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Kallemi P, Verret F, Andronis C, Ioannidis N, Glampedakis N, Kotzabasis K, Kalantidis K. Stress-related transcriptomic changes associated with GFP transgene expression and active transgene silencing in plants. Sci Rep 2024; 14:13314. [PMID: 38858413 PMCID: PMC11164987 DOI: 10.1038/s41598-024-63527-5] [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: 03/30/2023] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Plants respond to biotic and abiotic stress by activating and interacting with multiple defense pathways, allowing for an efficient global defense response. RNA silencing is a conserved mechanism of regulation of gene expression directed by small RNAs important in acquired plant immunity and especially virus and transgene repression. Several RNA silencing pathways in plants are crucial to control developmental processes and provide protection against abiotic and biotic stresses as well as invasive nucleic acids such as viruses and transposable elements. Various notable studies have shed light on the genes, small RNAs, and mechanisms involved in plant RNA silencing. However, published research on the potential interactions between RNA silencing and other plant stress responses is limited. In the present study, we tested the hypothesis that spreading and maintenance of systemic post-transcriptional gene silencing (PTGS) of a GFP transgene are associated with transcriptional changes that pertain to non-RNA silencing-based stress responses. To this end, we analyzed the structure and function of the photosynthetic apparatus and conducted whole transcriptome analysis in a transgenic line of Nicotiana benthamiana that spontaneously initiates transgene silencing, at different stages of systemic GFP-PTGS. In vivo analysis of chlorophyll a fluorescence yield and expression levels of key photosynthetic genes indicates that photosynthetic activity remains unaffected by systemic GFP-PTGS. However, transcriptomic analysis reveals that spreading and maintenance of GFP-PTGS are associated with transcriptional reprogramming of genes that are involved in abiotic stress responses and pattern- or effector-triggered immunity-based stress responses. These findings suggest that systemic PTGS may affect non-RNA-silencing-based defense pathways in N. benthamiana, providing new insights into the complex interplay between different plant stress responses.
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Affiliation(s)
- Paraskevi Kallemi
- Department of Biology, University of Crete, 70013, Heraklion, Greece
| | - Frederic Verret
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece
| | - Christos Andronis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece
| | | | | | | | - Kriton Kalantidis
- Department of Biology, University of Crete, 70013, Heraklion, Greece.
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece.
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Murmu S, Sinha D, Chaurasia H, Sharma S, Das R, Jha GK, Archak S. A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions. FRONTIERS IN PLANT SCIENCE 2024; 15:1292054. [PMID: 38504888 PMCID: PMC10948452 DOI: 10.3389/fpls.2024.1292054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/24/2024] [Indexed: 03/21/2024]
Abstract
Plants intricately deploy defense systems to counter diverse biotic and abiotic stresses. Omics technologies, spanning genomics, transcriptomics, proteomics, and metabolomics, have revolutionized the exploration of plant defense mechanisms, unraveling molecular intricacies in response to various stressors. However, the complexity and scale of omics data necessitate sophisticated analytical tools for meaningful insights. This review delves into the application of artificial intelligence algorithms, particularly machine learning and deep learning, as promising approaches for deciphering complex omics data in plant defense research. The overview encompasses key omics techniques and addresses the challenges and limitations inherent in current AI-assisted omics approaches. Moreover, it contemplates potential future directions in this dynamic field. In summary, AI-assisted omics techniques present a robust toolkit, enabling a profound understanding of the molecular foundations of plant defense and paving the way for more effective crop protection strategies amidst climate change and emerging diseases.
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Affiliation(s)
- Sneha Murmu
- Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Dipro Sinha
- Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Himanshushekhar Chaurasia
- Central Institute for Research on Cotton Technology, Indian Council of Agricultural Research (ICAR), Mumbai, India
| | - Soumya Sharma
- Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Ritwika Das
- Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Girish Kumar Jha
- Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Sunil Archak
- National Bureau of Plant Genetic Resources, Indian Council of Agricultural Research (ICAR), New Delhi, India
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Wu Y, Sun R, Huan T, Zhao Y, Yu D, Sun Y. An insight into the gene expression evolution in Gossypium species based on the leaf transcriptomes. BMC Genomics 2024; 25:179. [PMID: 38355396 PMCID: PMC10868065 DOI: 10.1186/s12864-024-10091-x] [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: 08/16/2023] [Accepted: 02/05/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Gene expression pattern is associated with biological phenotype and is widely used in exploring gene functions. Its evolution is also crucial in understanding species speciation and divergence. The genus Gossypium is a bona fide model for studying plant evolution and polyploidization. However, the evolution of gene expression during cotton species divergence has yet to be extensively discussed. RESULTS Based on the seedling leaf transcriptomes, this work analyzed the transcriptomic content and expression patterns across eight cotton species, including six diploids and two natural tetraploids. Our findings indicate that, while the biological function of these cotton transcriptomes remains largely conserved, there has been significant variation in transcriptomic content during species divergence. Furthermore, we conducted a comprehensive analysis of expression distances across cotton species. This analysis lends further support to the use of G. arboreum as a substitute for the A-genome donor of natural cotton polyploids. Moreover, our research highlights the evolution of stress-responsive pathways, including hormone signaling, fatty acid degradation, and flavonoid biosynthesis. These processes appear to have evolved under lower selection pressures, presumably reflecting their critical role in the adaptations of the studied cotton species to diverse environments. CONCLUSIONS In summary, this study provided insights into the gene expression variation within the genus Gossypium and identified essential genes/pathways whose expression evolution was closely associated with the evolution of cotton species. Furthermore, the method of characterizing genes and pathways under unexpected high or slow selection pressure can also serve as a new strategy for gene function exploration.
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Affiliation(s)
- Yuqing Wu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Rongnan Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Tong Huan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yanyan Zhao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Dongliang Yu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Yuqiang Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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Haq SAU, Bashir T, Roberts TH, Husaini AM. Ameliorating the effects of multiple stresses on agronomic traits in crops: modern biotechnological and omics approaches. Mol Biol Rep 2023; 51:41. [PMID: 38158512 DOI: 10.1007/s11033-023-09042-8] [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: 12/15/2022] [Accepted: 10/13/2023] [Indexed: 01/03/2024]
Abstract
While global climate change poses a significant environmental threat to agriculture, the increasing population is another big challenge to food security. To address this, developing crop varieties with increased productivity and tolerance to biotic and abiotic stresses is crucial. Breeders must identify traits to ensure higher and consistent yields under inconsistent environmental challenges, possess resilience against emerging biotic and abiotic stresses and satisfy customer demands for safer and more nutritious meals. With the advent of omics-based technologies, molecular tools are now integrated with breeding to understand the molecular genetics of genotype-based traits and develop better climate-smart crops. The rapid development of omics technologies offers an opportunity to generate novel datasets for crop species. Identifying genes and pathways responsible for significant agronomic traits has been made possible by integrating omics data with genetic and phenotypic information. This paper discusses the importance and use of omics-based strategies, including genomics, transcriptomics, proteomics and phenomics, for agricultural and horticultural crop improvement, which aligns with developing better adaptability in these crop species to the changing climate conditions.
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Affiliation(s)
- Syed Anam Ul Haq
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Tanzeel Bashir
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Thomas H Roberts
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, Sydney Institute of Agriculture, The University of Sydney, Eveleigh, Australia
| | - Amjad M Husaini
- Genome Engineering and Societal Biotechnology Lab, Division of Plant Biotechnology, SKUAST-K, Shalimar, Srinagar, Jammu and Kashmir, 190025, India.
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Fouché M, Bonnet H, Bonnet DMV, Wenden B. Transport capacity is uncoupled with endodormancy breaking in sweet cherry buds: physiological and molecular insights. FRONTIERS IN PLANT SCIENCE 2023; 14:1240642. [PMID: 38752012 PMCID: PMC11094712 DOI: 10.3389/fpls.2023.1240642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/25/2023] [Indexed: 05/18/2024]
Abstract
Introduction To avoid the negative impacts of winter unfavorable conditions for plant development, temperate trees enter a rest period called dormancy. Winter dormancy is a complex process that involves multiple signaling pathways and previous studies have suggested that transport capacity between cells and between the buds and the twig may regulate the progression throughout dormancy stages. However, the dynamics and molecular actors involved in this regulation are still poorly described in fruit trees. Methods Here, in order to validate the hypothesis that transport capacity regulates dormancy progression in fruit trees, we combined physiological, imaging and transcriptomic approaches to characterize molecular pathways and transport capacity during dormancy in sweet cherry (Prunus avium L.) flower buds. Results Our results show that transport capacity is reduced during dormancy and could be regulated by environmental signals. Moreover, we demonstrate that dormancy release is not synchronized with the transport capacity resumption but occurs when the bud is capable of growth under the influence of warmer temperatures. We highlight key genes involved in transport capacity during dormancy. Discussion Based on long-term observations conducted during six winter seasons, we propose hypotheses on the environmental and molecular regulation of transport capacity, in relation to dormancy and growth resumption in sweet cherry.
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Affiliation(s)
- Mathieu Fouché
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie 1332, Villenave d’Ornon, France
| | | | | | - Bénédicte Wenden
- INRAE, Univ. Bordeaux, UMR Biologie du Fruit et Pathologie 1332, Villenave d’Ornon, France
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Fu Q, Cao H, Wang L, Lei L, Di T, Ye Y, Ding C, Li N, Hao X, Zeng J, Yang Y, Wang X, Ye M, Huang J. Transcriptome Analysis Reveals That Ascorbic Acid Treatment Enhances the Cold Tolerance of Tea Plants through Cell Wall Remodeling. Int J Mol Sci 2023; 24:10059. [PMID: 37373207 DOI: 10.3390/ijms241210059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Cold stress is a major environmental factor that adversely affects the growth and productivity of tea plants. Upon cold stress, tea plants accumulate multiple metabolites, including ascorbic acid. However, the role of ascorbic acid in the cold stress response of tea plants is not well understood. Here, we report that exogenous ascorbic acid treatment improves the cold tolerance of tea plants. We show that ascorbic acid treatment reduces lipid peroxidation and increases the Fv/Fm of tea plants under cold stress. Transcriptome analysis indicates that ascorbic acid treatment down-regulates the expression of ascorbic acid biosynthesis genes and ROS-scavenging-related genes, while modulating the expression of cell wall remodeling-related genes. Our findings suggest that ascorbic acid treatment negatively regulates the ROS-scavenging system to maintain ROS homeostasis in the cold stress response of tea plants and that ascorbic acid's protective role in minimizing the harmful effects of cold stress on tea plants may occur through cell wall remodeling. Ascorbic acid can be used as a potential agent to increase the cold tolerance of tea plants with no pesticide residual concerns in tea.
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Affiliation(s)
- Qianyuan Fu
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongli Cao
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Food Science, Southwest University, Chongqing 400715, China
| | - Lu Wang
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Lei Lei
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Taimei Di
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Yufan Ye
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
- Key Laboratory of Tea Science in Universities of Fujian Province, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Changqing Ding
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Nana Li
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Xinyuan Hao
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Jianming Zeng
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Yajun Yang
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Xinchao Wang
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Meng Ye
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Jianyan Huang
- National Center for Tea Plant Improvement, Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
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Samarina L, Wang S, Malyukova L, Bobrovskikh A, Doroshkov A, Koninskaya N, Shkhalakhova R, Matskiv A, Fedorina J, Fizikova A, Manakhova K, Loshkaryova S, Tutberidze T, Ryndin A, Khlestkina E. Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant ( Camellia sinensis (L.) Kuntze). FRONTIERS IN PLANT SCIENCE 2023; 14:1145793. [PMID: 37235017 PMCID: PMC10206121 DOI: 10.3389/fpls.2023.1145793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/11/2023] [Indexed: 05/28/2023]
Abstract
Introduction Low temperatures and drought are two main environmental constraints reducing the yield and geographical distribution of horticultural crops worldwide. Understanding the genetic crosstalk between stress responses has potential importance for crop improvement. Methods In this study, Illumina RNA-seq and Pac-Bio genome resequencing were used to annotate genes and analyze transcriptome dynamics in tea plants under long-term cold, freezing, and drought. Results The highest number of differentially expressed genes (DEGs) was identified under long-term cold (7,896) and freezing (7,915), with 3,532 and 3,780 upregulated genes, respectively. The lowest number of DEGs was observed under 3-day drought (47) and 9-day drought (220), with five and 112 genes upregulated, respectively. The recovery after the cold had 6.5 times greater DEG numbers as compared to the drought recovery. Only 17.9% of cold-induced genes were upregulated by drought. In total, 1,492 transcription factor genes related to 57 families were identified. However, only 20 transcription factor genes were commonly upregulated by cold, freezing, and drought. Among the 232 common upregulated DEGs, most were related to signal transduction, cell wall remodeling, and lipid metabolism. Co-expression analysis and network reconstruction showed 19 genes with the highest co-expression connectivity: seven genes are related to cell wall remodeling (GATL7, UXS4, PRP-F1, 4CL, UEL-1, UDP-Arap, and TBL32), four genes are related to calcium-signaling (PXL1, Strap, CRT, and CIPK6), three genes are related to photo-perception (GIL1, CHUP1, and DnaJ11), two genes are related to hormone signaling (TTL3 and GID1C-like), two genes are involved in ROS signaling (ERO1 and CXE11), and one gene is related to the phenylpropanoid pathway (GALT6). Discussion Based on our results, several important overlapping mechanisms of long-term stress responses include cell wall remodeling through lignin biosynthesis, o-acetylation of polysaccharides, pectin biosynthesis and branching, and xyloglucan and arabinogalactan biosynthesis. This study provides new insight into long-term stress responses in woody crops, and a set of new target candidate genes were identified for molecular breeding aimed at tolerance to abiotic stresses.
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Affiliation(s)
- Lidiia Samarina
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Songbo Wang
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Lyudmila Malyukova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexandr Bobrovskikh
- Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey Doroshkov
- Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia Koninskaya
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Ruset Shkhalakhova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexandra Matskiv
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Jaroslava Fedorina
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Anastasia Fizikova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Karina Manakhova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Svetlana Loshkaryova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Tsiala Tutberidze
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexey Ryndin
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Elena Khlestkina
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
- Federal Research Center, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Saint Petersburg, Russia
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8
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Transcriptome and Physio-Biochemical Profiling Reveals Differential Responses of Rice Cultivars at Reproductive-Stage Drought Stress. Int J Mol Sci 2023; 24:ijms24021002. [PMID: 36674519 PMCID: PMC9863700 DOI: 10.3390/ijms24021002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/07/2023] Open
Abstract
Drought stress severely affects the growth and development of rice, especially at the reproductive stage, which results in disturbed metabolic processes, reduced seed-set/grain filling, deteriorated grain quality, declined productivity, and lower yield. Despite the recent advances in understanding the responses of rice to drought stress, there is a need to comprehensively integrate the morpho-physio-biochemical studies with the molecular responses/differential expression of genes and decipher the underlying pathways that regulate the adaptability of rice at various drought-sensitive growth stages. Our comparative analysis of immature panicle from a drought-tolerant (Nagina 22) and a drought-sensitive (IR 64) rice cultivar grown under control (well-watered) and water-deficit/drought stress (treatment, imposed at the reproductive stage) conditions unraveled some novel stress-responsive genes/pathways responsible for reproductive-stage drought stress tolerance. The results revealed a more important role of upregulated (6706) genes in the panicle of N 22 at reproductive-stage drought stress compared to that (5590) in IR 64. Functional enrichment and MapMan analyses revealed that majority of the DEGs were associated with the phytohormone, redox signalling/homeostasis, secondary metabolite, and transcription factor-mediated mitigation of the adverse effects of drought stress in N 22. The upregulated expression of the genes associated with starch/sucrose metabolism, secondary metabolites synthesis, transcription factors, glutathione, linoleic acid, and phenylalanine metabolism in N 22 was significantly more than that in the panicle of IR 64. Compared to IR 64, 2743 genes were upregulated in N 22 under control conditions, which further increased (4666) under drought stress in panicle of the tolerant cultivar. Interestingly, we observed 6706 genes to be upregulated in the panicle of N 22 over IR 64 under drought and 5814 genes get downregulated in the panicle of N 22 over IR 64 under the stress. In addition, RT-qPCR analysis confirmed differential expression patterns of the DEGs. These genes/pathways associated with the reproductive-stage drought tolerance might provide an important source of molecular markers for genetic manipulation of rice for enhanced drought tolerance.
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Yan M, Yu X, Zhou G, Sun D, Hu Y, Huang C, Zheng Q, Sun N, Wu J, Fu Z, Li L, Feng Z, Yu S. GhCDPK60 positively regulates drought stress tolerance in both transgenic Arabidopsis and cotton by regulating proline content and ROS level. FRONTIERS IN PLANT SCIENCE 2022; 13:1072584. [PMID: 36531339 PMCID: PMC9751749 DOI: 10.3389/fpls.2022.1072584] [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: 10/17/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Calcium-Dependent Protein Kinases (CDPKs) involved in regulating downstream components of calcium signaling pathways play a role in tolerance to abiotic stresses and seed development in plants. However, functions of only a few cotton CDPKs have been clarified at present. In this study, 80 conserved CDPKs in Gossypium hirsutum L. were identified and characterized, which was divided into four subgroups. Among them, the transcript level of GhCDPK60 was significantly upregulated under drought and several hormone treatments. And we found that the expression levels of several stress-inducible genes down-regulated in GhCDPK60-silence cotton and up-regulated in GhCDPK60-overexpressing Arabidopsis. In addition, physiological analyses demonstrated that GhCDPK60 improved drought stress tolerance by improving the osmotic adjustment ability and reducing the accumulation of reactive oxygen species (ROS) in plants. These findings broaden our understanding of the biological roles of GhCDPK60 and mechanisms underlying drought stress tolerance in cotton.
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Affiliation(s)
- Mengyuan Yan
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Xiaotian Yu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Gen Zhou
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Dongli Sun
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Yu Hu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Chenjue Huang
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Qintao Zheng
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Nan Sun
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Jiayan Wu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Zhaobin Fu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Libei Li
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Zhen Feng
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
| | - Shuxun Yu
- College of Advanced Agriculture Sciences, Zhejiang A&F University, Hangzhou, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, Henan, China
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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: 12] [Impact Index Per Article: 6.0] [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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11
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Li W, Mi X, Jin X, Zhang D, Zhu G, Shang X, Zhang D, Guo W. Thiamine functions as a key activator for modulating plant health and broad-spectrum tolerance in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:374-390. [PMID: 35506325 DOI: 10.1111/tpj.15793] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 04/23/2022] [Accepted: 05/01/2022] [Indexed: 06/14/2023]
Abstract
Global climate changes cause an increase of abiotic and biotic stresses that tremendously threaten the world's crop security. However, studies on broad-spectrum response pathways involved in biotic and abiotic stresses are relatively rare. Here, by comparing the time-dependent transcriptional changes and co-expression analysis of cotton (Gossypium hirsutum) root tissues under abiotic and biotic stress conditions, we discovered the common stress-responsive genes and stress metabolism pathways under different stresses, which included the circadian rhythm, thiamine and galactose metabolism, carotenoid, phenylpropanoid, flavonoid, and zeatin biosynthesis, and the mitogen-activated protein kinase signaling pathway. We found that thiamine metabolism was an important intersection between abiotic and biotic stresses; the key thiamine synthesis genes, GhTHIC and GhTHI1, were highly induced at the early stage of stresses. We confirmed that thiamine was crucial and necessary for cotton growth and development, and its deficiency could be recovered by exogenous thiamine supplement. Furthermore, we revealed that exogenous thiamine enhanced stress tolerance in cotton via increasing calcium signal transduction and activating downstream stress-responsive genes. Overall, our studies demonstrated that thiamine played a crucial role in the tradeoff between plant health and stress resistance. The thiamine deficiency caused by stresses could transiently induce upregulation of thiamine biosynthetic genes in vivo, while it could be totally salvaged by exogenous thiamine application, which could significantly improve cotton broad-spectrum stress tolerance and enhance plant growth and development.
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Affiliation(s)
- Weixi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Xinyue Mi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuanxiang Jin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Daiwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Guozhong Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoguang Shang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Dayong Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Germplasm Enhancement and Application Engineering Research Center (Ministry of Education), Nanjing Agricultural University, Nanjing, 210095, China
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12
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Zhang J, Liao J, Ling Q, Xi Y, Qian Y. Genome-wide identification and expression profiling analysis of maize AP2/ERF superfamily genes reveal essential roles in abiotic stress tolerance. BMC Genomics 2022; 23:125. [PMID: 35151253 PMCID: PMC8841118 DOI: 10.1186/s12864-022-08345-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/28/2022] [Indexed: 11/23/2022] Open
Abstract
Background As one of the largest transcription factor families in plants, the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is involved in various biological processes and plays significant roles in plant growth, development and responses to various stresses. Although identification and characterization of AP2/ERF superfamily genes have been accomplished in many plant species, very little is known regarding the structure and function of AP2/ERF genes in maize. Results In this study, a total of 214 genes encoding ZmAP2/ERF proteins with complete AP2/ERF domain were eventually identified according to the AGPv4 version of the maize B73 genome. Based on the number of AP2/ERF domain and similarities of amino acid sequences among AP2/ERF proteins from Arabidopsis, rice and maize, all 214 putative ZmAP2/ERF proteins were categorized into three distinct families, including the AP2 family (44), the ERF family (166) and the RAV family (4), respectively. Among them, the ERF family was further subdivided into two diverse subfamilies, including the DREB and ERF subfamilies with 61 and 105 members, respectively. Further, based on phylogenetic analysis, the members of DREB and ERF subfamilies were subdivided into four (Group I-IV) and eight (Group V-XII) groups, respectively. The characteristics of exon-intron structure of these putative ZmAP2/ERF genes and conserved protein motifs of their encoded ZmAP2/ERF proteins were also presented respectively, which was in accordance with the results of group classification. Promoter analysis suggested that ZmAP2/ERF genes shared many stress- and hormone-related cis-regulatory elements. Gene duplication and synteny analysis revealed that tandem or segmental duplication and purifying selection might play significant roles in evolution and functional differentiation of AP2/ERF superfamily genes among three various gramineous species (maize, rice and sorghum). Using RNA-seq data, transcriptome analysis indicated that the majority of ZmAP2/ERF genes displayed differential expression patterns at different developmental stages of maize. In addition, the following analyses of co-expression network among ZmAP2/ERF genes and protein protein interaction between ZmAP2 and ZmERF proteins further enabled us to understand the regulatory relationship among members of the AP2/ERF superfamily in maize. Furthermore, by quantitative real-time PCR analysis, twenty-seven selected ZmAP2/ERF genes were further confirmed to respond to three different abiotic stresses, suggesting their potential roles in various abiotic stress responses. Collectively, these results revealed that these ZmAP2/ERF genes play essential roles in abiotic stress tolerance. Conclusions Taken together, the present study will serve to present an important theoretical basis for further exploring the function and regulatory mechanism of ZmAP2/ERF genes in the growth, development, and adaptation to abiotic stresses in maize. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08345-7.
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Omics and CRISPR-Cas9 Approaches for Molecular Insight, Functional Gene Analysis, and Stress Tolerance Development in Crops. Int J Mol Sci 2021; 22:ijms22031292. [PMID: 33525517 PMCID: PMC7866018 DOI: 10.3390/ijms22031292] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
Abstract
Plants are regularly exposed to biotic and abiotic stresses that adversely affect agricultural production. Omics has gained momentum in the last two decades, fueled by statistical methodologies, computational capabilities, mass spectrometry, nucleic-acid sequencing, and peptide-sequencing platforms. Functional genomics—especially metabolomics, transcriptomics, and proteomics—have contributed substantially to plant molecular responses to stress. Recent progress in reverse and forward genetics approaches have mediated high-throughput techniques for identifying stress-related genes. Furthermore, web-based genetic databases have mediated bioinformatics techniques for detecting families of stress-tolerant genes. Gene ontology (GO) databases provide information on the gene product’s functional features and help with the computational estimation of gene function. Functional omics data from multiple platforms are useful for positional cloning. Stress-tolerant plants have been engineered using stress response genes, regulatory networks, and pathways. The genome-editing tool, CRISPR-Cas9, reveals the functional features of several parts of the plant genome. Current developments in CRISPR, such as de novo meristem induction genome-engineering in dicots and temperature-tolerant LbCas12a/CRISPR, enable greater DNA insertion precision. This review discusses functional omics for molecular insight and CRISPR-Cas9-based validation of gene function in crop plants. Omics and CRISPR-Cas9 are expected to garner knowledge on molecular systems and gene function and stress-tolerant crop production.
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Yang Y, Saand MA, Huang L, Abdelaal WB, Zhang J, Wu Y, Li J, Sirohi MH, Wang F. Applications of Multi-Omics Technologies for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:563953. [PMID: 34539683 PMCID: PMC8446515 DOI: 10.3389/fpls.2021.563953] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/06/2021] [Indexed: 05/19/2023]
Abstract
Multiple "omics" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the "phenotype to genotype" and "genotype to phenotype" concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.
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Affiliation(s)
- Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- *Correspondence: Yaodong Yang
| | - Mumtaz Ali Saand
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Department of Botany, Shah Abdul Latif University, Khairpur, Pakistan
| | - Liyun Huang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Walid Badawy Abdelaal
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jun Zhang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yi Wu
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Jing Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | | | - Fuyou Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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Xu Y, Hu D, Hou X, Shen J, Liu J, Cen X, Fu J, Li X, Hu H, Xiong L. OsTMF attenuates cold tolerance by affecting cell wall properties in rice. THE NEW PHYTOLOGIST 2020; 227:498-512. [PMID: 32176820 DOI: 10.1111/nph.16549] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 03/04/2020] [Indexed: 05/15/2023]
Abstract
Plant cell wall composition and structure can be modified as plants adapt to environmental stresses; however, the underlying regulatory mechanisms remain elusive. Here, we report that OsTMF, a homologue of the human TATA modulatory factor (TMF) in rice (Oryza sativa) and highly conserved in plants, negatively regulates cold tolerance through modification of cell wall properties. Cold stress increased the expression of OsTMF and accumulation of OsTMF in the nucleus, where OsTMF acts as a transcription activator and modulates the expression of genes involved in pectin degradation (OsBURP16), cellulose biosynthesis (OsCesA4 and OsCesA9), and cell wall structural maintenance (genes encoding proline-rich proteins and peroxidases). OsTMF directly activated the expression of OsBURP16, OsCesA4, and OsCesA9 through binding to the TATA cis-elements in their promoters. Under cold stress conditions, OsTMF negatively regulated pectin content and peroxidase activity and positively regulated cellulose content, causing corresponding alterations to cell wall properties, all of which collectively contribute to the negative effect of OsTMF on cold tolerance. Our findings unravel a previously unreported molecular mechanism of a conserved plant TMF protein in the regulation of cell wall changes under cold stress.
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Affiliation(s)
- Yan Xu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Biofuels, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Dan Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Hou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianqiang Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Juhong Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiang Cen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Fu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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Yuan H, Xu P, Xiao Y, Yang L, Yang X, Wu K. Infection of cotton bollworm by Helicoverpa armigera iflavirus decreases larval fitness. J Invertebr Pathol 2020; 173:107384. [PMID: 32302593 DOI: 10.1016/j.jip.2020.107384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/09/2020] [Accepted: 04/11/2020] [Indexed: 11/28/2022]
Abstract
Previously, we reported a novel iflavirus in Helicoverpa armigera (helicoverpa armigera iflavirus, HaIV) and here we report the effects of HaIV on its host. In a laboratory bioassay, HaIV-positive larvae and pupae developed more slowly and had higher mortality than HaIV-negative larvae, suggesting that the virus is pathogenic. The relative fitness of H. armigera decreased with HaIV infection by a ratio of 0.65. Transcriptional analysis indicated that infection significantly changed the expression levels of host genes, with more genes affected at 72 h after inoculation than at 48 h (138 up- and 229 downregulated at 48 h; 185 up- and 299 downregulated at 72 h). Interestingly, pathways related to digestion and absorption were significantly enriched, e.g., protein digestion and absorption, suggesting developmental regulation of the host by HaIV via these pathways. HaIV-infected H. armigera showed significantly downregulated expression of genes encoding cuticular proteins (CPs), essential for structural and protective functions, at 48 h and 72 h, suggesting that HaIV increased larval mortality by downregulating CP gene expression.
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Affiliation(s)
- He Yuan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, PR China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Pengjun Xu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, PR China
| | - Yutao Xiao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, PR China
| | - Liyu Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, PR China
| | - Xianming Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Kongming Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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Khizar M, Shi J, Saleem S, Liaquat F, Ashraf M, Latif S, Haroon U, Hassan SW, Rehman SU, Chaudhary HJ, Quraishi UM, Munis MFH. Resistance associated metabolite profiling of Aspergillus leaf spot in cotton through non-targeted metabolomics. PLoS One 2020; 15:e0228675. [PMID: 32049975 PMCID: PMC7015376 DOI: 10.1371/journal.pone.0228675] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/20/2020] [Indexed: 12/17/2022] Open
Abstract
Aspergillus tubingensis is an important pathogen of economically important crops. Different biotic stresses strongly influence the balance of metabolites in plants. The aim of this study was to understand the function and response of resistance associated metabolites which, in turn are involved in many secondary metabolomics pathways to influence defense mechanism of cotton plant. Analysis of non-targeted metabolomics using ultra high performance liquid chromatography-mass spectrometry (UPLC-MS) revealed abundant accumulation of key metabolites including flavonoids, phenylpropanoids, terpenoids, fatty acids and carbohydrates, in response to leaf spot of cotton. The principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA) and partial least squares discriminant analysis (PLS-DA) score plots illustrated the evidences of variation between two varieties of cotton under mock and pathogen inoculated treatments. Primary metabolism was affected by the up regulation of pyruvate and malate and by the accumulation of carbohydrates like cellobiose and inulobiose. Among 241 resistance related (RR) metabolites, 18 were identified as resistance related constitutive (RRC) and 223 as resistance related induced (RRI) metabolites. Several RRI metabolites, identified in the present study were the precursors for many secondary metabolic pathways. These included phenylpropanoids (stilbenes and furanocoumarin), flavonoids (phlorizin and kaempferol), alkaloids (indolizine and acetylcorynoline) and terpenoids (azelaic acid and oleanolic acid). Our results demonstrated that secondary metabolism, primary metabolism and energy metabolism were more active in resistant cultivar, as compared to sensitive cultivar. Differential protein and fatty acid metabolism was also depicted in both cultivars. Accumulation of these defense related metabolites in resistant cotton cultivar and their suppression in susceptible cotton cultivar revealed the reason of their respective tolerance and susceptibility against A. tubingensis.
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Affiliation(s)
- Maria Khizar
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jianxin Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Sadia Saleem
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fiza Liaquat
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Ashraf
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Sadia Latif
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Urooj Haroon
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Waqas Hassan
- Department of Bioscience, University of Wah, Quaid Avenue, Wah Cantt., Pakistan
| | - Shafiq ur Rehman
- College of Earth and Environmental Sciences, University of the Punjab, Lahore, Pakistan
| | - Hassan Javed Chaudhary
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Umar Masood Quraishi
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Zhang K, Cui H, Cao S, Yan L, Li M, Sun Y. Overexpression of CrCOMT from Carex rigescens increases salt stress and modulates melatonin synthesis in Arabidopsis thaliana. PLANT CELL REPORTS 2019; 38:1501-1514. [PMID: 31473792 DOI: 10.1007/s00299-019-02461-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/12/2019] [Indexed: 05/27/2023]
Abstract
CrCOMT, a COMT gene in Carex rigescens, was verified to enhance salt stress tolerance in transgenic Arabidopsis. High salinity severely restricts plant growth and development while melatonin can alleviate salt damage. Caffeic acid O-methyltransferase (COMT) plays an important role in regulating plant growth, development, and stress responses. COMT could also participate in melatonin biosynthesis. The objective of this study was to identify CrCOMT from Carex rigescens (Franch.) V. Krecz, a stress-tolerant grass species with a widespread distribution in north China, and to determine its physiological functions and regulatory mechanisms that impart tolerance to salt stress. The results showed that the transcription of CrCOMT exhibited different expression patterns under salt, drought, and ABA treatments. Transgenic Arabidopsis with the overexpression of CrCOMT exhibited improved growth and physiological performance under salt stress, such as higher lateral root numbers, proline level, and chlorophyll content, than in the wild type (WT). Overexpression of CrCOMT also increased dehydration tolerance in Arabidopsis. The transcription of salt response genes was more highly activated in transgenic plants than in the WT under salt stress conditions. In addition, the melatonin content in transgenic plants was higher than that in the WT after stress treatment. Taken together, our results indicated that CrCOMT may positively regulate stress responses and melatonin synthesis under salt stress.
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Affiliation(s)
- Kun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Huiting Cui
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Shihao Cao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Li Yan
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Mingna Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
| | - Yan Sun
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.
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Smitha PK, Vishnupriyan K, Kar AS, Anil Kumar M, Bathula C, Chandrashekara KN, Dhar SK, Das M. Genome wide search to identify reference genes candidates for gene expression analysis in Gossypium hirsutum. BMC PLANT BIOLOGY 2019; 19:405. [PMID: 31521126 PMCID: PMC6744693 DOI: 10.1186/s12870-019-1988-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/26/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cotton is one of the most important commercial crops as the source of natural fiber, oil and fodder. To protect it from harmful pest populations number of newer transgenic lines have been developed. For quick expression checks in successful agriculture qPCR (quantitative polymerase chain reaction) have become extremely popular. The selection of appropriate reference genes plays a critical role in the outcome of such experiments as the method quantifies expression of the target gene in comparison with the reference. Traditionally most commonly used reference genes are the "house-keeping genes", involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes for every experimental platform. This study presents a data science driven unbiased genome-wide search for the selection of reference genes by assessing variation of > 50,000 genes in a publicly available RNA-seq dataset of cotton species Gossypium hirsutum. RESULT Five genes (TMN5, TBL6, UTR5B, AT1g65240 and CYP76B6) identified by data-science driven analysis, along with two commonly used reference genes found in literature (PP2A1 and UBQ14) were taken through qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaluated using four algorithms - geNorm, BestKeeper, NormFinder and RefFinder. CONCLUSION Based on the results we recommend the usage of TMN5 and TBL6 as the optimal candidate reference genes in qPCR experiments with normal and transgenic cotton plant tissues. AT1g65240 and PP2A1 can also be used if expression study includes squares. This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes over the selection based on function alone.
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Affiliation(s)
- P. K. Smitha
- Department of Biotechnology, Research and Development Centre, Bharathiar University, Coimbatore, Tamil Nadu 641 046 India
- Beyond Antibody LLP, S-005 Krishna Greens, Krishna Temple Road, Dodda Bomasandra, Bangalore, Karnataka 560 097 India
| | - K. Vishnupriyan
- Tumor Immunology Program, DSRG1, MSCTR, MSMF, Mazumdar Shaw Medical Centre, 8th floor, Narayana Health City, Bommasandra, Bangalore, Karnataka 560 099 India
| | - Ananya S. Kar
- Tumor Immunology Program, DSRG1, MSCTR, MSMF, Mazumdar Shaw Medical Centre, 8th floor, Narayana Health City, Bommasandra, Bangalore, Karnataka 560 099 India
- School of Bio Sciences & Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632 014 India
| | - M. Anil Kumar
- Beyond Antibody LLP, S-005 Krishna Greens, Krishna Temple Road, Dodda Bomasandra, Bangalore, Karnataka 560 097 India
| | - Christopher Bathula
- Tumor Immunology Program, DSRG1, MSCTR, MSMF, Mazumdar Shaw Medical Centre, 8th floor, Narayana Health City, Bommasandra, Bangalore, Karnataka 560 099 India
| | - K. N. Chandrashekara
- Division of Plant Physiology and Biotechnology, UPASI Tea Research Foundation, Tea Research Institute, Nirar Dam, Valparai, Coimbatore, Tamil Nadu 642 127 India
| | - Sujan K. Dhar
- Beyond Antibody LLP, S-005 Krishna Greens, Krishna Temple Road, Dodda Bomasandra, Bangalore, Karnataka 560 097 India
| | - Manjula Das
- Tumor Immunology Program, DSRG1, MSCTR, MSMF, Mazumdar Shaw Medical Centre, 8th floor, Narayana Health City, Bommasandra, Bangalore, Karnataka 560 099 India
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Wu A, Hao P, Wei H, Sun H, Cheng S, Chen P, Ma Q, Gu L, Zhang M, Wang H, Yu S. Genome-Wide Identification and Characterization of Glycosyltransferase Family 47 in Cotton. Front Genet 2019; 10:824. [PMID: 31572442 PMCID: PMC6749837 DOI: 10.3389/fgene.2019.00824] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/09/2019] [Indexed: 01/06/2023] Open
Abstract
The glycosyltransferase (GT) 47 family is involved in the biosynthesis of xylose, pectin and xyloglucan and plays a significant role in maintaining the normal morphology of the plant cell wall. However, the functions of GT47s are less well known in cotton. In the present study, a total of 53, 53, 105 and 109 GT47 genes were detected by genome-wide identification in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. All the GT47s were classified into six major groups via phylogenetic analysis. The exon/intron structure and protein motifs indicated that each branch of the GT47 genes was highly conserved. Collinearity analysis showed that GT47 gene family expansion occurred in Gossypium spp. mainly through whole-genome duplication and that segmental duplication mainly promoted GT47 gene expansion within the A and D subgenomes. The Ka/Ks values suggested that the GT47 gene family has undergone purifying selection during the long-term evolutionary process. Transcriptomic data and qRT-PCR showed that GhGT47 genes exhibited different expression patterns in each tissue and during fiber development. Our results suggest that some genes in the GhGT47 family might be associated with fiber development and the abiotic stress response, which could promote further research involving functional analysis of GT47 genes in cotton.
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Affiliation(s)
- Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Huiru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Pengyun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qiang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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21
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Dossa K, Mmadi MA, Zhou R, Zhang T, Su R, Zhang Y, Wang L, You J, Zhang X. Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame ( Sesamum indicum L.). Int J Mol Sci 2019; 20:ijms20163930. [PMID: 31412539 PMCID: PMC6721054 DOI: 10.3390/ijms20163930] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/26/2019] [Accepted: 08/10/2019] [Indexed: 01/21/2023] Open
Abstract
Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that the plant reuses in response to an array of environmental stresses are unknown. We performed a meta-analysis of 72 RNA-Seq datasets from drought, waterlogging, salt and osmotic stresses and identified 543 genes constantly and differentially expressed in response to all stresses, representing the sesame CARG. Weighted gene co-expression network analysis of the CARG revealed three functional modules controlled by key transcription factors. Except for salt stress, the modules were positively correlated with the abiotic stresses. Network topology of the modules showed several hub genes predicted to play prominent functions. As proof of concept, we generated over-expressing Arabidopsis lines with hub and non-hub genes. Transgenic plants performed better under drought, waterlogging, and osmotic stresses than the wild-type plants but did not tolerate the salt treatment. As expected, the hub gene was significantly more potent than the non-hub gene. Overall, we discovered several novel candidate genes, which will fuel investigations on plant responses to multiple abiotic stresses.
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Affiliation(s)
- Komivi Dossa
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
| | - Marie A Mmadi
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Tianyuan Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruqi Su
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Yujuan Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Jun You
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan 430062, China.
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22
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Smita S, Katiyar A, Lenka SK, Dalal M, Kumar A, Mahtha SK, Yadav G, Chinnusamy V, Pandey DM, Bansal KC. Gene network modules associated with abiotic stress response in tolerant rice genotypes identified by transcriptome meta-analysis. Funct Integr Genomics 2019; 20:29-49. [PMID: 31286320 DOI: 10.1007/s10142-019-00697-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/31/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
Abiotic stress tolerance is a complex trait regulated by multiple genes and gene networks in plants. A range of abiotic stresses are known to limit rice productivity. Meta-transcriptomics has emerged as a powerful approach to decipher stress-associated molecular network in model crops. However, retaining specificity of gene expression in tolerant and susceptible genotypes during meta-transcriptome analysis is important for understanding genotype-dependent stress tolerance mechanisms. Addressing this aspect, we describe here "abiotic stress tolerant" (ASTR) genes and networks specifically and differentially expressing in tolerant rice genotypes in response to different abiotic stress conditions. We identified 6,956 ASTR genes, key hub regulatory genes, transcription factors, and functional modules having significant association with abiotic stress-related ontologies and cis-motifs. Out of the 6956 ASTR genes, 73 were co-located within the boundary of previously identified abiotic stress trait-related quantitative trait loci. Functional annotation of 14 uncharacterized ASTR genes is proposed using multiple computational methods. Around 65% of the top ASTR genes were found to be differentially expressed in at least one of the tolerant genotypes under different stress conditions (cold, salt, drought, or heat) from publicly available RNAseq data comparison. The candidate ASTR genes specifically associated with tolerance could be utilized for engineering rice and possibly other crops for broad-spectrum tolerance to abiotic stresses.
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Affiliation(s)
- Shuchi Smita
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amit Katiyar
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
- ICMR-AIIMS Computational Genomics Center, Div. of I.S.R.M., Indian Council of Medical Research, Ansari Nagar, New Delhi, 110029, India
| | - Sangram Keshari Lenka
- TERI-Deakin Nanobiotechnology Center, The Energy and Resources Institute, Gurgaon, Haryana, 122001, India
| | - Monika Dalal
- ICAR-National Research Center on Plant Biotechnology, Indian Agricultural Research Institute Campus, New Delhi, 110012, India
| | - Amish Kumar
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjeet Kumar Mahtha
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Viswanathan Chinnusamy
- ICAR-Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Dev Mani Pandey
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kailash Chander Bansal
- ICAR-National Bureau of Plant Genetic Resources, Indian Agricultural Research Institute Campus, New Delhi, 110012, India.
- TERI-Deakin Nanobiotechnology Center, The Energy and Resources Institute, Gurgaon, Haryana, 122001, India.
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Sawicki M, Rondeau M, Courteaux B, Rabenoelina F, Guerriero G, Gomès E, Soubigou-Taconnat L, Balzergue S, Clément C, Ait Barka E, Vaillant-Gaveau N, Jacquard C. On a Cold Night: Transcriptomics of Grapevine Flower Unveils Signal Transduction and Impacted Metabolism. Int J Mol Sci 2019; 20:E1130. [PMID: 30841651 PMCID: PMC6429367 DOI: 10.3390/ijms20051130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 02/02/2023] Open
Abstract
Low temperature is a critical environmental factor limiting plant productivity, especially in northern vineyards. To clarify the impact of this stress on grapevine flower, we used the Vitis array based on Roche-NimbleGen technology to investigate the gene expression of flowers submitted to a cold night. Our objectives were to identify modifications in the transcript levels after stress and during recovery. Consequently, our results confirmed some mechanisms known in grapes or other plants in response to cold stress, notably, (1) the pivotal role of calcium/calmodulin-mediated signaling; (2) the over-expression of sugar transporters and some genes involved in plant defense (especially in carbon metabolism), and (3) the down-regulation of genes encoding galactinol synthase (GOLS), pectate lyases, or polygalacturonases. We also identified some mechanisms not yet known to be involved in the response to cold stress, i.e., (1) the up-regulation of genes encoding G-type lectin S-receptor-like serine threonine-protein kinase, pathogen recognition receptor (PRR5), or heat-shock factors among others; (2) the down-regulation of Myeloblastosis (MYB)-related transcription factors and the Constans-like zinc finger family; and (3) the down-regulation of some genes encoding Pathogen-Related (PR)-proteins. Taken together, our results revealed interesting features and potentially valuable traits associated with stress responses in the grapevine flower. From a long-term perspective, our study provides useful starting points for future investigation.
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Affiliation(s)
- Mélodie Sawicki
- Unité de Recherche Résistance Induite et Bioprotection des Plantes-EA 4707, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, SFR Condorcet FR CNRS 3417, Moulin de la Housse-Bâtiment 18, BP 1039, 51687 REIMS Cedex 2, France.
| | - Marine Rondeau
- Unité de Recherche Résistance Induite et Bioprotection des Plantes-EA 4707, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, SFR Condorcet FR CNRS 3417, Moulin de la Housse-Bâtiment 18, BP 1039, 51687 REIMS Cedex 2, France.
| | - Barbara Courteaux
- Unité de Recherche Résistance Induite et Bioprotection des Plantes-EA 4707, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, SFR Condorcet FR CNRS 3417, Moulin de la Housse-Bâtiment 18, BP 1039, 51687 REIMS Cedex 2, France.
| | - Fanja Rabenoelina
- Unité de Recherche Résistance Induite et Bioprotection des Plantes-EA 4707, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, SFR Condorcet FR CNRS 3417, Moulin de la Housse-Bâtiment 18, BP 1039, 51687 REIMS Cedex 2, France.
| | - Gea Guerriero
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) Department, 41 rue du Brill, L- 4422 Belvaux, Luxembourg.
| | - Eric Gomès
- Institute of Vine and Wine Sciences, UMR 1287 Ecophysiology and Grape Functional Genomics, University of Bordeaux, INRA 210 Chemin de Leysotte - CS 50008, 33882 Villenave d'Ornon CEDEX, France.
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France.
| | - Sandrine Balzergue
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France.
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France.
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071 Beaucouzé CEDEX, France.
| | - Christophe Clément
- Unité de Recherche Résistance Induite et Bioprotection des Plantes-EA 4707, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, SFR Condorcet FR CNRS 3417, Moulin de la Housse-Bâtiment 18, BP 1039, 51687 REIMS Cedex 2, France.
| | - Essaïd Ait Barka
- Unité de Recherche Résistance Induite et Bioprotection des Plantes-EA 4707, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, SFR Condorcet FR CNRS 3417, Moulin de la Housse-Bâtiment 18, BP 1039, 51687 REIMS Cedex 2, France.
| | - Nathalie Vaillant-Gaveau
- Unité de Recherche Résistance Induite et Bioprotection des Plantes-EA 4707, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, SFR Condorcet FR CNRS 3417, Moulin de la Housse-Bâtiment 18, BP 1039, 51687 REIMS Cedex 2, France.
| | - Cédric Jacquard
- Unité de Recherche Résistance Induite et Bioprotection des Plantes-EA 4707, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, SFR Condorcet FR CNRS 3417, Moulin de la Housse-Bâtiment 18, BP 1039, 51687 REIMS Cedex 2, France.
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Vangelisti A, Zambrano LS, Caruso G, Macheda D, Bernardi R, Usai G, Mascagni F, Giordani T, Gucci R, Cavallini A, Natali L. How an ancient, salt-tolerant fruit crop, Ficus carica L., copes with salinity: a transcriptome analysis. Sci Rep 2019; 9:2561. [PMID: 30796285 PMCID: PMC6385202 DOI: 10.1038/s41598-019-39114-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/17/2019] [Indexed: 12/20/2022] Open
Abstract
Although Ficus carica L. (fig) is one of the most resistant fruit tree species to salinity, no comprehensive studies are currently available on its molecular responses to salinity. Here we report a transcriptome analysis of F. carica cv. Dottato exposed to 100 mM sodium chloride for 7 weeks, where RNA-seq analysis was performed on leaf samples at 24 and 48 days after the beginning of salinization; a genome-derived fig transcriptome was used as a reference. At day 24, 224 transcripts were significantly up-regulated and 585 were down-regulated, while at day 48, 409 genes were activated and 285 genes were repressed. Relatively small transcriptome changes were observed after 24 days of salt treatment, showing that fig plants initially tolerate salt stress. However, after an early down-regulation of some cell functions, major transcriptome changes were observed after 48 days of salinity. Seven weeks of 100 mM NaCl dramatically changed the repertoire of expressed genes, leading to activation or reactivation of many cell functions. We also identified salt-regulated genes, some of which had not been previously reported to be involved in plant salinity responses. These genes could be potential targets for the selection of favourable genotypes, through breeding or biotechnology, to improve salt tolerance in fig or other crops.
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Affiliation(s)
- Alberto Vangelisti
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy
| | - Liceth Solorzano Zambrano
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy
| | - Giovanni Caruso
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy
| | - Desiré Macheda
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy
| | - Rodolfo Bernardi
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy
| | - Gabriele Usai
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy
| | - Flavia Mascagni
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy
| | - Riccardo Gucci
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy
| | - Lucia Natali
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto 80, I-56124, Pisa, Italy.
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25
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Luo D, Wu Y, Liu J, Zhou Q, Liu W, Wang Y, Yang Q, Wang Z, Liu Z. Comparative Transcriptomic and Physiological Analyses of Medicago sativa L. Indicates that Multiple Regulatory Networks Are Activated during Continuous ABA Treatment. Int J Mol Sci 2018; 20:E47. [PMID: 30583536 PMCID: PMC6337461 DOI: 10.3390/ijms20010047] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022] Open
Abstract
Alfalfa is the most extensively cultivated forage legume worldwide. However, the molecular mechanisms underlying alfalfa responses to exogenous abscisic acid (ABA) are still unknown. In this study, the first global transcriptome profiles of alfalfa roots under ABA treatments for 1, 3 and 12 h (three biological replicates for each time point, including the control group) were constructed using a BGISEQ-500 sequencing platform. A total of 50,742 isoforms with a mean length of 2541 bp were generated, and 4944 differentially expressed isoforms (DEIs) were identified after ABA deposition. Metabolic analyses revealed that these DEIs were involved in plant hormone signal transduction, transcriptional regulation, antioxidative defense and pathogen immunity. Notably, several well characterized hormone signaling pathways, for example, the core ABA signaling pathway, was activated, while salicylic acid, jasmonate and ethylene signaling pathways were mainly suppressed by exogenous ABA. Moreover, the physiological work showed that catalase and peroxidase activity and glutathione and proline content were increased after ABA deposition, which is in accordance with the dynamic transcript profiles of the relevant genes in antioxidative defense system. These results indicate that ABA has the potential to improve abiotic stress tolerance, but that it may negatively regulate pathogen resistance in alfalfa.
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Affiliation(s)
- Dong Luo
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Yuguo Wu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Jie Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Qiang Zhou
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Wenxian Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Qingchuan Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China.
| | - Zengyu Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
- Core Research & Transformation, Noble Research Institute, Ardmore, OK 73401, USA.
| | - Zhipeng Liu
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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27
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Lanna AC, Silva RA, Ferraresi TM, Mendonça JA, Coelho GRC, Moreira AS, Valdisser PAMR, Brondani C, Vianello RP. Physiological characterization of common bean (Phaseolus vulgaris L.) under abiotic stresses for breeding purposes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:31149-31164. [PMID: 30187414 DOI: 10.1007/s11356-018-3012-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/20/2018] [Indexed: 05/13/2023]
Abstract
In the Brazilian wet and dry seasons, common beans (Phaseolus vulgaris L.) are grown under rainfed conditions with unexpected episodes of drought and high temperatures. The objective of this study was to evaluate the physiological mechanisms associated with drought adaptation traits in landraces and line/cultivars of beans from the Andean and Mesoamerican gene pools. Twenty-five genotypes, contrasting in terms of drought tolerance, were evaluated in a phenotyping platform under irrigated and rainfed conditions. Agronomic and physiological parameters such as grain yield, shoot structures, gas exchange, water potential, and osmotic adjustment were evaluated. The stress intensity was estimated to be 0.57, and the grain yield reduction ranged from 22 to 89%. Seven accessions, representative of the Andean and Mesoamerican germplasm (CF 200012, CF 240056, CF 250002, CF 900004, CNF 4497, CNF 7382, and SEA 5), presented superior performance in grain yield with and without stresses. The physiological responses under abiotic stresses were highly variable among the genotypes, and two Mesoamerican accessions (CF 200012 and SEA 5) showed more favorable adaptive responses. As the main secondary physiological traits, gas exchange and osmotic adjustment should be evaluated together with the grain yield to increase the selection efficiency of abiotic stresses-tolerant common bean lines.
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Affiliation(s)
- Anna Cristina Lanna
- Embrapa Rice and Beans, Rodovia GO-462, Km 12, C.P. 179, Santo Antônio de Goiás, GO, 75375-000, Brazil.
| | - Renato Adolfo Silva
- Limagrain Brazil S. A, Rodovia Br 060, km 171, Goiânia, GO, 74000-000, Brazil
| | - Tatiana Maris Ferraresi
- Embrapa Rice and Beans, Rodovia GO-462, Km 12, C.P. 179, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | - João Antônio Mendonça
- Embrapa Rice and Beans, Rodovia GO-462, Km 12, C.P. 179, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | | | - Alécio Souza Moreira
- Embrapa Cassava and Fruticulture/Araraquara Advanced Field, Araraquara, SP, 14807-040, Brazil
| | | | - Claudio Brondani
- Embrapa Rice and Beans, Rodovia GO-462, Km 12, C.P. 179, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | - Rosana Pereira Vianello
- Embrapa Rice and Beans, Rodovia GO-462, Km 12, C.P. 179, Santo Antônio de Goiás, GO, 75375-000, Brazil
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Das P, Majumder AL. Transcriptome analysis of grapevine under salinity and identification of key genes responsible for salt tolerance. Funct Integr Genomics 2018; 19:61-73. [PMID: 30046943 DOI: 10.1007/s10142-018-0628-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 06/04/2018] [Accepted: 07/11/2018] [Indexed: 02/02/2023]
Abstract
The negative effects of soil salinity towards grape yield depend upon salt concentration, cultivar type, developmental stage, and rootstock. Thompson Seedless variety of grape plant is considered moderately sensitive to salinity when grown upon its own root stock. In recent epoch, identification of key genes responsive to salinity offers hope to generate salinity-tolerant crop plants by their overexpression through genetic manipulation. In the present report, salt responsive transcriptome analysis of Thompson Seedless grape variety was done to identify vital genes involved in salinity tolerance which could be used further to generate salt liberal grape plant or other crop plants. Transcriptome libraries for control and 150-mM-NaCl-treated grape leaves were sequenced on Illumina platform where 714 genes were found to be differentially expressed. Gene ontology analysis indicated that under salinity conditions, the genes involved in metabolic process were highly enriched. Keto Encyclopedia of Genes and Genomes analysis revealed that, among the top 22 enriched pathways for the salt stress upregulated genes, the carbohydrate metabolism, signal transduction, energy metabolism, amino acid metabolism, biosynthesis of secondary metabolite, and lipid metabolism pathways possessed the largest number of transcripts. Key salinity-induced genes were selected and validated through qRT-PCR analysis which was comparable to RNA-seq results. Real-time PCR analysis also revealed that after 24 days of salinity, the expression of most of the selected key genes was highest. These salinity-induced genes will be characterized further in a model plant and also in Vitis vinifera through transgenic approach to disclose their role towards salt tolerance.
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Affiliation(s)
- Priyanka Das
- Division of Plant Biology, Bose Institute, P1/12, CIT Scheme, VIIM, Kankurgachi, Kolkata, West Bengal, 700054, India.
| | - Arun Lahiri Majumder
- Division of Plant Biology, Bose Institute, P1/12, CIT Scheme, VIIM, Kankurgachi, Kolkata, West Bengal, 700054, India.
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Yan J, Li G, Guo X, Li Y, Cao X. Genome-wide classification, evolutionary analysis and gene expression patterns of the kinome in Gossypium. PLoS One 2018; 13:e0197392. [PMID: 29768506 PMCID: PMC5955557 DOI: 10.1371/journal.pone.0197392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 05/01/2018] [Indexed: 11/18/2022] Open
Abstract
The protein kinase (PK, kinome) family is one of the largest families in plants and regulates almost all aspects of plant processes, including plant development and stress responses. Despite their important functions, comprehensive functional classification, evolutionary analysis and expression patterns of the cotton PK gene family has yet to be performed on PK genes. In this study, we identified the cotton kinomes in the Gossypium raimondii, Gossypium arboretum, Gossypium hirsutum and Gossypium barbadense genomes and classified them into 7 groups and 122-24 subfamilies using software HMMER v3.0 scanning and neighbor-joining (NJ) phylogenetic analysis. Some conserved exon-intron structures were identified not only in cotton species but also in primitive plants, ferns and moss, suggesting the significant function and ancient origination of these PK genes. Collinearity analysis revealed that 16.6 million years ago (Mya) cotton-specific whole genome duplication (WGD) events may have played a partial role in the expansion of the cotton kinomes, whereas tandem duplication (TD) events mainly contributed to the expansion of the cotton RLK group. Synteny analysis revealed that tetraploidization of G. hirsutum and G. barbadense contributed to the expansion of G. hirsutum and G. barbadense PKs. Global expression analysis of cotton PKs revealed stress-specific and fiber development-related expression patterns, suggesting that many cotton PKs might be involved in the regulation of the stress response and fiber development processes. This study provides foundational information for further studies on the evolution and molecular function of cotton PKs.
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Affiliation(s)
- Jun Yan
- College of Information Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, PR China
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Guilin Li
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Xingqi Guo
- College of Life Sciences, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Yang Li
- College of Information Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, PR China
| | - Xuecheng Cao
- College of Information Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, PR China
- * E-mail:
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Ashoub A, Müller N, Jiménez-Gómez JM, Brüggemann W. Prominent alterations of wild barley leaf transcriptome in response to individual and combined drought acclimation and heat shock conditions. PHYSIOLOGIA PLANTARUM 2018; 163:18-29. [PMID: 29111595 DOI: 10.1111/ppl.12667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/19/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
Under field conditions, drought and heat stress typically happen simultaneously and their negative impact on the agricultural production is expected to increase worldwide under the climate change scenario. In this study, we performed RNA-sequencing analysis on leaves of wild barley (Hordeum spontaneum) originated from the northern coastal region of Egypt following individual drought acclimation (DA) and heat shock (HS) treatments and their combination (CS, combined stresses) to distinguish the unique and shared differentially expressed genes (DEG). Results indicated that the number of unique genes that were differentially expressed following HS treatment exceeded the number of those expressed following DA. In addition, the number of genes that were uniquely differentially expressed in response to CS treatment exceeded the number of those of shared responses to individual DA and HS treatments. These results indicate a better adaptation of the Mediterranean wild barley to drought conditions when compared with heat stress. It also manifests that the wild barley response to CS tends to be unique rather than common. Annotation of DEG showed that metabolic processes were the most influenced biological function in response to the applied stresses.
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Affiliation(s)
- Ahmed Ashoub
- Institute of Ecology, Evolution, and Diversity, Johann Wolfgang Goethe-University Frankfurt, Frankfurt am Main, Germany
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Niels Müller
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - José M Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Wolfgang Brüggemann
- Institute of Ecology, Evolution, and Diversity, Johann Wolfgang Goethe-University Frankfurt, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
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Joseph JT, Poolakkalody NJ, Shah JM. Plant reference genes for development and stress response studies. J Biosci 2018; 43:173-187. [PMID: 29485125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Many reference genes are used by different laboratories for gene expression analyses to indicate the relative amount of input RNA/DNA in the experiment. These reference genes are supposed to show least variation among the treatments and with the control sets in a given experiment. However, expression of reference genes varies significantly from one set of experiment to the other. Thus, selection of reference genes depends on the experimental conditions. Sometimes the average expression of two or three reference genes is taken as standard. This review consolidated the details of about 120 genes attempted for normalization during comparative expression analysis in 16 different plants. Plant species included in this review are Arabidopsis thaliana, cotton (Gossypium hirsutum), tobacco (Nicotiana benthamiana and N. tabacum), soybean (Glycine max), rice (Oryza sativa), blueberry (Vaccinium corymbosum), tomato (Solanum lycopersicum), wheat (Triticum aestivum), potato (Solanum tuberosum), sugar cane (Saccharum sp.), carrot (Daucus carota), coffee (Coffea arabica), cucumber (Cucumis sativus), kiwi (Actinidia deliciosa) and grape (Vitis vinifera). The list includes model and cultivated crop plants from both monocot and dicot classes. We have categorized plant-wise the reference genes that have been used for expression analyses in any or all of the four different conditions such as biotic stress, abiotic stress, developmental stages and various organs and tissues, reported till date. This review serves as a guide during the reference gene hunt for gene expression analysis studies.
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Affiliation(s)
- Joyous T Joseph
- Department of Plant Science, Central University of Kerala, Padannakkad, Kasaragod 671 314, India
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Cai J, Li P, Luo X, Chang T, Li J, Zhao Y, Xu Y. Selection of appropriate reference genes for the detection of rhythmic gene expression via quantitative real-time PCR in Tibetan hulless barley. PLoS One 2018; 13:e0190559. [PMID: 29309420 PMCID: PMC5757941 DOI: 10.1371/journal.pone.0190559] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/16/2017] [Indexed: 11/18/2022] Open
Abstract
Hulless barley (Hordeum vulgare L. var. nudum. hook. f.) has been cultivated as a major crop in the Qinghai-Tibet plateau of China for thousands of years. Compared to other cereal crops, the Tibetan hulless barley has developed stronger endogenous resistances to survive in the severe environment of its habitat. To understand the unique resistant mechanisms of this plant, detailed genetic studies need to be performed. The quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is the most commonly used method in detecting gene expression. However, the selection of stable reference genes under limited experimental conditions was considered to be an essential step for obtaining accurate results in qRT-PCR. In this study, 10 candidate reference genes—ACT (Actin), E2 (Ubiquitin conjugating enzyme 2), TUBα (Alpha-tubulin), TUBβ6 (Beta-tubulin 6), GAPDH (Glyceraldehyde 3-phosphate dehydrogenase), EF-1α (Elongation factor 1-alpha), SAMDC (S-adenosylmethionine decarboxylase), PKABA1 (Gene for protein kinase HvPKABA1), PGK (Phosphoglycerate kinase), and HSP90 (Heat shock protein 90)—were selected from the NCBI gene database of barley. Following qRT-PCR amplifications of all candidate reference genes in Tibetan hulless barley seedlings under various stressed conditions, the stabilities of these candidates were analyzed by three individual software packages including geNorm, NormFinder, and BestKeeper. The results demonstrated that TUBβ6, E2, TUBα, and HSP90 were generally the most suitable sets under all tested conditions; similarly, TUBα and HSP90 showed peak stability under salt stress, TUBα and EF-1α were the most suitable reference genes under cold stress, and ACT and E2 were the most stable under drought stress. Finally, a known circadian gene CCA1 was used to verify the service ability of chosen reference genes. The results confirmed that all recommended reference genes by the three software were suitable for gene expression analysis under tested stress conditions by the qRT-PCR method.
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Affiliation(s)
- Jing Cai
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi’an, China
- Life Sciences School of Northwest University, Xi’an, China
- Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi’an, China
| | - Pengfei Li
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi’an, China
- Life Sciences School of Northwest University, Xi’an, China
- Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi’an, China
| | - Xiao Luo
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi’an, China
- Life Sciences School of Northwest University, Xi’an, China
- Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi’an, China
| | - Tianliang Chang
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi’an, China
- Life Sciences School of Northwest University, Xi’an, China
- Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi’an, China
| | - Jiaxing Li
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi’an, China
- Life Sciences School of Northwest University, Xi’an, China
- Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi’an, China
| | - Yuwei Zhao
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi’an, China
- Life Sciences School of Northwest University, Xi’an, China
- Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi’an, China
- * E-mail:
| | - Yao Xu
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Xi’an, China
- Life Sciences School of Northwest University, Xi’an, China
- Key Laboratory of Resource Biology and Biotechnology in western China (Ministry of Education), Xi’an, China
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Zeng C, Ding Z, Zhou F, Zhou Y, Yang R, Yang Z, Wang W, Peng M. The Discrepant and Similar Responses of Genome-Wide Transcriptional Profiles between Drought and Cold Stresses in Cassava. Int J Mol Sci 2017; 18:ijms18122668. [PMID: 29231846 PMCID: PMC5751270 DOI: 10.3390/ijms18122668] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 11/16/2022] Open
Abstract
Background: Cassava, an important tropical crop, has remarkable drought tolerance, but is very sensitive to cold. The growth, development, and root productivity of cassava are all adversely affected under cold and drought. Methods: To profile the transcriptional response to cold and drought stresses, cassava seedlings were respectively subjected to 0, 6, 24, and 48 h of cold stress and 0, 4, 6, and 10 days of drought stress. Their folded leaves, fully extended leaves, and roots were respectively investigated using RNA-seq. Results: Many genes specifically and commonly responsive to cold and drought were revealed: genes related to basic cellular metabolism, tetrapyrrole synthesis, and brassinosteroid metabolism exclusively responded to cold; genes related to abiotic stress and ethylene metabolism exclusively responded to drought; and genes related to cell wall, photosynthesis, and carbohydrate metabolism, DNA synthesis/chromatic structure, abscisic acid and salicylic acid metabolism, and calcium signaling commonly responded to both cold and drought. Discussion: Combined with cold- and/or drought-responsive transcription factors, the regulatory networks responding to cold and drought in cassava were constructed. All these findings will improve our understanding of the specific and common responses to cold and drought in cassava, and shed light on genetic improvement of cold and drought tolerance in cassava.
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Affiliation(s)
- Changying Zeng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Fang Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Yufei Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Ruiju Yang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Zi Yang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
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Ma L, Hu L, Fan J, Amombo E, Khaldun ABM, Zheng Y, Chen L. Cotton GhERF38 gene is involved in plant response to salt/drought and ABA. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:841-854. [PMID: 28536792 DOI: 10.1007/s10646-017-1815-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/05/2017] [Indexed: 05/06/2023]
Abstract
ERF (ethylene-responsive factor) transcription factors play important roles in plant stress signaling transduction pathways. However, their specific roles during diverse abiotic stresses tolerance in Gossypium hirsutum are largely unknown. Here, a novel ERF transcription factor, designated GhERF38, homologous to AtERF38 in Arabidopsis, was isolated from cotton (Gossypium hirsutum L). GhERF38 expression was up-regulated by salt, drought and ABA treatments. Subcellular localization results indicated that GhERF38 was localized in the cell nucleus. Over-expression of GhERF38 in Arabidopsis reduced plant tolerance to salt and drought stress as indicated by a decline of seed germination, plant greenness frequency, primary roots length and the survival rate in transgenic plants compared to those of wild type plants under salt or drought treatment. Besides, stress tolerance related physiological parameters such as proline content, relative water content, soluble sugar and chlorophyll content were all significantly lower in transgenic plants than those of wild type plants under salt or drought treatment. Furthermore, over-expression of GhERF38 in Arabidopsis resulted in ABA sensitivity in transgenic plants during both seed germination and seedling growth. Interestingly, the stomatal aperture of guard cells in the transgenic plants was larger than that in transgenic plant after ABA treatment, suggesting that GhERF38-overexpressing plants were insensitive to ABA in terms of stomatal closure. Furthermore, expressions of the stress-related genes were altered in the GhERF38 transgenic plants under high salinity, drought or ABA treatment. Together, our results revealed that GhERF38 functions as a novel regulator that is involved in response to salt/drought stress and ABA signaling during plant development.
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Affiliation(s)
- Liufeng Ma
- College of Biology and Geography Sciences, Kashgal University, Xinjiang, 844000, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Longxing Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- Department of Turfgrass Sciences, College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jibiao Fan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Erick Amombo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - A B M Khaldun
- Oilseed Research Centre, Bangladesh Agricultural Research Institute (BARI), Gazipur, 1701, Bangladesh
| | - Yong Zheng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
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Li J, Liu H, Xia W, Mu J, Feng Y, Liu R, Yan P, Wang A, Lin Z, Guo Y, Zhu J, Chen X. De Novo Transcriptome Sequencing and the Hypothetical Cold Response Mode of Saussurea involucrata in Extreme Cold Environments. Int J Mol Sci 2017; 18:E1155. [PMID: 28590406 PMCID: PMC5485979 DOI: 10.3390/ijms18061155] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/18/2017] [Accepted: 05/23/2017] [Indexed: 11/16/2022] Open
Abstract
Saussurea involucrata grows in high mountain areas covered by snow throughout the year. The temperature of this habitat can change drastically in one day. To gain a better understanding of the cold response signaling pathways and molecular metabolic reactions involved in cold stress tolerance, genome-wide transcriptional analyses were performed using RNA-Seq technologies. A total of 199,758 transcripts were assembled, producing 138,540 unigenes with 46.8 Gb clean data. Overall, 184,416 (92.32%) transcripts were successfully annotated. The 365 transcription factors identified (292 unigenes) belonged to 49 transcription factor families associated with cold stress responses. A total of 343 transcripts on the signal transduction (132 upregulated and 212 downregulated in at least any one of the conditions) were strongly affected by cold temperature, such as the CBL-interacting serine/threonine-protein kinase (CIPKs), receptor-like protein kinases, and protein kinases. The circadian rhythm pathway was activated by cold adaptation, which was necessary to endure the severe temperature changes within a day. There were 346 differentially expressed genes (DEGs) related to transport, of which 138 were upregulated and 22 were downregulated in at least any one of the conditions. Under cold stress conditions, transcriptional regulation, molecular transport, and signal transduction were involved in the adaptation to low temperature in S. involucrata. These findings contribute to our understanding of the adaptation of plants to harsh environments and the survival traits of S. involucrata. In addition, the present study provides insight into the molecular mechanisms of chilling and freezing tolerance.
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Affiliation(s)
- Jin Li
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Hailiang Liu
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai 200065, China.
| | - Wenwen Xia
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Jianqiang Mu
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Yujie Feng
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Ruina Liu
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Panyao Yan
- ShengTing Bioinformatics Institute, Christiansburg, VA 24073, USA.
| | - Aiying Wang
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Zhongping Lin
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
- College of Life Sciences, Perking University, Beijing 100871, China.
| | - Yong Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianbo Zhu
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
| | - Xianfeng Chen
- College of Life Sciences, Shihezi University, Shihezi 832000, China.
- ShengTing Bioinformatics Institute, Christiansburg, VA 24073, USA.
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Kong X, Luo Z, Dong H, Li W, Chen Y. Non-uniform salinity in the root zone alleviates salt damage by increasing sodium, water and nutrient transport genes expression in cotton. Sci Rep 2017; 7:2879. [PMID: 28588258 PMCID: PMC5460137 DOI: 10.1038/s41598-017-03302-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/25/2017] [Indexed: 11/09/2022] Open
Abstract
Non-uniform salinity alleviates salt damage through sets of physiological adjustments in Na+ transport in leaf and water and nutrient uptake in the non-saline root side. However, little is known of how non-uniform salinity induces these adjustments. In this study, RNA sequencing (RNA-Seq) analysis shown that the expression of sodium transport and photosynthesis related genes in the non-uniform treatment were higher than that in the uniform treatment, which may be the reason for the increased photosynthetic (Pn) rate and decreased Na+ content in leaves of the non-uniform salinity treatment. Most of the water and nutrient transport related genes were up-regulated in the non-saline root side but down-regulated in roots of the high-saline side, which might be the key reason for the increased water and nutrient uptake in the non-saline root side. Furthermore, the expression pattern of most differentially expressed transcription factor and hormone related genes in the non-saline root side was similar to that in the high-saline side. The alleviated salt damage by non-uniform salinity was probably attributed to the increased expression of salt tolerance related genes in the leaf and that of water and nutrient uptake genes in the non-saline root side.
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Affiliation(s)
- Xiangqiang Kong
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China
| | - Zhen Luo
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China
| | - Hezhong Dong
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China.
| | - Weijiang Li
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China
| | - Yizhen Chen
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, 250100, PR China
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Wei Y, Xu Y, Lu P, Wang X, Li Z, Cai X, Zhou Z, Wang Y, Zhang Z, Lin Z, Liu F, Wang K. Salt stress responsiveness of a wild cotton species (Gossypium klotzschianum) based on transcriptomic analysis. PLoS One 2017; 12:e0178313. [PMID: 28552980 PMCID: PMC5446155 DOI: 10.1371/journal.pone.0178313] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/11/2017] [Indexed: 11/22/2022] Open
Abstract
Cotton is a pioneer of saline land crop, while salt stress still causes its growth inhibition and fiber production decrease. Phenotype identification showed better salt tolerance of a wild diploid cotton species Gossypium klotzschianum. To elucidate the salt-tolerant mechanisms in G. klotzschianum, we firstly detected the changes in hormones, H2O2 and glutathione (GSSH and GSH), then investigated the gene expression pattern of roots and leaves treated with 300 mM NaCl for 0, 3, 12, 48 h, and each time control by RNA-seq on the Illumina-Solexa platform. Physiological determination proved that the significant increase in hormone ABA at 48 h, while that in H2O2 was at 12 h, likewise, the GSH content decrease at 48 h and the GSSH content increase at 48 h, under salt stress. In total, 37,278 unigenes were identified from the transcriptome data, 8,312 and 6,732 differentially expressed genes (DEGs) were discovered to be involved in salt stress tolerance in roots and leaves, respectively. Gene function annotation and expression analysis elucidated hormone biosynthesis and signal transduction, reactive oxygen species (ROS), and salt overly sensitive (SOS) signal transduction related genes revealed the important roles of them in signal transmission, oxidation balance and ion homeostasis in response to salinity stress. This is a report which focuses on primary response to highly salty stress (upto 300 mM NaCl) in cotton using a wild diploid Gossypium species, broadening our understanding of the salt tolerance mechanism in cotton and laying a solid foundation of salt resistant for the genetic improvement of upland cotton with the resistance to salt stress.
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Affiliation(s)
- Yangyang Wei
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Pu Lu
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Xingxing Wang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhenqing Li
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhenmei Zhang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement (Wuhan), Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail: (ZL); (FL); (KW)
| | - Fang Liu
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
- * E-mail: (ZL); (FL); (KW)
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology, / Institute of Cotton Research of Chinese Academy of Agricultural Science (ICR-CAAS), Anyang, Henan, China
- * E-mail: (ZL); (FL); (KW)
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Ullah A, Sun H, Yang X, Zhang X. Drought coping strategies in cotton: increased crop per drop. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:271-284. [PMID: 28055133 PMCID: PMC5316925 DOI: 10.1111/pbi.12688] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/06/2016] [Accepted: 12/27/2016] [Indexed: 05/04/2023]
Abstract
The growth and yield of many crops, including cotton, are affected by water deficit. Cotton has evolved drought specific as well as general morpho-physiological, biochemical and molecular responses to drought stress, which are discussed in this review. The key physiological responses against drought stress in cotton, including stomata closing, root development, cellular adaptations, photosynthesis, abscisic acid (ABA) and jasmonic acid (JA) production and reactive oxygen species (ROS) scavenging, have been identified by researchers. Drought stress induces the expression of stress-related transcription factors and genes, such as ROS scavenging, ABA or mitogen-activated protein kinases (MAPK) signalling genes, which activate various drought-related pathways to induce tolerance in the plant. It is crucial to elucidate and induce drought-tolerant traits via quantitative trait loci (QTL) analysis, transgenic approaches and exogenous application of substances. The current review article highlights the natural as well as engineered drought tolerance strategies in cotton.
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Affiliation(s)
- Abid Ullah
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Heng Sun
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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40
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Li S, Yu X, Cheng Z, Yu X, Ruan M, Li W, Peng M. Global Gene Expression Analysis Reveals Crosstalk between Response Mechanisms to Cold and Drought Stresses in Cassava Seedlings. FRONTIERS IN PLANT SCIENCE 2017; 8:1259. [PMID: 28769962 PMCID: PMC5513928 DOI: 10.3389/fpls.2017.01259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/04/2017] [Indexed: 05/21/2023]
Abstract
Abiotic stress negatively impacts cassava (Manihot esculenta) growth and yield. Several molecular mechanisms of plant response to cold and drought have been identified and described in the literature, however, little is known about the crosstalk of the responses of cassava to these two stresses. To elucidate this question, transcriptome analysis of cassava seedlings under cold or PEG-simulated drought stress treatment was performed. Our results showed that 6103 and 7462 transcripts were significantly regulated by cold and drought stress, respectively. Gene Ontology annotation revealed that the abscisic and jasmonic acid signaling pathways shared between the two stresses responses. We further identified 2434 common differentially expressed genes (DEGs), including 1130 up-regulated and 841 down-regulated DEGs by the two stresses. These co-induced or co-suppressed genes are grouped as stress signal perception and transduction, transcription factors (TFs), metabolism as well as transport facilitation according to the function annotation. Furthermore, a large proportion of well characterized protein kinases, TF families and ubiquitin proteasome system related genes, such as RLKs, MAPKs, AP2/ERFBPs, WRKYs, MYBs, E2 enzymes and E3 ligases, including three complexes of interacting proteins were shown as key points of crosstalk between cold and drought stress signaling transduction pathways in a hierarchical manner. Our research provides valuable information and new insights for genetically improving the tolerance of crops to multiple abiotic stresses.
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Affiliation(s)
- Shuxia Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Xiang Yu
- National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Zhihao Cheng
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Xiaoling Yu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Mengbin Ruan
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Wenbin Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesHaikou, China
- *Correspondence: Ming Peng,
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41
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Li A, Zhou M, Wei D, Chen H, You C, Lin J. Transcriptome Profiling Reveals the Negative Regulation of Multiple Plant Hormone Signaling Pathways Elicited by Overexpression of C-Repeat Binding Factors. FRONTIERS IN PLANT SCIENCE 2017; 8:1647. [PMID: 28983312 PMCID: PMC5613223 DOI: 10.3389/fpls.2017.01647] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 09/07/2017] [Indexed: 05/18/2023]
Abstract
C-repeat binding factors (CBF) are a subfamily of AP2 transcription factors that play critical roles in the regulation of plant cold tolerance and growth in low temperature. In the present work, we sought to perform a detailed investigation into global transcriptional regulation of plant hormone signaling associated genes in transgenic plants engineered with CBF genes. RNA samples from Arabidopsis thaliana plants overexpressing two CBF genes, CBF2 and CBF3, were subjected to Illumina HiSeq 2000 RNA sequencing (RNA-Seq). Our results showed that more than half of the hormone associated genes that were differentially expressed in CBF2 or CBF3 transgenic plants were related to auxin signal transduction and metabolism. Most of these alterations in gene expression could lead to repression of auxin signaling. Accordingly, the IAA content was significantly decreased in young tissues of plants overexpressing CBF2 and CBF3 compared with wild type. In addition, genes associated with the biosynthesis of Jasmonate (JA) and Salicylic acid (SA), as well as the signal sensing of Brassinolide (BR) and SA, were down-regulated, while genes associated with Gibberellin (GA) deactivation were up-regulated. In general, overexpression of CBF2 and CBF3 negatively affects multiple plant hormone signaling pathways in Arabidopsis. The transcriptome analysis using CBF2 and CBF3 transgenic plants provides novel and integrated insights into the interaction between CBFs and plant hormones, particularly the modulation of auxin signaling, which may contribute to the improvement of crop yields under abiotic stress via molecular engineering using CBF genes.
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Svoboda P, Janská A, Spiwok V, Prášil IT, Kosová K, Vítámvás P, Ovesná J. Global Scale Transcriptional Profiling of Two Contrasting Barley Genotypes Exposed to Moderate Drought Conditions: Contribution of Leaves and Crowns to Water Shortage Coping Strategies. FRONTIERS IN PLANT SCIENCE 2016; 7:1958. [PMID: 28083001 PMCID: PMC5187378 DOI: 10.3389/fpls.2016.01958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/09/2016] [Indexed: 05/07/2023]
Abstract
Drought is a serious threat for sustainable agriculture. Barley represents a species well adapted to environmental stresses including drought. To elucidate the adaptive mechanism of barley on transcriptional level we evaluated transcriptomic changes of two contrasting barley cultivars upon drought using the microarray technique on the level of leaves and crowns. Using bioinformatic tools, differentially expressed genes in treated vs. non-treated plants were identified. Both genotypes revealed tissue dehydration under drought conditions as shown at water saturation deficit and osmotic potential data; however, dehydration was more severe in Amulet than in drought-resistant Tadmor under the same ambient conditions. Performed analysis showed that Amulet enhanced expression of genes related to active plant growth and development, while Tadmor regarding the stimulated genes revealed conservative, water saving strategy. Common reactions of both genotypes and tissues included an induction of genes encoding several stress-responsive signaling proteins, transcription factors as well as effector genes encoding proteins directly involved in stress acclimation. In leaf, tolerant cultivar effectively stimulated mainly the expression of genes encoding proteins and enzymes involved in protein folding, sulfur metabolism, ROS detoxification or lipid biosynthesis and transport. The crown specific reaction of tolerant cultivar was an enhanced expression of genes encoding proteins and enzymes involved in cell wall lignification, ABRE-dependent abscisic acid (ABA) signaling, nucleosome remodeling, along with genes for numerous jasmonate induced proteins.
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Affiliation(s)
- Pavel Svoboda
- Division of Crop Genetics and Breeding, Crop Research InstitutePrague, Czechia
| | - Anna Janská
- Faculty of Science, Charles University in PraguePrague, Czechia
| | - Vojtěch Spiwok
- Faculty of Food and Biochemical Technology, University of Chemistry and TechnologyPrague, Czechia
| | - Ilja T. Prášil
- Division of Crop Genetics and Breeding, Crop Research InstitutePrague, Czechia
| | - Klára Kosová
- Division of Crop Genetics and Breeding, Crop Research InstitutePrague, Czechia
| | - Pavel Vítámvás
- Division of Crop Genetics and Breeding, Crop Research InstitutePrague, Czechia
| | - Jaroslava Ovesná
- Division of Crop Genetics and Breeding, Crop Research InstitutePrague, Czechia
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43
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Hanson AD, Beaudoin GA, McCarty DR, Gregory JF. Does Abiotic Stress Cause Functional B Vitamin Deficiency in Plants? PLANT PHYSIOLOGY 2016; 172:2082-2097. [PMID: 27807106 PMCID: PMC5129723 DOI: 10.1104/pp.16.01371] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/19/2016] [Indexed: 05/20/2023]
Abstract
B vitamins are the precursors of essential metabolic cofactors but are prone to destruction under stress conditions. It is therefore a priori reasonable that stressed plants suffer B vitamin deficiencies and that certain stress symptoms are metabolic knock-on effects of these deficiencies. Given the logic of these arguments, and the existence of data to support them, it is a shock to realize that the roles of B vitamins in plant abiotic stress have had minimal attention in the literature (100-fold less than hormones) and continue to be overlooked. In this article, we therefore aim to explain the connections among B vitamins, enzyme cofactors, and stress conditions in plants. We first outline the chemistry and biochemistry of B vitamins and explore the concept of vitamin deficiency with the help of information from mammals. We then summarize classical and recent evidence for stress-induced vitamin deficiencies and for plant responses that counter these deficiencies. Lastly, we consider potential implications for agriculture.
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Affiliation(s)
- Andrew D Hanson
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Guillaume A Beaudoin
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Donald R McCarty
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Jesse F Gregory
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
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Sivankalyani V, Sela N, Feygenberg O, Zemach H, Maurer D, Alkan N. Transcriptome Dynamics in Mango Fruit Peel Reveals Mechanisms of Chilling Stress. FRONTIERS IN PLANT SCIENCE 2016; 7:1579. [PMID: 27812364 PMCID: PMC5072284 DOI: 10.3389/fpls.2016.01579] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/06/2016] [Indexed: 05/24/2023]
Abstract
Cold storage is considered the most effective method for prolonging fresh produce storage. However, subtropical fruit is sensitive to cold. Symptoms of chilling injury (CI) in mango include red and black spots that start from discolored lenticels and develop into pitting. The response of 'Keitt' mango fruit to chilling stress was monitored by transcriptomic, physiological, and microscopic analyses. Transcriptomic changes in the mango fruit peel were evaluated during optimal (12°C) and suboptimal (5°C) cold storage. Two days of chilling stress upregulated genes involved in the plant stress response, including those encoding transmembrane receptors, calcium-mediated signal transduction, NADPH oxidase, MAP kinases, and WRKYs, which can lead to cell death. Indeed, cell death was observed around the discolored lenticels after 19 days of cold storage at 5°C. Localized cell death and cuticular opening in the lumen of discolored lenticels were correlated with increased general decay during shelf-life storage, possibly due to fungal penetration. We also observed increased phenolics accumulation around the discolored lenticels, which was correlated with the biosynthesis of phenylpropanoids that were probably transported from the resin ducts. Increased lipid peroxidation was observed during CI by both the biochemical malondialdehyde method and a new non-destructive luminescent technology, correlated to upregulation of the α-linolenic acid oxidation pathway. Genes involved in sugar metabolism were also induced, possibly to maintain osmotic balance. This analysis provides an in-depth characterization of mango fruit response to chilling stress and could lead to the development of new tools, treatments and strategies to prolong cold storage of subtropical fruit.
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Affiliation(s)
- Velu Sivankalyani
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani CenterRishon LeZion, Israel
| | - Noa Sela
- Department of Plant Pathology, Agricultural Research Organization, Volcani CenterRishon LeZion, Israel
| | - Oleg Feygenberg
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani CenterRishon LeZion, Israel
| | - Hanita Zemach
- Department of Plant Science, Agricultural Research Organization, Volcani CenterRishon LeZion, Israel
| | - Dalia Maurer
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani CenterRishon LeZion, Israel
| | - Noam Alkan
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani CenterRishon LeZion, Israel
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45
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Wang Q, Liu N, Yang X, Tu L, Zhang X. Small RNA-mediated responses to low- and high-temperature stresses in cotton. Sci Rep 2016; 6:35558. [PMID: 27752116 PMCID: PMC5067717 DOI: 10.1038/srep35558] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 09/30/2016] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are one class of endogenous non-coding RNAs modulating the expression of target genes involved in plant development and stress tolerance, by degrading mRNA or repressing translation. In this study, small RNA and mRNA degradome sequencing were used to identify low- and high-temperature stress-responsive miRNAs and their targets in cotton (Gossypium hirsutum). Cotton seedlings were treated under different temperature conditions (4, 12, 25, 35, and 42 °C) and then the effects were investigated. In total, 319 known miRNAs and 800 novel miRNAs were identified, and 168 miRNAs were differentially expressed between different treatments. The targets of these miRNAs were further analysed by degradome sequencing. Based on studies from Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, the majority of the miRNAs are from genes that are likely involved in response to hormone stimulus, oxidation-reduction reaction, photosynthesis, plant-pathogen interaction and plant hormone signal transduction pathways. This study provides new insight into the molecular mechanisms of plant response to extreme temperature stresses, and especially the roles of miRNAs under extreme temperatures.
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Affiliation(s)
- Qiongshan Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Nian Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Liang C, Meng Z, Meng Z, Malik W, Yan R, Lwin KM, Lin F, Wang Y, Sun G, Zhou T, Zhu T, Li J, Jin S, Guo S, Zhang R. GhABF2, a bZIP transcription factor, confers drought and salinity tolerance in cotton (Gossypium hirsutum L.). Sci Rep 2016; 6:35040. [PMID: 27713524 PMCID: PMC5054369 DOI: 10.1038/srep35040] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/23/2016] [Indexed: 11/16/2022] Open
Abstract
The bZIP transcription factor (TF) act as an important regulator for the abscisic acid (ABA) mediated abiotic stresses signaling pathways in plants. Here, we reported the cloning and characterization of GhABF2, encoding for typical cotton bZIP TF. Overexpression of GhABF2 significantly improved drought and salt stress tolerance both in Arabidopsis and cotton. However, silencing of GhABF2 made transgenic cotton sensitive to PEG osmotic and salt stress. Expression of GhABF2 was induced by drought and ABA treatments but repressed by high salinity. Transcriptome analysis indicated that GhABF2 increases drought and salt tolerance by regulating genes related to ABA, drought and salt response. The proline contents, activity of superoxide dismutase (SOD) and catalase (CAT) were also significantly increased in GhABF2-overexpression cottons in comparison to wild type after drought and salt treatment. Further, an increase in fiber yield under drought and saline-alkali wetland exhibited the important role of GhABF2 in enhancing the drought and salt tolerance in transgenic lines. In conclusion, manipulation of GhABF2 by biotechnological tools could be a sustainable strategy to deploy drought and salt tolerance in cotton.
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Affiliation(s)
- Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaohong Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Waqas Malik
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Rong Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Khin Myat Lwin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,Biotechnology Research Department, Ministry of Science and Technology, Naypyidaw, Myanmar
| | - Fazhuang Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guoqing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tao Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tao Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Liu X, Song Y, Xing F, Wang N, Wen F, Zhu C. GhWRKY25, a group I WRKY gene from cotton, confers differential tolerance to abiotic and biotic stresses in transgenic Nicotiana benthamiana. PROTOPLASMA 2016; 253:1265-81. [PMID: 26410829 DOI: 10.1007/s00709-015-0885-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 09/16/2015] [Indexed: 05/03/2023]
Abstract
WRKY transcription factors are involved in various processes, ranging from plant growth to abiotic and biotic stress responses. Group I WRKY members have been rarely reported compared with group II or III members, particularly in cotton (Gossypium hirsutum). In this study, a group I WRKY gene, namely, GhWRKY25, was cloned from cotton and characterized. Expression analysis revealed that GhWRKY25 can be induced or deduced by the treatments of abiotic stresses and multiple defense-related signaling molecules. Overexpression of GhWRKY25 in Nicotiana benthamiana reduced plant tolerance to drought stress but enhanced tolerance to salt stress. Moreover, more MDA and ROS accumulated in transgenic plants after drought treatment with lower activities of SOD, POD, and CAT. Our study further demonstrated that GhWRKY25 overexpression in plants enhanced sensitivity to the fungal pathogen Botrytis cinerea by reducing the expression of SA or ET signaling related genes and inducing the expression of genes involved in the JA signaling pathway. These results indicated that GhWRKY25 plays negative or positive roles in response to abiotic stresses, and the reduced pathogen resistance may be related to the crosstalk of the SA and JA/ET signaling pathways.
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Affiliation(s)
- Xiufang Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Yunzhi Song
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Fangyu Xing
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Ning Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Fujiang Wen
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China
| | - Changxiang Zhu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, People's Republic of China.
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48
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Shen L, Liu Z, Yang S, Yang T, Liang J, Wen J, Liu Y, Li J, Shi L, Tang Q, Shi W, Hu J, Liu C, Zhang Y, Lin W, Wang R, Yu H, Mou S, Hussain A, Cheng W, Cai H, He L, Guan D, Wu Y, He S. Pepper CabZIP63 acts as a positive regulator during Ralstonia solanacearum or high temperature-high humidity challenge in a positive feedback loop with CaWRKY40. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2439-51. [PMID: 26936828 PMCID: PMC4809298 DOI: 10.1093/jxb/erw069] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
CaWRKY40 is known to act as a positive regulator in the response of pepper (Capsicum annuum) to Ralstonia solanacearum inoculation (RSI) or high temperature-high humidity (HTHH), but the underlying mechanism remains elusive. Herein, we report that CabZIP63, a pepper bZIP family member, participates in this process by regulating the expression of CaWRKY40. CabZIP63 was found to localize in the nuclei, be up-regulated by RSI or HTHH, bind to promoters of both CabZIP63(pCabZIP63) and CaWRKY40(pCaWRKY40), and activate pCabZIP63- and pCaWRKY40-driven β-glucuronidase expression in a C- or G-box-dependent manner. Silencing of CabZIP63 by virus-induced gene silencing (VIGS) in pepper plants significantly attenuated their resistance to RSI and tolerance to HTHH, accompanied by down-regulation of immunity- or thermotolerance-associated CaPR1, CaNPR1, CaDEF1, and CaHSP24. Hypersensitive response-mediated cell death and expression of the tested immunity- and thermotolerance-associated marker genes were induced by transient overexpression (TOE) of CabZIP63, but decreased by that of CabZIP63-SRDX. Additionally, binding of CabZIP63 to pCaWRKY40 was up-regulated by RSI or HTHH, and the transcript level of CaWRKY40 and binding of CaWRKY40 to the promoters of CaPR1, CaNPR1, CaDEF1 and CaHSP24 were up-regulated by TOE of CabZIP63. On the other hand, CabZIP63 was also up-regulated transcriptionally by TOE of CaWRKY40. The data suggest collectively that CabZIP63 directly or indirectly regulates the expression of CaWRKY40 at both the transcriptional and post-transcriptional level, forming a positive feedback loop with CaWRKY40 during pepper's response to RSI or HTHH. Altogether, our data will help to elucidate the underlying mechanism of crosstalk between pepper's response to RSI and HTHH.
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Affiliation(s)
- Lei Shen
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Zhiqin Liu
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Sheng Yang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Tong Yang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiaqi Liang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiayu Wen
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Yanyan Liu
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiazhi Li
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Lanping Shi
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Qian Tang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Wei Shi
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Jiong Hu
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Cailing Liu
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Yangwen Zhang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Wei Lin
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Rongzhang Wang
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Huanxin Yu
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Shaoliang Mou
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Ansar Hussain
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Wei Cheng
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Hanyang Cai
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Li He
- College of Life Science, Jinggang Shan University, Ji'an, Jiangxi 343000, PR China
| | - Deyi Guan
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
| | - Yang Wu
- College of Life Science, Jinggang Shan University, Ji'an, Jiangxi 343000, PR China
| | - Shuilin He
- National Education Minister, Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China
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Transcriptome analysis in different rice cultivars provides novel insights into desiccation and salinity stress responses. Sci Rep 2016; 6:23719. [PMID: 27029818 PMCID: PMC4814823 DOI: 10.1038/srep23719] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/14/2016] [Indexed: 01/18/2023] Open
Abstract
Drought and salinity are the major environmental factors that affect rice productivity. Comparative transcriptome analysis between tolerant and sensitive rice cultivars can provide insights into the regulatory mechanisms involved in these stress responses. In this study, the comparison of transcriptomes of a drought-tolerant [Nagina 22 (N22)] and a salinity-tolerant (Pokkali) rice cultivar with IR64 (susceptible cultivar) revealed variable transcriptional responses under control and stress conditions. A total of 801 and 507 transcripts were exclusively differentially expressed in N22 and Pokkali rice cultivars, respectively, under stress conditions. Gene ontology analysis suggested the enrichment of transcripts involved in response to abiotic stress and regulation of gene expression in stress-tolerant rice cultivars. A larger number of transcripts encoding for members of NAC and DBP transcription factor (TF) families in N22 and members of bHLH and C2H2 TF families in Pokkali exhibited differential regulation under desiccation and salinity stresses, respectively. Transcripts encoding for thioredoxin and involved in phenylpropanoid metabolism were up-regulated in N22, whereas transcripts involved in wax and terpenoid metabolism were up-regulated in Pokkali. Overall, common and cultivar-specific stress-responsive transcripts identified in this study can serve as a helpful resource to explore novel candidate genes for abiotic stress tolerance in rice.
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Zhang H, Ni Z, Chen Q, Guo Z, Gao W, Su X, Qu Y. Proteomic responses of drought-tolerant and drought-sensitive cotton varieties to drought stress. Mol Genet Genomics 2016; 291:1293-303. [PMID: 26941218 DOI: 10.1007/s00438-016-1188-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 02/24/2016] [Indexed: 12/27/2022]
Abstract
Drought, one of the most widespread factors reducing agricultural crop productivity, affects biological processes such as development, architecture, flowering and senescence. Although protein analysis techniques and genome sequencing have made facilitated the proteomic study of cotton, information on genetic differences associated with proteomic changes in response to drought between different cotton genotypes is lacking. To determine the effects of drought stress on cotton seedlings, we used two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry to comparatively analyze proteome of drought-responsive proteins during the seedling stage in two cotton (Gossypium hirsutum L.) cultivars, drought-tolerant KK1543 and drought-sensitive Xinluzao26. A total of 110 protein spots were detected on 2-DE maps, of which 56 were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified proteins were mainly associated with metabolism (46.4 %), antioxidants (14.2 %), and transport and cellular structure (23.2 %). Some key proteins had significantly different expression patterns between the two genotypes. In particular, 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase, UDP-D-glucose pyrophosphorylase and ascorbate peroxidase were up-regulated in KK1543 compared with Xinluzao26. Under drought stress conditions, the vacuolar H(+)-ATPase catalytic subunit, a 14-3-3g protein, translation initiation factor 5A and pathogenesis-related protein 10 were up-regulated in KK1543, whereas ribosomal protein S12, actin, cytosolic copper/zinc superoxide dismutase, protein disulfide isomerase, S-adenosylmethionine synthase and cysteine synthase were down-regulated in Xinluzao26. This work represents the first characterization of proteomic changes that occur in response to drought in roots of cotton plants. These differentially expressed proteins may be related to biochemical pathways responsible for drought tolerance in KK1543. Although further studies are needed, this proteomic analysis underlines the role of post-translational events. The differentially expressed proteins and their corresponding genes may be used as markers for the breeding of drought tolerance in cotton.
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Affiliation(s)
- Haiyan Zhang
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zhiyong Ni
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zhongjun Guo
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Wenwei Gao
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Xiujuan Su
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Yanying Qu
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052, China.
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