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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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Gao T, Zhou X, Han M, Shen Y, Zhang Y, Wu Q, Dan H, Wang T, Ye H, Liu L, Chai M, Wang Y. Identification and expression responses of TCP gene family in Opisthopappus taihangensis under abiotic stress. FRONTIERS IN PLANT SCIENCE 2025; 16:1499244. [PMID: 40115945 PMCID: PMC11922953 DOI: 10.3389/fpls.2025.1499244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 02/17/2025] [Indexed: 03/23/2025]
Abstract
The TCP gene family plays pivotal roles in the development and abiotic stress responses of plants; however, no data has been provided for this gene family in Opisthopappus taihangensis. Based on O. taihangensis genome, 14 TCP genes were identified and divided into two classes (I and II). After tandem and segmental duplication/whole-genome duplication (WGD), more loss and less gain events of OtTCPs occurred, which might be related with the underwent purifying selection during the evolution. The conserved motifs and structures of OtTCP genes contained light response, growth and development, hormone response, and stress-related cis-acting elements. Different OtTCP genes, even duplicated gene pairs, could be expressed in different tissues, which implied that OtTCP genes had diverse function. Among OtTCPs, OtTCP4, 9 and 11 of CYC clade (Class II) presented a relative wide expression pattern with no or one intron. The three TCP genes could be regarded as important candidate factors for O. taihangensis in growth, development and stress response. These results provided some clues and references for the further in-depth exploration of O. taihangensis resistance mechanisms, as well as those of other unique eco-environment plants.
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Affiliation(s)
- Ting Gao
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Xiaojuan Zhou
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Mian Han
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Yuexin Shen
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Yimeng Zhang
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Qi Wu
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Haoyuan Dan
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Tingyu Wang
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Li Liu
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Min Chai
- School of Life Science, Shanxi Normal University, Taiyuan, China
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Taiyuan, China
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Nie J, Zhao H, Guo X, Zhang T, Han B, Liu H. Genome-wide identification of oat TCP gene family and expression patterns under abiotic stress. Front Genet 2025; 16:1533562. [PMID: 39967685 PMCID: PMC11832536 DOI: 10.3389/fgene.2025.1533562] [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: 11/26/2024] [Accepted: 01/17/2025] [Indexed: 02/20/2025] Open
Abstract
TCP transcription factors are a unique class of transcription factors that play important roles in alleviating abiotic stresses such as drought and salt. In this study, the whole-genome data of three cultivated varieties, namely, "SFS", "Sang" and "OT3098v2", were utilized to identify and analyze the members of the TCP gene family in oats, and their responses to two abiotic stresses, drought and salt, were also investigated. Results showed that there are 83, 65, and 30 non-redundant TCP genes in the three oats, with the highest number of TCP genes specific to the "SFS", reaching 22 genes. The oat TCP genes can be classified into three subfamilies: PCF, CIN, and CYC/TB1. Most AsTCP genes have important motifs, Motif 1 and Motif 2, which are part of the bHLH domain. Additionally, various cis-acting elements related to hormone response, abiotic stress, light response, and growth and development were found in the promoters of AsTCP genes. The main amplification mechanism of the oat TCP gene family is fragment duplication. Two tandem duplications, AsTCP058/AsTCP059 and AsTCP023/AsTCP025, are stably present in the three oats. The highest number of AsTCP collinear relationships exist in the "SFS" with 89 pairs. After drought and salt stress treatments, significant differences in gene expression were observed among different oat cultivars and treatment periods. Genes that showed significant expression changes under both treatments (AsTCP021, AsTCP033, AsTCP044, AsTCP053, and AsTCP058) may play important roles in oat's response to abiotic stresses. Notably, AsTCP053 gene was significantly upregulated at 24 h of stress treatment and showed a more sensitive response to salt stress. This study provides insights into the functional characterization of the oat TCP gene family and its molecular mechanisms underlying stress tolerance.
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Affiliation(s)
- Jiaming Nie
- Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Wheat Germplasm Innovation and Utilization Autonomous Region Higher School, Hohhot, China
| | - Hongbin Zhao
- Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Wheat Germplasm Innovation and Utilization Autonomous Region Higher School, Hohhot, China
- Key Laboratory of Grassland Resources of the Ministry of Education, Hohhot, China
| | - Xiaodong Guo
- Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Wheat Germplasm Innovation and Utilization Autonomous Region Higher School, Hohhot, China
| | - Tao Zhang
- Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Wheat Germplasm Innovation and Utilization Autonomous Region Higher School, Hohhot, China
| | - Bing Han
- Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Wheat Germplasm Innovation and Utilization Autonomous Region Higher School, Hohhot, China
- Key Laboratory of Grassland Resources of the Ministry of Education, Hohhot, China
| | - Huiyan Liu
- Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Wheat Germplasm Innovation and Utilization Autonomous Region Higher School, Hohhot, China
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Lv W, Yang H, Zheng Q, Liao W, Chen L, Lian Y, Lin Q, Huo S, Rehman OU, Liu W, Zheng K, Zhang Y, Cao S. Identification and Expression Analysis of TCP Transcription Factors Under Abiotic Stress in Phoebe bournei. PLANTS (BASEL, SWITZERLAND) 2024; 13:3095. [PMID: 39520013 PMCID: PMC11548437 DOI: 10.3390/plants13213095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2024] [Revised: 10/29/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024]
Abstract
The TCP gene family encodes plant transcription factors crucial for regulating growth and development. While TCP genes have been identified in various species, they have not been studied in Phoebe bournei (Hemsl.). This study identified 29 TCP genes in the P. bournei genome, categorizing them into Class I (PCF) and Class II (CYC/TB1 and CIN). We conducted analyses on the PbTCP gene at both the protein level (physicochemical properties) and the gene sequence level (subcellular localization, chromosomal distribution, phylogenetic relationships, conserved motifs, and gene structure). Most P. bournei TCP genes are localized in the nucleus, except PbTCP9 in the mitochondria and PbTCP8 in both the chloroplast and nucleus. Chromosomal mapping showed 29 TCP genes unevenly distributed across 10 chromosomes, except chromosome 8 and 9. We also analyzed the promoter cis-regulatory elements, which are mainly involved in plant growth and development and hormone responses. Notably, most PbTCP transcription factors respond highly to light. Further analysis revealed three subfamily genes expressed in five P. bournei tissues: leaves, root bark, root xylem, stem xylem, and stem bark, with predominant PCF genes. Using qRT-PCR, we examined six representative genes-PbTCP16, PbTCP23, PbTCP7, PbTCP29, PbTCP14, and PbTCP15-under stress conditions such as high temperature, drought, light exposure, and dark. PbTCP14 and PbTCP15 showed significantly higher expression under heat, drought, light and dark stress. We hypothesize that TCP transcription factors play a key role in growth under varying light conditions, possibly mediated by auxin hormones. This work provides insights into the TCP gene family's functional characteristics and stress resistance regulation in P. bournei.
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Affiliation(s)
- Wenzhuo Lv
- College of Jun Cao Science and Ecology (College of Carbon Neutrality), Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Hao Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Y.); (Q.Z.); (W.L.); (L.C.)
| | - Qiumian Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Y.); (Q.Z.); (W.L.); (L.C.)
| | - Wenhai Liao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Y.); (Q.Z.); (W.L.); (L.C.)
| | - Li Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Y.); (Q.Z.); (W.L.); (L.C.)
| | - Yiran Lian
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (Q.L.)
| | - Qinmin Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.L.); (Q.L.)
| | - Shuhao Huo
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (S.H.); (O.U.R.)
| | - Obaid Ur Rehman
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; (S.H.); (O.U.R.)
| | - Wei Liu
- Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, China;
| | - Kehui Zheng
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yanzi Zhang
- Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Y.); (Q.Z.); (W.L.); (L.C.)
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Gao Y, Regad F, Li Z, Pirrello J, Bouzayen M, Van Der Rest B. Class I TCP in fruit development: much more than growth. FRONTIERS IN PLANT SCIENCE 2024; 15:1411341. [PMID: 38863555 PMCID: PMC11165105 DOI: 10.3389/fpls.2024.1411341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Fruit development can be viewed as the succession of three main steps consisting of the fruit initiation, growth and ripening. These processes are orchestrated by different factors, notably the successful fertilization of flowers, the environmental conditions and the hormones whose action is coordinated by a large variety of transcription factors. Among the different transcription factor families, TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR (TCP) family has received little attention in the frame of fruit biology despite its large effects on several developmental processes and its action as modulator of different hormonal pathways. In this respect, the comprehension of TCP functions in fruit development remains an incomplete puzzle that needs to be assembled. Building on the abundance of genomic and transcriptomic data, this review aims at collecting available TCP expression data to allow their integration in the light of the different functional genetic studies reported so far. This reveals that several Class I TCP genes, already known for their involvement in the cell proliferation and growth, display significant expression levels in developing fruit, although clear evidence supporting their functional significance in this process remains scarce. The extensive expression data compiled in our study provide convincing elements that shed light on the specific involvement of Class I TCP genes in fruit ripening, once these reproductive organs acquire their mature size. They also emphasize their putative role in the control of specific biological processes such as fruit metabolism and hormonal dialogue.
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Affiliation(s)
- Yushuo Gao
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Farid Regad
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Julien Pirrello
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
| | - Mondher Bouzayen
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, China
| | - Benoît Van Der Rest
- Laboratoire de Recherche en Sciences Veígeítales - Génomique et Biotechnologie des Fruits, Universiteí de Toulouse, Centre national de la recherche scientifique (CNRS), Université Toulouse III - Paul Sabatier (UPS), Toulouse-Institut National Polytechnique (INP), Toulouse, France
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Liu S, An Z, Lai Z. Amaranth's Growth and Physiological Responses to Salt Stress and the Functional Analysis of AtrTCP1 Gene. Int J Mol Sci 2024; 25:5437. [PMID: 38791475 PMCID: PMC11121779 DOI: 10.3390/ijms25105437] [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: 05/03/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Amaranth species are C4 plants that are rich in betalains, and they are tolerant to salinity stress. A small family of plant-specific TCP transcription factors are involved in the response to salt stress. However, it has not been investigated whether amaranth TCP1 is involved in salt stress. We elucidated that the growth and physiology of amaranth were affected by salt concentrations of 50-200 mmol·L-1 NaCl. The data showed that shoot and root growth was inhibited at 200 mmol·L-1, while it was promoted at 50 mmol·L-1. Meanwhile, the plants also showed physiological responses, which indicated salt-induced injuries and adaptation to the salt stress. Moreover, AtrTCP1 promoted Arabidopsis seed germination. The germination rate of wild-type (WT) and 35S::AtrTCP1-GUS Arabidopsis seeds reached around 92% by the seventh day and 94.5% by the second day under normal conditions, respectively. With 150 mmol·L-1 NaCl treatment, the germination rate of the WT and 35S::AtrTCP1-GUS plant seeds was 27.0% by the seventh day and 93.0% by the fourth day, respectively. Under salt stress, the transformed 35S::AtrTCP1 plants bloomed when they grew 21.8 leaves after 16.2 days of treatment, which was earlier than the WT plants. The transformed Arabidopsis plants flowered early to resist salt stress. These results reveal amaranth's growth and physiological responses to salt stress, and provide valuable information on the AtrTCP1 gene.
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Affiliation(s)
- Shengcai Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zixian An
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
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Panzade KP, Vishwakarma H, Kharate PS, Azameti MK. Genome-wide analysis and expression profile of TCP gene family under drought and salinity stress condition in cowpea ( Vigna unguiculata (L.) Walp.). 3 Biotech 2024; 14:138. [PMID: 38682097 PMCID: PMC11052985 DOI: 10.1007/s13205-024-03976-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/13/2024] [Indexed: 05/01/2024] Open
Abstract
TCP transcription factors are known to regulate abiotic stress condition, but their role in V. unguiculata remains unexplored. So, in silico analysis and expression profile of the TCP gene family were performed in V. unguiculata to understand its role in response to heat and drought stress. A genome-wide search detected 28 TCPs (designated as VuTCPs) that were grouped into three subclasses by phylogenetic analysis. Gene structure, synteny, and phylogeny analyses of VuTCPs have shown a typical evolutionary path. One tandem and eight segmental duplication events were identified. Furthermore, identified duplicated, and orthologous VuTCP genes were under strong purifying selection pressure. A total of 15 SSRs were identified in the 12 VuTCPs, while 10 VuTCP genes were regulated by different miRNAs having a major role in abiotic stress tolerance. Analysed physicochemical properties, cis-acting elements, and gene ontology suggested that VuTCPs play various roles, including salinity and drought stress tolerance. qRT-PCR analysis showed that 11 and 15 VuTCPs were upregulated under drought and salinity stress conditions, respectively. Our findings provide comprehensive insights into the genomic characterization of the VuTCPs gene family in V. unguiculata, offering a foundation for understanding their structure, evolution, and role in abiotic stress tolerance. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03976-x.
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Affiliation(s)
- Kishor Prabhakar Panzade
- Department of Plant Biotechnology, SDMVM College of Agricultural Biotechnology, Georai Tanda, Chh. Sambhaji Nagar (Aurangabad), Maharashtra, 431002 India
| | - Harinder Vishwakarma
- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012 India
| | - Pawankumar S. Kharate
- Department of Plant Biotechnology, SDMVM College of Agricultural Biotechnology, Georai Tanda, Chh. Sambhaji Nagar (Aurangabad), Maharashtra, 431002 India
| | - Mawuli K. Azameti
- Department of Applied Biology, C. K. Tedam University of Technology and Applied Sciences, Navrongo, Upper East Region Ghana
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Pan J, Ju Z, Ma X, Duan L, Jia Z. Genome-wide characterization of TCP family and their potential roles in abiotic stress resistance of oat ( Avena sativa L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1382790. [PMID: 38654900 PMCID: PMC11036127 DOI: 10.3389/fpls.2024.1382790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
The TCP gene family members play multiple functions in plant growth and development and were named after the first three family members found in this family, TB1 (TEOSINTE BRANCHED 1), CYCLOIDEA (CYC), and Proliferating Cell Factor 1/2 (PCF1/2). Nitrogen (N) is a crucial element for forage yield; however, over-application of N fertilizer can increase agricultural production costs and environmental stress. Therefore, the discovery of low N tolerance genes is essential for the genetic improvement of superior oat germplasm and ecological protection. Oat (Avena sativa L.), is one of the world's staple grass forages, but no genome-wide analysis of TCP genes and their roles in low-nitrogen stress has been performed. This study identified the oat TCP gene family members using bioinformatics techniques. It analyzed their phylogeny, gene structure analysis, and expression patterns. The results showed that the AsTCP gene family includes 49 members, and most of the AsTCP-encoded proteins are neutral or acidic proteins; the phylogenetic tree classified the AsTCP gene family members into three subfamilies, and each subfamily has different conserved structural domains and functions. In addition, multiple cis-acting elements were detected in the promoter of the AsTCP genes, which were associated with abiotic stress, light response, and hormone response. The 49 AsTCP genes identified from oat were unevenly distributed on 18 oat chromosomes. The results of real-time quantitative polymerase chain reaction (qRT-PCR) showed that the AsTCP genes had different expression levels in various tissues under low nitrogen stress, which indicated that these genes (such as AsTCP01, AsTCP03, AsTCP22, and AsTCP38) played multiple roles in the growth and development of oat. In conclusion, this study analyzed the AsTCP gene family and their potential functions in low nitrogen stress at the genome-wide level, which lays a foundation for further analysis of the functions of AsTCP genes in oat and provides a theoretical basis for the exploration of excellent stress tolerance genes in oat. This study provides an essential basis for future in-depth studies of the TCP gene family in other oat genera and reveals new research ideas to improve gene utilization.
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Affiliation(s)
| | | | | | | | - Zhifeng Jia
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Husbandry and Veterinary Sciences, Qinghai University, Xining, China
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Wei X, Yuan M, Zheng BQ, Zhou L, Wang Y. Genome-wide identification and characterization of TCP gene family in Dendrobium nobile and their role in perianth development. FRONTIERS IN PLANT SCIENCE 2024; 15:1352119. [PMID: 38375086 PMCID: PMC10875090 DOI: 10.3389/fpls.2024.1352119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
TCP is a widely distributed, essential plant transcription factor that regulates plant growth and development. An in-depth study of TCP genes in Dendrobium nobile, a crucial parent in genetic breeding and an excellent model material to explore perianth development in Dendrobium, has not been conducted. We identified 23 DnTCP genes unevenly distributed across 19 chromosomes and classified them as Class I PCF (12 members), Class II: CIN (10 members), and CYC/TB1 (1 member) based on the conserved domain and phylogenetic analysis. Most DnTCPs in the same subclade had similar gene and motif structures. Segmental duplication was the predominant duplication event for TCP genes, and no tandem duplication was observed. Seven genes in the CIN subclade had potential miR319 and -159 target sites. Cis-acting element analysis showed that most DnTCP genes contained many developmental stress-, light-, and phytohormone-responsive elements in their promoter regions. Distinct expression patterns were observed among the 23 DnTCP genes, suggesting that these genes have diverse regulatory roles at different stages of perianth development or in different organs. For instance, DnTCP4 and DnTCP18 play a role in early perianth development, and DnTCP5 and DnTCP10 are significantly expressed during late perianth development. DnTCP17, 20, 21, and 22 are the most likely to be involved in perianth and leaf development. DnTCP11 was significantly expressed in the gynandrium. Specially, MADS-specific binding sites were present in most DnTCP genes putative promoters, and two Class I DnTCPs were in the nucleus and interacted with each other or with the MADS-box. The interactions between TCP and the MADS-box have been described for the first time in orchids, which broadens our understanding of the regulatory network of TCP involved in perianth development in orchids.
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Affiliation(s)
| | | | | | | | - Yan Wang
- State Key Laboratory of Tree Genetics and Breeding; Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Faysal Ahmed F, Dola FS, Zohra FT, Rahman SM, Konak JN, Sarkar MAR. Genome-wide identification, classification, and characterization of lectin gene superfamily in sweet orange (Citrus sinensis L.). PLoS One 2023; 18:e0294233. [PMID: 37956187 PMCID: PMC10642848 DOI: 10.1371/journal.pone.0294233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Lectins are sugar-binding proteins found abundantly in plants. Lectin superfamily members have diverse roles, including plant growth, development, cellular processes, stress responses, and defense against microbes. However, the genome-wide identification and functional analysis of lectin genes in sweet orange (Citrus sinensis L.) remain unexplored. Therefore, we used integrated bioinformatics approaches (IBA) for in-depth genome-wide identification, characterization, and regulatory factor analysis of sweet orange lectin genes. Through genome-wide comparative analysis, we identified a total of 141 lectin genes distributed across 10 distinct gene families such as 68 CsB-Lectin, 13 CsLysin Motif (LysM), 4 CsChitin-Bind1, 1 CsLec-C, 3 CsGal-B, 1 CsCalreticulin, 3 CsJacalin, 13 CsPhloem, 11 CsGal-Lec, and 24 CsLectinlegB.This classification relied on characteristic domain and phylogenetic analysis, showing significant homology with Arabidopsis thaliana's lectin gene families. A thorough analysis unveiled common similarities within specific groups and notable variations across different protein groups. Gene Ontology (GO) enrichment analysis highlighted the predicted genes' roles in diverse cellular components, metabolic processes, and stress-related regulation. Additionally, network analysis of lectin genes with transcription factors (TFs) identified pivotal regulators like ERF, MYB, NAC, WRKY, bHLH, bZIP, and TCP. The cis-acting regulatory elements (CAREs) found in sweet orange lectin genes showed their roles in crucial pathways, including light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and more. These findings will aid in the in-depth molecular examination of these potential genes and their regulatory elements, contributing to targeted enhancements of sweet orange species in breeding programs.
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Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Farah Sumaiya Dola
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Fatema Tuz Zohra
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Shaikh Mizanur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Jesmin Naher Konak
- Department of Biochemistry and Molecular Biology, Faculty of LifeScience, Mawlana Bhashani Science and Technology University, Santosh, Tangail, Bangladesh
| | - Md. Abdur Rauf Sarkar
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
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Xiao F, Zhao Y, Wang X, Sun Y. Comparative Transcriptome Analysis of Gleditsia sinensis Thorns at Different Stages of Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:1456. [PMID: 37050082 PMCID: PMC10096692 DOI: 10.3390/plants12071456] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
G. sinensis thorn (called "zào jiǎo cì", ZJC) has important medicinal and economic value, however, little is known about the molecular mechanisms behind the development of ZJC. In this study, we measured the content of soluble sugar and starch during the growth and development of the thorn, and performed transcriptome sequencing of the thorn segment, non-thorn segment, apex, and root tip at five distinct stages of thorn formation. The results showed that, with the growth of ZJC, the soluble sugar content of the roots, hypocotyls, thorn stems, thornless stems, leaves, and the starch content of the roots and leaves all firstly increased and then decreased after the basic structure of thorns was formed; the soluble sugar content and starch content of ZJC showed an overall downward trend (decreased by 59.26% and 84.56%, respectively). Myb-like, YABBY2, Growth-regulating factor 3, TCP2, Zinc transporter 8, and another 25 genes may be related to the maintenance and growth of thorns. Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) between stems with thorn and thorn-free stems found that a significant number of DEGs were annotated with terms related to the positive regulation of development, heterochronic (GO:0045962), the positive regulation of photomorphogenesis (GO:2000306), and other biological process (BP) terms. The developmental initiation regulation of ZJC may be regulated by TCP transcription factors (TFs). Eight genes were selected randomly to validate the RNA-seq results using real-time quantitative PCR (RT-qPCR) and they indicated that the transcriptome data were reliable. Our work provided a comprehensive review of the thorn development of G. sinensis.
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Affiliation(s)
- Feng Xiao
- Institute for Forest Resources and Environment of Guizhou/Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province/College of Forestry, Guizhou University, Guiyang 550025, China; (F.X.); (X.W.)
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Yang Zhao
- Institute for Forest Resources and Environment of Guizhou/Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province/College of Forestry, Guizhou University, Guiyang 550025, China; (F.X.); (X.W.)
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Xiurong Wang
- Institute for Forest Resources and Environment of Guizhou/Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province/College of Forestry, Guizhou University, Guiyang 550025, China; (F.X.); (X.W.)
| | - Yanan Sun
- Institute for Forest Resources and Environment of Guizhou/Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province/College of Forestry, Guizhou University, Guiyang 550025, China; (F.X.); (X.W.)
- Forestry Bureau of Xingren, Xingren 562300, China
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