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Li Y, Zhu G, Sun H, Xiang D, Zhang C, Li Z, Liu P. Genome-wide analysis of LOG family genes in castor and RcLOG5 enhances drought, salt, and cold stress tolerance in Arabidopsis thaliana. Gene 2024; 913:148398. [PMID: 38518901 DOI: 10.1016/j.gene.2024.148398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
The gene encoding the specific phosphohydrolase LONELY GUY (LOG) plays an important role in the activation of cytokinin and the stress response in plant cells. However, the role of LOG genes in castor bean (Ricinus communis) has not been reported. In this study, we identified a total of nine members of the LOG gene family in the castor bean genome and investigated the upregulated expression of the RcLOG5 gene using transcriptome data analysis. We found that the RcLOG5 gene exhibited tissue-specific expression and was activated by polyethylene glycol, NaCl, low temperature, and abscisic acid stress. The subcellular localization results showed that the RcLOG5 gene is mainly located in the cytoplasm. Based on phenotypic and physiological indicators, namely root length, peroxidase activity, and malondialdehyde content, overexpression of the RcLOG5 gene not only improved the drought resistance, salt tolerance, and cold tolerance of transgenic Arabidopsis, but also shortened the dormancy period of the transgenic plants. Transcriptomic sequencing revealed that the overexpression of the RcLOG5 gene led to the enrichment of differentially expressed genes in the glutathione metabolism pathway in transgenic Arabidopsis. Moreover, the overexpression plants had higher levels of glutathione and a higher GSH/GSSG ratio under stress compared to the wild type. Therefore, we inferred that the RcLOG5 gene may be responsible for regulating cell membrane homeostasis by reducing the accumulation of reactive oxygen species through the glutathione pathway. Overall, the overexpression of the RcLOG5 gene positively regulated the stress resistance of transgenic Arabidopsis. This study provides valuable gene resources for breeding stress-tolerant castor bean varieties.
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Affiliation(s)
- Yanxiao Li
- College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Guishuang Zhu
- College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Haonan Sun
- College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Dianjun Xiang
- College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China.
| | - Chunlan Zhang
- College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Zhigang Li
- College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Peng Liu
- College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China.
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Rathore RS, Mishra M, Pareek A, Singla-Pareek SL. Concurrent improvement of rice grain yield and abiotic stress tolerance by overexpression of cytokinin activating enzyme LONELY GUY (OsLOG). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108635. [PMID: 38688114 DOI: 10.1016/j.plaphy.2024.108635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 03/25/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Meristem activity is important for normal plant growth as well as adaptive plastic development under abiotic stresses. Cytokinin has been recognized to have a major role in regulating meristem function which is controlled by cytokinin activating enzymes by fine-tuning the concentrations and spatial distribution of its bioactive forms. It was previously reported that LONELY GUY (LOG) acts in the direct activation pathway of cytokinin in rice shoot meristems. LOG has a cytokinin specific phosphoribohydrolase activity, which transforms inactive cytokinin nucleotides into active free bases. Here, we explored the role of OsLOG in controlling meristem activity mediated by cytokinin and its effects on growth, development, and stress resilience of rice plants. Overexpression of OsLOG in rice led to significant alterations in cytokinin levels in the inflorescence meristem, leading to enhanced plant growth, biomass and grain yield under both non-stress as well as stress conditions such as drought and salinity. Moreover, our study provides insight into how overexpression of OsLOG improves the ability of plants to withstand stress. The OsLOG-overexpressing lines exhibit reduced accumulation of H2O2 along with elevated antioxidant enzyme activities, thereby maintaining better redox homeostasis under stress conditions. This ultimately reduces the negative impact of stresses on grain yield and improves harvest index, as evidenced by observations in the OsLOG-overexpressing lines. In summary, our study emphasizes the diverse role of OsLOG, not only in regulating plant growth and yield via cytokinin but also in enhancing adaptability to abiotic stresses. This highlights its potential to improve crop yield and promote sustainable agriculture.
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Affiliation(s)
- Ray Singh Rathore
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Manjari Mishra
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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Su Z, Jiao Y, Jiang Z, Liu P, Chen Q, Qu Y, Deng X. GBSOT4 Enhances the Resistance of Gossypium barbadense to Fusarium oxysporum f. sp. vasinfectum (FOV) by Regulating the Content of Flavonoid. PLANTS (BASEL, SWITZERLAND) 2023; 12:3529. [PMID: 37895991 PMCID: PMC10609824 DOI: 10.3390/plants12203529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/07/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023]
Abstract
Sulfotransferases (SOTs) (EC 2.8.2.-) are sulfate regulatory proteins in a variety of organisms that have been previously shown to be involved in regulating a variety of physiological and biological processes, such as growth, development, adaptation to land, stomatal closure, drought tolerance, and response to pathogen infection. However, there is a lack of comprehensive identification and systematic analysis of SOT in cotton, especially in G. barbadense. In this study, we used bioinformatics methods to analyze the structural characteristics, phylogenetic relationships, gene structure, expression patterns, evolutionary relationships, selection pressure and stress response of SOT gene family members in G. barbadense. In this study, a total of 241 SOT genes were identified in four cotton species, among which 74 SOT gene members were found in G. barbadense. According to the phylogenetic tree, 241 SOT protein sequences were divided into five distinct subfamilies. We also mapped the physical locations of these genes on chromosomes and visualized the structural information of SOT genes in G. barbadense. We also predicted the cis-acting elements of the SOT gene in G. barbadense, and we identified the repetitive types and collinearity analysis of SOT genes in four cotton species. We calculated the Ka/Ks ratio between homologous gene pairs to elucidate the selective pressure between SOT genes. Transcriptome data were used to explore the expression patterns of SOT genes, and then qRT-PCR was used to detect the expression patterns of GBSOT4, GBSOT17 and GBSOT33 under FOV stress. WGCNA (weighted gene co-expression network analysis) showed that GB_A01G0479 (GBSOT4) belonged to the MEblue module, which may regulate the resistance mechanism of G. barbadense to FOV through plant hormones, signal transduction and glutathione metabolism. In addition, we conducted a VIGS (virus-induced gene silencing) experiment on GBSOT4, and the results showed that after FOV inoculation, the plants with a silenced target gene had more serious leaf wilting, drying and cracking than the control group, and the disease index of the plants with the silenced target gene was significantly higher than that of the control group. This suggests that GBSOT4 may be involved in protecting the production of G. barbadense from FOV infection. Subsequent metabolomics analysis showed that some flavonoid metabolites, such as Eupatorin-5-methylether (3'-hydroxy-5,6,7,4'-tetramethoxyflavone, were accumulated in cotton plants in response to FOV infection.
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Affiliation(s)
- Zhanlian Su
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (Z.S.); (Y.J.); (Z.J.); (P.L.); (Y.Q.)
| | - Yang Jiao
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (Z.S.); (Y.J.); (Z.J.); (P.L.); (Y.Q.)
- Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi 832000, China
| | - Zhengwen Jiang
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (Z.S.); (Y.J.); (Z.J.); (P.L.); (Y.Q.)
| | - Pengfei Liu
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (Z.S.); (Y.J.); (Z.J.); (P.L.); (Y.Q.)
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (Z.S.); (Y.J.); (Z.J.); (P.L.); (Y.Q.)
| | - Yanying Qu
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (Z.S.); (Y.J.); (Z.J.); (P.L.); (Y.Q.)
| | - Xiaojuan Deng
- College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China; (Z.S.); (Y.J.); (Z.J.); (P.L.); (Y.Q.)
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4
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Du P, Deng Q, Wang W, Garg V, Lu Q, Huang L, Wang R, Li H, Huai D, Chen X, Varshney RK, Hong Y, Liu H. scRNA-seq Reveals the Mechanism of Fatty Acid Desaturase 2 Mutation to Repress Leaf Growth in Peanut ( Arachis hypogaea L.). Cells 2023; 12:2305. [PMID: 37759528 PMCID: PMC10527976 DOI: 10.3390/cells12182305] [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: 06/14/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Fatty Acid Desaturase 2 (FAD2) controls the conversion of oleic acids into linoleic acids. Mutations in FAD2 not only increase the high-oleic content, but also repress the leaf growth. However, the mechanism by which FAD2 regulates the growth pathway has not been elucidated in peanut leaves with single-cell resolution. In this study, we isolated fad2 mutant leaf protoplast cells to perform single-cell RNA sequencing. Approximately 24,988 individual cells with 10,249 expressed genes were classified into five major cell types. A comparative analysis of 3495 differentially expressed genes (DEGs) in distinct cell types demonstrated that fad2 inhibited the expression of the cytokinin synthesis gene LOG in vascular cells, thereby repressing leaf growth. Further, pseudo-time trajectory analysis indicated that fad2 repressed leaf cell differentiation, and cell-cycle evidence displayed that fad2 perturbed the normal cell cycle to induce the majority of cells to drop into the S phase. Additionally, important transcription factors were filtered from the DEG profiles that connected the network involved in high-oleic acid accumulation (WRKY6), activated the hormone pathway (WRKY23, ERF109), and potentially regulated leaf growth (ERF6, MYB102, WRKY30). Collectively, our study describes different gene atlases in high-oleic and normal peanut seedling leaves, providing novel biological insights to elucidate the molecular mechanism of the high-oleic peanut-associated agronomic trait at the single-cell level.
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Affiliation(s)
- Puxuan Du
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou 510640, China; (P.D.); (Q.D.); (Q.L.); (L.H.); (R.W.); (H.L.); (X.C.)
| | - Quanqing Deng
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou 510640, China; (P.D.); (Q.D.); (Q.L.); (L.H.); (R.W.); (H.L.); (X.C.)
| | - Wenyi Wang
- College of Agriculture, South China Agriculture University, Guangzhou 510642, China;
| | - Vanika Garg
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University (MU), Murdoch, WA 6150, Australia; (V.G.); (R.K.V.)
| | - Qing Lu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou 510640, China; (P.D.); (Q.D.); (Q.L.); (L.H.); (R.W.); (H.L.); (X.C.)
| | - Lu Huang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou 510640, China; (P.D.); (Q.D.); (Q.L.); (L.H.); (R.W.); (H.L.); (X.C.)
| | - Runfeng Wang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou 510640, China; (P.D.); (Q.D.); (Q.L.); (L.H.); (R.W.); (H.L.); (X.C.)
| | - Haifen Li
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou 510640, China; (P.D.); (Q.D.); (Q.L.); (L.H.); (R.W.); (H.L.); (X.C.)
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan 430062, China;
| | - Xiaoping Chen
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou 510640, China; (P.D.); (Q.D.); (Q.L.); (L.H.); (R.W.); (H.L.); (X.C.)
| | - Rajeev K. Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University (MU), Murdoch, WA 6150, Australia; (V.G.); (R.K.V.)
| | - Yanbin Hong
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou 510640, China; (P.D.); (Q.D.); (Q.L.); (L.H.); (R.W.); (H.L.); (X.C.)
| | - Hao Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences (GDAAS), Guangzhou 510640, China; (P.D.); (Q.D.); (Q.L.); (L.H.); (R.W.); (H.L.); (X.C.)
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Peng Z, Rehman A, Li X, Jiang X, Tian C, Wang X, Li H, Wang Z, He S, Du X. Comprehensive Evaluation and Transcriptome Analysis Reveal the Salt Tolerance Mechanism in Semi-Wild Cotton ( Gossypium purpurascens). Int J Mol Sci 2023; 24:12853. [PMID: 37629034 PMCID: PMC10454576 DOI: 10.3390/ijms241612853] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Elevated salinity significantly threatens cotton growth, particularly during the germination and seedling stages. The utilization of primitive species of Gossypium hirsutum, specifically Gossypium purpurascens, has the potential to facilitate the restoration of genetic diversity that has been depleted due to selective breeding in modern cultivars. This investigation evaluated 45 G. purpurascens varieties and a salt-tolerant cotton variety based on 34 morphological, physiological, and biochemical indicators and comprehensive salt tolerance index values. This study effectively identified a total of 19 salt-tolerant and two salt-resistant varieties. Furthermore, transcriptome sequencing of a salt-tolerant genotype (Nayanmian-2; NY2) and a salt-sensitive genotype (Sanshagaopao-2; GP2) revealed 2776, 6680, 4660, and 4174 differentially expressed genes (DEGs) under 0.5, 3, 12, and 24 h of salt stress. Gene ontology enrichment analysis indicated that the DEGs exhibited significant enrichment in biological processes like metabolic (GO:0008152) and cellular (GO:0009987) processes. MAPK signaling, plant-pathogen interaction, starch and sucrose metabolism, plant hormone signaling, photosynthesis, and fatty acid metabolism were identified as key KEGG pathways involved in salinity stress. Among the DEGs, including NAC, MYB, WRKY, ERF, bHLH, and bZIP, transcription factors, receptor-like kinases, and carbohydrate-active enzymes were crucial in salinity tolerance. Weighted gene co-expression network analysis (WGCNA) unveiled associations of salt-tolerant genotypes with flavonoid metabolism, carbon metabolism, and MAPK signaling pathways. Identifying nine hub genes (MYB4, MYB105, MYB36, bZIP19, bZIP43, FRS2 SMARCAL1, BBX21, F-box) across various intervals offered insights into the transcriptional regulation mechanism of salt tolerance in G. purpurascens. This study lays the groundwork for understanding the important pathways and gene networks in response to salt stress, thereby providing a foundation for enhancing salt tolerance in upland cotton.
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Affiliation(s)
- Zhen Peng
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572025, China
| | - Abdul Rehman
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Xiawen Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Xuran Jiang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Chunyan Tian
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Xiaoyang Wang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
| | - Hongge Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Zhenzhen Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
| | - Shoupu He
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572025, China
| | - Xiongming Du
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Z.P.); (A.R.); (X.L.); (X.J.); (C.T.); (X.W.); (H.L.)
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China;
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572025, China
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Kabir N, Wang X, Lu L, Qanmber G, Liu L, Si A, Zhang L, Cao W, Yang Z, Yu Y, Liu Z. Functional characterization of TBL genes revealed the role of GhTBL7 and GhTBL58 in cotton fiber elongation. Int J Biol Macromol 2023; 241:124571. [PMID: 37100328 DOI: 10.1016/j.ijbiomac.2023.124571] [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: 12/06/2022] [Revised: 04/01/2023] [Accepted: 04/14/2023] [Indexed: 04/28/2023]
Abstract
TBL (Trichome Birefringence Like) gene family members are involved in trichome initiation and xylan acetylation in several plant species. In our research, we identified 102 TBLs from G. hirsutum. The phylogenetic tree classified TBL genes into five groups. Collinearity analysis of TBL genes indicated 136 paralogous gene pairs in G. hirsutum. Gene duplication indicated that WGD or segmental duplication contributed to the GhTBL gene family expansion. Promoter cis-elements of GhTBLs were related to growth and development, seed-specific regulation, light, and stress responses. GhTBL genes (GhTBL7, GhTBL15, GhTBL21, GhTBL25, GhTBL45, GhTBL54, GhTBL67, GhTBL72, and GhTBL77) exhibited upregulated response under exposure to cold, heat, NaCl, and PEG. GhTBL genes exhibited high expression during fiber development stages. Two GhTBL genes (GhTBL7 and GhTBL58) showed differential expression at 10 DPA fiber, as 10 DPA is a fast fiber elongation stage and fiber elongation is a very important stage of cotton fiber development. Subcellular localization of GhTBL7 and GhTBL58 revealed that these genes reside inside the cell membrane. Promoter GUS activity of GhTBL7 and GhTBL58 exhibited deep staining in roots. To further validate the role of these genes in cotton fiber elongation, we silenced these genes and observed a significant reduction in the fiber length at 10 DPA. In conclusion, the functional study of cell membrane-associated genes (GhTBL7 and GhTBL58) showed deep staining in root tissues and potential function during cotton fiber elongation at 10 DPA fiber.
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Affiliation(s)
- Nosheen Kabir
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xuwen Wang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Ghulam Qanmber
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Le Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Aijun Si
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China
| | - Lian Zhang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China
| | - Wei Cao
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China
| | - Zuoren Yang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Yu Yu
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute, Xinjiang Academy Agricultural and Reclamation Science, Shihezi 832003, China.
| | - Zhao Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China.
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7
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Shuya M, Le L, Huiyun S, Yu G, Yujun L, Qanmber G. Genomic identification of cotton SAC genes branded ovule and stress-related key genes in Gossypium hirsutum. FRONTIERS IN PLANT SCIENCE 2023; 14:1123745. [PMID: 36818879 PMCID: PMC9935941 DOI: 10.3389/fpls.2023.1123745] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
SAC genes have been identified to play a variety of biological functions and responses to various stresses. Previously, SAC genes have been recognized in animals and Arabidopsis. For the very first time, we identified 157 SAC genes in eight cotton species including three diploids and five tetraploids with 23 SAC members in G. hirsutum. Evolutionary analysis classified all cotton SAC gene family members into five distinct groups. Cotton SAC genes showed conserved sequence logos and WGD or segmental duplication. Multiple synteny and collinearity analyses revealed gene family expansion and purifying selection pressure during evolution. G. hirsutum SAC genes showed uneven chromosomal distribution, multiple exons/introns, conserved protein motifs, and various growth and stress-related cis-elements. Expression pattern analysis revealed three GhSAC genes (GhSAC3, GhSAC14, and GhSAC20) preferentially expressed in flower, five genes (GhSAC1, GhSAC6, GhSAC9, GhSAC13, and GhSAC18) preferentially expressed in ovule and one gene (GhSAC5) preferentially expressed in fiber. Similarly, abiotic stress treatment verified that GhSAC5 was downregulated under all stresses, GhSAC6 and GhSAC9 were upregulated under NaCl treatment, and GhSAC9 and GhSAC18 were upregulated under PEG and heat treatment respectively. Overall, this study identified key genes related to flower, ovule, and fiber development and important genetic material for breeding cotton under abiotic stress conditions.
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Affiliation(s)
- Ma Shuya
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Liu Le
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Shi Huiyun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Gu Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Li Yujun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education, Xinjiang Agricultural University, Urumqi, China
| | - Ghulam Qanmber
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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Cui C, Ma Z, Wan H, Gao J, Zhou B. GhALKBH10 negatively regulates salt tolerance in cotton. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 192:87-100. [PMID: 36215791 DOI: 10.1016/j.plaphy.2022.09.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/28/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The alpha-ketoglutarate-dependent dioxygenase (AlkB) gene family plays an essential role in regulating plant development and stress response. However, the AlkB gene family is still not well understood in cotton. In this study, 40 AlkB genes in cotton and Arabidopsis are identified and classified into three classes based on phylogenetic analysis. Their protein motifs and exon/intron structures are highly conserved. Chromosomal localization and synteny analysis suggested that segmental or whole-genome duplication and polyploidization events contributed to the expansion of the cotton AlkB gene family. Furthermore, the AlkB genes showed dynamic spatiotemporal expression patterns and diverse responses to abiotic stresses. Among them, GhALKBH10 was down-regulated under various abiotic stresses and its subcellular expression was localized in cytoplasm and nucleus. Silencing GhALKBH10 in cotton increased antioxidant capacity and reduced cytoplasmic Na+ concentration, thereby improved the plant tolerance to salinity. Conversely, overexpression (OE) of GhALKBH10 in Arabidopsis markedly weakened the plant tolerance to salinity. The global m6A levels measured in VIGS and OE transgenic lines showed that they were significantly higher in TRV: GhALKBH10 plants (VIGS) than in TRV: 00 plants but significantly lower in OE plants than wild-type plants under salt stress, which could be considered as a potential m6A demethylase in cotton. Our results suggest that the GhALKBH10 gene negatively regulates salt tolerance in plants, which provides information of the cotton AlkB family and an understanding of GhALKBH10 function under salt condition as well as a new gene for salt-tolerant cotton breeding.
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Affiliation(s)
- Changjiang Cui
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Zhifeng Ma
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Hui Wan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Jianbo Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production Co-sponsored By Province and Ministry, Nanjing Agricultural University, Nanjing, China.
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9
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Wei L, Zhang R, Zhang M, Xia G, Liu S. Functional analysis of long non-coding RNAs involved in alkaline stress responses in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5698-5714. [PMID: 35595260 DOI: 10.1093/jxb/erac211] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Saline-alkali soil is a major environmental problem affecting crop productivity. One of the most effective approaches to combat it is to breed stress-tolerant plants through genetic engineering. Shanrong No. 4 (SR4) is an alkaline-tolerant cultivar of bread wheat (Triticum aestivum) derived from asymmetric somatic hybridization between the common wheat cultivar Jinan 177 (JN177) and tall wheatgrass. In this study, we aimed to explore the structure and function of alkalinity stress-responsive long non-coding RNAs (lncRNAs) in wheat. Sequencing was employed to identify the lncRNAs associated with stress tolerance and their corresponding targets. Approximately 19 000 novel lncRNA sequences were detected in SR4 and JN177. Upon exposure to alkaline stress, SR4 differentially expressed 5691 lncRNAs, whilst JN177 differentially expressed 5932. We selected five of them (L0760, L6247, L0208, L2098, and L3065) and generated seedlings of transiently knocked down strains using the virus-induced gene-silencing method. Knockdown of L0760 and L2098 caused the plants to exhibit sensitivity to alkaline stress, whereas knockdown of L6247, L0208, and L3065 increased the ability of plants to tolerate alkaline stress. We constructed lncRNA-miRNA-target-mRNA networks and alkali-response-related lncRNA-target-mRNA association networks to analyse the functions of lncRNAs. Collectively, our results demonstrate that lncRNAs may perform different roles under alkaline stress conditions.
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Affiliation(s)
- Lin Wei
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Rong Zhang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Min Zhang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Guangmin Xia
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Shuwei Liu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
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Liu K, Kabir N, Wei Z, Sun Z, Wang J, Qi J, Liu M, Liu J, Zhou K. Genome-wide identification and expression profile of GhGRF gene family in Gossypium hirsutum L.. PeerJ 2022; 10:e13372. [PMID: 35586135 PMCID: PMC9109687 DOI: 10.7717/peerj.13372] [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: 11/18/2021] [Accepted: 04/12/2022] [Indexed: 01/13/2023] Open
Abstract
Background Cotton is the primary source of renewable natural fiber in the textile industry and an important biodiesel crop. Growth regulating factors (GRFs) are involved in regulating plant growth and development. Methods Using genome-wide analysis, we identified 35 GRF genes in Gossypium hirsutum. Results Chromosomal location information revealed an uneven distribution of GhGRF genes, with maximum genes on chromosomes A02, A05, and A12 from the At sub-genome and their corresponding D05 and D12 from the Dt sub-genome. In the phylogenetic tree, 35 GRF genes were divided into five groups, including G1, G2, G3, G4, and G5. The majority of GhGRF genes have two to three introns and three to four exons, and their deduced proteins contained conserved QLQ and WRC domains in the N-terminal end of GRFs in Arabidopsis and rice. Sequence logos revealed that GRF genes were highly conserved during the long-term evolutionary process. The CDS of the GhGRF gene can complement MiRNA396a. Moreover, most GhGRF genes transcripts developed high levels of ovules and fibers. Analyses of promoter cis-elements and expression patterns indicated that GhGRF genes play an essential role in regulating plant growth and development by coordinating the internal and external environment and multiple hormone signaling pathways. Our analysis indicated that GhGRFs are ideal target genes with significant potential for improving the molecular structure of cotton.
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Affiliation(s)
- Kun Liu
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhenzhen Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jian Wang
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Jing Qi
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Miaoyang Liu
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Kehai Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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11
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Cytokinins: Wide-Spread Signaling Hormones from Plants to Humans with High Medical Potential. Nutrients 2022; 14:nu14071495. [PMID: 35406107 PMCID: PMC9003334 DOI: 10.3390/nu14071495] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 02/04/2023] Open
Abstract
Nature is a rich source of biologically active novel compounds. Sixty years ago, the plant hormones cytokinins were first discovered. These play a major role in cell division and cell differentiation. They affect organogenesis in plant tissue cultures and contribute to many other physiological and developmental processes in plants. Consequently, the effect of cytokinins on mammalian cells has caught the attention of researchers. Many reports on the contribution and potential of cytokinins in the therapy of different human diseases and pathophysiological conditions have been published and are reviewed here. We compare cytokinin effects and pathways in plants and mammalian systems and highlight the most important biological activities. We present the strong profile of the biological actions of cytokinins and their possible therapeutic applications.
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Chen L, Jameson GB, Guo Y, Song J, Jameson PE. The LONELY GUY gene family: from mosses to wheat, the key to the formation of active cytokinins in plants. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:625-645. [PMID: 35108444 PMCID: PMC8989509 DOI: 10.1111/pbi.13783] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/06/2022] [Accepted: 01/13/2022] [Indexed: 05/19/2023]
Abstract
LONELY GUY (LOG) was first identified in a screen of rice mutants with defects in meristem maintenance. In plants, LOG codes for cytokinin riboside 5'-monophosphate phosphoribohydrolase, which converts inactive cytokinin nucleotides directly to the active free bases. Many enzymes with the PGGxGTxxE motif have been misannotated as lysine decarboxylases; conversely not all enzymes containing this motif are cytokinin-specific LOGs. As LOG mutants clearly impact yield in rice, we investigated the LOG gene family in bread wheat. By interrogating the wheat (Triticum aestivum) genome database, we show that wheat has multiple LOGs. The close alignment of TaLOG1, TaLOG2 and TaLOG6 with the X-ray structures of two functional Arabidopsis thaliana LOGs allows us to infer that the wheat LOGs 1-11 are functional LOGs. Using RNA-seq data sets, we assessed TaLOG expression across 70 tissue types, their responses to various stressors, the pattern of cis-regulatory elements (CREs) and intron/exon patterns. TaLOG gene family members are expressed variously across tissue types. When the TaLOG CREs are compared with those of the cytokinin dehydrogenases (CKX) and glucosyltransferases (CGT), there is close alignment of CREs between TaLOGs and TaCKXs reflecting the key role of CKX in maintaining cytokinin homeostasis. However, we suggest that the main homeostatic mechanism controlling cytokinin levels in response to biotic and abiotic challenge resides in the CGTs, rather than LOG or CKX. However, LOG transgenics and identified mutants in rice variously impact yield, providing interesting avenues for investigation in wheat.
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Affiliation(s)
- Lei Chen
- School of Life SciencesYantai UniversityYantaiChina
| | | | - Yichu Guo
- School of Life SciencesYantai UniversityYantaiChina
| | - Jiancheng Song
- School of Life SciencesYantai UniversityYantaiChina
- Yantai Jien Biological Science & Technology LtdYEDAYantaiChina
| | - Paula E. Jameson
- School of Life SciencesYantai UniversityYantaiChina
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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13
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Kabir N, Zhang X, Liu L, Qanmber G, Zhang L, Wang YX, Sun Z, Zhao N, Wang G. RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum. BMC Genomics 2022; 23:40. [PMID: 35012446 PMCID: PMC8744286 DOI: 10.1186/s12864-021-08248-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/09/2021] [Indexed: 12/25/2022] Open
Abstract
Background RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton. Results Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes. Conclusions Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08248-z.
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Affiliation(s)
- Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xin Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Le Liu
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lian Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Henan, 450001, Zhengzhou, China
| | - Yu Xuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100122, China
| | - Na Zhao
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
| | - Gang Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Henan, 450001, Zhengzhou, China.
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14
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Kabir N, Lin H, Kong X, Liu L, Qanmber G, Wang Y, Zhang L, Sun Z, Yang Z, Yu Y, Zhao N. Identification, evolutionary analysis and functional diversification of RAV gene family in cotton (G. hirsutum L.). PLANTA 2021; 255:14. [PMID: 34862931 DOI: 10.1007/s00425-021-03782-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Genome wide analysis, expression pattern analysis, and functional characterization of RAV genes highlight their roles in roots, stem development and hormonal response. RAV (Related to ABI3 and VP1) gene family members have been involved in tissues/organs growth and hormone signaling in various plant species. Here, we identified 247 RAVs from 12 different species with 33 RAV genes from G. hirsutum. Phylogenetic analysis classified RAV genes into four distinct groups. Analysis of gene structure showed that most GhRAVs lack introns. Motif distribution pattern and protein sequence logos indicated that GhRAV genes were highly conserved during the process of evolution. Promotor cis-acting elements revealed that promotor regions of GhRAV genes encode numerous elements related to plant growth, abiotic stresses and phytohormones. Chromosomal location information showed uneven distribution of 33 GhRAV genes on different chromosomes. Collinearity analysis identified 628 and 52 orthologous/ paralogous gene pairs in G. hirsutum and G. barbadense, respectively. Ka/Ks values indicated that GhRAV and GbRAV genes underwent strong purifying selection pressure. Selecton model and codon model selection revealed that GhRAV amino acids were under purifying selection and adaptive evolution exists among GhRAV proteins. Three dimensional structure of GhRAVs indicated the presence of numerous alpha helix and beta-barrels. Expression level revealed that some GhRAV genes exhibited high expression in roots (GhRAV3, GhRAV4, GhRAV11, GhRAV18, GhRAV20 and GhRAV30) and stem (GhRAV3 and GhRAV18), indicating their potential role in roots and stem development. GhRAV genes can be regulated by phytohormonal stresses (BL, JA and IAA). Our study provides a reference for future studies related to the functional analysis of GhRAVs in cotton.
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Affiliation(s)
- Nosheen Kabir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hai Lin
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Xianhui Kong
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Le Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - YuXuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Lian Zhang
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Zhuojing Sun
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs, Beijing, 100122, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Yu Yu
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture and Rural Affairs, Cotton Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
| | - Na Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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Systematic Characterization of TCP Gene Family in Four Cotton Species Revealed That GhTCP62 Regulates Branching in Arabidopsis. BIOLOGY 2021; 10:biology10111104. [PMID: 34827097 PMCID: PMC8614845 DOI: 10.3390/biology10111104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 01/14/2023]
Abstract
TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play an essential role in regulating various physiological and biochemical functions during plant growth. However, the function of TCP transcription factors in G. hirsutum has not yet been studied. In this study, we performed genome-wide identification and correlation analysis of the TCP transcription factor family in G. hirsutum. We identified 72 non-redundant GhTCP genes and divided them into seven subfamilies, based on phylogenetic analysis. Most GhTCP genes in the same subfamily displayed similar exon and intron structures and featured highly conserved motif structures in their subfamily. Additionally, the pattern of chromosomal distribution demonstrated that GhTCP genes were unevenly distributed on 24 out of 26 chromosomes, and that fragment replication was the main replication event of GhTCP genes. In TB1 sub-family genes, GhTCP62 was highly expressed in the axillary buds, suggesting that GhTCP62 significantly affected cotton branching. Additionally, subcellular localization results indicated that GhTCP62 is located in the nucleus and possesses typical transcription factor characteristics. The overexpression of GhTCP62 in Arabidopsis resulted in fewer rosette-leaf branches and cauline-leaf branches. Furthermore, the increased expression of HB21 and HB40 genes in Arabidopsis plants overexpressing GhTCP62 suggests that GhTCP62 may regulate branching by positively regulating HB21 and HB40.
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