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Hou Y, Li Q, Zhou H, Kafle S, Li W, Tan L, Liang J, Meng L, Xin H. SMRT sequencing of a full-length transcriptome reveals cold induced alternative splicing in Vitis amurensis root. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108863. [PMID: 38917739 DOI: 10.1016/j.plaphy.2024.108863] [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: 03/02/2024] [Revised: 05/31/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Alternative splicing enhances diversity at the transcriptional and protein levels that widely involved in plant response to biotic and abiotic stresses. V. amurensis is an extremely cold-tolerant wild grape variety, however, studies on alternative splicing (AS) in amur grape at low temperatures are currently poorly understood. In this study, we analyzed full-length transcriptome and RNA seq data at 0, 2, and 24 h after cold stress in V. amurensis roots. Following quality control and correction, 221,170 high-quality full-length non-concatemer (FLNC) reads were identified. A total of 16,181 loci and 30,733 isoforms were identified. These included 22,868 novel isoforms from annotated genes and 2815 isoforms from 2389 novel genes. Among the distinguished novel isoforms, 673 Long non-coding RNAs (LncRNAs) and 18,164 novel isoforms open reading frame (ORF) region were found. A total of 2958 genes produced 8797 AS events, of which 189 genes were involved in the low-temperature response. Twelve transcription factors show AS during cold treatment and VaMYB108 was selected for initial exploration. Two transcripts, Chr05.63.1 (VaMYB108short) and Chr05.63.2 (VaMYB108normal) of VaMYB108, display up-regulated expression after cold treatment in amur grape roots and are both localized in the nucleus. Only VaMYB108normal exhibits transcriptional activation activity. Overexpression of either VaMYB108short or VaMYB108normal in grape roots leads to increased expression of the other transcript and both increased chilling resistance of amur grape roots. The results improve and supplement the genome annotations and provide insights for further investigation into AS mechanisms during cold stress in V. amurensis.
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Affiliation(s)
- Yujun Hou
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingyun Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huimin Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Subash Kafle
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjuan Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lisha Tan
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ju Liang
- Turpan Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang, 830091, China
| | - Lin Meng
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Haiping Xin
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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2
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Ganie SA, McMulkin N, Devoto A. The role of priming and memory in rice environmental stress adaptation: Current knowledge and perspectives. PLANT, CELL & ENVIRONMENT 2024; 47:1895-1915. [PMID: 38358119 DOI: 10.1111/pce.14855] [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: 09/06/2023] [Revised: 12/21/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Plant responses to abiotic stresses are dynamic, following the unpredictable changes of physical environmental parameters such as temperature, water and nutrients. Physiological and phenotypical responses to stress are intercalated by periods of recovery. An earlier stress can be remembered as 'stress memory' to mount a response within a generation or transgenerationally. The 'stress priming' phenomenon allows plants to respond quickly and more robustly to stressors to increase survival, and therefore has significant implications for agriculture. Although evidence for stress memory in various plant species is accumulating, understanding of the mechanisms implicated, especially for crops of agricultural interest, is in its infancy. Rice is a major food crop which is susceptible to abiotic stresses causing constraints on its cultivation and yield globally. Advancing the understanding of the stress response network will thus have a significant impact on rice sustainable production and global food security in the face of climate change. Therefore, this review highlights the effects of priming on rice abiotic stress tolerance and focuses on specific aspects of stress memory, its perpetuation and its regulation at epigenetic, transcriptional, metabolic as well as physiological levels. The open questions and future directions in this exciting research field are also laid out.
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Affiliation(s)
- Showkat Ahmad Ganie
- Department of Biological Sciences, Plant Molecular Science and Centre of Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, UK
| | - Nancy McMulkin
- Department of Biological Sciences, Plant Molecular Science and Centre of Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, UK
| | - Alessandra Devoto
- Department of Biological Sciences, Plant Molecular Science and Centre of Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, UK
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Xu WB, Cao F, Liu P, Yan K, Guo QH. The multifaceted role of RNA-based regulation in plant stress memory. FRONTIERS IN PLANT SCIENCE 2024; 15:1387575. [PMID: 38736453 PMCID: PMC11082352 DOI: 10.3389/fpls.2024.1387575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024]
Abstract
Plants have evolved interconnected regulatory pathways which enable them to respond and adapt to their environments. In plants, stress memory enhances stress tolerance through the molecular retention of prior stressful experiences, fostering rapid and robust responses to subsequent challenges. Mounting evidence suggests a close link between the formation of stress memories and effective future stress responses. However, the mechanism by which environmental stressors trigger stress memory formation is poorly understood. Here, we review the current state of knowledge regarding the RNA-based regulation on stress memory formation in plants and discuss research challenges and future directions. Specifically, we focus on the involvement of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and alternative splicing (AS) in stress memory formation. miRNAs regulate target genes via post-transcriptional silencing, while siRNAs trigger stress memory formation through RNA-directed DNA methylation (RdDM). lncRNAs guide protein complexes for epigenetic regulation, and AS of pre-mRNAs is crucial to plant stress memory. Unraveling the mechanisms underpinning RNA-mediated stress memory formation not only advances our knowledge of plant biology but also aids in the development of improved stress tolerance in crops, enhancing crop performance and global food security.
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Affiliation(s)
- Wei-Bo Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Fan Cao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Peng Liu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Qian-Huan Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
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Kim N, Lee J, Yeom SI, Kang NJ, Kang WH. The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper. Sci Data 2024; 11:381. [PMID: 38615136 PMCID: PMC11016105 DOI: 10.1038/s41597-024-03239-7] [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: 09/12/2023] [Accepted: 04/05/2024] [Indexed: 04/15/2024] Open
Abstract
Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA-seq datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. We report RNA-seq datasets (350.7 Gb) from Capsicum annuum inoculated with one of three bacteria, one virus, or one oomycete and obtained additional existing transcriptome datasets. In this study, we investigated the landscape of AS in response to environmental stressors, signaling molecules, and tissues from 425 total samples comprising 841.49 Gb. In addition, we identified genes that undergo AS under specific and shared stress conditions to obtain potential genes that may be involved in enhancing tolerance to stressors. We uncovered 1,642,007 AS events and identified 4,354 differential alternative splicing genes related to environmental stressors, tissues, and signaling molecules. This information and approach provide useful data for basic-research focused on enhancing tolerance to environmental stressors in hot pepper or establishing breeding programs.
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Affiliation(s)
- Nayoung Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
| | - Junesung Lee
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
| | - Seon-In Yeom
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
- Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, South Korea
| | - Nam-Jun Kang
- Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, South Korea
| | - Won-Hee Kang
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea.
- Department of Horticulture, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, South Korea.
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Han M, Niu M, Gao T, Shen Y, Zhou X, Zhang Y, Liu L, Chai M, Sun G, Wang Y. Responsive Alternative Splicing Events of Opisthopappus Species against Salt Stress. Int J Mol Sci 2024; 25:1227. [PMID: 38279226 PMCID: PMC10816081 DOI: 10.3390/ijms25021227] [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: 11/06/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
Salt stress profoundly affects plant growth, prompting intricate molecular responses, such as alternative splicing (AS), for environmental adaptation. However, the response of AS events to salt stress in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear, which is a Taihang Mountain cliff-dwelling species. Using RNA-seq data, differentially expressed genes (DEGs) were identified under time and concentration gradients of salt stress. Two types of AS, skipped exon (SE) and mutually exclusive exons (MXE), were found. Differentially alternative splicing (DAS) genes in both species were significantly enriched in "protein phosphorylation", "starch and sucrose metabolism", and "plant hormone signal transduction" pathways. Meanwhile, distinct GO terms and KEGG pathways of DAS occurred between two species. Only a small subset of DAS genes overlapped with DEGs under salt stress. Although both species likely adopted protein phosphorylation to enhance salt stress tolerance, they exhibited distinct responses. The results indicated that the salt stress mechanisms of both Opisthopappus species exhibited similarities and differences in response to salt stress, which suggested that adaptive divergence might have occurred between them. This study initially provides a comprehensive description of salt responsive AS events in Opisthopappus and conveys some insights into the molecular mechanisms behind species tolerance on the Taihang Mountains.
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Affiliation(s)
- Mian Han
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Mengfan Niu
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Ting Gao
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Yuexin Shen
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Xiaojuan Zhou
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Yimeng Zhang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Li Liu
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Min Chai
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
| | - Genlou Sun
- Department of Botany, Saint Mary’s University, Halifax, NS B3H 3C3, Canada
| | - Yiling Wang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China; (M.H.)
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Du Y, Cao L, Wang S, Guo L, Tan L, Liu H, Feng Y, Wu W. Differences in alternative splicing and their potential underlying factors between animals and plants. J Adv Res 2023:S2090-1232(23)00354-5. [PMID: 37981087 DOI: 10.1016/j.jare.2023.11.017] [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: 05/07/2023] [Revised: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed. AIM OF REVIEW This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants. KEY SCIENTIFIC CONCEPTS OF REVIEW We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.
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Affiliation(s)
- Yunfei Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lu Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Ying Feng
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
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Ye LX, Wu YM, Zhang JX, Zhang JX, Zhou H, Zeng RF, Zheng WX, Qiu MQ, Zhou JJ, Xie ZZ, Hu CG, Zhang JZ. A bZIP transcription factor (CiFD) regulates drought- and low-temperature-induced flowering by alternative splicing in citrus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:674-691. [PMID: 36250511 DOI: 10.1111/jipb.13390] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/13/2022] [Indexed: 05/20/2023]
Abstract
Drought and low temperature are two key environmental factors that induce adult citrus flowering. However, the underlying regulation mechanism is poorly understood. The bZIP transcription factor FD is a key component of the florigen activation complex (FAC) which is composed of FLOWERING LOCUS T (FT), FD, and 14-3-3 proteins. In this study, isolation and characterization of CiFD in citrus found that there was alternative splicing (AS) of CiFD, forming two different proteins (CiFDα and CiFDβ). Further investigation found that their expression patterns were similar in different tissues of citrus, but the subcellular localization and transcriptional activity were different. Overexpression of the CiFD DNA sequence (CiFD-DNA), CiFDα, or CiFDβ in tobacco and citrus showed early flowering, and CiFD-DNA transgenic plants were the earliest, followed by CiFDβ and CiFDα. Interestingly, CiFDα and CiFDβ were induced by low temperature and drought, respectively. Further analysis showed that CiFDα can form a FAC complex with CiFT, Ci14-3-3, and then bind to the citrus APETALA1 (CiAP1) promoter and promote its expression. However, CiFDβ can directly bind to the CiAP1 promoter independently of CiFT and Ci14-3-3. These results showed that CiFDβ can form a more direct and simplified pathway that is independent of the FAC complex to regulate drought-induced flowering through AS. In addition, a bHLH transcription factor (CibHLH96) binds to CiFD promoter and promotes the expression of CiFD under drought condition. Transgenic analysis found that CibHLH96 can promote flowering in transgenic tobacco. These results suggest that CiFD is involved in drought- and low-temperature-induced citrus flowering through different regulatory patterns.
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Affiliation(s)
- Li-Xia Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Yan-Mei Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin-Xia Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin-Xin Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huan Zhou
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ren-Fang Zeng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei-Xuan Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei-Qi Qiu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing-Jing Zhou
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zong-Zhou Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
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Kambona CM, Koua PA, Léon J, Ballvora A. Stress memory and its regulation in plants experiencing recurrent drought conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:26. [PMID: 36788199 PMCID: PMC9928933 DOI: 10.1007/s00122-023-04313-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Developing stress-tolerant plants continues to be the goal of breeders due to their realized yields and stability. Plant responses to drought have been studied in many different plant species, but the occurrence of stress memory as well as the potential mechanisms for memory regulation is not yet well described. It has been observed that plants hold on to past events in a way that adjusts their response to new challenges without altering their genetic constitution. This ability could enable training of plants to face future challenges that increase in frequency and intensity. A better understanding of stress memory-associated mechanisms leading to alteration in gene expression and how they link to physiological, biochemical, metabolomic and morphological changes would initiate diverse opportunities to breed stress-tolerant genotypes through molecular breeding or biotechnological approaches. In this perspective, this review discusses different stress memory types and gives an overall view using general examples. Further, focusing on drought stress, we demonstrate coordinated changes in epigenetic and molecular gene expression control mechanisms, the associated transcription memory responses at the genome level and integrated biochemical and physiological responses at cellular level following recurrent drought stress exposures. Indeed, coordinated epigenetic and molecular alterations of expression of specific gene networks link to biochemical and physiological responses that facilitate acclimation and survival of an individual plant during repeated stress.
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Affiliation(s)
- Carolyn Mukiri Kambona
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany
| | - Patrice Ahossi Koua
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany
- Deutsche Saatveredelung AG, Thüler Str. 30, 33154, Salzkotten-Thüle, Germany
| | - Jens Léon
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany
- Field Lab Campus Klein-Altendorf, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Agim Ballvora
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany.
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ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data. Int J Mol Sci 2022; 23:ijms23084079. [PMID: 35456896 PMCID: PMC9031537 DOI: 10.3390/ijms23084079] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) is an essential co-transcriptional regulatory mechanism in eukaryotes. The accumulation of plant RNA-Seq data provides an unprecedented opportunity to investigate the global landscape of plant AS events. However, most existing AS identification tools were originally designed for animals, and their performance in plants was not rigorously benchmarked. In this work, we developed a simple and easy-to-use bioinformatics tool named ASTool for detecting AS events from plant RNA-Seq data. As an exon-based method, ASTool can detect 4 major AS types, including intron retention (IR), exon skipping (ES), alternative 5′ splice sites (A5SS), and alternative 3′ splice sites (A3SS). Compared with existing tools, ASTool revealed a favorable performance when tested in simulated RNA-Seq data, with both recall and precision values exceeding 95% in most cases. Moreover, ASTool also showed a competitive computational speed and consistent detection results with existing tools when tested in simulated or real plant RNA-Seq data. Considering that IR is the most predominant AS type in plants, ASTool allowed the detection and visualization of novel IR events based on known splice sites. To fully present the functionality of ASTool, we also provided an application example of ASTool in processing real RNA-Seq data of Arabidopsis in response to heat stress.
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10
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Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice. Int J Mol Sci 2022; 23:ijms23031608. [PMID: 35163531 PMCID: PMC8836195 DOI: 10.3390/ijms23031608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/16/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS56 showed different alternate splicing (AS) events between genotypes and day length conditions. OsMADS56 was expressed in PSRR-1 but not in Cypress under both LD and SD conditions. Based on variations in both sequence and expression, the unique flowering response in PSRR-1 may be due to the high-impact variants of flowering genes, and OsMADS56 is proposed as a key regulator for its day-neutral flowering response.
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11
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Jacques C, Salon C, Barnard RL, Vernoud V, Prudent M. Drought Stress Memory at the Plant Cycle Level: A Review. PLANTS (BASEL, SWITZERLAND) 2021; 10:1873. [PMID: 34579406 PMCID: PMC8466371 DOI: 10.3390/plants10091873] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/07/2021] [Accepted: 09/07/2021] [Indexed: 05/25/2023]
Abstract
Plants are sessile organisms whose survival depends on their strategy to cope with dynamic, stressful conditions. It is urgent to improve the ability of crops to adapt to recurrent stresses in order to alleviate the negative impacts on their productivity. Although our knowledge of plant adaptation to drought has been extensively enhanced during the last decades, recent studies have tackled plant responses to recurrent stresses. The present review synthesizes the major findings from studies addressing plant responses to multiple drought events, and demonstrates the ability of plants to memorize drought stress. Stress memory is described as a priming effect allowing a different response to a reiterated stress when compared to a single stress event. Here, by specifically focusing on water stress memory at the plant cycle level, we describe the different underlying processes at the molecular, physiological and morphological levels in crops as well as in the model species Arabidopsis thaliana. Moreover, a conceptual analysis framework is proposed to study drought stress memory. Finally, the essential role of interactions between plants and soil microorganisms is emphasized during reiterated stresses because their plasticity can play a key role in supporting overall plant resilience.
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Affiliation(s)
| | | | | | | | - Marion Prudent
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Université Bourgogne Franche-Comté, F-21000 Dijon, France; (C.J.); (C.S.); (R.L.B.); (V.V.)
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Ganie SA, Reddy ASN. Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance. BIOLOGY 2021; 10:309. [PMID: 33917813 PMCID: PMC8068108 DOI: 10.3390/biology10040309] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/20/2022]
Abstract
Improvements in yield and quality of rice are crucial for global food security. However, global rice production is substantially hindered by various biotic and abiotic stresses. Making further improvements in rice yield is a major challenge to the rice research community, which can be accomplished through developing abiotic stress-resilient rice varieties and engineering durable agrochemical-independent pathogen resistance in high-yielding elite rice varieties. This, in turn, needs increased understanding of the mechanisms by which stresses affect rice growth and development. Alternative splicing (AS), a post-transcriptional gene regulatory mechanism, allows rapid changes in the transcriptome and can generate novel regulatory mechanisms to confer plasticity to plant growth and development. Mounting evidence indicates that AS has a prominent role in regulating rice growth and development under stress conditions. Several regulatory and structural genes and splicing factors of rice undergo different types of stress-induced AS events, and the functional significance of some of them in stress tolerance has been defined. Both rice and its pathogens use this complex regulatory mechanism to devise strategies against each other. This review covers the current understanding and evidence for the involvement of AS in biotic and abiotic stress-responsive genes, and its relevance to rice growth and development. Furthermore, we discuss implications of AS for the virulence of different rice pathogens and highlight the areas of further research and potential future avenues to develop climate-smart and disease-resistant rice varieties.
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Affiliation(s)
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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