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VanBuren R, Nguyen A, Marks RA, Mercado C, Pardo A, Pardo J, Schuster J, Aubin BS, Wilson ML, Rhee SY. Variability in drought gene expression datasets highlight the need for community standardization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578814. [PMID: 38370805 PMCID: PMC10871248 DOI: 10.1101/2024.02.04.578814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Physiologically relevant drought stress is difficult to apply consistently, and the heterogeneity in experimental design, growth conditions, and sampling schemes make it challenging to compare water deficit studies in plants. Here, we re-analyzed hundreds of drought gene expression experiments across diverse model and crop species and quantified the variability across studies. We found that drought studies are surprisingly uncomparable, even when accounting for differences in genotype, environment, drought severity, and method of drying. Many studies, including most Arabidopsis work, lack high-quality phenotypic and physiological datasets to accompany gene expression, making it impossible to assess the severity or in some cases the occurrence of water deficit stress events. From these datasets, we developed supervised learning classifiers that can accurately predict if RNA-seq samples have experienced a physiologically relevant drought stress, and suggest this can be used as a quality control for future studies. Together, our analyses highlight the need for more community standardization, and the importance of paired physiology data to quantify stress severity for reproducibility and future data analyses.
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Tiwari LD, Bdolach E, Prusty MR, Bodenheimer S, Be'ery A, Faigenboim-Doron A, Yamamoto E, Panzarová K, Kashkush K, Shental N, Fridman E. Cytonuclear interactions modulate the plasticity of photosynthetic rhythmicity and growth in wild barley. PHYSIOLOGIA PLANTARUM 2024; 176:e14192. [PMID: 38351880 DOI: 10.1111/ppl.14192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
In plants, the contribution of the plasmotype (mitochondria and chloroplast) in controlling the circadian clock plasticity and possible consequences on cytonuclear genetic makeup have yet to be fully elucidated. A genome-wide association study in the wild barley (Hordeum vulgare ssp. spontaneum) B1K collection identified overlap with our previously mapped DRIVERS OF CLOCKS (DOCs) loci in wild-cultivated interspecific population. Moreover, we identified non-random segregation and epistatic interactions between nuclear DOCs loci and the chloroplastic RpoC1 gene, indicating an adaptive value for specific cytonuclear gene combinations. Furthermore, we show that DOC1.1, which harbours the candidate SIGMA FACTOR-B (SIG-B) gene, is linked with the differential expression of SIG-B and CCA1 genes and contributes to the circadian gating response to heat. High-resolution temporal growth and photosynthesis measurements of B1K also link the DOCs loci to differential growth, Chl content and quantum yield. To validate the involvement of the Plastid encoded polymerase (PEP) complex, we over-expressed the two barley chloroplastic RpoC1 alleles in Arabidopsis and identified significant differential plasticity under elevated temperatures. Finally, enhanced clock plasticity of de novo ENU (N-Ethyl-N-nitrosourea) -induced barley rpoB1 mutant further implicates the PEP complex as a key player in regulating the circadian clock output. Overall, this study highlights the contribution of specific cytonuclear interaction between rpoC1 (PEP gene) and SIG-B with distinct circadian timing regulation under heat, and their pleiotropic effects on growth implicate an adaptive value.
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Affiliation(s)
- Lalit Dev Tiwari
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Eyal Bdolach
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Manas Ranjan Prusty
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Schewach Bodenheimer
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avital Be'ery
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Adi Faigenboim-Doron
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
| | - Eiji Yamamoto
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
| | - Eyal Fridman
- Plant Sciences Institute, Volcani Agricultural Research Organization (ARO), Bet Dagan, Israel
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Thathapalli Prakash P, Chebotarov D, Zhang J, Kudrna DA, Torres RO, Natividad MA, Quintana MR, Song J, Maldonado CE, Hechanova SL, Jena K, Wing RA, Henry A. Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice. PLANT PHYSIOLOGY 2023; 193:2381-2397. [PMID: 37665979 PMCID: PMC10663109 DOI: 10.1093/plphys/kiad485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/31/2023] [Accepted: 08/12/2023] [Indexed: 09/06/2023]
Abstract
Developing drought-resistant rice (Oryza sativa, L.) is essential for improving field productivity, especially in rain-fed areas affected by climate change. Wild relatives of rice are potential sources for drought-resistant traits. Therefore, we compared root growth and drought response among 22 wild Oryza species, from which Oryza glumaepatula was selected as a promising source for further exploration. A geographically diverse panel of 69 O. glumaepatula accessions was then screened for drought stress-related traits, and 6 of these accessions showed lower shoot dry weight (SDW) reduction, greater percentage of deep roots, and lower stomatal density (STO) under drought than the drought tolerant O. sativa variety, Sahbhagi dhan. Based on whole-genome resequencing of all 69 O. glumaepatula accessions and variant calling to a high-quality O. glumaepatula reference genome, we detected multiple genomic loci colocating for SDW, root dry weight at 30 to 45 cm depth, and STO in consecutive drought trials. Geo-referencing indicated that the potential drought donors originated in flood-prone locations, corroborating previous hypotheses about the coexistence of flood and drought tolerance within individual Oryza genomes. These findings present potential donor accessions, traits, and genomic loci from an AA genome wild relative of rice that, together with the recently developed reference genome, may be useful for further introgression of drought tolerance into the O. sativa backgrounds.
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Affiliation(s)
- Parthiban Thathapalli Prakash
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dmytro Chebotarov
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Rolando O Torres
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
| | - Mignon A Natividad
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
| | - Marinell R Quintana
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
| | - Jiaming Song
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Carlos E Maldonado
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Sherry Lou Hechanova
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
| | - Kshirod Jena
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Center for Desert Agriculture, King Abdullah University of Science & Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Amelia Henry
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
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Bedford JA, Carine M, Chapman MA. Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis. G3 (BETHESDA, MD.) 2023; 13:jkad194. [PMID: 37619981 PMCID: PMC10542315 DOI: 10.1093/g3journal/jkad194] [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: 07/19/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.
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Affiliation(s)
- James A Bedford
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark Carine
- Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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Fadiji AE, Yadav AN, Santoyo G, Babalola OO. Understanding the plant-microbe interactions in environments exposed to abiotic stresses: An overview. Microbiol Res 2023; 271:127368. [PMID: 36965460 DOI: 10.1016/j.micres.2023.127368] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/07/2023] [Accepted: 03/19/2023] [Indexed: 03/27/2023]
Abstract
Abiotic stress poses a severe danger to agriculture since it negatively impacts cellular homeostasis and eventually stunts plant growth and development. Abiotic stressors like drought and excessive heat are expected to occur more frequently in the future due to climate change, which would reduce the yields of important crops like maize, wheat, and rice which may jeopardize the food security of human populations. The plant microbiomes are a varied and taxonomically organized microbial community that is connected to plants. By supplying nutrients and water to plants, and regulating their physiology and metabolism, plant microbiota frequently helps plants develop and tolerate abiotic stresses, which can boost crop yield under abiotic stresses. In this present study, with emphasis on temperature, salt, and drought stress, we describe current findings on how abiotic stresses impact the plants, microbiomes, microbe-microbe interactions, and plant-microbe interactions as the way microorganisms affect the metabolism and physiology of the plant. We also explore crucial measures that must be taken in applying plant microbiomes in agriculture practices faced with abiotic stresses.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
| | - Ajar Nath Yadav
- Microbial Biotechnology Laboratory, Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich 58030, Mexico
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
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6
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Napier JD, Heckman RW, Juenger TE. Gene-by-environment interactions in plants: Molecular mechanisms, environmental drivers, and adaptive plasticity. THE PLANT CELL 2023; 35:109-124. [PMID: 36342220 PMCID: PMC9806611 DOI: 10.1093/plcell/koac322] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/03/2022] [Indexed: 05/13/2023]
Abstract
Plants demonstrate a broad range of responses to environmental shifts. One of the most remarkable responses is plasticity, which is the ability of a single plant genotype to produce different phenotypes in response to environmental stimuli. As with all traits, the ability of plasticity to evolve depends on the presence of underlying genetic diversity within a population. A common approach for evaluating the role of genetic variation in driving differences in plasticity has been to study genotype-by-environment interactions (G × E). G × E occurs when genotypes produce different phenotypic trait values in response to different environments. In this review, we highlight progress and promising methods for identifying the key environmental and genetic drivers of G × E. Specifically, methodological advances in using algorithmic and multivariate approaches to understand key environmental drivers combined with new genomic innovations can greatly increase our understanding about molecular responses to environmental stimuli. These developing approaches can be applied to proliferating common garden networks that capture broad natural environmental gradients to unravel the underlying mechanisms of G × E. An increased understanding of G × E can be used to enhance the resilience and productivity of agronomic systems.
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Affiliation(s)
- Joseph D Napier
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Robert W Heckman
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
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7
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Verslues PE, Bailey-Serres J, Brodersen C, Buckley TN, Conti L, Christmann A, Dinneny JR, Grill E, Hayes S, Heckman RW, Hsu PK, Juenger TE, Mas P, Munnik T, Nelissen H, Sack L, Schroeder JI, Testerink C, Tyerman SD, Umezawa T, Wigge PA. Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress. THE PLANT CELL 2023; 35:67-108. [PMID: 36018271 PMCID: PMC9806664 DOI: 10.1093/plcell/koac263] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/21/2022] [Indexed: 05/08/2023]
Abstract
We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.
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Affiliation(s)
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA
| | - Craig Brodersen
- School of the Environment, Yale University, New Haven, Connecticut 06511, USA
| | - Thomas N Buckley
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Lucio Conti
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Alexander Christmann
- School of Life Sciences, Technical University Munich, Freising-Weihenstephan 85354, Germany
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Erwin Grill
- School of Life Sciences, Technical University Munich, Freising-Weihenstephan 85354, Germany
| | - Scott Hayes
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Robert W Heckman
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Po-Kai Hsu
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona 08193, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Teun Munnik
- Department of Plant Cell Biology, Green Life Sciences Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam NL-1098XH, The Netherlands
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Lawren Sack
- Department of Ecology and Evolutionary Biology, Institute of the Environment and Sustainability, University of California, Los Angeles, California 90095, USA
| | - Julian I Schroeder
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Christa Testerink
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Stephen D Tyerman
- ARC Center Excellence, Plant Energy Biology, School of Agriculture Food and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
| | - Taishi Umezawa
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 6708 PB, Japan
| | - Philip A Wigge
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Großbeeren 14979, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
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8
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Cooper M, Messina CD. Breeding crops for drought-affected environments and improved climate resilience. THE PLANT CELL 2023; 35:162-186. [PMID: 36370076 PMCID: PMC9806606 DOI: 10.1093/plcell/koac321] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/01/2022] [Indexed: 05/12/2023]
Abstract
Breeding climate-resilient crops with improved levels of abiotic and biotic stress resistance as a response to climate change presents both opportunities and challenges. Applying the framework of the "breeder's equation," which is used to predict the response to selection for a breeding program cycle, we review methodologies and strategies that have been used to successfully breed crops with improved levels of drought resistance, where the target population of environments (TPEs) is a spatially and temporally heterogeneous mixture of drought-affected and favorable (water-sufficient) environments. Long-term improvement of temperate maize for the US corn belt is used as a case study and compared with progress for other crops and geographies. Integration of trait information across scales, from genomes to ecosystems, is needed to accurately predict yield outcomes for genotypes within the current and future TPEs. This will require transdisciplinary teams to explore, identify, and exploit novel opportunities to accelerate breeding program outcomes; both improved germplasm resources and improved products (cultivars, hybrids, clones, and populations) that outperform and replace the products in use by farmers, in combination with modified agronomic management strategies suited to their local environments.
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Affiliation(s)
| | - Carlos D Messina
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
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9
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Shelake RM, Kadam US, Kumar R, Pramanik D, Singh AK, Kim JY. Engineering drought and salinity tolerance traits in crops through CRISPR-mediated genome editing: Targets, tools, challenges, and perspectives. PLANT COMMUNICATIONS 2022; 3:100417. [PMID: 35927945 PMCID: PMC9700172 DOI: 10.1016/j.xplc.2022.100417] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/07/2022] [Accepted: 07/27/2022] [Indexed: 05/10/2023]
Abstract
Prolonged periods of drought triggered by climate change hamper plant growth and cause substantial agricultural yield losses every year. In addition to drought, salinity is one of the major abiotic stresses that severely affect crop health and agricultural production. Plant responses to drought and salinity involve multiple processes that operate in a spatiotemporal manner, such as stress sensing, perception, epigenetic modifications, transcription, post-transcriptional processing, translation, and post-translational changes. Consequently, drought and salinity stress tolerance are polygenic traits influenced by genome-environment interactions. One of the ideal solutions to these challenges is the development of high-yielding crop varieties with enhanced stress tolerance, together with improved agricultural practices. Recently, genome-editing technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR) tools, have been effectively applied to elucidate how plants deal with drought and saline environments. In this work, we aim to portray that the combined use of CRISPR-based genome engineering tools and modern genomic-assisted breeding approaches are gaining momentum in identifying genetic determinants of complex traits for crop improvement. This review provides a synopsis of plant responses to drought and salinity stresses at the morphological, physiological, and molecular levels. We also highlight recent advances in CRISPR-based tools and their use in understanding the multi-level nature of plant adaptations to drought and salinity stress. Integrating CRISPR tools with modern breeding approaches is ideal for identifying genetic factors that regulate plant stress-response pathways and for the introgression of beneficial traits to develop stress-resilient crops.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea.
| | - Ulhas Sopanrao Kadam
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Ritesh Kumar
- Department of Agronomy & Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Anil Kumar Singh
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju 52828, Korea.
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10
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The Examination of the Role of Rice Lysophosphatidic Acid Acyltransferase 2 in Response to Salt and Drought Stresses. Int J Mol Sci 2022; 23:ijms23179796. [PMID: 36077191 PMCID: PMC9456497 DOI: 10.3390/ijms23179796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Phosphatidic acid (PA) is an important signal molecule in various biological processes including osmotic stress. Lysophosphatidic acid acyltransferase (LPAT) acylates the sn-2 position of the glycerol backbone of lysophosphatidic acid (LPA) to produce PA. The role of LPAT2 and its PA in osmotic stress response remains elusive in plants. Here we showed that LPAT2-derived PA is important for salt and drought stress tolerance in rice. Rice LPAT2 was localized to the endoplasmic reticulum (ER) to catalyze the PA synthesis. The LPAT2 transcript was induced by osmotic stress such as high salinity and water deficit. To reveal its role in osmotic stress response, an LPAT2 knockdown mutant, designated lpat2, was isolated from rice, which contained a reduced PA level relative to wild type (WT) plants under salt stress and water deficit. The lpat2 mutant was more susceptible to osmotic stress and less sensitive to abscisic acid (ABA) than that of WT, which was recovered by either PA supplementation or genetic LPAT2 complementation. Moreover, suppressed LPAT2 also led to a large number of differentially expressed genes (DEGs) involved in diverse processes, particularly, in ABA response, kinase signaling, and ion homeostasis in response to salt stress. Together, LPAT2-produced PA plays a positive role in osmotic tolerance through mediating ABA response, which leads to transcriptional alteration of genes related to ABA response, protein kinase signaling, and ion homeostasis.
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11
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Omae N, Tsuda K. Plant-Microbiota Interactions in Abiotic Stress Environments. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:511-526. [PMID: 35322689 DOI: 10.1094/mpmi-11-21-0281-fi] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Abiotic stress adversely affects cellular homeostasis and ultimately impairs plant growth, posing a serious threat to agriculture. Climate change modeling predicts increasing occurrences of abiotic stresses such as drought and extreme temperature, resulting in decreasing the yields of major crops such as rice, wheat, and maize, which endangers food security for human populations. Plants are associated with diverse and taxonomically structured microbial communities that are called the plant microbiota. Plant microbiota often assist plant growth and abiotic stress tolerance by providing water and nutrients to plants and modulating plant metabolism and physiology and, thus, offer the potential to increase crop production under abiotic stress. In this review, we summarize recent progress on how abiotic stress affects plants, microbiota, plant-microbe interactions, and microbe-microbe interactions, and how microbes affect plant metabolism and physiology under abiotic stress conditions, with a focus on drought, salt, and temperature stress. We also discuss important steps to utilize plant microbiota in agriculture under abiotic stress.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Natsuki Omae
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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Reynoso MA, Borowsky AT, Pauluzzi GC, Yeung E, Zhang J, Formentin E, Velasco J, Cabanlit S, Duvenjian C, Prior MJ, Akmakjian GZ, Deal RB, Sinha NR, Brady SM, Girke T, Bailey-Serres J. Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice. Dev Cell 2022; 57:1177-1192.e6. [PMID: 35504287 DOI: 10.1016/j.devcel.2022.04.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/10/2022] [Accepted: 04/07/2022] [Indexed: 12/11/2022]
Abstract
Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.
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Affiliation(s)
- Mauricio A Reynoso
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; IBBM, FCE-UNLP CONICET, La Plata 1900, Argentina
| | - Alexander T Borowsky
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Germain C Pauluzzi
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Elaine Yeung
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Jianhai Zhang
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Elide Formentin
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, University of Padova, Padova, Italy
| | - Joel Velasco
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Sean Cabanlit
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Christine Duvenjian
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew J Prior
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Garo Z Akmakjian
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Thomas Girke
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands.
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13
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Bin Rahman ANMR, Zhang J. The Coexistence of Flood and Drought Tolerance: An Opinion on the Development of Climate-Smart Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:860802. [PMID: 35350297 PMCID: PMC8957971 DOI: 10.3389/fpls.2022.860802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Affiliation(s)
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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14
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Cox KL. Adapting to change: Rice surviving drought conditions in the field. THE PLANT CELL 2022; 34:708-709. [PMID: 35231107 PMCID: PMC8824549 DOI: 10.1093/plcell/koab279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Kevin L Cox
- Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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