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Chen Y, Su WY, Ren CJ, Lin YL, Wang WQ, Zhang HQ, Yin XR, Liu XF. Restricted responses of AcMYB68 and AcERF74/75 enhanced waterlogging tolerance in kiwifruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38761127 DOI: 10.1111/tpj.16816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/20/2024]
Abstract
Most of kiwifruit cultivars (e.g. Actinidia chinensis cv. Donghong, "DH") were sensitive to waterlogging, thus, waterlogging resistant rootstocks (e.g. Actinidia valvata Dunn, "Dunn") were widely used for kiwifruit industry. Those different species provided ideal materials to understand the waterlogging responses in kiwifruit. Compared to the weaken growth and root activities in "DH", "Dunn" maintained the relative high root activities under the prolonged waterlogging. Based on comparative analysis, transcript levels of pyruvate decarboxylase (PDCs) and alcohol dehydrogenase (ADHs) showed significantly difference between these two species. Both PDCs and ADHs had been significantly increased by waterlogging in "DH", while they were only limitedly triggered by 2 days stress and subsided during the prolonged waterlogging in "Dunn". Thus, 19 differentially expressed transcript factors (DETFs) had been isolated using weighted gene co-expression network analysis combined with transcriptomics and transcript levels of PDCs and ADHs in waterlogged "DH". Among these DETFs, dual luciferase and electrophoretic mobility shift assays indicated AcMYB68 could bind to and trigger the activity of AcPDC2 promoter. The stable over-expression of AcMYB68 significantly up-regulated the transcript levels of PDCs but inhibited the plant growth, especially the roots. Moreover, the enzyme activities of PDC in 35S::AcMYB68 were significantly enhanced during the waterlogging response than that in wild type plants. Most interestingly, comparative analysis indicated that the expression patterns of AcMYB68 and the previously characterized AcERF74/75 (the direct regulator on ADHs) either showed no responses (AcMYB68 and AcERF74) or very limited response (AcERF75) in "Dunn". Taken together, the restricted responses of AcMYB68 and AcERF74/75 in "Dunn" endow its waterlogging tolerance.
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Affiliation(s)
- Yue Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
| | - Wen-Yue Su
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
| | - Chun-Jiang Ren
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
| | - Yi-Lai Lin
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
| | - Wen-Qiu Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
| | - Hui-Qin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, P.R. China
| | - Xue-Ren Yin
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Xiao-Fen Liu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, 310058, P.R. China
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
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Cheng T, Zhou X, Lin J, Zhou X, Wang H, Chen T. Transcriptomic and Metabolomic Analyses Reveal the Response Mechanism of Ophiopogon japonicus to Waterlogging Stress. BIOLOGY 2024; 13:197. [PMID: 38534466 DOI: 10.3390/biology13030197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Ophiopogon japonicus, a plant that thrives in river alluvial dams, often faces waterlogging stress due to sustained rainfall and flood seasons, which significantly impacts its growth and development. Currently, the mechanisms of waterlogging tolerance in Ophiopogon japonicus are still unclear. This study analyzed the transcriptome and metabolome data for Ophiopogon japonicus in the Sichuan region (referred to as CMD) under varying degrees of waterlogging stress: mild, moderate, and severe. The results indicate that the group exposed to flooding stress exhibited a higher number of differentially expressed genes (DEGs) compared to the control group. Notably, most DEGs were downregulated and primarily enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction pathways. A total of 5151 differentially accumulated metabolites (DAMs) were identified, with significantly upregulated DAMs annotated to two clusters, namely flavonoids such as apiin, pelargonin, and others. Furthermore, our study revealed significant upregulation in the expression of C2H2 (C2H2 zinc finger proteins) and AP2/ERF-ERF (the subfamily ERF proteins of APETALA2/ethylene-responsive element binding factors) transcription factors in CMD under flooding stress, suggesting their critical roles in enabling CMD to adapt to these conditions. In conclusion, this research provides insights into the intricate molecular mechanisms underlying CMD's response to flooding stress and reports valuable genetic data for the development of transgenic plants with improved waterlogging tolerance.
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Affiliation(s)
- Tingting Cheng
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Xia Zhou
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Juan Lin
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Xianjian Zhou
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Hongsu Wang
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
| | - Tiezhu Chen
- Sichuan Academy of Chinese Medicine Sciences, Chengdu 610041, China
- Sichuan Provincial Key Laboratory of Quality and Innovation Research of Chinese Materia Medica, Chengdu 610041, China
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Renziehausen T, Frings S, Schmidt-Schippers R. 'Against all floods': plant adaptation to flooding stress and combined abiotic stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1836-1855. [PMID: 38217848 DOI: 10.1111/tpj.16614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/28/2023] [Accepted: 12/15/2023] [Indexed: 01/15/2024]
Abstract
Current climate change brings with it a higher frequency of environmental stresses, which occur in combination rather than individually leading to massive crop losses worldwide. In addition to, for example, drought stress (low water availability), also flooding (excessive water) can threaten the plant, causing, among others, an energy crisis due to hypoxia, which is responded to by extensive transcriptional, metabolic and growth-related adaptations. While signalling during flooding is relatively well understood, at least in model plants, the molecular mechanisms of combinatorial flooding stress responses, for example, flooding simultaneously with salinity, temperature stress and heavy metal stress or sequentially with drought stress, remain elusive. This represents a significant gap in knowledge due to the fact that dually stressed plants often show unique responses at multiple levels not observed under single stress. In this review, we (i) consider possible effects of stress combinations from a theoretical point of view, (ii) summarize the current state of knowledge on signal transduction under single flooding stress, (iii) describe plant adaptation responses to flooding stress combined with four other abiotic stresses and (iv) propose molecular components of combinatorial flooding (hypoxia) stress adaptation based on their reported dual roles in multiple stresses. This way, more future emphasis may be placed on deciphering molecular mechanisms of combinatorial flooding stress adaptation, thereby potentially stimulating development of molecular tools to improve plant resilience towards multi-stress scenarios.
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Affiliation(s)
- Tilo Renziehausen
- Plant Biotechnology, Faculty of Biology, University of Bielefeld, 33615, Bielefeld, Germany
- Center for Biotechnology, University of Bielefeld, 33615, Bielefeld, Germany
| | - Stephanie Frings
- Plant Biotechnology, Faculty of Biology, University of Bielefeld, 33615, Bielefeld, Germany
- Center for Biotechnology, University of Bielefeld, 33615, Bielefeld, Germany
| | - Romy Schmidt-Schippers
- Plant Biotechnology, Faculty of Biology, University of Bielefeld, 33615, Bielefeld, Germany
- Center for Biotechnology, University of Bielefeld, 33615, Bielefeld, Germany
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Jiang W, He J, Babla M, Wu T, Tong T, Riaz A, Zeng F, Qin Y, Chen G, Deng F, Chen ZH. Molecular evolution and interaction of 14-3-3 proteins with H+-ATPases in plant abiotic stresses. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:689-707. [PMID: 37864845 DOI: 10.1093/jxb/erad414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/20/2023] [Indexed: 10/23/2023]
Abstract
Environmental stresses severely affect plant growth and crop productivity. Regulated by 14-3-3 proteins (14-3-3s), H+-ATPases (AHAs) are important proton pumps that can induce diverse secondary transport via channels and co-transporters for the abiotic stress response of plants. Many studies demonstrated the roles of 14-3-3s and AHAs in coordinating the processes of plant growth, phytohormone signaling, and stress responses. However, the molecular evolution of 14-3-3s and AHAs has not been summarized in parallel with evolutionary insights across multiple plant species. Here, we comprehensively review the roles of 14-3-3s and AHAs in cell signaling to enhance plant responses to diverse environmental stresses. We analyzed the molecular evolution of key proteins and functional domains that are associated with 14-3-3s and AHAs in plant growth and hormone signaling. The results revealed evolution, duplication, contraction, and expansion of 14-3-3s and AHAs in green plants. We also discussed the stress-specific expression of those 14-3-3and AHA genes in a eudicotyledon (Arabidopsis thaliana), a monocotyledon (Hordeum vulgare), and a moss (Physcomitrium patens) under abiotic stresses. We propose that 14-3-3s and AHAs respond to abiotic stresses through many important targets and signaling components of phytohormones, which could be promising to improve plant tolerance to single or multiple environmental stresses.
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Affiliation(s)
- Wei Jiang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Jing He
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Mohammad Babla
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Ting Wu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Tao Tong
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Adeel Riaz
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Fanrong Zeng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Yuan Qin
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Fenglin Deng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, College of Agriculture, Yangtze University, Jingzhou, 434025, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
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O'Lone CE, Juhász A, Nye-Wood M, Dunn H, Moody D, Ral JP, Colgrave ML. Proteomic exploration reveals a metabolic rerouting due to low oxygen during controlled germination of malting barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1305381. [PMID: 38186599 PMCID: PMC10771735 DOI: 10.3389/fpls.2023.1305381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/20/2023] [Indexed: 01/09/2024]
Abstract
Barley (Hordeum vulgare L.) is used in malt production for brewing applications. Barley malting involves a process of controlled germination that modifies the grain by activating enzymes to solubilize starch and proteins for brewing. Initially, the grain is submerged in water to raise grain moisture, requiring large volumes of water. Achieving grain modification at reduced moisture levels can contribute to the sustainability of malting practices. This study combined proteomics, bioinformatics, and biochemical phenotypic analysis of two malting barley genotypes with observed differences in water uptake and modification efficiency. We sought to reveal the molecular mechanisms at play during controlled germination and explore the roles of protein groups at 24 h intervals across the first 72 h. Overall, 3,485 protein groups were identified with 793 significant differentially abundant (DAP) within and between genotypes, involved in various biological processes, including protein synthesis, carbohydrate metabolism, and hydrolysis. Functional integration into metabolic pathways, such as glycolysis, pyruvate, starch and sucrose metabolism, revealed a metabolic rerouting due to low oxygen enforced by submergence during controlled germination. This SWATH-MS study provides a comprehensive proteome reference, delivering new insights into the molecular mechanisms underlying the impacts of low oxygen during controlled germination. It is concluded that continued efficient modification of malting barley subjected to submergence is largely due to the capacity to reroute energy to maintain vital processes, particularly protein synthesis.
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Affiliation(s)
- Clare E. O'Lone
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, Joondalup, WA, Australia
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, ACT, Canberra, ACT, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, Joondalup, WA, Australia
| | - Mitchell Nye-Wood
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, Joondalup, WA, Australia
| | - Hugh Dunn
- Pilot Malting Australia, Edith Cowan University, School of Science, Joondalup, WA, Australia
| | - David Moody
- Barley Breeding, InterGrain Pty Ltd, Bibra Lake, WA, Australia
| | - Jean-Philippe Ral
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, ACT, Canberra, ACT, Australia
| | - Michelle L. Colgrave
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, Joondalup, WA, Australia
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Brisbane, QLD, Australia
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Aslam A, Mahmood A, Ur-Rehman H, Li C, Liang X, Shao J, Negm S, Moustafa M, Aamer M, Hassan MU. Plant Adaptation to Flooding Stress under Changing Climate Conditions: Ongoing Breakthroughs and Future Challenges. PLANTS (BASEL, SWITZERLAND) 2023; 12:3824. [PMID: 38005721 PMCID: PMC10675391 DOI: 10.3390/plants12223824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/24/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023]
Abstract
Climate-change-induced variations in temperature and rainfall patterns are a serious threat across the globe. Flooding is the foremost challenge to agricultural productivity, and it is believed to become more intense under a changing climate. Flooding is a serious form of stress that significantly reduces crop yields, and future climatic anomalies are predicted to make the problem even worse in many areas of the world. To cope with the prevailing flooding stress, plants have developed different morphological and anatomical adaptations in their roots, aerenchyma cells, and leaves. Therefore, researchers are paying more attention to identifying developed and adopted molecular-based plant mechanisms with the objective of obtaining flooding-resistant cultivars. In this review, we discuss the various physiological, anatomical, and morphological adaptations (aerenchyma cells, ROL barriers (redial O2 loss), and adventitious roots) and the phytohormonal regulation in plants under flooding stress. This review comprises ongoing innovations and strategies to mitigate flooding stress, and it also provides new insights into how this knowledge can be used to improve productivity in the scenario of a rapidly changing climate and increasing flood intensity.
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Affiliation(s)
- Amna Aslam
- Department of Botany, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (A.A.); (H.U.-R.)
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan;
| | - Hafeez Ur-Rehman
- Department of Botany, University of Agriculture Faisalabad, Faisalabad 38040, Pakistan; (A.A.); (H.U.-R.)
| | - Cunwu Li
- Guangxi Key Laboratory of Water Engineering Materials and Structures, Guangxi Institute of Water Resources Research, Nanning 530023, China; (C.L.); (J.S.)
| | - Xuewen Liang
- Guangxi Key Laboratory of Water Engineering Materials and Structures, Guangxi Institute of Water Resources Research, Nanning 530023, China; (C.L.); (J.S.)
| | - Jinhua Shao
- Guangxi Key Laboratory of Water Engineering Materials and Structures, Guangxi Institute of Water Resources Research, Nanning 530023, China; (C.L.); (J.S.)
| | - Sally Negm
- Department of Life Sciences, College of Science and Art Mahyel Aseer, King Khalid University, Abha 62529, Saudi Arabia;
| | - Mahmoud Moustafa
- Department of Biology, College of Science, King Khalid University, Abha 61421, Saudi Arabia;
| | - Muhammad Aamer
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (M.A.); (M.U.H.)
| | - Muhammad Umair Hassan
- Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (M.A.); (M.U.H.)
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Jeffery HR, Mudukuti N, Buell CR, Childs KL, Cichy K. Gene expression profiling of soaked dry beans (Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time. THE PLANT GENOME 2023; 16:e20364. [PMID: 37415293 DOI: 10.1002/tpg2.20364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/20/2023] [Accepted: 05/26/2023] [Indexed: 07/08/2023]
Abstract
Dry beans (Phaseolus vulgaris L.) are a nutritious food, but their lengthy cooking requirements are barriers to consumption. Presoaking is one strategy to reduce cooking time. Soaking allows hydration to occur prior to cooking, and enzymatic changes to pectic polysaccharides also occur during soaking that shorten the cooking time of beans. Little is known about how gene expression during soaking influences cooking times. The objectives of this study were to (1) identify gene expression patterns that are altered by soaking and (2) compare gene expression in fast-cooking and slow-cooking bean genotypes. RNA was extracted from four bean genotypes at five soaking time points (0, 3, 6, 12, and 18 h) and expression abundances were detected using Quant-seq. Differential gene expression analysis and weighted gene coexpression network analysis were used to identify candidate genes within quantitative trait loci for water uptake and cooking time. Genes related to cell wall growth and development as well as hypoxic stress were differentially expressed between the fast- and slow-cooking beans due to soaking. Candidate genes identified in the slow-cooking beans included enzymes that increase intracellular calcium concentrations and cell wall modification enzymes. The expression of cell wall-strengthening enzymes in the slow-cooking beans may increase their cooking time and ability to resist osmotic stress by preventing cell separation and water uptake in the cotyledon.
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Affiliation(s)
- Hannah R Jeffery
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Nyasha Mudukuti
- Keough School of Global Affairs, University of Notre Dame, Notre Dame, IN, USA
| | - Carol Robin Buell
- Department of Crop & Soil Sciences, Center for Applied Genetic Technologies, and Institute of Plant Breeding, Genetics, & Genomics, University of Georgia, Athens, GA, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Karen Cichy
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Sugarbeet and Bean Research Unit, USDA-ARS, East Lansing, MI, USA
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Gedam PA, Khandagale K, Shirsat D, Thangasamy A, Kulkarni O, Kulkarni A, Patil SS, Barvkar VT, Mahajan V, Gupta AJ, Bhagat KP, Khade YP, Singh M, Gawande S. Elucidating the molecular responses to waterlogging stress in onion ( Allium cepa L.) leaf by comparative transcriptome profiling. FRONTIERS IN PLANT SCIENCE 2023; 14:1150909. [PMID: 37615019 PMCID: PMC10442827 DOI: 10.3389/fpls.2023.1150909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
Introduction Waterlogging is a major stress that severely affects onion cultivation worldwide, and developing stress-tolerant varieties could be a valuable measure for overcoming its adverse effects. Gathering information regarding the molecular mechanisms and gene expression patterns of waterlogging-tolerant and sensitive genotypes is an effective method for improving stress tolerance in onions. To date, the waterlogging tolerance-governing molecular mechanism in onions is unknown. Methods This study identified the differentially expressed genes (DEGs) through transcriptome analysis in leaf tissue of two onion genotypes (Acc. 1666; tolerant and W-344; sensitive) presenting contrasting responses to waterlogging stress. Results Differential gene expression analysis revealed that in Acc. 1666, 1629 and 3271 genes were upregulated and downregulated, respectively. In W-344, 2134 and 1909 genes were upregulated and downregulated, respectively, under waterlogging stress. The proteins coded by these DEGs regulate several key biological processes to overcome waterlogging stress such as phytohormone production, antioxidant enzymes, programmed cell death, and energy production. The clusters of orthologous group pathway analysis revealed that DEGs contributed to the post-translational modification, energy production, and carbohydrate metabolism-related pathways under waterlogging stress. The enzyme assay demonstrated higher activity of antioxidant enzymes in Acc. 1666 than in W-344. The differential expression of waterlogging tolerance related genes, such as those related to antioxidant enzymes, phytohormone biosynthesis, carbohydrate metabolism, and transcriptional factors, suggested that significant fine reprogramming of gene expression occurs in response to waterlogging stress in onion. A few genes such as ADH, PDC, PEP carboxylase, WRKY22, and Respiratory burst oxidase D were exclusively upregulated in Acc. 1666. Discussion The molecular information about DEGs identified in the present study would be valuable for improving stress tolerance and for developing waterlogging tolerant onion varieties.
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Affiliation(s)
- Pranjali A. Gedam
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Kiran Khandagale
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Dhananjay Shirsat
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - A. Thangasamy
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Onkar Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
| | | | | | - Vijay Mahajan
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Amar Jeet Gupta
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Kiran P. Bhagat
- Indian Council of Agricultural Research (ICAR)-Directorate of Floriculture Research, Pune, India
| | - Yogesh P. Khade
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Major Singh
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Suresh Gawande
- Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
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Miricescu A, Brazel AJ, Beegan J, Wellmer F, Graciet E. Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response. PLANT DIRECT 2023; 7:e518. [PMID: 37577136 PMCID: PMC10422865 DOI: 10.1002/pld3.518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/15/2023]
Abstract
Waterlogging leads to major crop losses globally, particularly for waterlogging-sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related quantitative trait loci have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called "core hypoxia response genes," thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study "predisposition" to waterlogging tolerance or sensitivity in barley.
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Affiliation(s)
- Alexandra Miricescu
- Department of BiologyMaynooth UniversityMaynoothIreland
- Pesticide Registration DivisionDepartment of Agriculture, Food and the Marine, Backweston CampusCelbridgeIreland
| | | | - Joseph Beegan
- Smurfit Institute of GeneticsTrinity College DublinDublinIreland
| | - Frank Wellmer
- Smurfit Institute of GeneticsTrinity College DublinDublinIreland
| | - Emmanuelle Graciet
- Department of BiologyMaynooth UniversityMaynoothIreland
- Kathleen Lonsdale Institute for Human Health ResearchMaynooth UniversityMaynoothIreland
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10
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Karunarathne S, Walker E, Sharma D, Li C, Han Y. Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance. J Zhejiang Univ Sci B 2023; 24:1069-1092. [PMID: 38057266 PMCID: PMC10710907 DOI: 10.1631/jzus.b2200552] [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: 10/31/2022] [Accepted: 01/17/2023] [Indexed: 07/11/2023]
Abstract
Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern gene-editing platforms. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.
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Affiliation(s)
- Sakura Karunarathne
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Darshan Sharma
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.
| | - Yong Han
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.
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11
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Hill RD, de Castro J, Mira MM, Igamberdiev AU, Hebelstrup KH, Renault S, Xu W, Badea A, Stasolla C. Over-expression of the barley Phytoglobin 1 (HvPgb1) evokes leaf-specific transcriptional responses during root waterlogging. JOURNAL OF PLANT PHYSIOLOGY 2023; 283:153944. [PMID: 36933369 DOI: 10.1016/j.jplph.2023.153944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Oxygen deprivation (hypoxia) in the root due to waterlogging causes profound metabolic changes in the aerial organs depressing growth and limiting plant productivity in barley (Hordeum vulgare L.). Genome-wide analyses in waterlogged wild type (WT) barley (cv. Golden Promise) plants and plants over-expressing the phytoglobin 1 HvPgb1 [HvPgb1(OE)] were performed to determine leaf specific transcriptional responses during waterlogging. Normoxic WT plants outperformed their HvPgb1(OE) counterparts for dry weight biomass, chlorophyll content, photosynthetic rate, stomatal conductance, and transpiration. Root waterlogging severely depressed all these parameters in WT plants but not in HvPgb1(OE) plants, which exhibited an increase in photosynthetic rate. In leaftissue, root waterlogging repressed genes encoding photosynthetic components and chlorophyll biosynthetic enzymes, while induced those of reactive oxygen species (ROS)-generating enzymes. This repression was alleviated in HvPgb1(OE) leaves which also exhibited an induction of enzymes participating in antioxidant responses. In the same leaves, the transcript levels of several genes participating in nitrogen metabolism were also higher relative to WT leaves. Ethylene levels were diminished by root waterlogging in leaves of WT plants, but not in HvPgb1(OE), which were enriched in transcripts of ethylene biosynthetic enzymes and ethylene response factors. Pharmacological treatments increasing the level or action of ethylene further suggested the requirement of ethylene in plant response to root waterlogging. In natural germplasm an elevation in foliar HvPgb1 between 16h and 24h of waterlogging occurred in tolerant genotypes but not in susceptible ones. By integrating morpho-physiological parameters with transcriptome data, this study provides a framework defining leaf responses to root waterlogging and indicates that the induction of HvPgb1 may be used as a selection tool to enhance resilience to excess moisture.
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Affiliation(s)
- Robert D Hill
- Department of Plant Science, University of Manitoba, Winnipeg, R3T2N2, MB, Canada
| | - James de Castro
- Department of Plant Science, University of Manitoba, Winnipeg, R3T2N2, MB, Canada
| | - Mohammed M Mira
- Department of Plant Science, University of Manitoba, Winnipeg, R3T2N2, MB, Canada; Department of Botany and Microbiology, Tanta University, Tanta, Egypt.
| | - Abir U Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1C5S7, Canada
| | - Kim H Hebelstrup
- Department of Molecular Biology and Genetics, University of Aarhus, Forsogsvej 1, 4200, Slagelse, Denmark
| | - Sylvie Renault
- Department of Biological Sciences, University of Manitoba, Winnipeg, R3T2N2, MB, Canada
| | - Wayne Xu
- Brandon Research and Development Center, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB, R7A 5Y3, Canada
| | - Ana Badea
- Brandon Research and Development Center, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB, R7A 5Y3, Canada
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, R3T2N2, MB, Canada.
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12
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Li T, Li Y, Shangguan H, Bian J, Luo R, Tian Y, Li Z, Nie X, Cui L. BarleyExpDB: an integrative gene expression database for barley. BMC PLANT BIOLOGY 2023; 23:170. [PMID: 37003963 PMCID: PMC10064564 DOI: 10.1186/s12870-023-04193-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND RNA-sequencing (RNA-seq) has been widely used to study the dynamic expression patterns of transcribed genes, which can lead to new biological insights. However, processing and analyzing these huge amounts of histological data remains a great challenge for wet labs and field researchers who lack bioinformatics experience and computational resources. RESULTS We present BarleyExpDB, an easy-to-operate, free, and web-accessible database that integrates transcriptional profiles of barley at different growth and developmental stages, tissues, and stress conditions, as well as differential expression of mutants and populations to build a platform for barley expression and visualization. The expression of a gene of interest can be easily queried by searching by known gene ID or sequence similarity. Expression data can be displayed as a heat map, along with functional descriptions as well as Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Proteins Families Database, and Simple Modular Architecture Research Tool annotations. CONCLUSIONS BarleyExpDB will serve as a valuable resource for the barley research community to leverage the vast publicly available RNA-seq datasets for functional genomics research and crop molecular breeding.
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Affiliation(s)
- Tingting Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Hongbin Shangguan
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325 Shandong China
| | - Ruihan Luo
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Yuan Tian
- Xintai Urban and Rural Development Group Co., Ltd, Taian, 271200 Shandong China
| | - Zhimin Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
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13
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Mazhar HSUD, Shafiq M, Ali H, Ashfaq M, Anwar A, Tabassum J, Ali Q, Jilani G, Awais M, Sahu R, Javed MA. Genome-Wide Identification, and In-Silico Expression Analysis of YABBY Gene Family in Response to Biotic and Abiotic Stresses in Potato (Solanum tuberosum). Genes (Basel) 2023; 14:genes14040824. [PMID: 37107580 PMCID: PMC10137784 DOI: 10.3390/genes14040824] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
YABBY is among the specific transcription factor (TF) gene family in plants and plays an important role in the development of the leaves and floral organs. Its specific roles include lateral organ development, the establishment of dorsoventral polarity, and response to abiotic stress. Potato is an important crop worldwide and YABBY genes are not still identified and characterized in potato. So, little has been known about YABBY genes in potato until now. This study was carried out to perform genome-wide analysis, which will provide an in-depth analysis about the role of YABBY genes in potato. There have been seven StYAB genes identified, which are found to be located on seven different chromosomes. Through multiple sequence analyses, it has been predicted that the YABBY domain was present in all seven genes while the C2-C2 domain was found to be absent only in StYAB2. With the help of cis-element analysis, the involvement of StYAB genes in light, stress developmental, and hormonal responsiveness has been found. Furthermore, expression analysis from RNA-seq data of different potato organs indicated that all StYAB genes have a role in the vegetative growth of the potato plant. In addition to this, RNA-seq data also identified StYAB3, StYAB5, and StYAB7 genes showing expression during cadmium, and drought stress, while StYAB6 was highly expressed during a viral attack. Moreover, during the attack of Phytophthora infestans on a potato plant StYAB3, StYAB5, StYAB6, and StYAB7 showed high expression. This study provides significant knowledge about the StYAB gene structures and functions, which can later be used for gene cloning, and functional analysis; this information may be utilized by molecular biologists and plant breeders for the development of new potato lines.
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Hao Z, Tan Y, Feng J, Lin H, Sun Z, Zhuang JY, Chen Q, Jin X, Sun Y. Integrated metabolomic and transcriptomic analysis reveal the effect of mechanical stress on sugar metabolism in tea leaves ( Camellia sinensis) post-harvest. PeerJ 2023; 11:e14869. [PMID: 36785711 PMCID: PMC9921968 DOI: 10.7717/peerj.14869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
Sugar metabolites not only act as the key compounds in tea plant response to stress but are also critical for tea quality formation during the post-harvest processing of tea leaves. However, the mechanisms by which sugar metabolites in post-harvest tea leaves respond to mechanical stress are unclear. In this study, we aimed to investigate the effects of mechanical stress on saccharide metabolites and related post-harvest tea genes. Withered (C15) and mechanically-stressed (V15) for 15 min Oolong tea leaves were used for metabolome and transcriptome sequencing analyses. We identified a total of 19 sugar metabolites, most of which increased in C15 and V15. A total of 69 genes related to sugar metabolism were identified using transcriptome analysis, most of which were down-regulated in C15 and V15. To further understand the relationship between the down-regulated genes and sugar metabolites, we analyzed the sucrose and starch, galactose, and glycolysis metabolic pathways, and found that several key genes of invertase (INV), α-amylase (AMY), β-amylase (BMY), aldose 1-epimerase (AEP), and α-galactosidase (AGAL) were down-regulated. This inhibited the hydrolysis of sugars and might have contributed to the enrichment of galactose and D-mannose in V15. Additionally, galactinol synthase (Gols), raffinose synthase (RS), hexokinase (HXK), 6-phosphofructokinase 1 (PFK-1), and pyruvate kinase (PK) genes were significantly upregulated in V15, promoting the accumulation of D-fructose-6-phosphate (D-Fru-6P), D-glucose-6-phosphate (D-glu-6P), and D-glucose. Transcriptome and metabolome association analysis showed that the glycolysis pathway was enhanced and the hydrolysis rate of sugars related to hemicellulose synthesis slowed in response to mechanical stress. In this study, we explored the role of sugar in the response of post-harvest tea leaves to mechanical stress by analyzing differences in the expression of sugar metabolites and related genes. Our results improve the understanding of post-harvest tea's resistance to mechanical stress and the associated mechanism of sugar metabolism. The resulting treatment may be used to control the quality of Oolong tea.
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15
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Luan H, Li H, Li Y, Chen C, Li S, Wang Y, Yang J, Xu M, Shen H, Qiao H, Wang J. Transcriptome analysis of barley (Hordeum vulgare L.) under waterlogging stress, and overexpression of the HvADH4 gene confers waterlogging tolerance in transgenic Arabidopsis. BMC PLANT BIOLOGY 2023; 23:62. [PMID: 36710329 PMCID: PMC9885653 DOI: 10.1186/s12870-023-04081-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Waterlogging is one of the major abiotic stresses in barley and greatly reduces grain yield and quality. To explore the mechanism controlling waterlogging tolerance in barley, physiological, anatomical and transcriptional analyses were performed in two contrasting barley varieties, viz. Franklin (susceptible) and TX9425 (tolerant). RESULTS Compared to Franklin, TX9425 had more adventitious roots and aerenchymas and higher antioxidant enzyme activities. A total of 3064 and 5693 differentially expressed genes (DEGs) were identified in TX9425 after 24 h and 72 h of waterlogging treatment, respectively, while 2297 and 8462 DEGs were identified in Franklin. The results suggested that TX9425 was less affected by waterlogging stress after 72 h of treatment. The DEGs were enriched mainly in energy metabolism, hormone regulation, reactive oxygen species (ROS) scavenging, and cell wall-modifying enzymes. Alcohol dehydrogenase (ADH) plays an important role in response to waterlogging stress. We found that HvADH4 was significantly upregulated under waterlogging stress in TX9425. Transgenic Arabidopsis overexpressing HvADH4 displayed higher activity of antioxidant enzymes and was more tolerant to waterlogging than the wild type (WT). CONCLUSIONS The current results provide valuable information that will be of great value for the exploration of new candidate genes for molecular breeding of waterlogging tolerance in barley.
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Affiliation(s)
- Haiye Luan
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, 224002 Jiangsu China
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng, 224002 Jiangsu China
| | - Hongtao Li
- Lianyungang Academy of Agricultural Sciences, Lianyungang, 222000 China
| | - Yu Li
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, 224002 Jiangsu China
| | - Changyu Chen
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, 224002 Jiangsu China
| | - Shufeng Li
- Lianyungang Academy of Agricultural Sciences, Lianyungang, 222000 China
| | - Yu Wang
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, 224002 Jiangsu China
| | - Ju Yang
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, 224002 Jiangsu China
| | - Meng Xu
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, 224002 Jiangsu China
| | - Huiquan Shen
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, 224002 China
| | - Hailong Qiao
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, 224002 China
| | - Jun Wang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, 222000 China
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16
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Hu S, Qin Q, Liu J, Yin H, Meng Q, Yu J, Huang S, Ma Z. The Correlations of Barley Vitality and Storage Reserve Mobilization during Early Germination. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2023. [DOI: 10.1080/03610470.2022.2161270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Shumin Hu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Qingqing Qin
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Jia Liu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Hua Yin
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Qingshang Meng
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Junhong Yu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Shuxia Huang
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
| | - Zengxin Ma
- State Key Laboratory of Biological Fermentation Engineering of Beer, Tsingtao Brewery Co. Ltd, Qingdao, Shandong, China
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, China
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17
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Pais IP, Moreira R, Semedo JN, Ramalho JC, Lidon FC, Coutinho J, Maçãs B, Scotti-Campos P. Wheat Crop under Waterlogging: Potential Soil and Plant Effects. PLANTS (BASEL, SWITZERLAND) 2022; 12:149. [PMID: 36616278 PMCID: PMC9823972 DOI: 10.3390/plants12010149] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Inundation, excessive precipitation, or inadequate field drainage can cause waterlogging of cultivated land. It is anticipated that climate change will increase the frequency, intensity, and unpredictability of flooding events. This stress affects 10-15 million hectares of wheat every year, resulting in 20-50% yield losses. Since this crop greatly sustains a population's food demands, providing ca. 20% of the world's energy and protein diets requirements, it is crucial to understand changes in soil and plant physiology under excess water conditions. Variations in redox potential, pH, nutrient availability, and electrical conductivity of waterlogged soil will be addressed, as well as their impacts in major plant responses, such as root system and plant development. Waterlogging effects at the leaf level will also be addressed, with a particular focus on gas exchanges, photosynthetic pigments, soluble sugars, membrane integrity, lipids, and oxidative stress.
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Affiliation(s)
- Isabel P. Pais
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, Av. República, 2784-505 Oeiras, Portugal
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Rita Moreira
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, Av. República, 2784-505 Oeiras, Portugal
| | - José N. Semedo
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, Av. República, 2784-505 Oeiras, Portugal
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José C. Ramalho
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- PlantStress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, 2784-505 Oeiras, Portugal
| | - Fernando C. Lidon
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Earth Sciences Department, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - José Coutinho
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estrada Gil Vaz, Ap. 6, 7350-901 Elvas, Portugal
| | - Benvindo Maçãs
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Estrada Gil Vaz, Ap. 6, 7350-901 Elvas, Portugal
| | - Paula Scotti-Campos
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Quinta do Marquês, Av. República, 2784-505 Oeiras, Portugal
- GeoBioTec Research Center, Faculdade de Ciências e Tecnologia, Campus da Caparica, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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18
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Luan H, Chen C, Yang J, Qiao H, Li H, Li S, Zheng J, Shen H, Xu X, Wang J. Genome-wide association scan and transcriptome analysis reveal candidate genes for waterlogging tolerance in cultivated barley. FRONTIERS IN PLANT SCIENCE 2022; 13:1048939. [PMID: 36589094 PMCID: PMC9798782 DOI: 10.3389/fpls.2022.1048939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Waterlogging is the primary abiotic factor that destabilizes the yield and quality of barley (Hordeum vulgare L.). However, the genetic basis of waterlogging tolerance remains poorly understood. In this study, we conducted a genome-wide association study (GWAS) by involving 106,131 single-nucleotide polymorphisms (SNPs) with a waterlogging score (WLS) of 250 barley accessions in two years. Out of 72 SNPs that were found to be associated with WLS, 34 were detected in at least two environments. We further performed the transcriptome analysis in root samples from TX9425 (waterlogging tolerant) and Franklin (waterlogging sensitive), resulting in the identification of 5,693 and 8,462 differentially expressed genes (DEGs) in these genotypes, respectively. The identified DEGs included various transcription factor (TF) genes, primarily including AP2/ERF, bZIP and MYB. By combining GWAS and RNA-seq, we identified 27 candidate genes associated with waterlogging, of which three TFs (HvDnaJ, HvMADS and HvERF1) were detected in multiple treatments. Moreover, by overexpressing barley HvERF1 in Arabidopsis, the transgenic lines were detected with enhanced waterlogging tolerance. Altogether, our results provide new insights into the genetic mechanisms of waterlogging, which have implications in the molecular breeding of waterlogging-tolerant barley varieties.
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Affiliation(s)
- Haiye Luan
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Changyu Chen
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Ju Yang
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu, China
| | - Hailong Qiao
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, China
| | - Hongtao Li
- Lianyungang academy of agricultural sciences, Lianyungang, China
| | - Shufeng Li
- Lianyungang academy of agricultural sciences, Lianyungang, China
| | - Junyi Zheng
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu, China
- Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng, Jiangsu, China
| | - Huiquan Shen
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, China
| | - Xiao Xu
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng, China
| | - Jun Wang
- Lianyungang academy of agricultural sciences, Lianyungang, China
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19
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Jiang W, Tong T, Chen X, Deng F, Zeng F, Pan R, Zhang W, Chen G, Chen ZH. Molecular response and evolution of plant anion transport systems to abiotic stress. PLANT MOLECULAR BIOLOGY 2022; 110:397-412. [PMID: 34846607 DOI: 10.1007/s11103-021-01216-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/31/2021] [Indexed: 06/13/2023]
Abstract
We propose that anion channels are essential players for green plants to respond and adapt to the abiotic stresses associated changing climate via reviewing the literature and analyzing the molecular evolution, comparative genetic analysis, and bioinformatics analysis of the key anion channel gene families. Climate change-induced abiotic stresses including heatwave, elevated CO2, drought, and flooding, had a major impact on plant growth in the last few decades. This scenario could lead to the exposure of plants to various stresses. Anion channels are confirmed as the key factors in plant stress responses, which exist in the green lineage plants. Numerous studies on anion channels have shed light on their protein structure, ion selectivity and permeability, gating characteristics, and regulatory mechanisms, but a great quantity of questions remain poorly understand. Here, we review function of plant anion channels in cell signaling to improve plant response to environmental stresses, focusing on climate change related abiotic stresses. We investigate the molecular response and evolution of plant slow anion channel, aluminum-activated malate transporter, chloride channel, voltage-dependent anion channel, and mechanosensitive-like anion channel in green plant. Furthermore, comparative genetic and bioinformatic analysis reveal the conservation of these anion channel gene families. We also discuss the tissue and stress specific expression, molecular regulation, and signaling transduction of those anion channels. We propose that anion channels are essential players for green plants to adapt in a diverse environment, calling for more fundamental and practical studies on those anion channels towards sustainable food production and ecosystem health in the future.
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Affiliation(s)
- Wei Jiang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Tao Tong
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Xuan Chen
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Fenglin Deng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Fanrong Zeng
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Rui Pan
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou, China.
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia.
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
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20
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Waterlogging Stress Induces Antioxidant Defense Responses, Aerenchyma Formation and Alters Metabolisms of Banana Plants. PLANTS 2022; 11:plants11152052. [PMID: 35956531 PMCID: PMC9370344 DOI: 10.3390/plants11152052] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/28/2022]
Abstract
Flooding caused or exacerbated by climate change has threatened plant growth and food production worldwide. The lack of knowledge on how crops respond and adapt to flooding stress imposes a major barrier to enhancing their productivity. Hence, understanding the flooding-responsive mechanisms of crops is indispensable for developing new flooding-tolerant varieties. Here, we examined the banana (Musa acuminata cv. Berangan) responses to soil waterlogging for 1, 3, 5, 7, 14, and 24 days. After waterlogging stress, banana root samples were analyzed for their molecular and biochemical changes. We found that waterlogging treatment induced the formation of adventitious roots and aerenchyma with conspicuous gas spaces. In addition, the antioxidant activities, hydrogen peroxide, and malondialdehyde contents of the waterlogged bananas increased in response to waterlogging stress. To assess the initial response of bananas toward waterlogging stress, we analyzed the transcriptome changes of banana roots. A total of 3508 unigenes were differentially expressed under 1-day waterlogging conditions. These unigenes comprise abiotic stress-related transcription factors, such as ethylene response factors, basic helix-loop-helix, myeloblastosis, plant signal transduction, and carbohydrate metabolisms. The findings of the study provide insight into the complex molecular events of bananas in response to waterlogging stress, which could later help develop waterlogging resilient crops for the future climate.
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Xiong J, Chen D, Su T, Shen Q, Wu D, Zhang G. Genome-Wide Identification, Expression Pattern and Sequence Variation Analysis of SnRK Family Genes in Barley. PLANTS 2022; 11:plants11070975. [PMID: 35406955 PMCID: PMC9002700 DOI: 10.3390/plants11070975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 02/02/2023]
Abstract
Sucrose non-fermenting 1 (SNF1)-related protein kinase (SnRK) is a large family of protein kinases that play a significant role in plant stress responses. Although intensive studies have been conducted on SnRK members in some crops, little is known about the SnRK in barley. Using phylogenetic and conserved motif analyses, we discovered 46 SnRK members scattered across barley’s 7 chromosomes and classified them into 3 sub-families. The gene structures of HvSnRKs showed the divergence among three subfamilies. Gene duplication and synteny analyses on the genomes of barley and rice revealed the evolutionary features of HvSnRKs. The promoter regions of HvSnRK family genes contained many ABRE, MBS and LTR elements responding to abiotic stresses, and their expression patterns varied with different plant tissues and abiotic stresses. HvSnRKs could interact with the components of ABA signaling pathway to respond to abiotic stress. Moreover, the haplotypes of HvSnRK2.5 closely associated with drought tolerance were detected in a barley core collection. The current results could be helpful for further exploration of the HvSnRK genes responding to abiotic stress tolerance in barley.
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Affiliation(s)
- Jiangyan Xiong
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; (J.X.); (D.C.); (T.S.); (Q.S.)
| | - Danyi Chen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; (J.X.); (D.C.); (T.S.); (Q.S.)
| | - Tingting Su
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; (J.X.); (D.C.); (T.S.); (Q.S.)
| | - Qiufang Shen
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; (J.X.); (D.C.); (T.S.); (Q.S.)
| | - Dezhi Wu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Correspondence: (D.W.); (G.Z.)
| | - Guoping Zhang
- Department of Agronomy, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China; (J.X.); (D.C.); (T.S.); (Q.S.)
- Linyi Institute of Agricultural Sciences, Zhejiang University, Linyi 276000, China
- Correspondence: (D.W.); (G.Z.)
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Sun S, Wang B, Jiang Q, Li Z, Jia S, Wang Y, Guo H. Genome-wide analysis of BpDof genes and the tolerance to drought stress in birch ( Betula platyphylla). PeerJ 2021; 9:e11938. [PMID: 34513325 PMCID: PMC8395574 DOI: 10.7717/peerj.11938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/19/2021] [Indexed: 01/23/2023] Open
Abstract
Background DNA binding with one finger (Dof) proteins are plant-specific transcription factors playing vital roles in developmental processes and stress responses in plants. Nevertheless, the characterizations, expression patterns, and functions of the Dof family under drought stress (a key determinant of plant physiology and metabolic homeostasis) in woody plants remain unclear. Methods The birch (Betula platyphylla var. mandshuric) genome and plant TFDB database were used to identify Dof gene family members in birch plants. ClustalW2 of BioEdit v7.2.1, MEGA v7.0, ExPASy ProtParam tool, Subloc, TMHMM v2.0, GSDS v2.0, MEME, TBtools, KaKs Calculator v2.0, and PlantCARE were respectively used to align the BpDof sequences, build a phylogenetic tree, identify the physicochemical properties, analyze the chromosomal distribution and synteny, and identify the cis-elements in the promoter regions of the 26 BpDof genes. Additionally, the birch seedlings were exposed to PEG6000-simulated drought stress, and the expression patterns of the BpDof genes in different tissues were analyzed by qRT-PCR. The histochemical staining and the evaluation of physiological indexes were performed to assess the plant tolerance to drought with transient overexpression of BpDof4, BpDof11, and BpDof17 genes. SPSS software and ANOVA were used to conduct all statistical analyses and determine statistically significant differences between results. Results A total of 26 BpDof genes were identified in birch via whole-genome analysis. The conserved Dof domain with a C(x)2C(x)21C(x)2C zinc finger motif was present in all BpDof proteins. These birch BpDofs were classified into four groups (A to D) according to the phylogenetic analysis of Arabidopsis thaliana Dof genes. BpDof proteins within the same group mostly possessed similar motifs, as detected by conserved motif analysis. The exon–intron analysis revealed that the structures of BpDof genes differed, indicating probable gene gain and lose during the BpDof evolution. The chromosomal distribution and synteny analysis showed that the 26 BpDofs were unevenly distributed on 14 chromosomes, and seven duplication events among six chromosomes were found. Cis-acting elements were abundant in the promoter regions of the 26 BpDof genes. qRT-PCR revealed that the expression of the 26 BpDof genes was differentially regulated by drought stress among roots, stems, and leaves. Most BpDof genes responded to drought stress, and BpDof4, BpDof11, and BpDof17 were significantly up-regulated. Therefore, plants overexpressing these three genes were generated to investigate drought stress tolerance. The BpDof4-, BpDof11-, and BpDof17-overexpressing plants showed promoted reactive oxygen species (ROS) scavenging capabilities and less severe cell damage, suggesting that they conferred enhanced drought tolerance in birch. This study provided an in-depth insight into the structure, evolution, expression, and function of the Dof gene family in plants.
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Affiliation(s)
- Shilin Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Bo Wang
- Department of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, Heilongjiang, China
| | - Qi Jiang
- Department of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, Heilongjiang, China
| | - Zhuoran Li
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Site Jia
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yucheng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Huiyan Guo
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China.,The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
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Borrego-Benjumea A, Carter A, Zhu M, Tucker JR, Zhou M, Badea A. Genome-Wide Association Study of Waterlogging Tolerance in Barley ( Hordeum vulgare L.) Under Controlled Field Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:711654. [PMID: 34512694 PMCID: PMC8427447 DOI: 10.3389/fpls.2021.711654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/21/2021] [Indexed: 06/01/2023]
Abstract
Waterlogging is one of the main abiotic stresses severely reducing barley grain yield. Barley breeding programs focusing on waterlogging tolerance require an understanding of genetic loci and alleles in the current germplasm. In this study, 247 worldwide spring barley genotypes grown under controlled field conditions were genotyped with 35,926 SNPs with minor allele frequency (MAF) > 0.05. Significant phenotypic variation in each trait, including biomass, spikes per plant, grains per plant, kernel weight per plant, plant height and chlorophyll content, was observed. A genome-wide association study (GWAS) based on linkage disequilibrium (LD) for waterlogging tolerance was conducted. Population structure analysis divided the population into three subgroups. A mixed linkage model using both population structure and kinship matrix (Q+K) was performed. We identified 17 genomic regions containing 51 significant waterlogging-tolerance-associated markers for waterlogging tolerance response, accounting for 5.8-11.5% of the phenotypic variation, with a majority of them localized on chromosomes 1H, 2H, 4H, and 5H. Six novel QTL were identified and eight potential candidate genes mediating responses to abiotic stresses were located at QTL associated with waterlogging tolerance. To our awareness, this is the first GWAS for waterlogging tolerance in a worldwide barley collection under controlled field conditions. The marker-trait associations could be used in the marker-assisted selection of waterlogging tolerance and will facilitate barley breeding.
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Affiliation(s)
- Ana Borrego-Benjumea
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Adam Carter
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Min Zhu
- College of Agriculture, Yangzhou University, Yangzhou, China
| | - James R. Tucker
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Ana Badea
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
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24
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Tong C, Hill CB, Zhou G, Zhang XQ, Jia Y, Li C. Opportunities for Improving Waterlogging Tolerance in Cereal Crops-Physiological Traits and Genetic Mechanisms. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10081560. [PMID: 34451605 PMCID: PMC8401455 DOI: 10.3390/plants10081560] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/12/2021] [Accepted: 07/28/2021] [Indexed: 05/22/2023]
Abstract
Waterlogging occurs when soil is saturated with water, leading to anaerobic conditions in the root zone of plants. Climate change is increasing the frequency of waterlogging events, resulting in considerable crop losses. Plants respond to waterlogging stress by adventitious root growth, aerenchyma formation, energy metabolism, and phytohormone signalling. Genotypes differ in biomass reduction, photosynthesis rate, adventitious roots development, and aerenchyma formation in response to waterlogging. We reviewed the detrimental effects of waterlogging on physiological and genetic mechanisms in four major cereal crops (rice, maize, wheat, and barley). The review covers current knowledge on waterlogging tolerance mechanism, genes, and quantitative trait loci (QTL) associated with waterlogging tolerance-related traits, the conventional and modern breeding methods used in developing waterlogging tolerant germplasm. Lastly, we describe candidate genes controlling waterlogging tolerance identified in model plants Arabidopsis and rice to identify homologous genes in the less waterlogging-tolerant maize, wheat, and barley.
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Affiliation(s)
- Cen Tong
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Camilla Beate Hill
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Gaofeng Zhou
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Xiao-Qi Zhang
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Yong Jia
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Chengdao Li
- Western Crop Genetic Alliance, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; (C.T.); (C.B.H.); (G.Z.); (X.-Q.Z.); (Y.J.)
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
- Department of Primary Industries and Regional Development, 3-Baron-Hay Court, South Perth, WA 6151, Australia
- Correspondence: ; Tel.: +61-893-607-519
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25
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Shen C, Yuan J, Ou X, Ren X, Li X. Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat ( Triticum aestivum). PeerJ 2021; 9:e11861. [PMID: 34386306 PMCID: PMC8312495 DOI: 10.7717/peerj.11861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Background Alcohol dehydrogenase (ADH) plays an important role in plant survival under anaerobic conditions. Although some research about ADH in many plants have been carried out, the bioinformatics analysis of the ADH gene family from Triticum aestivum and their response to abiotic stress is unclear. Methods A total of 22 ADH genes were identified from the wheat genome, and these genes could be divided into two subfamilies (subfamily I and subfamily II). All TaADH genes belonged to the Medium-chain ADH subfamily. Sequence alignment analysis showed that all TaADH proteins contained a conservative GroES-like domain and Zinc-binding domain. A total of 64 duplicated gene pairs were found, and the Ka/Ks value of these gene pairs was less than 1, which indicated that these genes were relatively conservative and did not change greatly in the process of duplication. Results The organizational analysis showed that nine TaADH genes were highly expressed in all organs, and the rest of TaADH genes had tissue specificity. Cis-acting element analysis showed that almost all of the TaADH genes contained an anaerobic response element. The expression levels of ADH gene in waterlogging tolerant and waterlogging sensitive wheat seeds were analyzed by quantitative real-time PCR (qRT-PCR). This showed that some key ADH genes were significantly responsive to waterlogging stress at the seed germination stage, and the response of waterlogging tolerant and waterlogging sensitive wheat seeds to waterlogging stress was regulated by different ADH genes. The results may be helpful to further study the function of TaADH genes and to determine the candidate gene for wheat stress resistance breeding.
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Affiliation(s)
- Changwei Shen
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Jingping Yuan
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xingqi Ou
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xiujuan Ren
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xinhua Li
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan, China
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26
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Wang X, He Y, Zhang C, Tian YA, Lei X, Li D, Bai S, Deng X, Lin H. Physiological and transcriptional responses of Phalaris arundinacea under waterlogging conditions. JOURNAL OF PLANT PHYSIOLOGY 2021; 261:153428. [PMID: 33957505 DOI: 10.1016/j.jplph.2021.153428] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
As a high-yielding forage grass, Phalaris arundinacea widely distributed in the Qinghai-Tibet Plateau region of China. To explore physiological and molecular response mechanism of Phalaris arundinacea under waterlogging, we analyzed the biomass and physiological indexes of three locally grown strains under the submerged condition of 10 cm. The material Z0611 showed the strongest waterlogging resistance while the YS showed the weakest performance. Transcriptome sequencing analysis demonstrated that the YS and Z0611 had 17010 and 7566 differently expression genes (DEGs), respectively, which were mainly concentrated in the metabolic process, cell, ribosome, phenylpropanoid biosynthesis pathway in GO and KEGG databases. We also identified a large number of genes involved in carbohydrate metabolism, hormone signaling regulation, transcription factors, antioxidant system, and ethylene signaling. Our research may provide a scientific basis for the restoration of wetland environment on the Qinghai-Tibet Plateau, and lay a foundation for further exploration of the waterlogging resistance genes of Phalaris arundinacea and breeding of new strains resistant with waterlogging stress.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Ying He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Changbing Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731, China
| | - Yu-Ang Tian
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065 Sichuan, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731, China
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731, China.
| | - Xingguang Deng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065 Sichuan, China.
| | - Honghui Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065 Sichuan, China.
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Ji HS, Bang SG, Ahn MA, Kim G, Kim E, Eom SH, Hyun TK. Molecular Cloning and Functional Characterization of Heat Stress-Responsive Superoxide Dismutases in Garlic ( Allium sativum L.). Antioxidants (Basel) 2021; 10:antiox10050815. [PMID: 34065356 PMCID: PMC8161062 DOI: 10.3390/antiox10050815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/26/2022] Open
Abstract
Superoxide dismutases (SODs) are key antioxidant enzymes that can detoxify the superoxide radicals generated by various stresses. Although various plant SODs have been suggested to improve stress tolerance, SODs in garlic, an economically important vegetable grown worldwide, remain relatively unknown. In this study, we found that heat stress strongly induced the activities of Cu/ZnSODs, FeSODs, and MnSODs in garlic leaves. In addition, we cloned four garlic SODs (AsSODs) and suggest that heat stress-increased SOD activity was reflected at least by the induction of these AsSODs. The results of the agro-infiltration assay suggested that the cloned AsSODs encoded functional SOD enzymes belonging to the Cu/ZnSOD and MnSOD families. As a first step toward understanding the enzymatic antioxidant system in garlic plants, our results provide a solid foundation for an in-depth analysis of the physiological functions of the AsSOD family.
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28
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Kan J, Gao G, He Q, Gao Q, Jiang C, Ahmar S, Liu J, Zhang J, Yang P. Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley. Int J Mol Sci 2021; 22:5354. [PMID: 34069581 PMCID: PMC8160967 DOI: 10.3390/ijms22105354] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 12/19/2022] Open
Abstract
The WRKY transcription factors (WRKYs) are known for their crucial roles in biotic and abiotic stress responses, and developmental and physiological processes. In barley, early studies revealed their importance, whereas their diversity at the population scale remains hardly estimated. In this study, 98 HsWRKYs and 103 HvWRKYs have been identified from the reference genome of wild and cultivated barley, respectively. The tandem duplication and segmental duplication events from the cultivated barley were observed. By taking advantage of early released exome-captured sequencing datasets in 90 wild barley accessions and 137 landraces, the diversity analysis uncovered synonymous and non-synonymous variants instead of loss-of-function mutations that had occurred at all WRKYs. For majority of WRKYs, the haplotype and nucleotide diversity both decreased in cultivated barley relative to the wild population. Five WRKYs were detected to have undergone selection, among which haplotypes of WRKY9 were enriched, correlating with the geographic collection sites. Collectively, profiting from the state-of-the-art barley genomic resources, this work represented the characterization and diversity of barley WRKY transcription factors, shedding light on future deciphering of their roles in barley domestication and adaptation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (J.K.); (G.G.); (Q.H.); (Q.G.); (C.J.); (S.A.); (J.L.); (J.Z.)
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Shahzad R, Jamil S, Ahmad S, Nisar A, Amina Z, Saleem S, Zaffar Iqbal M, Muhammad Atif R, Wang X. Harnessing the potential of plant transcription factors in developing climate resilient crops to improve global food security: Current and future perspectives. Saudi J Biol Sci 2021; 28:2323-2341. [PMID: 33911947 PMCID: PMC8071895 DOI: 10.1016/j.sjbs.2021.01.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/09/2020] [Accepted: 01/12/2021] [Indexed: 12/20/2022] Open
Abstract
Crop plants should be resilient to climatic factors in order to feed ever-increasing populations. Plants have developed stress-responsive mechanisms by changing their metabolic pathways and switching the stress-responsive genes. The discovery of plant transcriptional factors (TFs), as key regulators of different biotic and abiotic stresses, has opened up new horizons for plant scientists. TFs perceive the signal and switch certain stress-responsive genes on and off by binding to different cis-regulatory elements. More than 50 families of plant TFs have been reported in nature. Among them, DREB, bZIP, MYB, NAC, Zinc-finger, HSF, Dof, WRKY, and NF-Y are important with respect to biotic and abiotic stresses, but the potential of many TFs in the improvement of crops is untapped. In this review, we summarize the role of different stress-responsive TFs with respect to biotic and abiotic stresses. Further, challenges and future opportunities linked with TFs for developing climate-resilient crops are also elaborated.
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Affiliation(s)
- Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Amina Nisar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
| | - Zarmaha Amina
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
| | - Shazmina Saleem
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Zaffar Iqbal
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad, University Road, 38040, Faisalabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an 716000, China
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30
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Kaur G, Vikal Y, Kaur L, Kalia A, Mittal A, Kaur D, Yadav I. Elucidating the morpho-physiological adaptations and molecular responses under long-term waterlogging stress in maize through gene expression analysis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110823. [PMID: 33568312 DOI: 10.1016/j.plantsci.2021.110823] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 12/31/2020] [Accepted: 01/06/2021] [Indexed: 05/25/2023]
Abstract
Waterlogging stress in maize is one of the emerging abiotic stresses in the current climate change scenario. To gain insights in transcriptional reprogramming during late hours of waterlogging stress under field conditions, we aimed to elucidate the transcriptional and anatomical changes in two contrasting maize inbreds viz. I110 (susceptible) and I172 (tolerant). Waterlogging stress reduced dry matter translocations from leaves and stems to ears, resulting in a lack of sink capacity and inadequate grain filling in I110, thus decreased the grain yield drastically. The development of aerenchyma cells within 48 h in I172 enabled hypoxia tolerance. The upregulation of alanine aminotransferase, ubiquitin activating enzyme E1, putative mitogen activated protein kinase and pyruvate kinase in I172 suggested that genes involved in protein degradation, signal transduction and carbon metabolism provided adaptive mechanisms during waterlogging. Overexpression of alcohol dehydrogenase, sucrose synthase, aspartate aminotransferase, NADP dependent malic enzyme and many miRNA targets in I110 indicated that more oxygen and energy consumption might have shortened plant survival during long-term waterlogging exposure. To the best of our knowledge, this is the first report of transcript profiling at late stage (24-96 h) of waterlogging stress under field conditions and provides new visions to understand the molecular basis of waterlogging tolerance in maize.
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Affiliation(s)
- Gurwinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
| | - Loveleen Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Anu Kalia
- Department of Nanoscience, Punjab Agricultural University, Ludhiana, India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Dasmeet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Inderjit Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
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Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions. Genes (Basel) 2021; 12:genes12020189. [PMID: 33525400 PMCID: PMC7912563 DOI: 10.3390/genes12020189] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/15/2021] [Accepted: 01/23/2021] [Indexed: 02/06/2023] Open
Abstract
Waterlogging (WL), excess water in the soil, is a phenomenon often occurring during plant cultivation causing low oxygen levels (hypoxia) in the soil. The aim of this study was to identify candidate genes involved in long-term waterlogging tolerance in cucumber using RNA sequencing. Here, we also determined how waterlogging pre-treatment (priming) influenced long-term memory in WL tolerant (WL-T) and WL sensitive (WL-S) i.e., DH2 and DH4 accessions, respectively. This work uncovered various differentially expressed genes (DEGs) activated in the long-term recovery in both accessions. De novo assembly generated 36,712 transcripts with an average length of 2236 bp. The results revealed that long-term waterlogging had divergent impacts on gene expression in WL-T DH2 and WL-S DH4 cucumber accessions: after 7 days of waterlogging, more DEGs in comparison to control conditions were identified in WL-S DH4 (8927) than in WL-T DH2 (5957). Additionally, 11,619 and 5007 DEGs were identified after a second waterlogging treatment in the WL-S and WL-T accessions, respectively. We identified genes associated with WL in cucumber that were especially related to enhanced glycolysis, adventitious roots development, and amino acid metabolism. qRT-PCR assay for hypoxia marker genes i.e., alcohol dehydrogenase (adh), 1-aminocyclopropane-1-carboxylate oxidase (aco) and long chain acyl-CoA synthetase 6 (lacs6) confirmed differences in response to waterlogging stress between sensitive and tolerant cucumbers and effectiveness of priming to enhance stress tolerance.
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