/ijms232012284] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022] Open
Abstract
Incessant development and introduction of novel cultivars with improved floral attributes are vital in the dynamic ornamental industry. Chrysanthemum (Chrysanthemum morifolium) is a highly favored ornamental plant, ranking second globally in the cut flower trade, after rose. Development of new chrysanthemum cultivars with improved and innovative modifications in ornamental attributes, including floral color, shape, plant architecture, flowering time, enhanced shelf life, and biotic and abiotic stress tolerance, is a major goal in chrysanthemum breeding. Despite being an economically important ornamental plant, the application of conventional and molecular breeding approaches to various key traits of chrysanthemum is hindered owing to its genomic complexity, heterozygosity, and limited gene pool availability. Although classical breeding of chrysanthemum has resulted in the development of several hundreds of cultivars with various morphological variations, the genetic and transcriptional control of various important ornamental traits remains unclear. The coveted blue colored flowers of chrysanthemums cannot be achieved through conventional breeding and mutation breeding due to technical limitations. However, blue-hued flower has been developed by genetic engineering, and transgenic molecular breeding has been successfully employed, leading to substantial progress in improving various traits. The recent availability of whole-genome sequences of chrysanthemum offers a platform to extensively employ MAS to identify a large number of markers for QTL mapping, and GWAS to dissect the genetic control of complex traits. The combination of NGS, multi-omic platforms, and genome editing technologies has provided a tremendous scope to decipher the molecular and regulatory mechanisms. However, the application and integration of these technologies remain inadequate for chrysanthemum. This review, therefore, details the significance of floral attributes, describes the efforts of recent advancements, and highlights the possibilities for future application towards the improvement of crucial ornamental traits in the globally popular chrysanthemum plant.
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