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Kaur R, Gupta S, Tripathi V, Bharadwaj A. Unravelling the secrets of soil microbiome and climate change for sustainable agroecosystems. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01194-9. [PMID: 39249146 DOI: 10.1007/s12223-024-01194-9] [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: 03/15/2024] [Accepted: 08/20/2024] [Indexed: 09/10/2024]
Abstract
The soil microbiota exhibits an important function in the ecosystem, and its response to climate change is of paramount importance for sustainable agroecosystems. The macronutrients, micronutrients, and additional constituents vital for the growth of plants are cycled biogeochemically under the regulation of the soil microbiome. Identifying and forecasting the effect of climate change on soil microbiomes and ecosystem services is the need of the hour to address one of the biggest global challenges of the present time. The impact of climate change on the structure and function of the soil microbiota is a major concern, explained by one or more sustainability factors around resilience, reluctance, and rework. However, the past research has revealed that microbial interventions have the potential to regenerate soils and improve crop resilience to climate change factors. The methods used therein include using soil microbes' innate capacity for carbon sequestration, rhizomediation, bio-fertilization, enzyme-mediated breakdown, phyto-stimulation, biocontrol of plant pathogens, antibiosis, inducing the antioxidative defense pathways, induced systemic resistance response (ISR), and releasing volatile organic compounds (VOCs) in the host plant. Microbial phytohormones have a major role in altering root shape in response to exposure to drought, salt, severe temperatures, and heavy metal toxicity and also have an impact on the metabolism of endogenous growth regulators in plant tissue. However, shelf life due to the short lifespan and storage time of microbial formulations is still a major challenge, and efforts should be made to evaluate their effectiveness in crop growth based on climate change. This review focuses on the influence of climate change on soil physico-chemical status, climate change adaptation by the soil microbiome, and its future implications.
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Affiliation(s)
- Rasanpreet Kaur
- Department of Biotechnology, IAH, GLA University, Mathura, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Saurabh Gupta
- Department of Biotechnology, IAH, GLA University, Mathura, India.
| | - Vishal Tripathi
- Department of Biotechnology, Graphic Era (Deemed to Be University), Dehradun, 248002, Uttarakhand, India.
| | - Alok Bharadwaj
- Department of Biotechnology, IAH, GLA University, Mathura, India
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2
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Yan T, Shu X, Ning C, Li Y, Wang Z, Wang T, Zhuang W. Functions and Regulatory Mechanisms of bHLH Transcription Factors during the Responses to Biotic and Abiotic Stresses in Woody Plants. PLANTS (BASEL, SWITZERLAND) 2024; 13:2315. [PMID: 39204751 PMCID: PMC11360703 DOI: 10.3390/plants13162315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/06/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Environmental stresses, including abiotic and biotic stresses, have complex and diverse effects on the growth and development of woody plants, which have become a matter of contention due to concerns about the outcomes of climate change on plant resources, genetic diversity, and world food safety. Plant basic helix-loop-helix (bHLH) transcription factors (TFs) are involved in a variety of physiological processes and play an important role in biotic and abiotic stress responses of woody plants. In recent years, an increasing body of studies have been conducted on the bHLH TFs in woody plants, and the roles of bHLH TFs in response to various stresses are increasingly clear and precise. Therefore, it is necessary to conduct a systematic and comprehensive review of the progress of the research of woody plants. In this review, the structural characteristics, research history and roles in the plant growth process of bHLH TFs are summarized, the gene families of bHLH TFs in woody plants are summarized, and the roles of bHLH TFs in biotic and abiotic stresses in woody plants are highlighted. Numerous studies mentioned in this review have shown that bHLH transcription factors play a crucial role in the response of woody plants to biotic and abiotic stresses. This review serves as a reference for further studies about enhancing the stress resistance and breeding of woody plants. Also, the future possible research directions of bHLH TFs in response to various stresses in woody plants will be discussed.
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Affiliation(s)
- Tengyue Yan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (T.Y.)
| | - Xiaochun Shu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (T.Y.)
| | - Chuanli Ning
- Yantai Agricultural Technology Extension Center, Yantai 264001, China
| | - Yuhang Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (T.Y.)
| | - Zhong Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (T.Y.)
| | - Tao Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (T.Y.)
| | - Weibing Zhuang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Memorial Sun Yat-Sen), Nanjing 210014, China; (T.Y.)
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Khan N, Choi SH, Lee CH, Qu M, Jeon JS. Photosynthesis: Genetic Strategies Adopted to Gain Higher Efficiency. Int J Mol Sci 2024; 25:8933. [PMID: 39201620 PMCID: PMC11355022 DOI: 10.3390/ijms25168933] [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: 07/10/2024] [Revised: 08/11/2024] [Accepted: 08/13/2024] [Indexed: 09/02/2024] Open
Abstract
The global challenge of feeding an ever-increasing population to maintain food security requires novel approaches to increase crop yields. Photosynthesis, the fundamental energy and material basis for plant life on Earth, is highly responsive to environmental conditions. Evaluating the operational status of the photosynthetic mechanism provides insights into plants' capacity to adapt to their surroundings. Despite immense effort, photosynthesis still falls short of its theoretical maximum efficiency, indicating significant potential for improvement. In this review, we provide background information on the various genetic aspects of photosynthesis, explain its complexity, and survey relevant genetic engineering approaches employed to improve the efficiency of photosynthesis. We discuss the latest success stories of gene-editing tools like CRISPR-Cas9 and synthetic biology in achieving precise refinements in targeted photosynthesis pathways, such as the Calvin-Benson cycle, electron transport chain, and photorespiration. We also discuss the genetic markers crucial for mitigating the impact of rapidly changing environmental conditions, such as extreme temperatures or drought, on photosynthesis and growth. This review aims to pinpoint optimization opportunities for photosynthesis, discuss recent advancements, and address the challenges in improving this critical process, fostering a globally food-secure future through sustainable food crop production.
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Affiliation(s)
- Naveed Khan
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea; (N.K.); (S.-H.C.)
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
| | - Seok-Hyun Choi
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea; (N.K.); (S.-H.C.)
| | - Choon-Hwan Lee
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea;
- Department of Molecular Biology, Pusan National University, Busan 46241, Republic of Korea
| | - Mingnan Qu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea; (N.K.); (S.-H.C.)
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Wang Y, Zhang M, Wu C, Chen C, Meng L, Zhang G, Zhuang K, Shi Q. SlWRKY51 regulates proline content to enhance chilling tolerance in tomato. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39148214 DOI: 10.1111/pce.15081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/09/2024] [Accepted: 07/30/2024] [Indexed: 08/17/2024]
Abstract
Chilling stress is a major environmental factor that significantly reduces crop production. To adapt to chilling stress, plants activate a series of cellular responses and accumulate an array of metabolites, particularly proline. Here, we report that the transcription factor SlWRKY51 increases proline contents in tomato (Solanum lycopersicum) under chilling stress. SlWRKY51 expression is induced under chilling stress. Knockdown or knockout of SlWRKY51 led to chilling-sensitive phenotypes, with lower photosynthetic capacity and more reactive oxygen species (ROS) accumulation than the wild type (WT). The proline contents were significantly reduced in SlWRKY51 knockdown and knockout lines under chilling stress, perhaps explaining the phenotypes of these lines. D-1-pyrroline-5-carboxylate synthetase (P5CS), which catalyses the rate-limiting step of proline biosynthesis, is encoded by two closely related P5CS genes (P5CS1 and P5CS2). We demonstrate that SlWRKY51 directly activates the expression of P5CS1 under chilling stress. In addition, the VQ (a class of plant-specific proteins containing the conserved motif FxxhVQxhTG) family member SlVQ10 physically interacts with SlWRKY51 to enhance its activation of P5CS1. Our study reveals that the chilling-induced transcription factor SlWRKY51 enhances chilling tolerance in tomato by promoting proline accumulation.
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Affiliation(s)
- Yixuan Wang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, China
- College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Meihui Zhang
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Chuanzhao Wu
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Chong Chen
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
- College of Agriculture and Bioengineering, Heze University, He'ze, China
| | - Lun Meng
- Shandong Shike Modern Agriculture Investment Co. Ltd, He'ze, China
| | - Guangqiang Zhang
- College of Agriculture and Bioengineering, Heze University, He'ze, China
| | - Kunyang Zhuang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, China
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Qinghua Shi
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai'an, China
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Liu B, Su J, Fu C, Xian K, He J, Huang N. Comparative transcriptomic profiles of Paulownia catalpifolia under different degrees of chilling stress during the seedling stage. BMC Genomics 2024; 25:716. [PMID: 39048935 PMCID: PMC11270786 DOI: 10.1186/s12864-024-10613-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 07/11/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Paulownia, an ecologically and economically valuable plant species native to China, is notable for its excellent timber quality and strong adaptability. Among them, Paulownia catalpifolia displays the ability to survive in cold climate, a trait associated with northern China. Yet, the molecular information for its cold-tolerance has not been explored. This study was to investigate the changes in physiological indices and transcript levels of P. catalpifolia following cold exposure, which could provide evidence for revealing whether there were differences in the genetic basis of inducing physiological perturbations between moderate low temperature (MLT) and extreme low temperature (ELT). RESULTS The detection of physiological indices under diverse degrees of chilling stress showed similar patterns of alteration. Enhanced accumulation of osmoregulatory substances, such as soluble sugar and soluble protein, were more conducive under ELT compared to MLT in P. catalpifolia. Moreover, we observed leaf wilting symptoms distinctly after exposure to ELT for 48 h, while this effect was not obvious after MLT exposure for 48 h. Comparative transcriptomic analysis between MLT and ELT demonstrated 13,688 differentially expressed genes (DEGs), most of them appeared after 12 h and 48 h of treatment. GO and KEGG analyses elucidated prominent enrichment in aromatic-L-amino-acid decarboxylase activity term and carbohydrate metabolism pathways. Therefore, it was speculated that the DEGs involved in the above processes might be related to the difference in the contents of soluble protein and soluble sugar between MLT and ELT. Time series clustering analyses further highlighted several key genes engaged in the 'Glycosyltransferases', 'Galactose metabolism' and 'Starch and sucrose metabolism' pathways as well as the 'tyrosine decarboxylase activity' term. For instance, cellulose synthase-like A (CLSA2/9), raffinose synthase (RafS2), β-amylase (BAM1) and tyrosine/DOPA decarboxylase (TYDC1/2/5) genes, diverging in their expression trends between MLT and ELT, might significantly affect the soluble sugar and soluble protein abundance within P. catalpifolia. CONCLUSION Between MLT and ELT treatments, partial overlaps in response pathways of P. catalpifolia were identified, while several genes regulating the accumulation of osmotic adjustment substances had disparate expression patterns. These findings could provide a novel physiological and molecular perspective for P. catalpifolia to adapt to complex low temperature habitats.
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Affiliation(s)
- Baojun Liu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Jiang Su
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Chuanming Fu
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Kanghua Xian
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Jinxiang He
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Ningzhen Huang
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China.
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Wei Y, Kong Y, Li H, Yao A, Han J, Zhang W, Li X, Li W, Han D. Genome-Wide Characterization and Expression Profiling of the AP2/ERF Gene Family in Fragaria vesca L. Int J Mol Sci 2024; 25:7614. [PMID: 39062854 PMCID: PMC11277216 DOI: 10.3390/ijms25147614] [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: 05/24/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
The wild strawberry (Fragaria vesca L.; F. vesca) represents a resilient and extensively studied model organism. While the AP2/ERF gene family plays a pivotal role in plant development, its exploration within F. vesca remains limited. In this study, we characterized the AP2/ERF gene family in wild strawberries using the recently released genomic data (F. vesca V6.0). We conducted an analysis of the gene family expansion pattern, we examined gene expression in stem segments and leaves under cold conditions, and we explored its functional attributes. Our investigation revealed that the FvAP2/ERF family comprises 86 genes distributed among four subfamilies: AP2 (17), RAV (6), ERF (62), and Soloist (1). Tandem and segmental duplications significantly contributed to the growth of this gene family. Furthermore, predictive analysis identified several cis-acting elements in the promoter region associated with meristematic tissue expression, hormone regulation, and resistance modulation. Transcriptomic analysis under cold stress unveiled diverse responses among multiple FvAP2/ERFs in stem segments and leaves. Real-time fluorescence quantitative reverse transcription PCR (RT-qPCR) results confirmed elevated expression levels of select genes following the cold treatment. Additionally, overexpression of FvERF23 in Arabidopsis enhanced cold tolerance, resulting in significantly increased fresh weight and root length compared to the wild-type control. These findings lay the foundation for further exploration into the functional roles of FvAP2/ERF genes.
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Affiliation(s)
| | | | | | | | | | | | | | - Wenhui Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.W.); (Y.K.); (H.L.); (A.Y.); (J.H.); (W.Z.); (X.L.)
| | - Deguo Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Development and Utilization of Small Fruits in Cold Regions, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (Y.W.); (Y.K.); (H.L.); (A.Y.); (J.H.); (W.Z.); (X.L.)
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Zhou R, Jiang F, Liu Y, Yu X, Song X, Wu Z, Cammarano D. Environmental changes impact on vegetables physiology and nutrition - Gaps between vegetable and cereal crops. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173180. [PMID: 38740212 DOI: 10.1016/j.scitotenv.2024.173180] [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: 03/04/2024] [Revised: 04/17/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Projected changes in climate patterns, increase of weather extreme, water scarcity, and land degradation are going to challenge agricultural production and food security. Currently, studies concerning effects of climate change on agriculture mainly focus on yield and quality of cereal crops. In contrast, there has been little attention on the effects of environmental changes on vegetables that are necessary and key nutrition component for human beings, but quite sensitive to these climatic changes. Therefore, we reviewed the main changes of environmental factors under the current scenario as well as the impacts of these factors on the physiological responses and nutritional alteration of vegetables and the key findings based on modelling. The gaps between cereal crops and vegetables were pinpointed and the actions to take in the future were proposed. The review will enhance our understanding concerning the effects of environmental changes on production, physiological responses, nutrition, and modelling of vegetable plants.
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Affiliation(s)
- Rong Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; Department of Food Science, Aarhus University, Agro Food Park 48, DK-8200 Aarhus N, Denmark.
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yi Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaqing Yu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Zhen Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Davide Cammarano
- Department of Agroecology, iClimate, CBIO, Aarhus University, Tjele 8830, Denmark.
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Chen M, Dai S, Chen D, Zhu P, Feng N, Zheng D. Comparative Analysis Highlights Uniconazole's Efficacy in Enhancing the Cold Stress Tolerance of Mung Beans by Targeting Photosynthetic Pathways. PLANTS (BASEL, SWITZERLAND) 2024; 13:1885. [PMID: 39065416 PMCID: PMC11280120 DOI: 10.3390/plants13141885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024]
Abstract
Soybean (Glycine max) and mung bean (Vigna radiata) are key legumes with global importance, but their mechanisms for coping with cold stress-a major challenge in agriculture-have not been thoroughly investigated, especially in a comparative study. This research aimed to fill this gap by examining how these two major legumes respond differently to cold stress and exploring the role of uniconazole, a potential stress mitigator. Our comprehensive approach involved transcriptomic and metabolomic analyses, revealing distinct responses between soybean and mung bean under cold stress conditions. Notably, uniconazole was found to significantly enhance cold tolerance in mung bean by upregulating genes associated with photosynthesis, while its impact on soybean was either negligible or adverse. To further understand the molecular interactions, we utilized advanced machine learning algorithms for protein structure prediction, focusing on photosynthetic pathways. This enabled us to identify LOC106780309 as a direct binding target for uniconazole, confirmed through isothermal titration calorimetry. This research establishes a new comparative approach to explore how soybean and mung bean adapt to cold stress, offers key insights to improve the hardiness of legumes against environmental challenges, and contributes to sustainable agricultural practices and food security.
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Affiliation(s)
- Mingming Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
- Shenzhen Research Institute of Guangdong Ocean University, Guangdong Ocean University, Shenzhen 518108, China
| | - Shuangfeng Dai
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
- Shenzhen Research Institute of Guangdong Ocean University, Guangdong Ocean University, Shenzhen 518108, China
| | - Daming Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
| | - Peiyi Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
- Shenzhen Research Institute of Guangdong Ocean University, Guangdong Ocean University, Shenzhen 518108, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (S.D.); (D.C.); (P.Z.)
- Shenzhen Research Institute of Guangdong Ocean University, Guangdong Ocean University, Shenzhen 518108, China
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Zhang L, Jiang G, Wang X, Bai Y, Zhang P, Liu J, Li L, Huang L, Qin P. Identifying Core Genes Related to Low-Temperature Stress Resistance in Quinoa Seedlings Based on WGCNA. Int J Mol Sci 2024; 25:6885. [PMID: 38999994 PMCID: PMC11241592 DOI: 10.3390/ijms25136885] [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: 06/03/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024] Open
Abstract
Quinoa is a nutritious crop that is tolerant to extreme environmental conditions; however, low-temperature stress can affect quinoa growth, development, and quality. Considering the lack of molecular research on quinoa seedlings under low-temperature stress, we utilized a Weighted Gene Co-Expression Network Analysis to construct weighted gene co-expression networks associated with physiological indices and metabolites related to low-temperature stress resistance based on transcriptomic data. We screened 11 co-expression modules closely related to low-temperature stress resistance and selected 12 core genes from the two modules that showed the highest associations with the target traits. Following the functional annotation of these genes to determine the key biological processes and metabolic pathways involved in low-temperature stress, we identified four important transcription factors involved in resistance to low-temperature stress: gene-LOC110731664, gene-LOC110736639, gene-LOC110684437, and gene-LOC110720903. These results provide insights into the molecular genetic mechanism of quinoa under low-temperature stress and can be used to breed lines with tolerance to low-temperature stress.
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Affiliation(s)
- Lingyuan Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Guofei Jiang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Xuqin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Yutao Bai
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Liubin Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
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10
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Moulick D, Majumdar A, Choudhury A, Das A, Chowardhara B, Pattnaik BK, Dash GK, Murmu K, Bhutia KL, Upadhyay MK, Yadav P, Dubey PK, Nath R, Murmu S, Jana S, Sarkar S, Garai S, Ghosh D, Mondal M, Chandra Santra S, Choudhury S, Brahmachari K, Hossain A. Emerging concern of nano-pollution in agro-ecosystem: Flip side of nanotechnology. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108704. [PMID: 38728836 DOI: 10.1016/j.plaphy.2024.108704] [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: 01/29/2024] [Revised: 04/24/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024]
Abstract
Nanomaterials (NMs) have proven to be a game-changer in agriculture, showcasing their potential to boost plant growth and safeguarding crops. The agricultural sector has widely adopted NMs, benefiting from their small size, high surface area, and optical properties to augment crop productivity and provide protection against various stressors. This is attributed to their unique characteristics, contributing to their widespread use in agriculture. Human exposure from various components of agro-environmental sectors (soil, crops) NMs residues are likely to upsurge with exposure paths may stimulates bioaccumulation in food chain. With the aim to achieve sustainability, nanotechnology (NTs) do exhibit its potentials in various domains of agriculture also have its flip side too. In this review article we have opted a fusion approach using bibliometric based analysis of global research trend followed by a holistic assessment of pros and cons i.e. toxicological aspect too. Moreover, we have also tried to analyse the current scenario of policy associated with the application of NMs in agro-environment.
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Affiliation(s)
- Debojyoti Moulick
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal, 741235, India; Plant Stress Biology and Metabolomics Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, 788 011, India.
| | - Arnab Majumdar
- School of Environmental Studies, Jadavpur University, Kolkata, 700032, India.
| | - Abir Choudhury
- Department of Agricultural Chemistry and Soil Science, F/Ag., Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741252, India.
| | - Anupam Das
- Department of Soil Science and Agricultural Chemistry, Bihar Agricultural University, Sabour, Bhagalpur, India.
| | - Bhaben Chowardhara
- Department of Botany, Faculty of Science and Technology, Arunachal University of Studies, Arunachal Pradesh, 792103, India.
| | - Binaya Kumar Pattnaik
- Institute of Environment Education and Research, Bharati Vidyapeeth (Deemed to be University), Pune-411043, Maharastra, India.
| | - Goutam Kumar Dash
- Department of Biochemistry and Crop Physiology, MS Swaminathan School of Agriculture, Centurion University of Technology and Management, Paralakhemundi, Gajapati, Odisha, India.
| | - Kanu Murmu
- Department of Agronomy, F/Ag., Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741252, India.
| | - Karma Landup Bhutia
- Deptt. Agri. Biotechnology & Molecular Biology, College of Basic Sciences and Humanities, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur, Bihar, 848 125, India.
| | - Munish Kumar Upadhyay
- Department of Civil Engineering, Indian Institute of Technology Kanpur, Uttar Pradesh, 208016, India.
| | - Poonam Yadav
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
| | - Pradeep Kumar Dubey
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
| | - Ratul Nath
- Microbiology Laboratory, Department of Life Sciences, Dibrugarh University, Dibrugarh, Assam, India.
| | - Sidhu Murmu
- Department of Agricultural Chemistry and Soil Science, F/Ag., Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741252, India.
| | - Soujanya Jana
- Division of Agronomy, School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur Campus, Kolkata, 700103, India.
| | - Sukamal Sarkar
- Division of Agronomy, School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur Campus, Kolkata, 700103, India.
| | - Sourav Garai
- Division of Agronomy, School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda Educational and Research Institute, Narendrapur Campus, Kolkata, 700103, India.
| | - Dibakar Ghosh
- Division of Agronomy, ICAR-Indian Institute of Water Management, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
| | - Mousumi Mondal
- School of Agriculture and Allied Sciences, Neotia University, Sarisha, India.
| | - Subhas Chandra Santra
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal, 741235, India.
| | - Shuvasish Choudhury
- Plant Stress Biology and Metabolomics Laboratory, Department of Life Science and Bioinformatics, Assam University, Silchar, 788 011, India.
| | - Koushik Brahmachari
- Department of Agronomy, F/Ag., Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741252, India.
| | - Akbar Hossain
- Department of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur, 5200, Bangladesh.
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Terletskaya NV, Shadenova EA, Litvinenko YA, Ashimuly K, Erbay M, Mamirova A, Nazarova I, Meduntseva ND, Kudrina NO, Korbozova NK, Djangalina ED. Influence of Cold Stress on Physiological and Phytochemical Characteristics and Secondary Metabolite Accumulation in Microclones of Juglans regia L. Int J Mol Sci 2024; 25:4991. [PMID: 38732208 PMCID: PMC11084536 DOI: 10.3390/ijms25094991] [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: 04/16/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
The current study investigated the impact of cold stress on the morphological, physiological, and phytochemical properties of Juglans regia L. (J. regia) using in vitro microclone cultures. The study revealed significant stress-induced changes in the production of secondary antioxidant metabolites. According to gas chromatography-mass spectrometry (GC-MS) analyses, the stress conditions profoundly altered the metabolism of J. regia microclones. Although the overall spectrum of metabolites was reduced, the production of key secondary antioxidant metabolites significantly increased. Notably, there was a sevenfold (7×) increase in juglone concentration. These findings are crucial for advancing walnut metabolomics and enhancing our understanding of plant responses to abiotic stress factors. Additionally, study results aid in identifying the role of individual metabolites in these processes, which is essential for developing strategies to improve plant resilience and tolerance to adverse conditions.
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Affiliation(s)
- Nina V. Terletskaya
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Elvira A. Shadenova
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Yuliya A. Litvinenko
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Kazhybek Ashimuly
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Malika Erbay
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Aigerim Mamirova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
| | - Irada Nazarova
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
- Faculty of Chemistry, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan
| | - Nataliya D. Meduntseva
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Nataliya O. Kudrina
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Nazym K. Korbozova
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan; (M.E.); (A.M.); (N.O.K.); (N.K.K.)
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
| | - Erika D. Djangalina
- Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan; (E.A.S.); (Y.A.L.); (K.A.); (N.D.M.)
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12
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Fatahi B, Sorkheh K, Sofo A. Deciphering the possible role of RNA-helicase genes mechanism in response to abiotic stresses in rapeseed (Brassica napus L.). BMC PLANT BIOLOGY 2024; 24:206. [PMID: 38509484 PMCID: PMC10953219 DOI: 10.1186/s12870-024-04893-0] [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: 08/05/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Plants mediate several defense mechanisms to withstand abiotic stresses. Several gene families respond to stress as well as multiple transcription factors to minimize abiotic stresses without minimizing their effects on performance potential. RNA helicase (RH) is one of the foremost critical gene families that can play an influential role in tolerating abiotic stresses in plants. However, little knowledge is present about this protein family in rapeseed (canola). Here, we performed a comprehensive survey analysis of the RH protein family in rapeseed (Brassica napus L.). RESULTS A total of 133 BnRHs genes have been discovered in this study. By phylogenetic analysis, RHs genes were divided into one main group and a subgroup. Examination of the chromosomal position of the identified genes showed that most of the genes (27%) were located on chromosome 3. All 133 identified sequences contained the main DEXDC domain, the HELICC domain, and a number of sub-domains. The results of biological process studies showed that about 17% of the proteins acted as RHs, 22% as ATP binding, and 14% as mRNA binding. Each part of the conserved motifs, communication network, and three-dimensional structure of the proteins were examined separately. The results showed that the RWC in leaf tissue decreased with higher levels of drought stress and in both root and leaf tissues sodium concentration was increased upon increased levels of salt stress treatments. The proline content were found to be increased in leaf and root with the increased level of stress treatment. Finally, the expression patterns of eight selected RHs genes that have been exposed to drought, salinity, cold, heat and cadmium stresses were investigated by qPCR. The results showed the effect of genes under stress. Examination of gene expression in the Hayola #4815 cultivar showed that all primers except primer #79 had less expression in both leaves and roots than the control level. CONCLUSIONS New finding from the study have been presented new insights for better understanding the function and possible mechanism of RH in response to abiotic stress in rapeseed.
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Affiliation(s)
- Bahareh Fatahi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box 61355/144, Ahvaz, Iran
| | - Karim Sorkheh
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P.O. Box 61355/144, Ahvaz, Iran.
| | - Adriano Sofo
- Department of European and Mediterranean Cultures, Architecture, Environment, Cultural Heritage (DiCEM), Università degli Studi della Basilicata, Via Lanera 20, 75100, Matera, MT, Italy
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13
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Jan S, Rustgi S, Barmukh R, Shikari AB, Leske B, Bekuma A, Sharma D, Ma W, Kumar U, Kumar U, Bohra A, Varshney RK, Mir RR. Advances and opportunities in unraveling cold-tolerance mechanisms in the world's primary staple food crops. THE PLANT GENOME 2024; 17:e20402. [PMID: 37957947 DOI: 10.1002/tpg2.20402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023]
Abstract
Temperatures below or above optimal growth conditions are among the major stressors affecting productivity, end-use quality, and distribution of key staple crops including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays L.). Among temperature stresses, cold stress induces cellular changes that cause oxidative stress and slowdown metabolism, limit growth, and ultimately reduce crop productivity. Perception of cold stress by plant cells leads to the activation of cold-responsive transcription factors and downstream genes, which ultimately impart cold tolerance. The response triggered in crops to cold stress includes gene expression/suppression, the accumulation of sugars upon chilling, and signaling molecules, among others. Much of the information on the effects of cold stress on perception, signal transduction, gene expression, and plant metabolism are available in the model plant Arabidopsis but somewhat lacking in major crops. Hence, a complete understanding of the molecular mechanisms by which staple crops respond to cold stress remain largely unknown. Here, we make an effort to elaborate on the molecular mechanisms employed in response to low-temperature stress. We summarize the effects of cold stress on the growth and development of these crops, the mechanism of cold perception, and the role of various sensors and transducers in cold signaling. We discuss the progress in cold tolerance research at the genome, transcriptome, proteome, and metabolome levels and highlight how these findings provide opportunities for designing cold-tolerant crops for the future.
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Affiliation(s)
- Sofora Jan
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore Kashmir, India
| | - Sachin Rustgi
- Department of Plant and Environmental Sciences, Clemson University, Florence, South Carolina, USA
| | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Asif B Shikari
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore Kashmir, India
| | - Brenton Leske
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Amanuel Bekuma
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Darshan Sharma
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Wujun Ma
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- College of Agronomy, Qingdao Agriculture University, Qingdao, China
| | - Upendra Kumar
- Department of Plant Science, Mahatma Jyotiba Phule Rohilkhand University, Bareilly, Uttar Pradesh, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, Punjab, India
| | - Abhishek Bohra
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore Kashmir, India
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Liu L, Xie Y, Yahaya BS, Wu F. GIGANTEA Unveiled: Exploring Its Diverse Roles and Mechanisms. Genes (Basel) 2024; 15:94. [PMID: 38254983 PMCID: PMC10815842 DOI: 10.3390/genes15010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
GIGANTEA (GI) is a conserved nuclear protein crucial for orchestrating the clock-associated feedback loop in the circadian system by integrating light input, modulating gating mechanisms, and regulating circadian clock resetting. It serves as a core component which transmits blue light signals for circadian rhythm resetting and overseeing floral initiation. Beyond circadian functions, GI influences various aspects of plant development (chlorophyll accumulation, hypocotyl elongation, stomatal opening, and anthocyanin metabolism). GI has also been implicated to play a pivotal role in response to stresses such as freezing, thermomorphogenic stresses, salinity, drought, and osmotic stresses. Positioned at the hub of complex genetic networks, GI interacts with hormonal signaling pathways like abscisic acid (ABA), gibberellin (GA), salicylic acid (SA), and brassinosteroids (BRs) at multiple regulatory levels. This intricate interplay enables GI to balance stress responses, promoting growth and flowering, and optimize plant productivity. This review delves into the multifaceted roles of GI, supported by genetic and molecular evidence, and recent insights into the dynamic interplay between flowering and stress responses, which enhance plants' adaptability to environmental challenges.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644000, China;
| | - Yuxin Xie
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
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He Z, Li M, Pan X, Peng Y, Shi Y, Han Q, Shi M, She L, Borovskii G, Chen X, Gu X, Cheng X, Zhang W. R-loops act as regulatory switches modulating transcription of COLD-responsive genes in rice. THE NEW PHYTOLOGIST 2024; 241:267-282. [PMID: 37849024 DOI: 10.1111/nph.19315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/22/2023] [Indexed: 10/19/2023]
Abstract
COLD is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in crops. R-loops function in various cellular processes, including development and stress responses, in plants. However, how R-loops function in COLD responses is largely unknown in COLD susceptible crops like rice (Oryza sativa L.). We conducted DRIP-Seq along with other omics data (RNA-Seq, DNase-Seq and ChIP-Seq) in rice with or without COLD treatment. COLD treatment caused R-loop reprogramming across the genome. COLD-biased R-loops had higher GC content and novel motifs for the binding of distinct transcription factors (TFs). Moreover, R-loops can directly/indirectly modulate the transcription of a subset of COLD-responsive genes, which can be mediated by R-loop overlapping TF-centered or cis-regulatory element-related regulatory networks and lncRNAs, accounting for c. 60% of COLD-induced expression of differential genes in rice, which is different from the findings in Arabidopsis. We validated two R-loop loci with contrasting (negative/positive) roles in the regulation of two individual COLD-responsive gene expression, as potential targets for enhanced COLD resistance. Our study provides detailed evidence showing functions of R-loop reprogramming during COLD responses and provides some potential R-loop loci for genetic and epigenetic manipulation toward breeding of rice varieties with enhanced COLD tolerance.
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Affiliation(s)
- Zexue He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Mengqi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Xiucai Pan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
- Xiangyang Academy of Agricultural Sciences, Xiangyang, Hubei Province, 441057, China
| | - Yulian Peng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Yining Shi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Qi Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Manli Shi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Linwei She
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Gennadii Borovskii
- Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of Russian Academy of Sciences (SB RAS) Irkutsk, Lermontova, 664033, Russia
| | - Xiaojun Chen
- Key Lab of Agricultural Biotechnology of Ningxia, Ningxia Academy of Agriculture and Forestry Sciences, YinChuan, 750002, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xuejiao Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, China
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16
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Pandey V, Singh S. Plant Adaptation and Tolerance to Heat Stress: Advance Approaches and Future Aspects. Comb Chem High Throughput Screen 2024; 27:1701-1715. [PMID: 38441014 DOI: 10.2174/0113862073300371240229100613] [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: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/21/2024] [Indexed: 03/06/2024]
Abstract
Heat stress impacts plant growth at all phases of development, although the particular threshold for heat tolerance varies significantly across different developmental stages. During seed germination, elevated temperatures can either impede or completely halt the process, contingent upon the plant type and the severity of the stress. During advanced stages, high temperatures can have a negative impact on photosynthesis, respiration, water balance, and membrane integrity. Additionally, they can also influence the levels of hormones and primary and secondary metabolites. In addition, during the growth and development of plants, there is an increased expression of various heat shock proteins, as well as other proteins related to stress, and the generation of reactive oxygen species (ROS). These are significant plant responses to heat stress. Plants employ several strategies to deal with heat stress, such as maintaining the stability of their cell membranes, removing harmful reactive oxygen species (ROS), producing antioxidants, accumulating and adjusting compatible solutes, activating mitogen-activated protein kinase (MAPK) and calcium-dependent protein kinase (CDPK) cascades, and, crucially, signaling through chaperones and activating transcription. These molecular-level systems boost the ability of plants to flourish in heat stress. Potential genetic methods to enhance plant heat stress resistance encompass old and modern molecular breeding techniques and transgenic approaches, all of which rely on a comprehensive comprehension of these systems. Although several plants exhibit enhanced heat tolerance through traditional breeding methods, the effectiveness of genetic transformation techniques has been somewhat restricted. The latter results from the current constraints in our understanding and access to genes that have known impacts on plant heat stress tolerance. However, these challenges may be overcome in the future. Besides genetic methods, crops' heat tolerance can be improved through the pre-treatment of plants with various environmental challenges or the external application of osmoprotectants such as glycine betaine and proline. Thermotolerance is achieved through an active process in which plants allocate significant energy to maintain their structure and function to avoid damage induced by heat stress. The practice of nanoparticles has been shown to upgrade both the standard and the quantity of produce when crops are under heat stress. This review provides information on the effects of heat stress on plants and explores the importance of nanoparticles, transgenics, and genomic techniques in reducing the negative consequences of heat stress. Furthermore, it explores how plants might adapt to heat stress by modifying their biochemical, physiological, and molecular reactions.
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Affiliation(s)
- Vineeta Pandey
- Faculty of Agricultural Sciences, Institute of Applied Sciences and Humanities, GLA University, 17 km Stone, NH-2, Mathura, Delhi Road Mathura, Chaumuhan, Uttar Pradesh, 281406, India
| | - Sonia Singh
- Institute of Pharmaceutical Research, GLA University, 17 km Stone, NH-2, Mathura-Delhi Road Mathura, Chaumuhan, Uttar Pradesh, 281406, India
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17
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Rehman M, Kundu B, Regon P, Tanti B. Biochemical and molecular properties of Boro rice ( Oryza sativa L.) cultivars under abiotic stresses. 3 Biotech 2023; 13:422. [PMID: 38047036 PMCID: PMC10689613 DOI: 10.1007/s13205-023-03840-4] [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: 06/27/2023] [Accepted: 10/31/2023] [Indexed: 12/05/2023] Open
Abstract
The present investigation was conducted so as to unravel the various underlying antioxidant enzyme and non-enzyme defence mechanisms in some selected Boro rice cultivars that differ in temperature stress tolerance. Oxidative injury under heat and cold stress, H2O2 level showed a decline in roots and shoots of Boro in stressed condition whilst significant rise in the susceptible varieties was observed under both the stresses. However, susceptible varieties, such as Disang (shoots), Moricha (shoots) and China Boro (roots), showed a decreased H2O2 content at recovery. Under cold stress, roots and shoots of Boro and Laal Bihari showed a decreased level of lipid peroxidises and Boro and Kolong under heat stress. In contrast, significant enhancement of lipid peroxidase was revealed in the susceptible varieties. Remarkable increase in non-enzymatic antioxidants like proline, glutathione and ascorbate content was seen in the shoots of Boro in the treated and the recovery conditions. On the other hand, in enzymatic antioxidants like ascorbate peroxidase, guaiacol peroxidase, superoxide dismutase, catalase, and glutathione reductase activity, marked enhancement in ascorbate peroxidase activity was seen in the roots and the shoots of Boro and Kolong in treated and recovery samples and decreased in Swarnabh under heat stress. The guaiacol peroxidase activity of roots and shoots increased in Boro and Kolong under heat stress, and decreased in China boro and Swarnabh. The superoxide dismutase activity in the roots and shoot of Boro increased significantly under both the stress conditions in treated and recovery. Root and shoots of Swarnabh and Moricha showed decline in SOD activity in stressed conditions. The catalase activity in the case of Boro, showed a significant increase in both its roots and shoots under cold and heat stresses in the treated and the recovery samples. Moreover, under heat stress, the root and the shoots of Boro and Kolong showed the maximum glutathione activity, whilst Swarnabh and China Boro showed reduced glutathione activity at 96 h and recovery. On the other hand, the gene expression pattern of the cold-responsive genes (OsHAN1/OsCYP9B4 and FeSOD1) showed significant upregulation in the tolerant than the sensitive cultivars. Similarly, heat-responsive genes (OsTT1/OsPAB1 and OsHsfC1b) are also highly upregulated in the tolerant than the susceptible ones. Thus, the findings would provide a thorough insight into various non-enzymatic and enzymatic antioxidants and stress-responsive genes of Boro rice that could help in the future rice breeding programmes for cold and heat stresses.
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Affiliation(s)
- Mehzabin Rehman
- Department of Botany, Gauhati University, Guwahati, 781014 Assam India
- Department of Botany, University of Science and Technology, Meghalaya, Ri-Bhoi, Baridua, Meghalaya 793101 India
| | - Bikash Kundu
- Department of Botany, Gauhati University, Guwahati, 781014 Assam India
| | - Preetom Regon
- Department of Botany, Gauhati University, Guwahati, 781014 Assam India
| | - Bhaben Tanti
- Department of Botany, Gauhati University, Guwahati, 781014 Assam India
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Meng D, Li S, Feng X, Di Q, Zhou M, Yu X, He C, Yan Y, Wang J, Sun M, Li Y. CsBPC2 is essential for cucumber survival under cold stress. BMC PLANT BIOLOGY 2023; 23:566. [PMID: 37968586 PMCID: PMC10652477 DOI: 10.1186/s12870-023-04577-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023]
Abstract
Cold stress affects the growth and development of cucumbers. Whether the BPC2 transcription factor participates in cold tolerance and its regulatory mechanism in plants have not been reported. Here, we used wild-type (WT) cucumber seedlings and two mutant Csbpc2 lines as materials. The underlying mechanisms were studied by determining the phenotype, physiological and biochemical indicators, and transcriptome after cold stress. The results showed that CsBPC2 knockout reduced cucumber cold tolerance by increasing the chilling injury index, relative electrical conductivity and malondialdehyde (MDA) content and decreasing antioxidant enzyme activity. We then conducted RNA sequencing (RNA-seq) to explore transcript-level changes in Csbpc2 mutants. A large number of differentially expressed genes (1032) were identified and found to be unique in Csbpc2 mutants. However, only 489 down-regulated genes related to the synthesis and transport of amino acids and vitamins were found to be enriched through GO analysis. Moreover, both RNA-seq and qPT-PCR techniques revealed that CsBPC2 knockout also decreased the expression of some key cold-responsive genes, such as CsICE1, CsCOR413IM2, CsBZR1 and CsBZR2. These results strongly suggested that CsBPC2 knockout not only affected cold function genes but also decreased the levels of some key metabolites under cold stress. In conclusion, this study reveals for the first time that CsBPC2 is essential for cold tolerance in cucumber and provides a reference for research on the biological function of BPC2 in other plants.
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Affiliation(s)
- Di Meng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuzhen Li
- Ganzhou Key Laboratory of Greenhouse Vegetable, College of Life Science, Gannan Normal University, Ganzhou, 341000, China
| | - Xiaojie Feng
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qinghua Di
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mengdi Zhou
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianchang Yu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaoxing He
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yan Yan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jun Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mintao Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yansu Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Xu P, Zhang W, Wang X, Zhu Y, Liang W, He Y, Yu X. Multiomics analysis reveals a link between Brassica-specific miR1885 and rapeseed tolerance to low temperature. PLANT, CELL & ENVIRONMENT 2023; 46:3405-3419. [PMID: 37564020 DOI: 10.1111/pce.14690] [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: 06/30/2022] [Revised: 06/26/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Brassica crops include various edible vegetable and plant oil crops, and their production is limited by low temperature beyond their tolerant capability. The key regulators of low-temperature resistance in Brassica remain largely unexplored. To identify posttranscriptional regulators of plant response to low temperature, we performed small RNA profiling, and found that 16 known miRNAs responded to cold treatment in Brassica rapa. The cold response of seven of those miRNAs were further confirmed by qRT-PCR and/or northern blot analyses. In parallel, a genome-wide association study of 220 accessions of Brassica napus identified four candidate MIRNA genes, all of which were cold-responsive, at the loci associated with low-temperature resistance. Specifically, these large-scale data analyses revealed a link between miR1885 and the plant response to low temperature in both B. rapa and B. napus. Using 5' rapid amplification of cDNA ends approach, we validated that miR1885 can cleave its putative target gene transcripts, Bn.TIR.A09 and Bn.TNL.A03, in B. napus. Furthermore, overexpression of miR1885 in Semiwinter type B. napus decreased the mRNA abundance of Bn.TIR.A09 and Bn.TNL.A03 and resulted in increased sensitivity to low temperature. Knocking down of miR1885 in Spring type B. napus led to increased mRNA abundance of its targets and improved rapeseed tolerance to low temperature. Together, our results suggested that the loci of miR1885 and its targets could be potential candidates for the molecular breeding of low temperature-tolerant Spring type Brassica crops.
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Affiliation(s)
- Pengfei Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wenting Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xuan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yantao Zhu
- Hybrid Rape Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuke He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiang Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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20
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Wani SH. Editorial: Mechanisms of abiotic stress responses and tolerance in plants: physiological, biochemical and molecular interventions, volume II. FRONTIERS IN PLANT SCIENCE 2023; 14:1272255. [PMID: 37780497 PMCID: PMC10535095 DOI: 10.3389/fpls.2023.1272255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023]
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21
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Teh JT, Leitz V, Holzer VJC, Neusius D, Marino G, Meitzel T, García-Cerdán JG, Dent RM, Niyogi KK, Geigenberger P, Nickelsen J. NTRC regulates CP12 to activate Calvin-Benson cycle during cold acclimation. Proc Natl Acad Sci U S A 2023; 120:e2306338120. [PMID: 37549282 PMCID: PMC10433458 DOI: 10.1073/pnas.2306338120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 08/09/2023] Open
Abstract
NADPH-dependent thioredoxin reductase C (NTRC) is a chloroplast redox regulator in algae and plants. Here, we used site-specific mutation analyses of the thioredoxin domain active site of NTRC in the green alga Chlamydomonas reinhardtii to show that NTRC mediates cold tolerance in a redox-dependent manner. By means of coimmunoprecipitation and mass spectrometry, a redox- and cold-dependent binding of the Calvin-Benson Cycle Protein 12 (CP12) to NTRC was identified. NTRC was subsequently demonstrated to directly reduce CP12 of C. reinhardtii as well as that of the vascular plant Arabidopsis thaliana in vitro. As a scaffold protein, CP12 joins the Calvin-Benson cycle enzymes phosphoribulokinase (PRK) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to form an autoinhibitory supracomplex. Using size-exclusion chromatography, NTRC from both organisms was shown to control the integrity of this complex in vitro and thereby PRK and GAPDH activities in the cold. Thus, NTRC apparently reduces CP12, hence triggering the dissociation of the PRK/CP12/GAPDH complex in the cold. Like the ntrc::aphVIII mutant, CRISPR-based cp12::emx1 mutants also exhibited a redox-dependent cold phenotype. In addition, CP12 deletion resulted in robust decreases in both PRK and GAPDH protein levels implying a protein protection effect of CP12. Both CP12 functions are critical for preparing a repertoire of enzymes for rapid activation in response to environmental changes. This provides a crucial mechanism for cold acclimation.
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Affiliation(s)
- Jing Tsong Teh
- Department of Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Verena Leitz
- Department of Plant Metabolism, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Victoria J. C. Holzer
- Department of Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Daniel Neusius
- Department of Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Giada Marino
- Department of Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Tobias Meitzel
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben06466, Germany
| | - José G. García-Cerdán
- HHMI, University of California, Berkeley, CA94720-3102
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720-3102
| | - Rachel M. Dent
- HHMI, University of California, Berkeley, CA94720-3102
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720-3102
| | - Krishna K. Niyogi
- HHMI, University of California, Berkeley, CA94720-3102
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720-3102
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Peter Geigenberger
- Department of Plant Metabolism, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
| | - Jörg Nickelsen
- Department of Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität Munich, Planegg82152, Germany
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Zhu Y, Zhu G, Xu R, Jiao Z, Yang J, Lin T, Wang Z, Huang S, Chong L, Zhu J. A natural promoter variation of SlBBX31 confers enhanced cold tolerance during tomato domestication. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1033-1043. [PMID: 36704926 PMCID: PMC10106858 DOI: 10.1111/pbi.14016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 05/04/2023]
Abstract
Cold stress affects crop growth and productivity worldwide. Understanding the genetic basis of cold tolerance in germplasms is critical for crop improvement. Plants can coordinate environmental stimuli of light and temperature to regulate cold tolerance. However, it remains unknown which gene in germplasms could have such function. Here, we utilized genome-wide association study (GWAS) to investigate the cold tolerance of wild and cultivated tomato accessions and discovered that increased cold tolerance is accompanied with tomato domestication. We further identified a 27-bp InDel in the promoter of the CONSTANS-like transcription factor (TF) SlBBX31 is significantly linked with cold tolerance. Coincidentally, a key regulator of light signalling, SlHY5, can directly bind to the SlBBX31 promoter to activate SlBBX31 transcription while the 27-bp InDel can prevent S1HY5 from transactivating SlBBX31. Parallel to these findings, we observed that the loss of function of SlBBX31 results in impaired tomato cold tolerance. SlBBX31 can also modulate the cold-induced expression of several ERF TFs including CBF2 and DREBs. Therefore, our study has uncovered that SlBBX31 is possibly selected during tomato domestication for cold tolerance regulation, providing valuable insights for the development of hardy tomato varieties.
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Affiliation(s)
- Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
- Sanya Institute of Henan UniversitySanyaHainanChina
| | - Guangtao Zhu
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS‐YNNU Joint Academy of Potato SciencesYunnan Normal UniversityKunmingChina
| | - Rui Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
| | - Zhixin Jiao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
| | - Junwei Yang
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Tao Lin
- College of HorticultureChina Agricultural UniversityBeijingChina
| | - Zhen Wang
- School of Life SciencesAnhui Agricultural UniversityHefeiAnhuiChina
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenChina
| | - Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
| | - Jian‐Kang Zhu
- Institute of Advanced Biotechnology and School of Life SciencesSouthern University of Science and TechnologyShenzhenChina
- Center for Advanced Bioindustry TechnologiesChinese Academy of Agricultural SciencesBeijingChina
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23
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Pradhan UK, Meher PK, Naha S, Rao AR, Kumar U, Pal S, Gupta A. ASmiR: a machine learning framework for prediction of abiotic stress-specific miRNAs in plants. Funct Integr Genomics 2023; 23:92. [PMID: 36939943 DOI: 10.1007/s10142-023-01014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/18/2023] [Accepted: 03/06/2023] [Indexed: 03/21/2023]
Abstract
Abiotic stresses have become a major challenge in recent years due to their pervasive nature and shocking impacts on plant growth, development, and quality. MicroRNAs (miRNAs) play a significant role in plant response to different abiotic stresses. Thus, identification of specific abiotic stress-responsive miRNAs holds immense importance in crop breeding programmes to develop cultivars resistant to abiotic stresses. In this study, we developed a machine learning-based computational model for prediction of miRNAs associated with four specific abiotic stresses such as cold, drought, heat and salt. The pseudo K-tuple nucleotide compositional features of Kmer size 1 to 5 were used to represent miRNAs in numeric form. Feature selection strategy was employed to select important features. With the selected feature sets, support vector machine (SVM) achieved the highest cross-validation accuracy in all four abiotic stress conditions. The highest cross-validated prediction accuracies in terms of area under precision-recall curve were found to be 90.15, 90.09, 87.71, and 89.25% for cold, drought, heat and salt respectively. Overall prediction accuracies for the independent dataset were respectively observed 84.57, 80.62, 80.38 and 82.78%, for the abiotic stresses. The SVM was also seen to outperform different deep learning models for prediction of abiotic stress-responsive miRNAs. To implement our method with ease, an online prediction server "ASmiR" has been established at https://iasri-sg.icar.gov.in/asmir/ . The proposed computational model and the developed prediction tool are believed to supplement the existing effort for identification of specific abiotic stress-responsive miRNAs in plants.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Prabina Kumar Meher
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India.
| | - Sanchita Naha
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | | | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Soumen Pal
- Division of Computer Applications, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
| | - Ajit Gupta
- Division of Statistical Genetics, ICAR-Indian Agricultural Statistics Research Institute, PUSA, New Delhi, 110012, India
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Tang M, Liu L, Hu X, Zheng H, Wang Z, Liu Y, Zhu Q, Cui L, Xie S. Genome-wide characterization of R2R3-MYB gene family in Santalum album and their expression analysis under cold stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1142562. [PMID: 36938022 PMCID: PMC10017448 DOI: 10.3389/fpls.2023.1142562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Sandalwood (Santalum album) is a high-value multifunctional tree species that is rich in aromatic substances and is used in medicine and global cosmetics. Due to the scarcity of land resources in tropical and subtropical regions, land in temperate regions is a potential resource for the development of S. album plantations in order to meet the needs of S. album production and medicine. The R2R3-MYB transcription factor family is one of the largest in plants and plays an important role in the response to various abiotic stresses. However, the R2R3-MYB gene family of S. album has not been studied. In this study, 144 R2R3-MYB genes were successfully identified in the assembly genome sequence, and their characteristics and expression patterns were investigated under various durations of low temperature stress. According to the findings, 31 of the 114 R2R3-MYB genes showed significant differences in expression after cold treatment. Combining transcriptome and weighted gene co-expression network analysis (WGCNA) revealed three key candidate genes (SaMYB098, SaMYB015, and SaMYB068) to be significantly involved in the regulation of cold resistance in S. album. The structural characteristics, evolution, and expression pattern of the R2R3-MYB gene in S. album were systematically examined at the whole genome level for the first time in this study. It will provide important information for future research into the function of the R2R3-MYB genes and the mechanism of cold stress response in S. album.
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Affiliation(s)
- Minqiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Le Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Xu Hu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Haoyue Zheng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Zukai Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Yi Liu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Qing Zhu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Shangqian Xie
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
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25
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Ben Saad R, Ben Romdhane W, Baazaoui N, Bouteraa MT, Chouaibi Y, Mnif W, Ben Hsouna A, Kačániová M. Functional Characterization of Lobularia maritima LmTrxh2 Gene Involved in Cold Tolerance in Tobacco through Alleviation of ROS Damage to the Plasma Membrane. Int J Mol Sci 2023; 24:ijms24033030. [PMID: 36769352 PMCID: PMC9917683 DOI: 10.3390/ijms24033030] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Cold stress is a key environmental factor affecting plant growth and development, crop productivity, and geographic distribution. Thioredoxins (Trxs) are small proteins that are ubiquitously expressed in all organisms and implicated in several cellular processes, including redox reactions. However, their role in the regulation of cold stress in the halophyte plant Lobularia maritima remains unknown. We recently showed that overexpression of LmTrxh2, which is the gene that encodes the h-type Trx protein previously isolated from L. maritima, led to an enhanced tolerance to salt and osmotic stress in transgenic tobacco. This study functionally characterized the LmTrxh2 gene via its overexpression in tobacco and explored its cold tolerance mechanisms. Results of the RT-qPCR and western blot analyses indicated differential temporal and spatial regulation of LmTrxh2 in L. maritima under cold stress at 4 °C. LmTrxh2 overexpression enhanced the cold tolerance of transgenic tobacco, as evidenced by increased germination rate, fresh weight and catalase (CAT), superoxide dismutase (SOD) and peroxidase (POD) activities; reduced malondialdehyde levels, membrane leakage, superoxide anion (O2-), and hydrogen peroxide (H2O2) levels; and higher retention of chlorophyll than in non-transgenic plants (NT). Furthermore, the transcript levels of reactive oxygen species (ROS)-related genes (NtSOD and NtCAT1), stress-responsive late embryogenis abundant protein 5 (NtLEA5), early response to dehydration 10C (NtERD10C), DRE-binding proteins 1A (NtDREB1A), and cold-responsive (COR) genes (NtCOR15A, NtCOR47, and NtKIN1) were upregulated in transgenic lines compared with those in NT plants under cold stress, indicating that LmTrxh2 conferred cold stress tolerance by enhancing the ROS scavenging ability of plants, thus enabling them to maintain membrane integrity. These results suggest that LmTrxh2 promotes cold tolerance in tobacco and provide new insight into the improvement of cold-stress resistance to cold stress in non-halophyte plants and crops.
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Affiliation(s)
- Rania Ben Saad
- Centre of Biotechnology of Sfax, Biotechnology and Plant Improvement Laboratory, University of Sfax, B.P “1177”, Sfax 3018, Tunisia
- Correspondence: (R.B.S.); (M.K.)
| | - Walid Ben Romdhane
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Narjes Baazaoui
- Biology Department, College of Sciences and Arts Muhayil Assir, King Khalid University, Abha 61421, Saudi Arabia
| | - Mohamed Taieb Bouteraa
- Centre of Biotechnology of Sfax, Biotechnology and Plant Improvement Laboratory, University of Sfax, B.P “1177”, Sfax 3018, Tunisia
| | - Yosra Chouaibi
- Centre of Biotechnology of Sfax, Biotechnology and Plant Improvement Laboratory, University of Sfax, B.P “1177”, Sfax 3018, Tunisia
| | - Wissem Mnif
- Department of Chemistry, Faculty of Sciences and Arts in Balgarn, University of Bisha, Bisha 61922, Saudi Arabia
| | - Anis Ben Hsouna
- Centre of Biotechnology of Sfax, Biotechnology and Plant Improvement Laboratory, University of Sfax, B.P “1177”, Sfax 3018, Tunisia
- Department of Environmental Sciences and Nutrition, Higher Institute of Applied Sciences and Technology of Mahdia, University of Monastir, Mahdia 5100, Tunisia
| | - Miroslava Kačániová
- Faculty of Horticulture, Institute of Horticulture, Slovak University of Agriculture, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia
- Department of Bioenergy, Food Technology and Microbiology, Institute of Food Technology and Nutrition, University of Rzeszow, 4 Zelwerowicza St, 35601 Rzeszow, Poland
- Correspondence: (R.B.S.); (M.K.)
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26
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Das A, Dedon N, Enders DJ, Fjellheim S, Preston JC. Testing the chilling- before drought-tolerance hypothesis in Pooideae grasses. Mol Ecol 2023; 32:772-785. [PMID: 36420966 PMCID: PMC10107940 DOI: 10.1111/mec.16794] [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: 04/29/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022]
Abstract
Temperate Pooideae are a large clade of economically important grasses distributed in some of the Earth's coldest and driest terrestrial environments. Previous studies have inferred that Pooideae diversified from their tropical ancestors in a cold montane habitat, suggesting that above-freezing cold (chilling) tolerance evolved early in the subfamily. By contrast, drought tolerance is hypothesized to have evolved multiple times independently in response to global aridification that occurred after the split of Pooideae tribes. To independently test predictions of the chilling-before-drought hypothesis in Pooideae, we assessed conservation of whole plant and gene expression traits in response to chilling vs. drought. We demonstrated that both trait responses are more similar across tribes in cold as compared to drought, suggesting that chilling responses evolved before, and drought responses after, tribe diversification. Moreover, we found significantly more overlap between drought and chilling responsive genes within a species than between drought responsive genes across species, providing evidence that chilling tolerance genes acted as precursors for the novel acquisition of increased drought tolerance multiple times independently, partially through the cooption of chilling responsive genes.
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Affiliation(s)
- Aayudh Das
- Department of Plant Biology, The University of Vermont, Burlington, Vermont, USA
| | - Natalie Dedon
- Department of Plant Biology, The University of Vermont, Burlington, Vermont, USA
| | - Daniel J Enders
- Department of Plant Biology, The University of Vermont, Burlington, Vermont, USA
| | - Siri Fjellheim
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jill C Preston
- Department of Plant Biology, The University of Vermont, Burlington, Vermont, USA
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27
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Sahoo DK, Hegde C, Bhattacharyya MK. Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 13:1094462. [PMID: 36714785 PMCID: PMC9878698 DOI: 10.3389/fpls.2022.1094462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Cold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions. METHODS The genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes. RESULTS Investigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domain-containing proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier. DISCUSSION The 12.5% overlap between the genes identified in this genome-wide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Chinmay Hegde
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States
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Stawoska I, Myszkowska D, Oliwa J, Skoczowski A, Wesełucha-Birczyńska A, Saja-Garbarz D, Ziemianin M. Air pollution in the places of Betula pendula growth and development changes the physicochemical properties and the main allergen content of its pollen. PLoS One 2023; 18:e0279826. [PMID: 36696393 PMCID: PMC9876359 DOI: 10.1371/journal.pone.0279826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/14/2022] [Indexed: 01/26/2023] Open
Abstract
Pollen allergy becomes an increasing problem for humans, especially in the regions, where the air pollution level increases due to the traffic and urbanization. These factors may also affect the physiological activity of plants, causing changes in pollen allergenicity. The aim of the study was to estimate the influence of air pollutants on the chemical composition of birch pollen and the secondary structures of the Bet v1 protein. The research was conducted in seven locations in Malopolska region, South of Poland of a different pollution level. We have found slight fluctuations in the values of parameters describing the photosynthetic light reactions, similar spectra of leaf reflectance and the negligible differences in the discrimination values of the δ13C carbon isotope were found. The obtained results show a minor effect of a degree of pollution on the physiological condition B. pendula specimen. On the other hand, mean Bet v1 concentration measured in pollen samples collected in Kraków was significantly higher than in less polluted places (p = .03886), while FT-Raman spectra showed the most distinct variations in the wavenumbers characteristic of proteins. Pollen collected at sites of the increased NOx and PM concentration, show the highest percentage values of potential aggregated forms and antiparallel β-sheets in the expense of α-helix, presenting a substantial impact on chemical compounds of pollen, Bet v1 concentration and on formation of the secondary structure of proteins, what can influence their functions.
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Affiliation(s)
- Iwona Stawoska
- Institute of Biology, Pedagogical University of Krakow, Kraków, Poland
| | - Dorota Myszkowska
- Department of Clinical and Environmental Allergology, Jagiellonian University Medical College, Kraków, Poland
| | - Jakub Oliwa
- Institute of Biology, Pedagogical University of Krakow, Kraków, Poland
| | | | | | - Diana Saja-Garbarz
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland
| | - Monika Ziemianin
- Department of Clinical and Environmental Allergology, Jagiellonian University Medical College, Kraków, Poland
- * E-mail:
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Li Y, Han H, Fu M, Zhou X, Ye J, Xu F, Zhang W, Liao Y, Yang X. Genome-wide identification and expression analysis of NAC family genes in Ginkgo biloba L. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:107-118. [PMID: 36377299 DOI: 10.1111/plb.13486] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
NAC (NAM, ATAF, CUC2) transcription factors constitute one of the largest families of plant-specific transcription factors with important roles in plant growth and development and in biotic and abiotic stresses. The physicochemical properties, gene structure, cis-acting elements and expression patterns of NAC transcription factors in Ginkgo biloba were analysed using bioinformatics, and expression of this gene family was analysed via quantitative reverse transcription PCR. The family of G. biloba NAC transcription factors had 50 members, distributed on 12 chromosomes and divided into 11 groups. Members in the same group share a similar gene structure and motif distribution. Transcriptome data analysis of G. biloba showed that 35 genes were expressed in eight tissues. Correlation analysis suggested that GbNAC007 and GNAC008 might be involved in flavonoid biosynthesis. Expression levels of 12 GbNACs under cold, het, and salt stresses were analysed. Results indicate that NAC transcription factors play an important role in response to abiotic stresses. This study provides a reference for the functional analysis of the G. biloba family of NAC transcription factors, as well as a resource for studies on the involvement of this family in responses to abiotic stresses and flavonoid biosynthesis.
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Affiliation(s)
- Y Li
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - H Han
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - M Fu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - X Zhou
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - J Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - F Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - W Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - Y Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
| | - X Yang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, China
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Zang Z, Li Z, Wang J, Lu X, Lyu Q, Tang M, Cui HL, Yan S. Terahertz spectroscopic monitoring and analysis of citrus leaf water status under low temperature stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:52-59. [PMID: 36375327 DOI: 10.1016/j.plaphy.2022.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Low temperature stress, in the form of chilling and freezing, is one of the major environmental factors impacting on citrus yield, which changes plant's water state and results in the crops' sub-health or injury. The innovative terahertz (THz) spectroscopy and imaging based sensing technology has been shown to be a suitable tool for plant leaf water status determination, due to THz radiation's innate sensitivity to hydrogen bond vibration in aqueous solutions, which is usually related to plant phenotype change. We demonstrate experimentally that the THz absorption coefficient of leaf could be used for distinguishing plant's physiological stress status, exhibiting clear decreasing or increasing trend under chilling or freezing stress respectively. The underlying rationale might be that membrane damage shows a diverse pattern, changing the intra- or extra-cellular liquid environments, likely being linked to the various THz spectral characteristics. There were different adaptations in leaf morphology, leading to different leaf density, which in turn affects the water volume fraction. Moreover, different patterns of the dynamic equilibrium state of free water and bound water under chilling and freezing treatment were revealed by THz spectroscopy. Here, THz spectroscopic monitoring has shown unique potential for judging citrus's low temperature stress state through bio-water detection and discrimination.
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Affiliation(s)
- Ziyi Zang
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
| | - Zaoxia Li
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
| | - Jie Wang
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
| | - Xingxing Lu
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China
| | - Qiang Lyu
- Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Mingjie Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Hong-Liang Cui
- College of Instrumentation and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China; Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China.
| | - Shihan Yan
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
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31
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Dhaliwal LK, Angeles-Shim RB. Cell Membrane Features as Potential Breeding Targets to Improve Cold Germination Ability of Seeds. PLANTS (BASEL, SWITZERLAND) 2022; 11:3400. [PMID: 36501439 PMCID: PMC9738148 DOI: 10.3390/plants11233400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/22/2022] [Accepted: 12/01/2022] [Indexed: 05/13/2023]
Abstract
Cold stress breeding that focuses on the improvement of chilling tolerance at the germination stage is constrained by the complexities of the trait which involves integrated cellular, biochemical, hormonal and molecular responses. Biological membrane serves as the first line of plant defense under stress. Membranes receive cold stress signals and transduce them into intracellular responses. Low temperature stress, in particular, primarily and effectively affects the structure, composition and properties of cell membranes, which ultimately disturbs cellular homeostasis. Under cold stress, maintenance of membrane integrity through the alteration of membrane lipid composition is of prime importance to cope with the stress. This review describes the critical role of cell membranes in cold stress responses as well as the physiological and biochemical manifestations of cold stress in plants. The potential of cell membrane properties as breeding targets in developing strategies to improve cold germination ability is discussed using cotton (Gossypium hirsutum L.) as a model.
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Affiliation(s)
- Lakhvir Kaur Dhaliwal
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409-2122, USA
| | - Rosalyn B Angeles-Shim
- Department of Plant and Soil Science, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX 79409-2122, USA
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32
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Rahman MU, Zulfiqar S, Raza MA, Ahmad N, Zhang B. Engineering Abiotic Stress Tolerance in Crop Plants through CRISPR Genome Editing. Cells 2022; 11:3590. [PMID: 36429019 PMCID: PMC9688763 DOI: 10.3390/cells11223590] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental abiotic stresses challenge food security by depressing crop yields often exceeding 50% of their annual production. Different methods, including conventional as well as genomic-assisted breeding, mutagenesis, and genetic engineering have been utilized to enhance stress resilience in several crop species. Plant breeding has been partly successful in developing crop varieties against abiotic stresses owning to the complex genetics of the traits as well as the narrow genetic base in the germplasm. Irrespective of the fact that genetic engineering can transfer gene(s) from any organism(s), transgenic crops have become controversial mainly due to the potential risk of transgene-outcrossing. Consequently, the cultivation of transgenic crops is banned in certain countries, particularly in European countries. In this scenario, the discovery of the CRISPR tool provides a platform for producing transgene-free genetically edited plants-similar to the mutagenized crops that are not extensively regulated such as genetically modified organisms (GMOs). Thus, the genome-edited plants without a transgene would likely go into the field without any restriction. Here, we focused on the deployment of CRISPR for the successful development of abiotic stress-tolerant crop plants for sustaining crop productivity under changing environments.
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Affiliation(s)
- Mehboob-ur Rahman
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Sana Zulfiqar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Muhammad Ahmad Raza
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Niaz Ahmad
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Pakistan
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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33
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Soualiou S, Duan F, Li X, Zhou W. CROP PRODUCTION UNDER COLD STRESS: An understanding of plant responses, acclimation processes, and management strategies. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 190:47-61. [PMID: 36099808 DOI: 10.1016/j.plaphy.2022.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 06/15/2023]
Abstract
In the context of climate change, the magnitude and frequency of temperature extremes (low and high temperatures) are increasing worldwide. Changes to the lower extremes of temperature, known as cold stress (CS), are one of the recurrent stressors in many parts of the world, severely limiting agricultural production. A series of plant reactions to CS could be generalized into morphological, physiological, and biochemical responses based on commonalities among crop plants. However, the differing originality of crops revealed varying degrees of sensitivity to cold and, therefore, exhibited large differences in these responses among the crops. This review discusses the vegetative and reproductive growth effects of CS and highlights the species-specific aspect of each growth stage whereby the reproductive growth CS appears more detrimental in rice and wheat, with marginal yield losses. To mitigate CS negative effects, crop plants have evolved cold-acclimation mechanisms (with differing capability), characterized by specific protein accumulation, membrane modification, regulation of signaling pathways, osmotic regulation, and induction of endogenous hormones. In addition, we reviewed a comprehensive account of management strategies for regulating tolerance mechanisms of crop plants under CS.
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Affiliation(s)
- Soualihou Soualiou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fengying Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xia Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Figueroa N, Gómez R. Bolstered plant tolerance to low temperatures by overexpressing NAC transcription factors: identification of critical variables by meta-analysis. PLANTA 2022; 256:92. [PMID: 36181642 DOI: 10.1007/s00425-022-04007-w] [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: 08/24/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The potential biotechnological application of NAC overexpression has been challenged by meta-analysis, establishing a correlation between the magnitudes of several physiological and biochemical parameters and the enhanced tolerance to cold. Overexpression of various NAC (NAM/ATAF/CUC) transcription factors in different plant systems was shown to confer enhanced tolerance to low temperatures by inducing both common and distinctive stress response pathways. However, lack of consensus on the type of parameters evaluated, their magnitudes, and direction of the responses complicates drawing general conclusions on the effects of NAC expression in plant physiology. We report herein a meta-analysis summarizing the most critical response variables used to study the effect of overexpressing NAC regulators on cold stress tolerance. We found that NAC overexpression affected all of the outcome parameters in stressed plants, and one response in control conditions. Transformed plants displayed an increase of at least 40% in positive responses, while negative outcomes were reduced by at least 30%. The most reported parameters included survival, electrolyte leakage, and malondialdehyde contents, whereas the most sensitive to the treatments were the Fv/Fm parameter, survival, and the activity of catalases. We also explored how different experimental arrangements affected the magnitudes of the responses. NAC-mediated improvements were best observed after severe stress episodes and during brief treatments (ranging from 5 to 24 h), especially in terms of antioxidant activities, accumulation of free proline, and parameters related to membrane integrity. Use of heterologous expression also favored several indicators of plant fitness. Our findings should help both basic and applied research on the influence of NAC expression on enhanced tolerance to cold.
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Affiliation(s)
- Nicolás Figueroa
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina.
| | - Rodrigo Gómez
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario (UNR), 2123, Zavalla, Santa Fe, Argentina
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35
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Kao PH, Baiya S, Lai ZY, Huang CM, Jhan LH, Lin CJ, Lai YS, Kao CF. An advanced systems biology framework of feature engineering for cold tolerance genes discovery from integrated omics and non-omics data in soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:1019709. [PMID: 36247545 PMCID: PMC9562094 DOI: 10.3389/fpls.2022.1019709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Soybean is sensitive to low temperatures during the crop growing season. An urgent demand for breeding cold-tolerant cultivars to alleviate the production loss is apparent to cope with this scenario. Cold-tolerant trait is a complex and quantitative trait controlled by multiple genes, environmental factors, and their interaction. In this study, we proposed an advanced systems biology framework of feature engineering for the discovery of cold tolerance genes (CTgenes) from integrated omics and non-omics (OnO) data in soybean. An integrative pipeline was introduced for feature selection and feature extraction from different layers in the integrated OnO data using data ensemble methods and the non-parameter random forest prioritization to minimize uncertainties and false positives for accuracy improvement of results. In total, 44, 143, and 45 CTgenes were identified in short-, mid-, and long-term cold treatment, respectively, from the corresponding gene-pool. These CTgenes outperformed the remaining genes, the random genes, and the other candidate genes identified by other approaches in an independent RNA-seq database. Furthermore, we applied pathway enrichment and crosstalk network analyses to uncover relevant physiological pathways with the discovery of underlying cold tolerance in hormone- and defense-related modules. Our CTgenes were validated by using 55 SNP genotype data of 56 soybean samples in cold tolerance experiments. This suggests that the CTgenes identified from our proposed systematic framework can effectively distinguish cold-resistant and cold-sensitive lines. It is an important advancement in the soybean cold-stress response. The proposed pipelines provide an alternative solution to biomarker discovery, module discovery, and sample classification underlying a particular trait in plants in a robust and efficient way.
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Affiliation(s)
- Pei-Hsiu Kao
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Supaporn Baiya
- Department of Resource and Environment, Faculty of Science at Sriracha, Kasetsart University, Sriracha, Thailand
| | - Zheng-Yuan Lai
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Chih-Min Huang
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Li-Hsin Jhan
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Chian-Jiun Lin
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Ya-Syuan Lai
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Feng Kao
- Department of Agronomy, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
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Liu Z, Bi S, Meng J, Liu T, Li P, Yu C, Peng X. Arbuscular mycorrhizal fungi enhanced rice proline metabolism under low temperature with nitric oxide involvement. FRONTIERS IN PLANT SCIENCE 2022; 13:962460. [PMID: 36247649 PMCID: PMC9555847 DOI: 10.3389/fpls.2022.962460] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are known to improve plant stress tolerance by regulating proline accumulation, and nitric oxide (NO) plays an important signaling role in proline metabolism. Environmental nitrogen (N) affects AMF colonization and its contribution to host plants resistance to stress conditions. However, the relationship between proline metabolism and NO in mycorrhizal rice and the effect of N application on symbiont proline metabolism under low temperature have not been established. Pot culture experiments with different temperature, N and exogenous NO donor treatments were conducted with non-mycorrhizal and mycorrhizal rice. The results showed that AMF enhanced rice proline accumulation under low-temperature stress and decreased glutamate (Glu) and ornithine (Orn) concentrations significantly. In comparison with non-mycorrhizal rice, AMF colonization significantly decreased the Glu concentration, but had little effect on the Orn concentration under low-temperature stress, accompanied by increasing expression of OsP5CS2, OsOAT and OsProDH1. Exogenous application of NO increased proline concentration both under normal and low temperature, which exhibited a higher increase in mycorrhizal rice. NO also triggered the expression of key genes in the Glu and Orn pathways of proline synthesis as well as proline degradation. Higher N application decreased the AMF colonization, and AMF showed greater promotion of proline metabolism at low N levels under low temperature stress by regulating the Glu synthetic pathway. Meanwhile, AMF increased rice nitrate reductase (NR) and nitric oxide synthase (NOS) activities and then enhanced NO accumulation under low N levels. Consequently, it could be hypothesized that one of the mechanisms by which AMF improves plant resistance to low-temperature stress is the accumulation of proline via enhancement of the Glu and Orn synthetic pathways, with the involvement of the signaling molecule NO. However, the contribution of AMF to rice proline accumulation under low-temperature stress was attenuated by high N application.
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Affiliation(s)
- Zhilei Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Germplasm Innovation, Physiology and Ecology of Grain Crop in Cold Region (Northeast Agricultural University), Ministry of Education, Harbin, China
| | - Shiting Bi
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Jingrou Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Tingting Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Pengfei Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Germplasm Innovation, Physiology and Ecology of Grain Crop in Cold Region (Northeast Agricultural University), Ministry of Education, Harbin, China
| | - Cailian Yu
- The School of Material Science and Chemical Engineering, Harbin University of Science and Technology, Harbin, China
| | - Xianlong Peng
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
- Key Laboratory of Germplasm Innovation, Physiology and Ecology of Grain Crop in Cold Region (Northeast Agricultural University), Ministry of Education, Harbin, China
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Phour M, Sindhu SS. Mitigating abiotic stress: microbiome engineering for improving agricultural production and environmental sustainability. PLANTA 2022; 256:85. [PMID: 36125564 DOI: 10.1007/s00425-022-03997-x] [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: 03/26/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
The responses of plants to different abiotic stresses and mechanisms involved in their mitigation are discussed. Production of osmoprotectants, antioxidants, enzymes and other metabolites by beneficial microorganisms and their bioengineering ameliorates environmental stresses to improve food production. Progressive intensification of global agriculture, injudicious use of agrochemicals and change in climate conditions have deteriorated soil health, diminished the microbial biodiversity and resulted in environment pollution along with increase in biotic and abiotic stresses. Extreme weather conditions and erratic rains have further imposed additional stress for the growth and development of plants. Dominant abiotic stresses comprise drought, temperature, increased salinity, acidity, metal toxicity and nutrient starvation in soil, which severely limit crop production. For promoting sustainable crop production in environmentally challenging environments, use of beneficial microbes has emerged as a safer and sustainable means for mitigation of abiotic stresses resulting in improved crop productivity. These stress-tolerant microorganisms play an effective role against abiotic stresses by enhancing the antioxidant potential, improving nutrient acquisition, regulating the production of plant hormones, ACC deaminase, siderophore and exopolysaccharides and accumulating osmoprotectants and, thus, stimulating plant biomass and crop yield. In addition, bioengineering of beneficial microorganisms provides an innovative approach to enhance stress tolerance in plants. The use of genetically engineered stress-tolerant microbes as inoculants of crop plants may facilitate their use for enhanced nutrient cycling along with amelioration of abiotic stresses to improve food production for the ever-increasing population. In this chapter, an overview is provided about the current understanding of plant-bacterial interactions that help in alleviating abiotic stress in different crop systems in the face of climate change. This review largely focuses on the importance and need of sustainable and environmentally friendly approaches using beneficial microbes for ameliorating the environmental stresses in our agricultural systems.
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Affiliation(s)
- Manisha Phour
- Department of Microbiology, CCS Haryana Agricultural University, Hisar, 125004, India
- University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Satyavir S Sindhu
- Department of Microbiology, CCS Haryana Agricultural University, Hisar, 125004, India.
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38
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Guo X, Ullah A, Siuta D, Kukfisz B, Iqbal S. Role of WRKY Transcription Factors in Regulation of Abiotic Stress Responses in Cotton. Life (Basel) 2022; 12:life12091410. [PMID: 36143446 PMCID: PMC9504182 DOI: 10.3390/life12091410] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental factors are the major constraints in sustainable agriculture. WRKY proteins are a large family of transcription factors (TFs) that regulate various developmental processes and stress responses in plants, including cotton. On the basis of Gossypium raimondii genome sequencing, WRKY TFs have been identified in cotton and characterized for their functions in abiotic stress responses. WRKY members of cotton play a significant role in the regulation of abiotic stresses, i.e., drought, salt, and extreme temperatures. These TFs either activate or repress various signaling pathways such as abscisic acid, jasmonic acid, salicylic acid, mitogen-activated protein kinases (MAPK), and the scavenging of reactive oxygen species. WRKY-associated genes in cotton have been genetically engineered in Arabidopsis, Nicotiana, and Gossypium successfully, which subsequently enhanced tolerance in corresponding plants against abiotic stresses. Although a few review reports are available for WRKY TFs, there is no critical report available on the WRKY TFs of cotton. Hereby, the role of cotton WRKY TFs in environmental stress responses is studied to enhance the understanding of abiotic stress response and further improve in cotton plants.
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Affiliation(s)
- Xiaoqiang Guo
- College of Life Science and Technology, Longdong University, Qingyang 745000, China
- Correspondence: (X.G.); (A.U.)
| | - Abid Ullah
- Department of Botany, Post Graduate College Dargai, Malakand 23060, Khyber Pakhtunkhwa, Pakistan
- Correspondence: (X.G.); (A.U.)
| | - Dorota Siuta
- Faculty of Process and Environmental Engineering, Lodz University of Technology, Wolczanska Str. 213, 90-924 Lodz, Poland
| | - Bożena Kukfisz
- Faculty of Security Engineering and Civil Protection, The Main School of Fire Service, 01-629 Warsaw, Poland
| | - Shehzad Iqbal
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Yousefi S, Marchese A, Salami SA, Benny J, Giovino A, Perrone A, Caruso T, Gholami M, Sarikhani H, Buti M, Martinelli F. Identifying conserved genes involved in crop tolerance to cold stress. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:861-873. [PMID: 35785800 DOI: 10.1071/fp21290] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Low temperature is a limiting factor for crop productivity in tropical and subtropical climates. Cold stress response in plants involves perceiving and relaying the signal through a transcriptional cascade composed of different transduction components, resulting in altered gene activity. We performed a meta-analysis of four previously published datasets of cold-tolerant and cold-sensitive crops to better understand the gene regulatory networks and identify key genes involved in cold stress tolerance conserved across phylogenetically distant species. Re-analysing the raw data with the same bioinformatics pipeline, we identified common cold tolerance-related genes. We found 236 and 242 commonly regulated genes in sensitive and tolerant genotypes, respectively. Gene enrichment analysis showed that protein modifications, hormone metabolism, cell wall, and secondary metabolism are the most conserved pathways involved in cold tolerance. Upregulation of the abiotic stress (heat and drought/salt) related genes [heat shock N -terminal domain-containing protein, 15.7kDa class I-related small heat shock protein-like, DNAJ heat shock N -terminal domain-containing protein, and HYP1 (HYPOTHETICAL PROTEIN 1)] in sensitive genotypes and downregulation of the abiotic stress (heat and drought/salt) related genes (zinc ion binding and pollen Ole e 1 allergen and extensin family protein) in tolerant genotypes was observed across the species. Almost all development-related genes were upregulated in tolerant and downregulated in sensitive genotypes. Moreover, protein-protein network analysis identified highly interacting proteins linked to cold tolerance. Mapping of abiotic stress-related genes on analysed species genomes provided information that could be essential to developing molecular markers for breeding and building up genetic improvement strategies using CRISPR/Cas9 technologies.
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Affiliation(s)
- Sanaz Yousefi
- Department of Horticultural Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Annalisa Marchese
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze - Ed. 4, 90128 Palermo, Italy
| | - Seyed Alireza Salami
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Tehran, Karaj 31587-77871, Iran
| | - Jubina Benny
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze - Ed. 4, 90128 Palermo, Italy
| | - Antonio Giovino
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification (CREA-DC), 90011 Bagheria, Italy
| | - Anna Perrone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, Palermo 90128, Italy
| | - Tiziano Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze - Ed. 4, 90128 Palermo, Italy
| | - Mansour Gholami
- Department of Horticultural Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Hassan Sarikhani
- Department of Horticultural Science, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Matteo Buti
- Department of Agriculture, Food, Environment and Forestry, University of Florence, Firenze, Italy
| | - Federico Martinelli
- Department of Biology, University of Florence, Firenze, Italy; and Istituto di Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Rome, Italy
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Luo Z, Zhou Z, Li Y, Tao S, Hu ZR, Yang JS, Cheng X, Hu R, Zhang W. Transcriptome-based gene regulatory network analyses of differential cold tolerance of two tobacco cultivars. BMC PLANT BIOLOGY 2022; 22:369. [PMID: 35879667 PMCID: PMC9316383 DOI: 10.1186/s12870-022-03767-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 07/20/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND Cold is one of the main abiotic stresses that severely affect plant growth and development, and crop productivity as well. Transcriptional changes during cold stress have already been intensively studied in various plant species. However, the gene networks involved in the regulation of differential cold tolerance between tobacco varieties with contrasting cold resistance are quite limited. RESULTS Here, we conducted multiple time-point transcriptomic analyses using Tai tobacco (TT, cold susceptibility) and Yan tobacco (YT, cold resistance) with contrasting cold responses. We identified similar DEGs in both cultivars after comparing with the corresponding control (without cold treatment), which were mainly involved in response to abiotic stimuli, metabolic processes, kinase activities. Through comparison of the two cultivars at each time point, in contrast to TT, YT had higher expression levels of the genes responsible for environmental stresses. By applying Weighted Gene Co-Expression Network Analysis (WGCNA), we identified two main modules: the pink module was similar while the brown module was distinct between the two cultivars. Moreover, we obtained 100 hub genes, including 11 important transcription factors (TFs) potentially involved in cold stress, 3 key TFs in the brown module and 8 key TFs in the pink module. More importantly, according to the genetic regulatory networks (GRNs) between TFs and other genes or TFs by using GENIE3, we identified 3 TFs (ABI3/VP1, ARR-B and WRKY) mainly functioning in differential cold responses between two cultivars, and 3 key TFs (GRAS, AP2-EREBP and C2H2) primarily involved in cold responses. CONCLUSION Collectively, our study provides valuable resources for transcriptome- based gene network studies of cold responses in tobacco. It helps to reveal how key cold responsive TFs or other genes are regulated through network. It also helps to identify the potential key cold responsive genes for the genetic manipulation of tobacco cultivars with enhanced cold tolerance in the future.
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Affiliation(s)
- Zhenyu Luo
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Zhicheng Zhou
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Yangyang Li
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Zheng-Rong Hu
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Jia-Shuo Yang
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China.
| | - Risheng Hu
- Hunan Tobacco Research Institute, Changsha, 410128, Hunan, China.
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China.
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Olechowska E, Słomnicka R, Kaźmińska K, Olczak-Woltman H, Bartoszewski G. The genetic basis of cold tolerance in cucumber (Cucumis sativus L.)-the latest developments and perspectives. J Appl Genet 2022; 63:597-608. [PMID: 35838983 DOI: 10.1007/s13353-022-00710-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/18/2022] [Accepted: 06/28/2022] [Indexed: 10/17/2022]
Abstract
Cold stress is one of the main causes of yield losses in plant production in temperate climate areas. Cold stress slows down and even stops plant growth and development and causes injuries that may result in the plant's death. Cucumber (Cucumis sativus L.), an economically important vegetable, is sensitive to low temperatures, thus improving cold tolerance in cucumber would benefit cucumber producers, particularly those farming in temperate climates and higher altitude areas. So far, single cucumber accessions showing different degrees of cold tolerance have been identified, and genetic studies have revealed biparentally and maternally inherited genetic factors responsible for chilling tolerance. Paternally transmitted chilling tolerance has also been suggested. Quantitative trait loci (QTL) associated with seed germination ability at low temperature and seedling recovery from chilling have been described. Several transgenic attempts have been made to improve cold tolerance in cucumber. Despite numerous studies, the molecular mechanisms of cold tolerance in cucumber have still not been sufficiently elucidated. In this review, we summarise the results of research focused on understanding the genetic basis of cold tolerance in cucumber and their implications for cucumber breeding.
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Affiliation(s)
- Emilia Olechowska
- Department of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, Poland
| | - Renata Słomnicka
- Department of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, Poland
| | - Karolina Kaźmińska
- Department of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, Poland
| | - Helena Olczak-Woltman
- Department of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences, Nowoursynowska 159, Warsaw, Poland.
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Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants. Int J Genomics 2022; 2022:1092894. [PMID: 35747076 PMCID: PMC9213152 DOI: 10.1155/2022/1092894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA machinery). Studies based on epigenetics have evolved over the years especially in understanding the mechanisms at transcriptional and posttranscriptional levels in plants against various environmental stimuli. Epigenomic changes in plants through induced methylation of specific genes that lead to changes in their expression can help to overcome various stress conditions. Recent studies suggested that epigenomics has a significant potential for crop improvement in plants. By the induction and modulation of various cellular processes like DNA methylation, histone modification, and biogenesis of noncoding RNAs, the plant genome can be activated which can help in achieving a quicker response against various plant stresses. Epigenetic modifications in plants allow them to adjust under varied environmental stresses by modulating their phenotypic plasticity and at the same time ensure the quality and yield of crops. The plasticity of the epigenome helps to adapt the plants during pre- and postdevelopmental processes. The variation in DNA methylation in different organisms exhibits variable phenotypic responses. The epigenetic changes also occur sequentially in the genome. Various studies indicated that environmentally stimulated epimutations produce variable responses especially in differentially methylated regions (DMR) that play a major role in the management of stress conditions in plants. Besides, it has been observed that environmental stresses cause specific changes in the epigenome that are closely associated with phenotypic modifications. However, the relationship between epigenetic modifications and phenotypic plasticity is still debatable. In this review, we will be discussing the role of various factors that allow epigenetic changes to modulate phenotypic plasticity against various abiotic stress in plants.
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Bhat KA, Mahajan R, Pakhtoon MM, Urwat U, Bashir Z, Shah AA, Agrawal A, Bhat B, Sofi PA, Masi A, Zargar SM. Low Temperature Stress Tolerance: An Insight Into the Omics Approaches for Legume Crops. FRONTIERS IN PLANT SCIENCE 2022; 13:888710. [PMID: 35720588 PMCID: PMC9204169 DOI: 10.3389/fpls.2022.888710] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/27/2022] [Indexed: 05/27/2023]
Abstract
The change in climatic conditions is the major cause for decline in crop production worldwide. Decreasing crop productivity will further lead to increase in global hunger rate. Climate change results in environmental stress which has negative impact on plant-like deficiencies in growth, crop yield, permanent damage, or death if the plant remains in the stress conditions for prolonged period. Cold stress is one of the main abiotic stresses which have already affected the global crop production. Cold stress adversely affects the plants leading to necrosis, chlorosis, and growth retardation. Various physiological, biochemical, and molecular responses under cold stress have revealed that the cold resistance is more complex than perceived which involves multiple pathways. Like other crops, legumes are also affected by cold stress and therefore, an effective technique to mitigate cold-mediated damage is critical for long-term legume production. Earlier, crop improvement for any stress was challenging for scientific community as conventional breeding approaches like inter-specific or inter-generic hybridization had limited success in crop improvement. The availability of genome sequence, transcriptome, and proteome data provides in-depth sight into different complex mechanisms under cold stress. Identification of QTLs, genes, and proteins responsible for cold stress tolerance will help in improving or developing stress-tolerant legume crop. Cold stress can alter gene expression which further leads to increases in stress protecting metabolites to cope up the plant against the temperature fluctuations. Moreover, genetic engineering can help in development of new cold stress-tolerant varieties of legume crop. This paper provides a general insight into the "omics" approaches for cold stress in legume crops.
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Affiliation(s)
- Kaisar Ahmad Bhat
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Reetika Mahajan
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
| | - Mohammad Maqbool Pakhtoon
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
- Department of Life Sciences, Rabindranath Tagore University, Bhopal, India
| | - Uneeb Urwat
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
| | - Zaffar Bashir
- Deparment of Microbiology, University of Kashmir, Srinagar, India
| | - Ali Asghar Shah
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ankit Agrawal
- Department of Life Sciences, Rabindranath Tagore University, Bhopal, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Parvaze A. Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, India
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Ding D, Li J, Xie J, Li N, Bakpa EP, Han K, Yang Y, Wang C. Exogenous Zeaxanthin Alleviates Low Temperature Combined with Low Light Induced Photosynthesis Inhibition and Oxidative Stress in Pepper (Capsicum annuum L.) Plants. Curr Issues Mol Biol 2022; 44:2453-2471. [PMID: 35735609 PMCID: PMC9221838 DOI: 10.3390/cimb44060168] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
Low temperature combined with low light (LL) affects crop production, especially the yield and quality of peppers, in northwest China during the winter and spring seasons. Zeaxanthin (Z) is a known lipid protectant and active oxygen scavenger. However, whether exogenous Z can mitigate LL-induced inhibition of photosynthesis and oxidative stress in peppers remains unclear. In this study, we investigated the effects of exogenous Z on photosynthesis and the antioxidant machinery of pepper seedlings subject to LL stress. The results showed that the growth and photosynthesis of pepper seedlings were significantly inhibited by LL stress. In addition, the antioxidant machinery was disturbed by the uneven production and elimination of reactive oxygen species (ROS), which resulted in damage to the pepper. For example, membrane lipid peroxidation increased ROS content, and so on. However, exogenous application of Z before LL stress significantly increased the plant height, stem diameter, net photosynthetic rate (Pn), and stomata, which were obviously closed at LL. The activities of antioxidant enzymes superoxide dismutase (SOD), catalase (CAT), mono de-hydroascorbate reductase (MDHAR), de-hydroascorbate reductase (DHAR), ascorbate peroxidase (APX), and ascorbate oxidase (AAO) improved significantly due to the increased expression of CaSOD, CaCAT, CaAPX, CaMDHAR, and CaDHAR. The ascorbic (AsA) and glutathione (GSH) contents and ascorbic/dehydroascorbate (AsA/DHA) and glutathione/oxidized glutathione (GSH/GSSG) ratios also increased significantly, resulting in the effective removal of hydrogen peroxide (H2O2) and superoxide anions (O2•−) caused by LL stress. Thus, pre-treatment with Z significantly reduced ROS accumulation in pepper seedlings under LL stress by enhancing the activity of antioxidant enzymes and accumulation of components of the ascorbate–glutathione (AsA–GSH) cycle and upregulated key genes in the AsA–GSH cycle.
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Burnett AC, Kromdijk J. Can we improve the chilling tolerance of maize photosynthesis through breeding? JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3138-3156. [PMID: 35143635 PMCID: PMC9126739 DOI: 10.1093/jxb/erac045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/02/2022] [Indexed: 05/11/2023]
Abstract
Chilling tolerance is necessary for crops to thrive in temperate regions where cold snaps and lower baseline temperatures place limits on life processes; this is particularly true for crops of tropical origin such as maize. Photosynthesis is often adversely affected by chilling stress, yet the maintenance of photosynthesis is essential for healthy growth and development, and most crucially for yield. In this review, we describe the physiological basis for enhancing chilling tolerance of photosynthesis in maize by examining nine key responses to chilling stress. We synthesize current knowledge of genetic variation for photosynthetic chilling tolerance in maize with respect to each of these traits and summarize the extent to which genetic mapping and candidate genes have been used to understand the genomic regions underpinning chilling tolerance. Finally, we provide perspectives on the future of breeding for photosynthetic chilling tolerance in maize. We advocate for holistic and high-throughput approaches to screen for chilling tolerance of photosynthesis in research and breeding programmes in order to develop resilient crops for the future.
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Affiliation(s)
- Angela C Burnett
- Department of Plant Sciences, University of CambridgeCambridge, UK
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46
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Freda PJ, Toxopeus J, Dowle EJ, Ali ZM, Heter N, Collier RL, Sower I, Tucker JC, Morgan TJ, Ragland GJ. Transcriptomic and functional genetic evidence for distinct ecophysiological responses across complex life cycle stages. J Exp Biol 2022; 225:275641. [PMID: 35578907 DOI: 10.1242/jeb.244063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/30/2022] [Indexed: 11/20/2022]
Abstract
Organisms with complex life cycles demonstrate a remarkable ability to change their phenotypes across development, presumably as an evolutionary adaptation to developmentally variable environments. Developmental variation in environmentally sensitive performance, and thermal sensitivity in particular, has been well documented in holometabolous insects. For example, thermal performance in adults and juvenile stages exhibit little genetic correlation (genetic decoupling) and can evolve independently, resulting in divergent thermal responses. Yet, we understand very little about how this genetic decoupling occurs. We tested the hypothesis that genetic decoupling of thermal physiology is driven by fundamental differences in physiology between life stages, despite a potentially conserved Cellular Stress Response. We used RNAseq to compare transcript expression in response to a cold stressor in Drosophila melanogaster larvae and adults and used RNAi (RNA interference) to test whether knocking down nine target genes differentially affected larval and adult cold tolerance. Transcriptomic responses of whole larvae and adults during and following exposure to -5°C were largely unique both in identity of responding transcripts and in temporal dynamics. Further, we analyzed the tissue-specificity of differentially-expressed transcripts from FlyAtlas 2 data, and concluded that stage-specific differences in transcription were not simply driven by differences in tissue composition. In addition, RNAi of target genes resulted in largely stage-specific and sometimes sex-specific effects on cold tolerance. The combined evidence suggests that thermal physiology is largely stage-specific at the level of gene expression, and thus natural selection may be acting on different loci during the independent thermal adaptation of different life stages.
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Affiliation(s)
- Philip J Freda
- Department of Entomology, Kansas State University, 1603 Old Claflin Place, Manhattan, KS 66506, USA
| | - Jantina Toxopeus
- Department of Integrative Biology, University of Colorado Denver, 1151 Arapahoe St., Denver, CO 80204, USA
| | - Edwina J Dowle
- Department of Integrative Biology, University of Colorado Denver, 1151 Arapahoe St., Denver, CO 80204, USA
| | - Zainab M Ali
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Nicholas Heter
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Rebekah L Collier
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Isaiah Sower
- Department of Integrative Biology, University of Colorado Denver, 1151 Arapahoe St., Denver, CO 80204, USA
| | - Joseph C Tucker
- Department of Integrative Biology, University of Colorado Denver, 1151 Arapahoe St., Denver, CO 80204, USA
| | - Theodore J Morgan
- Division of Biology, Kansas State University, 116 Ackert Hall, Manhattan, KS 66506, USA
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado Denver, 1151 Arapahoe St., Denver, CO 80204, USA
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Genome-Wide Analysis of the Trehalose-6-Phosphate Synthase Gene Family in Rose (Rosa chinensis) and Differential Expression under Heat Stress. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050429] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Trehalose and some members of the trehalose 6-phosphate synthase (TPS) gene family play important roles in response to abiotic stress in plants. However, no studies investigating the TPS gene in rose have been reported. In this study, the trehalose content in the stems and roots of Rosa chinensis was significantly increased under heat stress, and nine TPS family members were identified from the genome of R. chinensis. The R. chinensis TPS (RcTPS) family members could be divided into two subfamilies based on the structure and phylogenetic analysis. In this study, we found that segmental duplications contributed to the expansion of the RcTPS gene family, and the type II subfamily gene pairs RcTPS9–RcTPS10 and RcTPS7a–RcTPS7b were created by segmental duplication events. The type I subfamily RcTPS members contained 17 exons in the protein-coding region, whereas type II subfamily members only had 3 or 4 exons. Most cis-acting elements in the promoters of RcTPS members were related to plant hormones, especially ABA hormones. A phylogenetic tree of 78 TPS homologous amino acids from R. chinensis and another 7 species was constructed, which could be divided into 5 clades, and purity selection was observed to be the dominant evolutionary selection pressure. Under heat stress, except for RcTPS1b, the other eight RcTPS members were upregulated in the roots, stems, orleaves. The type II subfamily members RcTPS7a and RcTPS7b showed significantly high expression patterns in response to heat stress in all three tissues. Our findings indicate that RcTPS7a and RcTPS7b may play important roles in the heat tolerance of R. chinensis and are helpful for future functional studies of the two RcTPS members during heat stress.
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Tang B, Xie L, Yang H, Li X, Chen Y, Zou X, Liu F, Dai X. Analysis of the Expression and Function of Key Genes in Pepper Under Low-Temperature Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:852511. [PMID: 35599873 PMCID: PMC9116226 DOI: 10.3389/fpls.2022.852511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
The mechanism of resistance of plants to cold temperatures is very complicated, and the molecular mechanism and related gene network in pepper are largely unknown. Here, during cold treatment, we used cluster analysis (k-means) to classify all expressed genes into 15 clusters, 3,680 and 2,405 differentially expressed genes (DEGs) were observed in the leaf and root, respectively. The DEGs associated with certain important basic metabolic processes, oxidoreductase activity, and overall membrane compositions were most significantly enriched. In addition, based on the homologous sequence alignment of Arabidopsis genes, we identified 14 positive and negative regulators of the ICE-CBF-COR module in pepper, including CBF and ICE, and compared their levels in different data sets. The correlation matrix constructed based on the expression patterns of whole pepper genes in leaves and roots after exposure to cold stress showed the correlation between 14 ICE-CBF-COR signaling module genes, and provided insight into the relationship between these genes in pepper. These findings not only provide valuable resources for research on cold tolerance, but also lay the foundation for the genetic modification of cold stress regulators, which would help us achieve improved crop tolerance. To our knowledge, this is the first study to demonstrate the relationship between positive and negative regulators related to the ICE-CBF-COR module, which is of great significance to the study of low-temperature adaptive mechanisms in plants.
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Affiliation(s)
- Bingqian Tang
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Longping Branch, Graduate School of Hunan University, Changsha, China
- ERC for Germplasm Innovation and New Variety, Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Lingling Xie
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Huiping Yang
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Xiumin Li
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Ying Chen
- Longping Branch, Graduate School of Hunan University, Changsha, China
| | - Xuexiao Zou
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Longping Branch, Graduate School of Hunan University, Changsha, China
- ERC for Germplasm Innovation and New Variety, Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Feng Liu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Longping Branch, Graduate School of Hunan University, Changsha, China
- ERC for Germplasm Innovation and New Variety, Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
| | - Xiongze Dai
- College of Horticulture, Hunan Agricultural University, Changsha, China
- ERC for Germplasm Innovation and New Variety, Breeding of Horticultural Crops, Changsha, China
- Key Laboratory for Vegetable Biology of Hunan Province, Changsha, China
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A Circular Economy Approach to Restoring Soil Substrate Ameliorated by Sewage Sludge with Amendments. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095296. [PMID: 35564693 PMCID: PMC9103250 DOI: 10.3390/ijerph19095296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 02/05/2023]
Abstract
This study examined the use of an artificial soil substrate in a mine waste reclamation area and its effect on plant metabolic functions. Research was conducted by determining the relationship between the plants’ biochemical features and the properties of plant growth medium derived from post-flotation coal waste, sewage sludge, crushed stone and fly ash on the surface of the mine waste disposal area. Trees and shrubs were established on the material and allowed to grow for eight years. The study determined that the applied plants and the naturally occurring Taraxacum officinale were suitable for physio-biochemical assessment, identification of derelict areas and reclamation purposes. An evaluation of a soil substrate applied to post-mining areas indicated that it was beneficial for plant growth since it activated the metabolic functions of herbaceous plants, shrubs, and trees. The study showed that soil substrate can be targeted to improve plant stress tolerance to potentially toxic elements (PTEs). These data suggest the potential for growth and slower susceptible response to Cd, Cr, Cu, Fe, Mn, Ni, Pb and Zn. It is possible that the constructed soil-substitute substrate (biosolid material) would be an effective reclamation treatment in areas where natural soil materials are polluted by PTEs. This observation may reflect a more efficient use of soil substrate released from the cycling of organic biogene pools, in accordance with the circular economy approach. In further studies related to land reclamation using sewage sludge amendments, it would be necessary to extend the research to other stress factors, such as salinity or water deficiency.
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Kang Y, Lee K, Hoshikawa K, Kang M, Jang S. Molecular Bases of Heat Stress Responses in Vegetable Crops With Focusing on Heat Shock Factors and Heat Shock Proteins. FRONTIERS IN PLANT SCIENCE 2022; 13:837152. [PMID: 35481144 PMCID: PMC9036485 DOI: 10.3389/fpls.2022.837152] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/09/2022] [Indexed: 05/09/2023]
Abstract
The effects of the climate change including an increase in the average global temperatures, and abnormal weather events such as frequent and severe heatwaves are emerging as a worldwide ecological concern due to their impacts on plant vegetation and crop productivity. In this review, the molecular processes of plants in response to heat stress-from the sensing of heat stress, the subsequent molecular cascades associated with the activation of heat shock factors and their primary targets (heat shock proteins), to the cellular responses-have been summarized with an emphasis on the classification and functions of heat shock proteins. Vegetables contain many essential vitamins, minerals, antioxidants, and fibers that provide many critical health benefits to humans. The adverse effects of heat stress on vegetable growth can be alleviated by developing vegetable crops with enhanced thermotolerance with the aid of various genetic tools. To achieve this goal, a solid understanding of the molecular and/or cellular mechanisms underlying various responses of vegetables to high temperature is imperative. Therefore, efforts to identify heat stress-responsive genes including those that code for heat shock factors and heat shock proteins, their functional roles in vegetable crops, and also their application to developing vegetables tolerant to heat stress are discussed.
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Affiliation(s)
- Yeeun Kang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
| | - Kwanuk Lee
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju-gun, South Korea
| | - Ken Hoshikawa
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | | | - Seonghoe Jang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
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