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Tisarum R, Theerawitaya C, Praseartkul P, Chungloo D, Ullah H, Himanshu SK, Datta A, Cha-Um S. Screening cotton genotypes for their drought tolerance ability based on the expression level of dehydration-responsive element-binding protein and proline biosynthesis-related genes and morpho-physio-biochemical responses. PROTOPLASMA 2024; 261:783-798. [PMID: 38376598 DOI: 10.1007/s00709-024-01935-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024]
Abstract
Drought stress adversely affects growth, development, productivity, and fiber quality of cotton (Gossypium hirsutum L). Breeding strategies to enhance drought tolerance require an improved knowledge of plant drought responses necessitating proper identification of drought-tolerant genotypes of crops, including cotton. The objective of this study was to classify the selected cotton genotypes for their drought tolerance ability based on morpho-physio-biochemical traits using Hierarchical Ward's cluster analysis. Five genotypes of cotton (Takfa 3, Takfa 6, Takfa 7, Takfa 84-4, and Takfa 86-5) were selected as plant materials, and were grown under well-watered (WW; 98 ± 2% field capacity) and water-deficit (WD; 50 ± 2% field capacity) conditions for 16 days during the flower initiation stage. Data on morpho-physio-biochemical parameters and gene expression levels for these parameters were collected, and subsequently genotypes were classified either as a drought tolerant or drought susceptible one. Upregulation of GhPRP (proline-rich protein), GhP5CS (Δ1-pyrroline-5-carboxylate synthetase), and GhP5CR (Δ1-pyrroline-5-carboxylate reductase) in relation to free proline enrichment was observed in Takfa 3 genotype under WD condition. An accumulation of free proline, total soluble sugar, and potassium in plants under WD conditions was detected, which played a key role as major osmolytes controlling cellular osmotic potential. Magnesium and calcium concentrations were also enriched in leaves under WD conditions, functioning as essential elements and regulating photosynthetic abilities. Leaf greenness, net photosynthetic rate, stomatal conductance, and transpiration rate were also declined under WD conditions, leading to growth retardation, especially aboveground traits of Takfa 6, Takfa 7, Takfa 84-4, and Takfa 86-5 genotypes. An increase in leaf temperature (1.1 - 4.0 °C) and crop water stress index (CWSI > 0.75) in relation to stomatal closure and reduced transpiration rate was recorded in cotton genotypes under WD conditions compared with WW conditions. Based on the increase of free proline, soluble sugar, leaf temperature, and CWSI, as well as the decrease of aboveground growth traits and physiological attributes, five genotypes were categorized into two cluster groups: drought tolerant (Takfa 3) and drought susceptible (Takfa 6, Takfa 7, Takfa 84-4, and Takfa 86-5). The identified drought-tolerant cotton genotype, namely, Takfa 3, may be grown in areas experiencing drought conditions. It is recommended to further validate the yield traits of Takfa 3 under rainfed field conditions in drought-prone environments.
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Affiliation(s)
- Rujira Tisarum
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Cattarin Theerawitaya
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Patchara Praseartkul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Daonapa Chungloo
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Hayat Ullah
- Agricultural Systems and Engineering, Department of Food, Agriculture and Bioresources, School of Environment, Resources and Development, Asian Institute of Technology, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Sushil Kumar Himanshu
- Agricultural Systems and Engineering, Department of Food, Agriculture and Bioresources, School of Environment, Resources and Development, Asian Institute of Technology, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Avishek Datta
- Agricultural Systems and Engineering, Department of Food, Agriculture and Bioresources, School of Environment, Resources and Development, Asian Institute of Technology, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Suriyan Cha-Um
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand.
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Liu H, Lin M, Zhou D, Liu B, Li X, Wang H, Bi X. Characterization of the m 6A gene family in switchgrass and functional analysis of PvALKBH10 during flowering. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108781. [PMID: 38820914 DOI: 10.1016/j.plaphy.2024.108781] [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: 02/18/2024] [Revised: 04/30/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
N6-methyladenosine (m6A), a nucleotide modification that is frequently seen in RNA, plays a crucial role in plant growth, development and stress resistance. However, the m6A regulatory machinery in switchgrass (Panicum virgatum L.), a model plant for cellulose-to-ethanol conversion, remains largely unknown. In this study, we identified 57 candidate genes involved in m6A-regulation in the switchgrass genome, and analyzed their chromosomal distribution, evolutionary relationships, and functions. Notably, we observed distinct gene expression patterns under salt and drought stress, with salt stress inducing writer and eraser genes, alongside drought stress predominantly affecting reader genes. Additionally, we knocked out PvALKBH10, an m6A demethylase gene, via CRISPR/Cas9 and found its potential function in controlling flowering time. This study provides insight into the genomic organization and evolutionary features of m6A-associated putative genes in switchgrass, and therefore serves as the basis for further functional studies.
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Affiliation(s)
- Huayue Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mengzhuo Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Die Zhou
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Bowen Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xue Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hui Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiaojing Bi
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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Liu H, Lin M, Wang H, Li X, Zhou D, Bi X, Zhang Y. N 6-methyladenosine analysis unveils key mechanisms underlying long-term salt stress tolerance in switchgrass (Panicum virgatum). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112023. [PMID: 38320658 DOI: 10.1016/j.plantsci.2024.112023] [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: 10/12/2023] [Revised: 01/15/2024] [Accepted: 02/01/2024] [Indexed: 02/08/2024]
Abstract
N6-methyladenosine (m6A) RNA modification is critical for plant growth, development, and environmental stress response. While short-term stress impacts on m6A are well-documented, the consequences of prolonged stress remain underexplored. This study conducts a thorough transcriptome-wide analysis of m6A modifications following 28-day exposure to 200 mM NaCl. We detected 11,149 differentially expressed genes (DEGs) and 12,936 differentially methylated m6A peaks, along with a global decrease in m6A levels. Notably, about 62% of m6A-modified DEGs, including demethylase genes like PvALKBH6_N, PvALKBH9_K, and PvALKBH10_N, showed increased expression and reduced m6A peaks, suggesting that decreased m6A methylation may enhance gene expression under salt stress. Consistent expression and methylation patterns were observed in key genes related to ion homeostasis (e.g., H+-ATPase 1, High-affinity K+transporter 5), antioxidant defense (Catalase 1/2, Copper/zinc superoxide dismutase 2, Glutathione synthetase 1), and osmotic regulation (delta 1-pyrroline-5-carboxylate synthase 2, Pyrroline-5-carboxylate reductase). These findings provide insights into the adaptive mechanisms of switchgrass under long-term salt stress and highlight the potential of regulating m6A modifications as a novel approach for crop breeding strategies focused on stress resistance.
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Affiliation(s)
- Huayue Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Mengzhuo Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hui Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xue Li
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Die Zhou
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaojing Bi
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Yunwei Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China.
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Tian Y, Fang Y, Zhang K, Zhai Z, Yang Y, He M, Cao X. Applications of Virus-Induced Gene Silencing in Cotton. PLANTS (BASEL, SWITZERLAND) 2024; 13:272. [PMID: 38256825 PMCID: PMC10819639 DOI: 10.3390/plants13020272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/02/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024]
Abstract
Virus-induced gene silencing (VIGS) is an RNA-mediated reverse genetics technique that has become an effective tool to investigate gene function in plants. Cotton is one of the most important economic crops globally. In the past decade, VIGS has been successfully applied in cotton functional genomic studies, including those examining abiotic and biotic stress responses and vegetative and reproductive development. This article summarizes the traditional vectors used in the cotton VIGS system, the visible markers used for endogenous gene silencing, the applications of VIGS in cotton functional genomics, and the limitations of VIGS and how they can be addressed in cotton.
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Affiliation(s)
- Yue Tian
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Y.T.); (Y.F.); (K.Z.); (Z.Z.); (Y.Y.); (M.H.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Yao Fang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Y.T.); (Y.F.); (K.Z.); (Z.Z.); (Y.Y.); (M.H.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Kaixin Zhang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Y.T.); (Y.F.); (K.Z.); (Z.Z.); (Y.Y.); (M.H.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Zeyang Zhai
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Y.T.); (Y.F.); (K.Z.); (Z.Z.); (Y.Y.); (M.H.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Yujie Yang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Y.T.); (Y.F.); (K.Z.); (Z.Z.); (Y.Y.); (M.H.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Meiyu He
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Y.T.); (Y.F.); (K.Z.); (Z.Z.); (Y.Y.); (M.H.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Xu Cao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China; (Y.T.); (Y.F.); (K.Z.); (Z.Z.); (Y.Y.); (M.H.)
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
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Li B, Feng C, Zhang W, Sun S, Yue D, Zhang X, Yang X. Comprehensive non-coding RNA analysis reveals specific lncRNA/circRNA-miRNA-mRNA regulatory networks in the cotton response to drought stress. Int J Biol Macromol 2023; 253:126558. [PMID: 37659489 DOI: 10.1016/j.ijbiomac.2023.126558] [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: 03/06/2023] [Revised: 07/29/2023] [Accepted: 08/20/2023] [Indexed: 09/04/2023]
Abstract
Root and leaf are essential organs of plants in sensing and responding to drought stress. However, comparative knowledge of non-coding RNAs (ncRNAs) of root and leaf tissues in the regulation of drought response in cotton is limited. Here, we used deep sequencing data of leaf and root tissues of drought-resistant and drought-sensitive cotton varieties for identifying miRNAs, lncRNAs and circRNAs. A total of 1531 differentially expressed (DE) ncRNAs was identified, including 77 DE miRNAs, 1393 DE lncRNAs and 61 DE circRNAs. The tissue-specific and variety-specific competing endogenous RNA (ceRNA) networks of DE lncRNA-miRNA-mRNA response to drought were constructed. Furthermore, the novel drought-responsive lncRNA 1 (DRL1), specifically and differentially expressed in root, was verified to positively affect phenotypes of cotton seedlings under drought stress, competitively binding to miR477b with GhNAC1 and GhSCL3. In addition, we also constructed another ceRNA network consisting of 18 DE circRNAs, 26 DE miRNAs and 368 DE mRNAs. Fourteen circRNA were characterized, and a novel molecular regulatory system of circ125- miR7484b/miR7450b was proposed under drought stress. Our findings revealed the specificity of ncRNA expression in tissue- and variety-specific patterns involved in the response to drought stress, and uncovered novel regulatory pathways and potentially effective molecules in genetic improvement for crop drought resistance.
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Affiliation(s)
- Baoqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
| | - Cheng Feng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Wenhao Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Simin Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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Shen H, Zhou Y, Liao C, Xie Q, Chen G, Hu Z, Wu T. The AlkB Homolog SlALKBH10B Negatively Affects Drought and Salt Tolerance in Solanum lycopersicum. Int J Mol Sci 2023; 25:173. [PMID: 38203345 PMCID: PMC10778744 DOI: 10.3390/ijms25010173] [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: 10/26/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
ALKBH proteins, the homologs of Escherichia coli AlkB dioxygenase, constitute a single-protein repair system that safeguards cellular DNA and RNA against the harmful effects of alkylating agents. ALKBH10B, the first discovered N6-methyladenosine (m6A) demethylase in Arabidopsis (Arabidopsis thaliana), has been shown to regulate plant growth, development, and stress responses. However, until now, the functional role of the plant ALKBH10B has solely been reported in arabidopsis, cotton, and poplar, leaving its functional implications in other plant species shrouded in mystery. In this study, we identified the AlkB homolog SlALKBH10B in tomato (Solanum lycopersicum) through phylogenetic and gene expression analyses. SlALKBH10B exhibited a wide range of expression patterns and was induced by exogenous abscisic acid (ABA) and abiotic stresses. By employing CRISPR/Cas9 gene editing techniques to knock out SlALKBH10B, we observed an increased sensitivity of mutants to ABA treatment and upregulation of gene expression related to ABA synthesis and response. Furthermore, the Slalkbh10b mutants displayed an enhanced tolerance to drought and salt stress, characterized by higher water retention, accumulation of photosynthetic products, proline accumulation, and lower levels of reactive oxygen species and cellular damage. Collectively, these findings provide insights into the negative impact of SlALKBH10B on drought and salt tolerance in tomato plant, expanding our understanding of the biological functionality of SlALKBH10B.
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Affiliation(s)
- Hui Shen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Ying Zhou
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
| | - Changguang Liao
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
| | - Ting Wu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China; (H.S.); (Y.Z.); (C.L.); (Q.X.); (G.C.)
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