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Arouisse B, Thoen MPM, Kruijer W, Kunst JF, Jongsma MA, Keurentjes JJB, Kooke R, de Vos RCH, Mumm R, van Eeuwijk FA, Dicke M, Kloth KJ. Bivariate GWA mapping reveals associations between aliphatic glucosinolates and plant responses to thrips and heat stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39316617 DOI: 10.1111/tpj.17009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/20/2024] [Indexed: 09/26/2024]
Abstract
Although plants harbor a huge phytochemical diversity, only a fraction of plant metabolites is functionally characterized. In this work, we aimed to identify the genetic basis of metabolite functions during harsh environmental conditions in Arabidopsis thaliana. With machine learning algorithms we predicted stress-specific metabolomes for 23 (a)biotic stress phenotypes of 300 natural Arabidopsis accessions. The prediction models identified several aliphatic glucosinolates (GLSs) and their breakdown products to be implicated in responses to heat stress in siliques and herbivory by Western flower thrips, Frankliniella occidentalis. Bivariate GWA mapping of the metabolome predictions and their respective (a)biotic stress phenotype revealed genetic associations with MAM, AOP, and GS-OH, all three involved in aliphatic GSL biosynthesis. We, therefore, investigated thrips herbivory on AOP, MAM, and GS-OH loss-of-function and/or overexpression lines. Arabidopsis accessions with a combination of MAM2 and AOP3, leading to 3-hydroxypropyl dominance, suffered less from thrips feeding damage. The requirement of MAM2 for this effect could, however, not be confirmed with an introgression line of ecotypes Cvi and Ler, most likely due to other, unknown susceptibility factors in the Ler background. However, AOP2 and GS-OH, adding alkenyl or hydroxy-butenyl groups, respectively, did not have major effects on thrips feeding. Overall, this study illustrates the complex implications of aliphatic GSL diversity in plant responses to heat stress and a cell-content-feeding herbivore.
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Affiliation(s)
- Bader Arouisse
- Biometris, Wageningen University and Research, Wageningen, the Netherlands
| | - Manus P M Thoen
- Laboratory of Entomology, Wageningen University & Research, Wageningen, the Netherlands
- Enza Seeds, Enkhuizen, the Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University and Research, Wageningen, the Netherlands
| | - Jonathan F Kunst
- Biometris, Wageningen University and Research, Wageningen, the Netherlands
| | - Maarten A Jongsma
- Bioscience, Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Rik Kooke
- Biometris, Wageningen University and Research, Wageningen, the Netherlands
- Laboratory of Genetics, Wageningen University and Research, Wageningen, the Netherlands
| | - Ric C H de Vos
- Bioscience, Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Roland Mumm
- Bioscience, Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Fred A van Eeuwijk
- Biometris, Wageningen University and Research, Wageningen, the Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University & Research, Wageningen, the Netherlands
| | - Karen J Kloth
- Laboratory of Entomology, Wageningen University & Research, Wageningen, the Netherlands
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2
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Lei G, Huang J, Zhou H, Chen Y, Song J, Xie X, Vasseur L, You M, You S. Polygenic adaptation of a cosmopolitan pest to a novel thermal environment. INSECT MOLECULAR BIOLOGY 2024; 33:387-404. [PMID: 38488345 DOI: 10.1111/imb.12908] [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: 07/27/2023] [Accepted: 03/01/2024] [Indexed: 07/10/2024]
Abstract
The fluctuation in temperature poses a significant challenge for poikilothermic organisms, notably insects, particularly in the context of changing climatic conditions. In insects, temperature adaptation has been driven by polygenes. In addition to genes that directly affect traits (core genes), other genes (peripheral genes) may also play a role in insect temperature adaptation. This study focuses on two peripheral genes, the GRIP and coiled-coil domain containing 2 (GCC2) and karyopherin subunit beta 1 (KPNB1). These genes are differentially expressed at different temperatures in the cosmopolitan pest, Plutella xylostella. GCC2 and KPNB1 in P. xylostella were cloned, and their relative expression patterns were identified. Reduced capacity for thermal adaptation (development, reproduction and response to temperature extremes) in the GCC2-deficient and KPNB1-deficient P. xylostella strains, which were constructed by CRISPR/Cas9 technique. Deletion of the PxGCC2 or PxKPNB1 genes in P. xylostella also had a differential effect on gene expression for many traits including stress resistance, resistance to pesticides, involved in immunity, trehalose metabolism, fatty acid metabolism and so forth. The ability of the moth to adapt to temperature via different pathways is likely to be key to its ability to remain an important pest species under predicted climate change conditions.
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Affiliation(s)
- Gaoke Lei
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jieling Huang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huiling Zhou
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanting Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Plant Protection Fujian Academy of Agricultural Sciences, Fuzhou, China
| | | | | | - Liette Vasseur
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Minsheng You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijun You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- BGI Research, Sanya, China
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3
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Hufnagel B, Bernardino KC, Malosetti M, Sousa SM, Silva LA, Guimaraes CT, Coelho AM, Santos TT, Viana JHM, Schaffert RE, Kochian LV, Eeuwijk FA, Magalhaes JV. Multi-trait association mapping for phosphorous efficiency reveals flexible root architectures in sorghum. BMC PLANT BIOLOGY 2024; 24:562. [PMID: 38877425 PMCID: PMC11179229 DOI: 10.1186/s12870-024-05183-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND On tropical regions, phosphorus (P) fixation onto aluminum and iron oxides in soil clays restricts P diffusion from the soil to the root surface, limiting crop yields. While increased root surface area favors P uptake under low-P availability, the relationship between the three-dimensional arrangement of the root system and P efficiency remains elusive. Here, we simultaneously assessed allelic effects of loci associated with a variety of root and P efficiency traits, in addition to grain yield under low-P availability, using multi-trait genome-wide association. We also set out to establish the relationship between root architectural traits assessed in hydroponics and in a low-P soil. Our goal was to better understand the influence of root morphology and architecture in sorghum performance under low-P availability. RESULT In general, the same alleles of associated SNPs increased root and P efficiency traits including grain yield in a low-P soil. We found that sorghum P efficiency relies on pleiotropic loci affecting root traits, which enhance grain yield under low-P availability. Root systems with enhanced surface area stemming from lateral root proliferation mostly up to 40 cm soil depth are important for sorghum adaptation to low-P soils, indicating that differences in root morphology leading to enhanced P uptake occur exactly in the soil layer where P is found at the highest concentration. CONCLUSION Integrated QTLs detected in different mapping populations now provide a comprehensive molecular genetic framework for P efficiency studies in sorghum. This indicated extensive conservation of P efficiency QTL across populations and emphasized the terminal portion of chromosome 3 as an important region for P efficiency in sorghum. Increases in root surface area via enhancement of lateral root development is a relevant trait for sorghum low-P soil adaptation, impacting the overall architecture of the sorghum root system. In turn, particularly concerning the critical trait for water and nutrient uptake, root surface area, root system development in deeper soil layers does not occur at the expense of shallow rooting, which may be a key reason leading to the distinctive sorghum adaptation to tropical soils with multiple abiotic stresses including low P availability and drought.
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Affiliation(s)
- Barbara Hufnagel
- Embrapa Maize and Sorghum, Sete Lagoas, Minas Gerais, 35701-970, Brazil
- CIRAD, UMR AGAP Institut, Petit-Bourg, Guadeloupe, F-97170, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Marcos Malosetti
- Biometris, Wageningen University and Research Center, Wageningen, 6700AC, The Netherlands
- BASF - Nunhems, Nunhem, The Netherlands
| | - Sylvia M Sousa
- Embrapa Maize and Sorghum, Sete Lagoas, Minas Gerais, 35701-970, Brazil
| | - Lidianne A Silva
- Embrapa Maize and Sorghum, Sete Lagoas, Minas Gerais, 35701-970, Brazil
- Universidade Federal do Acre, Rio Branco, Acre, 69920-900, Brazil
| | | | | | | | - Joao H M Viana
- Embrapa Maize and Sorghum, Sete Lagoas, Minas Gerais, 35701-970, Brazil
| | | | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Fred A Eeuwijk
- Biometris, Wageningen University and Research Center, Wageningen, 6700AC, The Netherlands
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Ijaz U, Zhao C, Shabala S, Zhou M. Molecular Basis of Plant-Pathogen Interactions in the Agricultural Context. BIOLOGY 2024; 13:421. [PMID: 38927301 PMCID: PMC11200688 DOI: 10.3390/biology13060421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Biotic stressors pose significant threats to crop yield, jeopardizing food security and resulting in losses of over USD 220 billion per year by the agriculture industry. Plants activate innate defense mechanisms upon pathogen perception and invasion. The plant immune response comprises numerous concerted steps, including the recognition of invading pathogens, signal transduction, and activation of defensive pathways. However, pathogens have evolved various structures to evade plant immunity. Given these facts, genetic improvements to plants are required for sustainable disease management to ensure global food security. Advanced genetic technologies have offered new opportunities to revolutionize and boost plant disease resistance against devastating pathogens. Furthermore, targeting susceptibility (S) genes, such as OsERF922 and BnWRKY70, through CRISPR methodologies offers novel avenues for disrupting the molecular compatibility of pathogens and for introducing durable resistance against them in plants. Here, we provide a critical overview of advances in understanding disease resistance mechanisms. The review also critically examines management strategies under challenging environmental conditions and R-gene-based plant genome-engineering systems intending to enhance plant responses against emerging pathogens. This work underscores the transformative potential of modern genetic engineering practices in revolutionizing plant health and crop disease management while emphasizing the importance of responsible application to ensure sustainable and resilient agricultural systems.
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Affiliation(s)
- Usman Ijaz
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
| | - Sergey Shabala
- School of Biological Science, University of Western Australia, Crawley, WA 6009, Australia;
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Launceston, TAS 7250, Australia; (U.I.); (C.Z.)
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5
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Huang P, El-Soda M, Wolinska KW, Zhao K, Davila Olivas NH, van Loon JJA, Dicke M, Aarts MGM. Genome-wide association analysis reveals genes controlling an antagonistic effect of biotic and osmotic stress on Arabidopsis thaliana growth. MOLECULAR PLANT PATHOLOGY 2024; 25:e13436. [PMID: 38460112 PMCID: PMC10924621 DOI: 10.1111/mpp.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 03/11/2024]
Abstract
While the response of Arabidopsis thaliana to drought, herbivory or fungal infection has been well-examined, the consequences of exposure to a series of such (a)biotic stresses are not well studied. This work reports on the genetic mechanisms underlying the Arabidopsis response to single osmotic stress, and to combinatorial stress, either fungal infection using Botrytis cinerea or herbivory using Pieris rapae caterpillars followed by an osmotic stress treatment. Several small-effect genetic loci associated with rosette dry weight (DW), rosette water content (WC), and the projected rosette leaf area in response to combinatorial stress were mapped using univariate and multi-environment genome-wide association approaches. A single-nucleotide polymorphism (SNP) associated with DROUGHT-INDUCED 19 (DI19) was identified by both approaches, supporting its potential involvement in the response to combinatorial stress. Several SNPs were found to be in linkage disequilibrium with known stress-responsive genes such as PEROXIDASE 34 (PRX34), BASIC LEUCINE ZIPPER 25 (bZIP25), RESISTANCE METHYLATED GENE 1 (RMG1) and WHITE RUST RESISTANCE 4 (WRR4). An antagonistic effect between biotic and osmotic stress was found for prx34 and arf4 mutants, which suggests PRX34 and ARF4 play an important role in the response to the combinatorial stress.
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Affiliation(s)
- Pingping Huang
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
| | - Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Katarzyna W Wolinska
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
| | - Kaige Zhao
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
| | | | - Joop J A van Loon
- Laboratory of Entomology, Wageningen University & Research, Wageningen, Netherlands
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University & Research, Wageningen, Netherlands
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, Wageningen, Netherlands
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Kang X, Zhao L, Liu X. Calcium Signaling and the Response to Heat Shock in Crop Plants. Int J Mol Sci 2023; 25:324. [PMID: 38203495 PMCID: PMC10778685 DOI: 10.3390/ijms25010324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Climate change and the increasing frequency of high temperature (HT) events are significant threats to global crop yields. To address this, a comprehensive understanding of how plants respond to heat shock (HS) is essential. Signaling pathways involving calcium (Ca2+), a versatile second messenger in plants, encode information through temporal and spatial variations in ion concentration. Ca2+ is detected by Ca2+-sensing effectors, including channels and binding proteins, which trigger specific cellular responses. At elevated temperatures, the cytosolic concentration of Ca2+ in plant cells increases rapidly, making Ca2+ signals the earliest response to HS. In this review, we discuss the crucial role of Ca2+ signaling in raising plant thermotolerance, and we explore its multifaceted contributions to various aspects of the plant HS response (HSR).
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Affiliation(s)
| | - Liqun Zhao
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China;
| | - Xiaotong Liu
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China;
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Zhang X, Yu F, Lyu X, Chen J, Zeng H, Xu N, Wu Y, Zhu Q. Transcriptome profiling of Bergenia purpurascens under cold stress. BMC Genomics 2023; 24:754. [PMID: 38062379 PMCID: PMC10702111 DOI: 10.1186/s12864-023-09850-z] [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: 07/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Bergenia purpurascens is an important medicinal, edible and ornamental plant. It generally grows in high-altitude areas with complex climates. There have been no reports about how B. purpurascens survives under cold stress. Here, the B. purpurascens under low temperature were subjected to transcriptomics analysis to explore the candidate genes and pathways that involved in the cold tolerance of B. purpurascens. Compared with the control treatment, we found 9,600 up-regulated differentially expressed genes (DEGs) and 7,055 down-regulated DEGs. A significant number of DEGs were involved in the Ca2+ signaling pathway, mitogen-activated protein kinase (MAPK) cascade, plant hormone signaling pathway, and lipid metabolism. A total of 400 transcription factors were found to respond to cold stress, most of which belonged to the MYB and AP2/ERF families. Five novel genes were found to be potential candidate genes involved in the cold tolerance of B. purpurascens. The study provide insights into further investigation of the molecular mechanism of how B. purpurascens survives under cold stress.
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Affiliation(s)
- Xuebin Zhang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Fang Yu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Xin Lyu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Jingyu Chen
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Hongyan Zeng
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Nuomei Xu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yufeng Wu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Qiankun Zhu
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drug, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
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8
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Rogowska-van der Molen MA, Berasategui-Lopez A, Coolen S, Jansen RS, Welte CU. Microbial degradation of plant toxins. Environ Microbiol 2023; 25:2988-3010. [PMID: 37718389 DOI: 10.1111/1462-2920.16507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/05/2023] [Indexed: 09/19/2023]
Abstract
Plants produce a variety of secondary metabolites in response to biotic and abiotic stresses. Although they have many functions, a subclass of toxic secondary metabolites mainly serve plants as deterring agents against herbivores, insects, or pathogens. Microorganisms present in divergent ecological niches, such as soil, water, or insect and rumen gut systems have been found capable of detoxifying these metabolites. As a result of detoxification, microbes gain growth nutrients and benefit their herbivory host via detoxifying symbiosis. Here, we review current knowledge on microbial degradation of toxic alkaloids, glucosinolates, terpenes, and polyphenols with an emphasis on the genes and enzymes involved in breakdown pathways. We highlight that the insect-associated microbes might find application in biotechnology and become targets for an alternative microbial pest control strategy.
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Affiliation(s)
- Magda A Rogowska-van der Molen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Aileen Berasategui-Lopez
- Department of Microbiology and Biotechnology, University of Tübingen, Tübingen, Baden-Württemberg, Germany
- Amsterdam Institute for Life and Environment, Section Ecology and Evolution, Vrije Universiteit, Amsterdam, The Netherlands
| | - Silvia Coolen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Robert S Jansen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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9
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Reichelt N, Korte A, Krischke M, Mueller MJ, Maag D. Natural variation of warm temperature-induced raffinose accumulation identifies TREHALOSE-6-PHOSPHATE SYNTHASE 1 as a modulator of thermotolerance. PLANT, CELL & ENVIRONMENT 2023; 46:3392-3404. [PMID: 37427798 DOI: 10.1111/pce.14664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/11/2023]
Abstract
High-temperature stress limits plant growth and reproduction. Exposure to high temperature, however, also elicits a physiological response, which protects plants from the damage evoked by heat. This response involves a partial reconfiguration of the metabolome including the accumulation of the trisaccharide raffinose. In this study, we explored the intraspecific variation of warm temperature-induced raffinose accumulation as a metabolic marker for temperature responsiveness with the aim to identify genes that contribute to thermotolerance. By combining raffinose measurements in 250 Arabidopsis thaliana accessions following a mild heat treatment with genome-wide association studies, we identified five genomic regions that were associated with the observed trait variation. Subsequent functional analyses confirmed a causal relationship between TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) and warm temperature-dependent raffinose synthesis. Moreover, complementation of the tps1-1 null mutant with functionally distinct TPS1 isoforms differentially affected carbohydrate metabolism under more severe heat stress. While higher TPS1 activity was associated with reduced endogenous sucrose levels and thermotolerance, disruption of trehalose 6-phosphate signalling resulted in higher accumulation of transitory starch and sucrose and was associated with enhanced heat resistance. Taken together, our findings suggest a role of trehalose 6-phosphate in thermotolerance, most likely through its regulatory function in carbon partitioning and sucrose homoeostasis.
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Affiliation(s)
- Niklas Reichelt
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute of Biosciences, University of Würzburg, Würzburg, Germany
| | - Arthur Korte
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Markus Krischke
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute of Biosciences, University of Würzburg, Würzburg, Germany
| | - Martin J Mueller
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute of Biosciences, University of Würzburg, Würzburg, Germany
| | - Daniel Maag
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute of Biosciences, University of Würzburg, Würzburg, Germany
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Jin H, Tian Y, Zhang Y, Zhang R, Zhao H, Yang X, Song X, Dimitrov Y, Wu YE, Gao Q, Liu J, Zhang J, He Z. Genome-Wide Association Mapping of Processing Quality Traits in Common Wheat ( Triticum aestivum L.). Genes (Basel) 2023; 14:1816. [PMID: 37761956 PMCID: PMC10530800 DOI: 10.3390/genes14091816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Processing quality is an important economic wheat trait. The marker-assisted selection (MAS) method plays a vital role in accelerating genetic improvement of processing quality. In the present study, processing quality in a panel of 165 cultivars grown in four environments was evaluated by mixograph. An association mapping analysis using 90 K and 660 K single nucleotide polymorphism (SNP) arrays identified 24 loci in chromosomes 1A, 1B (4), 1D, 2A, 2B (2), 3A, 3B, 3D (2), 4A (3), 4B, 5D (2), 6A, 7B (2) and 7D (2), explaining 10.2-42.5% of the phenotypic variances. Totally, 15 loci were stably detected in two or more environments. Nine loci coincided with known genes or QTL, whereas the other fifteen were novel loci. Seven candidate genes encoded 3-ketoacyl-CoA synthase, lipoxygenase, pyridoxal phosphate-dependent decarboxylase, sucrose synthase 3 and a plant lipid transfer protein/Par allergen. SNPs significantly associated with processing quality and accessions with more favorable alleles can be used for marker-assisted selection.
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Affiliation(s)
- Hui Jin
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Yuanyuan Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China; (Y.T.); (Y.Z.); (J.L.)
| | - Yan Zhang
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China; (Y.T.); (Y.Z.); (J.L.)
| | - Rui Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Haibin Zhao
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Xue Yang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Xizhang Song
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Yordan Dimitrov
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Yu-e Wu
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Qiang Gao
- Horticultural Branch of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Jindong Liu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China; (Y.T.); (Y.Z.); (J.L.)
| | - Jumei Zhang
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (H.J.); (X.Y.); (X.S.); (Y.D.); (Y.W.)
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100000, China; (Y.T.); (Y.Z.); (J.L.)
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11
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Meyer RC, Weigelt-Fischer K, Tschiersch H, Topali G, Altschmied L, Heuermann MC, Knoch D, Kuhlmann M, Zhao Y, Altmann T. Dynamic growth QTL action in diverse light environments: characterization of light regime-specific and stable QTL in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5341-5362. [PMID: 37306093 DOI: 10.1093/jxb/erad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 06/10/2023] [Indexed: 06/13/2023]
Abstract
Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throughput phenotyping and genome-wide association studies. Daily automated non-invasive phenotyping of a collection of 382 Arabidopsis accessions provided growth data during developmental progression under different light regimes at high temporal resolution. Quantitative trait loci (QTL) for projected leaf area, relative growth rate, and PSII operating efficiency detected under the two light regimes were predominantly condition-specific and displayed distinct temporal activity patterns, with active phases ranging from 2 d to 9 d. Eighteen protein-coding genes and one miRNA gene were identified as potential candidate genes at 10 QTL regions consistently found under both light regimes. Expression patterns of three candidate genes affecting projected leaf area were analysed in time-series experiments in accessions with contrasting vegetative leaf growth. These observations highlight the importance of considering both environmental and temporal patterns of QTL/allele actions and emphasize the need for detailed time-resolved analyses under diverse well-defined environmental conditions to effectively unravel the complex and stage-specific contributions of genes affecting plant growth processes.
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Affiliation(s)
- Rhonda C Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Kathleen Weigelt-Fischer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Georgia Topali
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Dominic Knoch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Markus Kuhlmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Breeding Research, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department of Molecular Genetics, OT Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
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12
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Patel A, Miles A, Strackhouse T, Cook L, Leng S, Patel S, Klinger K, Rudrabhatla S, Potlakayala SD. Methods of crop improvement and applications towards fortifying food security. Front Genome Ed 2023; 5:1171969. [PMID: 37484652 PMCID: PMC10361821 DOI: 10.3389/fgeed.2023.1171969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023] Open
Abstract
Agriculture has supported human life from the beginning of civilization, despite a plethora of biotic (pests, pathogens) and abiotic (drought, cold) stressors being exerted on the global food demand. In the past 50 years, the enhanced understanding of cellular and molecular mechanisms in plants has led to novel innovations in biotechnology, resulting in the introduction of desired genes/traits through plant genetic engineering. Targeted genome editing technologies such as Zinc-Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) have emerged as powerful tools for crop improvement. This new CRISPR technology is proving to be an efficient and straightforward process with low cost. It possesses applicability across most plant species, targets multiple genes, and is being used to engineer plant metabolic pathways to create resistance to pathogens and abiotic stressors. These novel genome editing (GE) technologies are poised to meet the UN's sustainable development goals of "zero hunger" and "good human health and wellbeing." These technologies could be more efficient in developing transgenic crops and aid in speeding up the regulatory approvals and risk assessments conducted by the US Departments of Agriculture (USDA), Food and Drug Administration (FDA), and Environmental Protection Agency (EPA).
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Affiliation(s)
- Aayushi Patel
- Penn State Harrisburg, Middletown, PA, United States
| | - Andrew Miles
- Penn State University Park, State College, University Park, PA, United States
| | | | - Logan Cook
- Penn State Harrisburg, Middletown, PA, United States
| | - Sining Leng
- Shanghai United Cell Biotechnology Co Ltd, Shanghai, China
| | - Shrina Patel
- Penn State Harrisburg, Middletown, PA, United States
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13
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Coolen S, Van Dijen M, Van Pelt JA, Van Loon JJA, Pieterse CMJ, Van Wees SCM. Genome-wide association study reveals WRKY42 as a novel plant transcription factor that influences oviposition preference of Pieris butterflies. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:1690-1704. [PMID: 36560910 PMCID: PMC10010613 DOI: 10.1093/jxb/erac501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Insect herbivores are amongst the most destructive plant pests, damaging both naturally occurring and domesticated plants. As sessile organisms, plants make use of structural and chemical barriers to counteract herbivores. However, over 75% of herbivorous insect species are well adapted to their host's defenses and these specialists are generally difficult to ward off. By actively antagonizing the number of insect eggs deposited on plants, future damage by the herbivore's offspring can be limited. Therefore, it is important to understand which plant traits influence attractiveness for oviposition, especially for specialist insects that are well adapted to their host plants. In this study, we investigated the oviposition preference of Pieris butterflies (Lepidoptera: Pieridae) by offering them the choice between 350 different naturally occurring Arabidopsis accessions. Using a genome-wide association study of the oviposition data and subsequent fine mapping with full genome sequences of 164 accessions, we identified WRKY42 and AOC1 as candidate genes that are associated with the oviposition preference observed for Pieris butterflies. Host plant choice assays with Arabidopsis genotypes impaired in WRKY42 or AOC1 function confirmed a clear role for WRKY42 in oviposition preference of female Pieris butterflies, while for AOC1 the effect was mild. In contrast, WRKY42-impaired plants, which were preferred for oviposition by butterflies, negatively impacted offspring performance. These findings exemplify that plant genotype can have opposite effects on oviposition preference and caterpillar performance. This knowledge can be used for breeding trap crops or crops that are unattractive for oviposition by pest insects.
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Affiliation(s)
| | - Marcel Van Dijen
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Johan A Van Pelt
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Joop J A Van Loon
- Laboratory of Entomology, Wageningen University, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
| | - Saskia C M Van Wees
- Plant-Microbe Interactions, Department of Biology, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, The Netherlands
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14
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Tan QW, Lim PK, Chen Z, Pasha A, Provart N, Arend M, Nikoloski Z, Mutwil M. Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses. Nat Commun 2023; 14:986. [PMID: 36813788 PMCID: PMC9946954 DOI: 10.1038/s41467-023-36517-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 02/03/2023] [Indexed: 02/24/2023] Open
Abstract
Abiotic stresses negatively impact ecosystems and the yield of crops, and climate change will increase their frequency and intensity. Despite progress in understanding how plants respond to individual stresses, our knowledge of plant acclimatization to combined stresses typically occurring in nature is still lacking. Here, we used a plant with minimal regulatory network redundancy, Marchantia polymorpha, to study how seven abiotic stresses, alone and in 19 pairwise combinations, affect the phenotype, gene expression, and activity of cellular pathways. While the transcriptomic responses show a conserved differential gene expression between Arabidopsis and Marchantia, we also observe a strong functional and transcriptional divergence between the two species. The reconstructed high-confidence gene regulatory network demonstrates that the response to specific stresses dominates those of others by relying on a large ensemble of transcription factors. We also show that a regression model could accurately predict the gene expression under combined stresses, indicating that Marchantia performs arithmetic multiplication to respond to multiple stresses. Lastly, two online resources ( https://conekt.plant.tools and http://bar.utoronto.ca/efp_marchantia/cgi-bin/efpWeb.cgi ) are provided to facilitate the study of gene expression in Marchantia exposed to abiotic stresses.
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Affiliation(s)
- Qiao Wen Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Zhong Chen
- Amoeba Education Hub, 1 West Coast Road, 128020, Singapore, Singapore
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Marius Arend
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.,Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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15
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Thonglim A, Bortolami G, Delzon S, Larter M, Offringa R, Keurentjes JJB, Smets E, Balazadeh S, Lens F. Drought response in Arabidopsis displays synergistic coordination between stems and leaves. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:1004-1021. [PMID: 36350081 PMCID: PMC9899417 DOI: 10.1093/jxb/erac446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
The synergy between drought-responsive traits across different organs is crucial in the whole-plant mechanism influencing drought resilience. These organ interactions, however, are poorly understood, limiting our understanding of drought response strategies at the whole-plant level. Therefore, we need more integrative studies, especially on herbaceous species that represent many important food crops but remain underexplored in their drought response. We investigated inflorescence stems and rosette leaves of six Arabidopsis thaliana genotypes with contrasting drought tolerance, and combined anatomical observations with hydraulic measurements and gene expression studies to assess differences in drought response. The soc1ful double mutant was the most drought-tolerant genotype based on its synergistic combination of low stomatal conductance, largest stomatal safety margin, more stable leaf water potential during non-watering, reduced transcript levels of drought stress marker genes, and reduced loss of chlorophyll content in leaves, in combination with stems showing the highest embolism resistance, most pronounced lignification, and thickest intervessel pit membranes. In contrast, the most sensitive Cvi ecotype shows the opposite extreme of the same set of traits. The remaining four genotypes show variations in this drought syndrome. Our results reveal that anatomical, ecophysiological, and molecular adaptations across organs are intertwined, and multiple (differentially combined) strategies can be applied to acquire a certain level of drought tolerance.
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Affiliation(s)
| | - Giovanni Bortolami
- Naturalis Biodiversity Center, Research Group Functional Traits, PO Box 9517, 2300 RA Leiden, The Netherlands
| | | | | | - Remko Offringa
- Leiden University, Institute of Biology Leiden, Plant Developmental Genetics, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Erik Smets
- Naturalis Biodiversity Center, Research Group Functional Traits, PO Box 9517, 2300 RA Leiden, The Netherlands
- Leiden University, Institute of Biology Leiden, Plant Sciences, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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16
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Wei J, Luo B, Kong S, Liu W, Zhang C, Wei Z, Min X. Screening and identification of multiple abiotic stress responsive candidate genes based on hybrid-sequencing in Vicia sativa. Heliyon 2023; 9:e13536. [PMID: 36816321 PMCID: PMC9929474 DOI: 10.1016/j.heliyon.2023.e13536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023] Open
Abstract
Common vetch is an important leguminous forage for both livestock fodder and green manure and has a tremendous latent capacity in a sustainable agroecosystem. In the present study, a comprehensive transcriptome analysis of the aboveground leaves and underground roots of common vetch under multiple abiotic stress treatments, including NaCl, drought, cold, and cold drought, was performed using hybrid-sequencing technology, i. e. single-molecule real-time sequencing technology (SMRT) and supplemented by next-generation sequencing (NGS) technology. A total of 485,038 reads of insert (ROIs) with a mean length of 2606 bp and 228,261 full-length nonchimeric (FLNC) reads were generated. After deduplication, 39,709 transcripts were generated. Of these transcripts, we identified 1059 alternative splicing (AS) events, 17,227 simple sequence repeats (SSRs), and 1647 putative transcription factors (TFs). Furthermore, 640 candidates long noncoding RNAs (lncRNAs) and 28,256 complete coding sequences (CDSs) were identified. In gene annotation analyses, a total of 38,826 transcripts (97.78%) were annotated in eight public databases. Finally, seven multiple abiotic stress-responsive candidate genes were obtained through gene expression, annotation information, and protein-protein interaction (PPI) networks. Our research not only enriched the structural information of FL transcripts in common vetch, but also provided useful information for exploring the molecular mechanism of multiple abiotic stress tolerance between aboveground and underground tissues in common vetch and related legumes.
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Affiliation(s)
- Jia Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Bo Luo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Shiyi Kong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730000, People’s Republic of China
| | - Chuanjie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
| | - Xueyang Min
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu Province, 225009, People’s Republic of China
- Corresponding author.
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17
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Myers BK, Shin GY, Agarwal G, Stice SP, Gitaitis RD, Kvitko BH, Dutta B. Genome-wide association and dissociation studies in Pantoea ananatis reveal potential virulence factors affecting Allium porrum and Allium fistulosum × Allium cepa hybrid. Front Microbiol 2023; 13:1094155. [PMID: 36817114 PMCID: PMC9933511 DOI: 10.3389/fmicb.2022.1094155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/30/2022] [Indexed: 02/05/2023] Open
Abstract
Pantoea ananatis is a member of a Pantoea species complex that causes center rot of bulb onions (A. cepa) and also infects other Allium crops like leeks (Allium porrum), chives (Allium schoenoprasum), bunching onion or Welsh onion (Allium fistulosum), and garlic (Allium sativum). This pathogen relies on a chromosomal phosphonate biosynthetic gene cluster (HiVir) and a plasmid-borne thiosulfinate tolerance cluster (alt) for onion pathogenicity and virulence, respectively. However, pathogenicity and virulence factors associated with other Allium species remain unknown. We used phenotype-dependent genome-wide association (GWAS) and phenotype-independent gene-pair coincidence (GPC) analyses on a panel of diverse 92 P. ananatis strains, which were inoculated on A. porrum and A. fistulosum × A. cepa under greenhouse conditions. Phenotypic assays showed that, in general, these strains were more aggressive on A. fistulosum × A. cepa as opposed to A. porrum. Of the 92 strains, only six showed highly aggressive foliar lesions on A. porrum compared to A. fistulosum × A. cepa. Conversely, nine strains showed highly aggressive foliar lesions on A. fistulosum × A. cepa compared to A. porrum. These results indicate that there are underlying genetic components in P. ananatis that may drive pathogenicity in these two Allium spp. Based on GWAS for foliar pathogenicity, 835 genes were associated with P. ananatis' pathogenicity on A. fistulosum × A. cepa whereas 243 genes were associated with bacterial pathogenicity on A. porrum. The Hivir as well as the alt gene clusters were identified among these genes. Besides the 'HiVir' and the alt gene clusters that are known to contribute to pathogenicity and virulence from previous studies, genes annotated with functions related to stress responses, a potential toxin-antitoxin system, flagellar-motility, quorum sensing, and a previously described phosphonoglycan biosynthesis (pgb) cluster were identified. The GPC analysis resulted in the identification of 165 individual genes sorted into 39 significant gene-pair association components and 255 genes sorted into 50 significant gene-pair dissociation components. Within the coincident gene clusters, several genes that occurred on the GWAS outputs were associated with each other but dissociated with genes that did not appear in their respective GWAS output. To focus on candidate genes that could explain the difference in virulence between hosts, a comparative genomics analysis was performed on five P. ananatis strains that were differentially pathogenic on A. porrum or A. fistulosum × A. cepa. Here, we found a putative type III secretion system, and several other genes that occurred on both GWAS outputs of both Allium hosts. Further, we also demonstrated utilizing mutational analysis that the pepM gene in the HiVir cluster is important than the pepM gene in the pgb cluster for P. ananatis pathogenicity in A. fistulosum × A. cepa and A. porrum. Overall, our results support that P. ananatis may utilize a common set of genes or gene clusters to induce symptoms on A. fistulosum × A. cepa foliar tissue as well as A. cepa but implicates additional genes for infection on A. porrum.
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Affiliation(s)
- Brendon K. Myers
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Gi Yoon Shin
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Gaurav Agarwal
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Shaun P. Stice
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Ronald D. Gitaitis
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States,*Correspondence: Bhabesh Dutta, ✉
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18
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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: 11] [Impact Index Per Article: 11.0] [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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19
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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: 19] [Impact Index Per Article: 19.0] [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)
- Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Queensland 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Carlos D Messina
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, USA
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20
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Malinowska M, Ruud AK, Jensen J, Svane SF, Smith AG, Bellucci A, Lenk I, Nagy I, Fois M, Didion T, Thorup-Kristensen K, Jensen CS, Asp T. Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass. THE PLANT GENOME 2022; 15:e20253. [PMID: 35975565 DOI: 10.1002/tpg2.20253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
The growing demand for food and feed crops in the world because of growing population and more extreme weather events requires high-yielding and resilient crops. Many agriculturally important traits are polygenic, controlled by multiple regulatory layers, and with a strong interaction with the environment. In this study, 120 F2 families of perennial ryegrass (Lolium perenne L.) were grown across a water gradient in a semifield facility with subsoil irrigation. Genomic (single-nucleotide polymorphism [SNP]), transcriptomic (gene expression [GE]), and DNA methylomic (MET) data were integrated with feed quality trait data collected from control and drought sections in the semifield facility, providing a treatment effect. Deep root length (DRL) below 110 cm was assessed with convolutional neural network image analysis. Bayesian prediction models were used to partition phenotypic variance into its components and evaluated the proportion of phenotypic variance in all traits captured by different regulatory layers (SNP, GE, and MET). The spatial effects and effects of SNP, GE, MET, the interaction between GE and MET (GE × MET) and GE × treatment (GEControl and GEDrought ) interaction were investigated. Gene expression explained a substantial part of the genetic and spatial variance for all the investigated phenotypes, whereas MET explained residual variance not accounted for by SNPs or GE. For DRL, MET also contributed to explaining spatial variance. The study provides a statistically elegant analytical paradigm that integrates genomic, transcriptomic, and MET information to understand the regulatory mechanisms of polygenic effects for complex traits.
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Affiliation(s)
- Marta Malinowska
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Anja Karine Ruud
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Simon Fiil Svane
- Dep. of Plant and Environmental Sciences, Univ. of Copenhagen, Taastrup, Denmark
| | | | - Andrea Bellucci
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Ingo Lenk
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Mattia Fois
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Thomas Didion
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | | | | | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
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21
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Peláez JN, Gloss AD, Ray JF, Chaturvedi S, Haji D, Charboneau JLM, Verster KI, Whiteman NK. Evolution and genomic basis of the plant-penetrating ovipositor: a key morphological trait in herbivorous Drosophilidae. Proc Biol Sci 2022; 289:20221938. [PMID: 36350206 PMCID: PMC9653217 DOI: 10.1098/rspb.2022.1938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Herbivorous insects are extraordinarily diverse, yet are found in only one-third of insect orders. This skew may result from barriers to plant colonization, coupled with phylogenetic constraint on plant-colonizing adaptations. The plant-penetrating ovipositor, however, is one trait that surmounts host plant physical defences and may be evolutionarily labile. Ovipositors densely lined with hard bristles have evolved repeatedly in herbivorous lineages, including within the Drosophilidae. However, the evolution and genetic basis of this innovation has not been well studied. Here, we focused on the evolution of this trait in Scaptomyza, a genus sister to Hawaiian Drosophila, that contains a herbivorous clade. Our phylogenetic approach revealed that ovipositor bristle number increased as herbivory evolved in the Scaptomyza lineage. Through a genome-wide association study, we then dissected the genomic architecture of variation in ovipositor bristle number within S. flava. Top-associated variants were enriched for transcriptional repressors, and the strongest associations included genes contributing to peripheral nervous system development. Individual genotyping supported the association at a variant upstream of Gαi, a neural development gene, contributing to a gain of 0.58 bristles/major allele. These results suggest that regulatory variation involving conserved developmental genes contributes to this key morphological trait involved in plant colonization.
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Affiliation(s)
- Julianne N. Peláez
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | - Andrew D. Gloss
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10012, USA,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Julianne F. Ray
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Samridhi Chaturvedi
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | - Diler Haji
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | | | - Kirsten I. Verster
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA
| | - Noah K. Whiteman
- Department of Integrative Biology, University of California, Berkeley, 94720 CA, USA,Department of Molecular and Cell Biology, University of California, Berkeley, 94720 CA, USA
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22
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Reinert S. Quantitative genetics of pleiotropy and its potential for plant sciences. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153784. [PMID: 35944292 DOI: 10.1016/j.jplph.2022.153784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Stephan Reinert
- Friedrich-Alexander-University Erlangen-Nürnberg, Department of Biology, Division of Biochemistry, Biocomputing Lab, Staudtstraße 5, 91058, Erlangen, Germany.
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23
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Morales A, de Boer HJ, Douma JC, Elsen S, Engels S, Glimmerveen T, Sajeev N, Huber M, Luimes M, Luitjens E, Raatjes K, Hsieh C, Teapal J, Wildenbeest T, Jiang Z, Pareek A, Singla-Pareek S, Yin X, Evers J, Anten NPR, van Zanten M, Sasidharan R. Effects of sublethal single, simultaneous and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana. AOB PLANTS 2022; 14:plac029. [PMID: 35854681 PMCID: PMC9291396 DOI: 10.1093/aobpla/plac029] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 06/21/2022] [Indexed: 05/24/2023]
Abstract
Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sublethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analysed the phenotypic responses of 1782 individuals across these stresses and different developmental stages. Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analysed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses. This includes novel results regarding the lack of a response to drought after submergence and a decoupling between leaf number and flowering time after submergence. Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sublethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts.
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Affiliation(s)
| | - Hugo J de Boer
- Copernicus Institute of Sustainable Development, Utrecht University, 3584CB Utrecht, The Netherlands
| | - Jacob C Douma
- Centre for Crop Systems Analysis, Wageningen University & Research, 6700AK Wageningen, The Netherlands
| | - Saskia Elsen
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Sophie Engels
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Tobias Glimmerveen
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Nikita Sajeev
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Martina Huber
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Mathijs Luimes
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Emma Luitjens
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Kevin Raatjes
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Chenyun Hsieh
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Juliane Teapal
- Developmental Biology, Institute of Biodynamics and Biocomplexity, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Tessa Wildenbeest
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Zhang Jiang
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584CH Utrecht, The Netherlands
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sneh Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Xinyou Yin
- Centre for Crop Systems Analysis, Wageningen University & Research, 6700AK Wageningen, The Netherlands
| | - Jochem Evers
- Centre for Crop Systems Analysis, Wageningen University & Research, 6700AK Wageningen, The Netherlands
| | - Niels P R Anten
- Centre for Crop Systems Analysis, Wageningen University & Research, 6700AK Wageningen, The Netherlands
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24
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Coolen S, van der Molen MR, Welte CU. The secret life of insect-associated microbes and how they shape insect-plant interactions. FEMS Microbiol Ecol 2022; 98:6643329. [PMID: 35830517 PMCID: PMC9409087 DOI: 10.1093/femsec/fiac083] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/14/2022] [Accepted: 07/11/2022] [Indexed: 12/04/2022] Open
Abstract
Insects are associated with a plethora of different microbes of which we are only starting to understand their role in shaping insect–plant interactions. Besides directly benefitting from symbiotic microbial metabolism, insects obtain and transmit microbes within their environment, making them ideal vectors and potential beneficiaries of plant diseases and microbes that alter plant defenses. To prevent damage, plants elicit stress-specific defenses to ward off insects and their microbiota. However, both insects and microbes harbor a wealth of adaptations that allow them to circumvent effective plant defense activation. In the past decades, it has become apparent that the enormous diversity and metabolic potential of insect-associated microbes may play a far more important role in shaping insect–plant interactions than previously anticipated. The latter may have implications for the development of sustainable pest control strategies. Therefore, this review sheds light on the current knowledge on multitrophic insect–microbe–plant interactions in a rapidly expanding field of research.
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Affiliation(s)
- Silvia Coolen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, The Netherlands
| | - Magda Rogowska- van der Molen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, The Netherlands
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25
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Coulibaly M, Idohou R, Akohoue F, Peterson AT, Sawadogo M, Achigan-Dako EG. Coupling genetic structure analysis and ecological-niche modeling in Kersting’s groundnut in West Africa. Sci Rep 2022; 12:5590. [PMID: 35379846 PMCID: PMC8980027 DOI: 10.1038/s41598-022-09153-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/14/2022] [Indexed: 01/14/2023] Open
Abstract
Orphan legume crops play an important role in smallholder farmers’ food systems. Though less documented, they have the potential to contribute to adequate nutrition in vulnerable communities. Unfortunately, data are scarce about the potential of those crops to withstand current and future climate variations. Using Macrotyloma geocarpum as an example, we used ecological niche modeling to explore the role of ecology on the current and future distributions of genetic populations of Kersting’s groundnut. Our findings showed that: (1) the models had good predictive power, indicating that M. geocarpum’s distribution was correlated with both climatic and soil layers; (2) identity and similarity tests revealed that the two genetic groups have identical and similar environmental niches; (3) by integrating the genetic information in niche modeling, niches projections show divergence in the response of the species and genetic populations to ongoing climate change. This study highlights the importance of incorporating genetic data into Ecological Niche Modeling (ENM) approaches to obtain a finer information of species’ future distribution, and explores the implications for agricultural adaptation, with a particular focus on identifying priority actions in orphan crops conservation and breeding.
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26
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Zhu F, Ahchige MW, Brotman Y, Alseekh S, Zsögön A, Fernie AR. Bringing more players into play: Leveraging stress in genome wide association studies. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153657. [PMID: 35231821 DOI: 10.1016/j.jplph.2022.153657] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
In order to meet the demand of the burgeoning human population as well as to adapt crops to the enhanced abiotic and biotic stress caused by the global climatic change, breeders focus on identifying valuable genes to improve both crop stress tolerance and crop quality. Recently, with the development of next-generation sequencing methods, millions of high quality single-nucleotide polymorphisms (SNPs) have been made available and genome-wide association studies (GWAS) are widely used in crop improvement studies to identify the associations between genetic variants of genomes and relevant crop agronomic traits. Here, we review classic cases of use of GWAS to identify genetic variants associated with valuable traits such as geographic adaptation, crop quality and metabolites. We discuss the power of stress GWAS to identify further associations including those with genes that are not, or only lowly, expressed during optimal growth conditions. Finally, we emphasize recent demonstrations of the efficiency and accuracy of time-resolved dynamic stress GWAS and GWAS based on genomic gene expression and structural variations, which can be applied to resolve more comprehensively the genetic regulation mechanisms of complex traits.
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Affiliation(s)
- Feng Zhu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070, Wuhan, China
| | - Micha Wijesingha Ahchige
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Agustin Zsögön
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP 36570-900, Viçosa, MG, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
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27
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Bassetti N, Caarls L, Bukovinszkine'Kiss G, El-Soda M, van Veen J, Bouwmeester K, Zwaan BJ, Schranz ME, Bonnema G, Fatouros NE. Genetic analysis reveals three novel QTLs underpinning a butterfly egg-induced hypersensitive response-like cell death in Brassica rapa. BMC PLANT BIOLOGY 2022; 22:140. [PMID: 35331150 PMCID: PMC8944062 DOI: 10.1186/s12870-022-03522-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cabbage white butterflies (Pieris spp.) can be severe pests of Brassica crops such as Chinese cabbage, Pak choi (Brassica rapa) or cabbages (B. oleracea). Eggs of Pieris spp. can induce a hypersensitive response-like (HR-like) cell death which reduces egg survival in the wild black mustard (B. nigra). Unravelling the genetic basis of this egg-killing trait in Brassica crops could improve crop resistance to herbivory, reducing major crop losses and pesticides use. Here we investigated the genetic architecture of a HR-like cell death induced by P. brassicae eggs in B. rapa. RESULTS A germplasm screening of 56 B. rapa accessions, representing the genetic and geographical diversity of a B. rapa core collection, showed phenotypic variation for cell death. An image-based phenotyping protocol was developed to accurately measure size of HR-like cell death and was then used to identify two accessions that consistently showed weak (R-o-18) or strong cell death response (L58). Screening of 160 RILs derived from these two accessions resulted in three novel QTLs for Pieris brassicae-induced cell death on chromosomes A02 (Pbc1), A03 (Pbc2), and A06 (Pbc3). The three QTLs Pbc1-3 contain cell surface receptors, intracellular receptors and other genes involved in plant immunity processes, such as ROS accumulation and cell death formation. Synteny analysis with A. thaliana suggested that Pbc1 and Pbc2 are novel QTLs associated with this trait, while Pbc3 also contains an ortholog of LecRK-I.1, a gene of A. thaliana previously associated with cell death induced by a P. brassicae egg extract. CONCLUSIONS This study provides the first genomic regions associated with the Pieris egg-induced HR-like cell death in a Brassica crop species. It is a step closer towards unravelling the genetic basis of an egg-killing crop resistance trait, paving the way for breeders to further fine-map and validate candidate genes.
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Affiliation(s)
- Niccolò Bassetti
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Lotte Caarls
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Gabriella Bukovinszkine'Kiss
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Jeroen van Veen
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Klaas Bouwmeester
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Guusje Bonnema
- Laboratory of Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Nina E Fatouros
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands.
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28
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Rivero RM, Mittler R, Blumwald E, Zandalinas SI. Developing climate-resilient crops: improving plant tolerance to stress combination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:373-389. [PMID: 34482588 DOI: 10.1111/tpj.15483] [Citation(s) in RCA: 145] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/22/2021] [Accepted: 08/31/2021] [Indexed: 05/21/2023]
Abstract
Global warming and climate change are driving an alarming increase in the frequency and intensity of different abiotic stresses, such as droughts, heat waves, cold snaps, and flooding, negatively affecting crop yields and causing food shortages. Climate change is also altering the composition and behavior of different insect and pathogen populations adding to yield losses worldwide. Additional constraints to agriculture are caused by the increasing amounts of human-generated pollutants, as well as the negative impact of climate change on soil microbiomes. Although in the laboratory, we are trained to study the impact of individual stress conditions on plants, in the field many stresses, pollutants, and pests could simultaneously or sequentially affect plants, causing conditions of stress combination. Because climate change is expected to increase the frequency and intensity of such stress combination events (e.g., heat waves combined with drought, flooding, or other abiotic stresses, pollutants, and/or pathogens), a concentrated effort is needed to study how stress combination is affecting crops. This need is particularly critical, as many studies have shown that the response of plants to stress combination is unique and cannot be predicted from simply studying each of the different stresses that are part of the stress combination. Strategies to enhance crop tolerance to a particular stress may therefore fail to enhance tolerance to this specific stress, when combined with other factors. Here we review recent studies of stress combinations in different plants and propose new approaches and avenues for the development of stress combination- and climate change-resilient crops.
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Affiliation(s)
- Rosa M Rivero
- Department of Plant Nutrition, Campus Universitario de Espinardo, CEBAS-CSIC, Ed 25, Espinardo, Murcia, 30100, Spain
| | - Ron Mittler
- Division of Plant Sciences and Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO, 65201, USA
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Sara I Zandalinas
- Division of Plant Sciences and Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO, 65201, USA
- Departamento de Ciencias Agrarias y del Medio Natural, Universitat Jaume I, Av. de Vicent Sos Baynat, s/n, Castelló de la Plana, 12071, Spain
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29
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Libourel C, Baron E, Lenglet J, Amsellem L, Roby D, Roux F. The Genomic Architecture of Competitive Response of Arabidopsis thaliana Is Highly Flexible Among Plurispecific Neighborhoods. FRONTIERS IN PLANT SCIENCE 2021; 12:741122. [PMID: 34899774 PMCID: PMC8656689 DOI: 10.3389/fpls.2021.741122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/11/2021] [Indexed: 06/14/2023]
Abstract
Plants are daily challenged by multiple abiotic and biotic stresses. A major biotic constraint corresponds to competition with other plant species. Although plants simultaneously interact with multiple neighboring species throughout their life cycle, there is still very limited information about the genetics of the competitive response in the context of plurispecific interactions. Using a local mapping population of Arabidopsis thaliana, we set up a genome wide association study (GWAS) to estimate the extent of genetic variation of competitive response in 12 plant species assemblages, based on three competitor species (Poa annua, Stellaria media, and Veronica arvensis). Based on five phenotypic traits, we detected strong crossing reaction norms not only between the three bispecific neighborhoods but also among the plurispecific neighborhoods. The genetic architecture of competitive response was highly dependent on the identity and the relative abundance of the neighboring species. In addition, most of the enriched biological processes underlying competitive responses largely differ among neighborhoods. While the RNA related processes might confer a broad range response toolkit for multiple traits in diverse neighborhoods, some processes, such as signaling and transport, might play a specific role in particular assemblages. Altogether, our results suggest that plants can integrate and respond to different species assemblages depending on the identity and number of each neighboring species, through a large range of candidate genes associated with diverse and unexpected processes leading to developmental and stress responses.
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Affiliation(s)
- Cyril Libourel
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Etienne Baron
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, Villeneuve d’Ascq Cedex, France
| | - Juliana Lenglet
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, Villeneuve d’Ascq Cedex, France
| | - Laurent Amsellem
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, Villeneuve d’Ascq Cedex, France
| | - Dominique Roby
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
- Laboratoire Evolution, Ecologie et Paléontologie, UMR CNRS 8198, Université de Lille, Villeneuve d’Ascq Cedex, France
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Molecular characterization and expression of cyclic nucleotide gated ion channels 19 and 20 in Arabidopsis thaliana for their potential role in salt stress. Saudi J Biol Sci 2021; 28:5800-5807. [PMID: 34588894 PMCID: PMC8459076 DOI: 10.1016/j.sjbs.2021.06.027] [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: 02/21/2021] [Revised: 06/06/2021] [Accepted: 06/09/2021] [Indexed: 12/05/2022] Open
Abstract
Cyclic nucleotide gated ion channels (CNGCs) in plants have very important role in signaling and development. The study reports role of CNGC19 and CNGC20 in salt stress in A. thaliana. In-silico, genome wide analysis showed that CNGC19 and CNGC20 are related to salt stress with maximum expression after 6 h in A. thaliana. The position of inserted T-DNA was determined (in-vivo) through TAIL-PCR for activation tagged mutants of CNGC19 and CNGC20 under salt stress. The expression of AtCNGC19 and AtCNGC20 after cloning under 35S promoter of expression vectors pBCH1 and pEarleyGate100 was determined in A. thaliana by real-time PCR analysis. Genome wide analysis showed that AtCNGC11 had lowest and AtCNGC20 highest molecular weight as well as number of amino acid residues. In-vivo expression of AtCNGC19 and AtCNGC20 was enhanced through T-DNA insertion and 35S promoter in over-expressed plants under high salt concentration. AtCNGC19 was activated twice in control and about five times under 150 mM NaCl stress level, and expression value was also higher than AtCNGC20. Phenotypically, over-expressed plants and calli were healthier while knock-out plants and calli showed retarded growth under salinity stress. The study provides new insight for the role of AtCNGC19 and AtCNGC20 under salt stress regulation in A. thaliana and will be helpful for improvement of crop plants for salt stress to combat food shortage and security.
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Romero-Puertas MC, Terrón-Camero LC, Peláez-Vico MÁ, Molina-Moya E, Sandalio LM. An update on redox signals in plant responses to biotic and abiotic stress crosstalk: insights from cadmium and fungal pathogen interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5857-5875. [PMID: 34111283 PMCID: PMC8355756 DOI: 10.1093/jxb/erab271] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/07/2021] [Indexed: 05/09/2023]
Abstract
Complex signalling pathways are involved in plant protection against single and combined stresses. Plants are able to coordinate genome-wide transcriptional reprogramming and display a unique programme of transcriptional responses to a combination of stresses that differs from the response to single stresses. However, a significant overlap between pathways and some defence genes in the form of shared and general stress-responsive genes appears to be commonly involved in responses to multiple biotic and abiotic stresses. Reactive oxygen and nitrogen species, as well as redox signals, are key molecules involved at the crossroads of the perception of different stress factors and the regulation of both specific and general plant responses to biotic and abiotic stresses. In this review, we focus on crosstalk between plant responses to biotic and abiotic stresses, in addition to possible plant protection against pathogens caused by previous abiotic stress. Bioinformatic analyses of transcriptome data from cadmium- and fungal pathogen-treated plants focusing on redox gene ontology categories were carried out to gain a better understanding of common plant responses to abiotic and biotic stresses. The role of reactive oxygen and nitrogen species in the complex network involved in plant responses to changes in their environment is also discussed.
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Affiliation(s)
- María C Romero-Puertas
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin (EEZ), Consejo Superior de Investigaciones Cientificas (CSIC), Apartado 419, 18080 Granada, Spain
| | - Laura C Terrón-Camero
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin (EEZ), Consejo Superior de Investigaciones Cientificas (CSIC), Apartado 419, 18080 Granada, Spain
- Bioinformatics Unit, Institute of Parasitology and Biomedicine “López-Neyra” (IPBLN-CSIC), Granada, Spain
| | - M Ángeles Peláez-Vico
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin (EEZ), Consejo Superior de Investigaciones Cientificas (CSIC), Apartado 419, 18080 Granada, Spain
| | - Eliana Molina-Moya
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin (EEZ), Consejo Superior de Investigaciones Cientificas (CSIC), Apartado 419, 18080 Granada, Spain
| | - Luisa M Sandalio
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estacion Experimental del Zaidin (EEZ), Consejo Superior de Investigaciones Cientificas (CSIC), Apartado 419, 18080 Granada, Spain
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Thonglim A, Delzon S, Larter M, Karami O, Rahimi A, Offringa R, Keurentjes JJB, Balazadeh S, Smets E, Lens F. Intervessel pit membrane thickness best explains variation in embolism resistance amongst stems of Arabidopsis thaliana accessions. ANNALS OF BOTANY 2021; 128:171-182. [PMID: 33216143 PMCID: PMC8324034 DOI: 10.1093/aob/mcaa196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/13/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND AND AIMS The ability to avoid drought-induced embolisms in the xylem is one of the essential traits for plants to survive periods of water shortage. Over the past three decades, hydraulic studies have been focusing on trees, which limits our ability to understand how herbs tolerate drought. Here we investigate the embolism resistance in inflorescence stems of four Arabidopsis thaliana accessions that differ in growth form and drought response. We assess functional traits underlying the variation in embolism resistance amongst the accessions studied using detailed anatomical observations. METHODS Vulnerability to xylem embolism was evaluated via vulnerability curves using the centrifuge technique and linked with detailed anatomical observations in stems using light microscopy and transmission electron microscopy. KEY RESULTS The data show significant differences in stem P50, varying 2-fold from -1.58 MPa in the Cape Verde Island accession to -3.07 MPa in the woody soc1 ful double mutant. Out of all the anatomical traits measured, intervessel pit membrane thickness (TPM) best explains the differences in P50, as well as P12 and P88. The association between embolism resistance and TPM can be functionally explained by the air-seeding hypothesis. There is no evidence that the correlation between increased woodiness and increased embolism resistance is directly related to functional aspects. However, we found that increased woodiness is strongly linked to other lignification characters, explaining why mechanical stem reinforcement is indirectly related to increased embolism resistance. CONCLUSIONS The woodier or more lignified accessions are more resistant to embolism than the herbaceous accessions, confirming the link between increased stem lignification and increased embolism resistance, as also observed in other lineages. Intervessel pit membrane thickness and, to a lesser extent, theoretical vessel implosion resistance and vessel wall thickness are the missing functional links between stem lignification and embolism resistance.
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Affiliation(s)
- Ajaree Thonglim
- Naturalis Biodiversity Center, Research Group Functional Traits, RA Leiden, The Netherlands
| | | | - Maximilian Larter
- Naturalis Biodiversity Center, Research Group Functional Traits, RA Leiden, The Netherlands
| | - Omid Karami
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, BE Leiden, the Netherlands
| | - Arezoo Rahimi
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, BE Leiden, the Netherlands
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, BE Leiden, the Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg, PB Wageningen, The Netherlands
| | - Salma Balazadeh
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, BE Leiden, the Netherlands
| | - Erik Smets
- Naturalis Biodiversity Center, Research Group Functional Traits, RA Leiden, The Netherlands
| | - Frederic Lens
- Naturalis Biodiversity Center, Research Group Functional Traits, RA Leiden, The Netherlands
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Capador-Barreto HD, Bernhardsson C, Milesi P, Vos I, Lundén K, Wu HX, Karlsson B, Ingvarsson PK, Stenlid J, Elfstrand M. Killing two enemies with one stone? Genomics of resistance to two sympatric pathogens in Norway spruce. Mol Ecol 2021; 30:4433-4447. [PMID: 34218489 DOI: 10.1111/mec.16058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 12/31/2022]
Abstract
Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.
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Affiliation(s)
- Hernán D Capador-Barreto
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Carolina Bernhardsson
- Uppsala Biocentre, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Pascal Milesi
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ingrid Vos
- Forestry Research Institute of Sweden (Skogforsk), Ekebo, Sweden
| | - Karl Lundén
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Harry X Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Bo Karlsson
- Forestry Research Institute of Sweden (Skogforsk), Ekebo, Sweden
| | - Pär K Ingvarsson
- Uppsala Biocentre, Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Stenlid
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Malin Elfstrand
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Genetic variability assessment of 127 Triticum turgidum L. accessions for mycorrhizal susceptibility-related traits detection. Sci Rep 2021; 11:13426. [PMID: 34183734 PMCID: PMC8239029 DOI: 10.1038/s41598-021-92837-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Positive effects of arbuscular mycorrhizal fungi (AMF)-wheat plant symbiosis have been well discussed by research, while the actual role of the single wheat genotype in establishing this type of association is still poorly investigated. In this work, the genetic diversity of Triticum turgidum wheats was exploited to detect roots susceptibility to AMF and to identify genetic markers in linkage with chromosome regions involved in this symbiosis. A tetraploid wheat collection of 127 accessions was genotyped using 35K single-nucleotide polymorphism (SNP) array and inoculated with the AMF species Funneliformis mosseae (F. mosseae) and Rhizoglomus irregulare (R. irregulare), and a genome-wide association study (GWAS) was conducted. Six clusters of genetically related accessions were identified, showing a different mycorrhizal colonization among them. GWAS revealed four significant quantitative trait nucleotides (QTNs) involved in mycorrhizal symbiosis, located on chromosomes 1A, 2A, 2B and 6A. The results of this work enrich future breeding activities aimed at developing new grains on the basis of genetic diversity on low or high susceptibility to mycorrhization, and, possibly, maximizing the symbiotic effects.
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Zandalinas SI, Fritschi FB, Mittler R. Global Warming, Climate Change, and Environmental Pollution: Recipe for a Multifactorial Stress Combination Disaster. TRENDS IN PLANT SCIENCE 2021; 26:588-599. [PMID: 33745784 DOI: 10.1016/j.tplants.2021.02.011] [Citation(s) in RCA: 226] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 05/19/2023]
Abstract
Global warming, climate change, and environmental pollution present plants with unique combinations of different abiotic and biotic stresses. Although much is known about how plants acclimate to each of these individual stresses, little is known about how they respond to a combination of many of these stress factors occurring together, namely a multifactorial stress combination. Recent studies revealed that increasing the number of different co-occurring multifactorial stress factors causes a severe decline in plant growth and survival, as well as in the microbiome biodiversity that plants depend upon. This effect should serve as a dire warning to our society and prompt us to decisively act to reduce pollutants, fight global warming, and augment the tolerance of crops to multifactorial stress combinations.
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Affiliation(s)
- Sara I Zandalinas
- Division of Plant Sciences and Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65201, USA
| | - Felix B Fritschi
- Division of Plant Sciences and Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65201, USA
| | - Ron Mittler
- Division of Plant Sciences and Interdisciplinary Plant Group, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65201, USA; Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, MO 65201, USA.
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Plant Transcription Factors Involved in Drought and Associated Stresses. Int J Mol Sci 2021; 22:ijms22115662. [PMID: 34073446 PMCID: PMC8199153 DOI: 10.3390/ijms22115662] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors (TFs) play a significant role in signal transduction networks spanning the perception of a stress signal and the expression of corresponding stress-responsive genes. TFs are multi-functional proteins that may simultaneously control numerous pathways during stresses in plants-this makes them powerful tools for the manipulation of regulatory and stress-responsive pathways. In recent years, the structure-function relationships of numerous plant TFs involved in drought and associated stresses have been defined, which prompted devising practical strategies for engineering plants with enhanced stress tolerance. Vast data have emerged on purposely basic leucine zipper (bZIP), WRKY, homeodomain-leucine zipper (HD-Zip), myeloblastoma (MYB), drought-response elements binding proteins/C-repeat binding factor (DREB/CBF), shine (SHN), and wax production-like (WXPL) TFs that reflect the understanding of their 3D structure and how the structure relates to function. Consequently, this information is useful in the tailored design of variant TFs that enhances our understanding of their functional states, such as oligomerization, post-translational modification patterns, protein-protein interactions, and their abilities to recognize downstream target DNA sequences. Here, we report on the progress of TFs based on their interaction pathway participation in stress-responsive networks, and pinpoint strategies and applications for crops and the impact of these strategies for improving plant stress tolerance.
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Arouisse B, Theeuwen TPJM, van Eeuwijk FA, Kruijer W. Improving Genomic Prediction Using High-Dimensional Secondary Phenotypes. Front Genet 2021; 12:667358. [PMID: 34108993 PMCID: PMC8181460 DOI: 10.3389/fgene.2021.667358] [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: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 11/17/2022] Open
Abstract
In the past decades, genomic prediction has had a large impact on plant breeding. Given the current advances of high-throughput phenotyping and sequencing technologies, it is increasingly common to observe a large number of traits, in addition to the target trait of interest. This raises the important question whether these additional or “secondary” traits can be used to improve genomic prediction for the target trait. With only a small number of secondary traits, this is known to be the case, given sufficiently high heritabilities and genetic correlations. Here we focus on the more challenging situation with a large number of secondary traits, which is increasingly common since the arrival of high-throughput phenotyping. In this case, secondary traits are usually incorporated through additional relatedness matrices. This approach is however infeasible when secondary traits are not measured on the test set, and cannot distinguish between genetic and non-genetic correlations. An alternative direction is to extend the classical selection indices using penalized regression. So far, penalized selection indices have not been applied in a genomic prediction setting, and require plot-level data in order to reliably estimate genetic correlations. Here we aim to overcome these limitations, using two novel approaches. Our first approach relies on a dimension reduction of the secondary traits, using either penalized regression or random forests (LS-BLUP/RF-BLUP). We then compute the bivariate GBLUP with the dimension reduction as secondary trait. For simulated data (with available plot-level data), we also use bivariate GBLUP with the penalized selection index as secondary trait (SI-BLUP). In our second approach (GM-BLUP), we follow existing multi-kernel methods but replace secondary traits by their genomic predictions, with the advantage that genomic prediction is also possible when secondary traits are only measured on the training set. For most of our simulated data, SI-BLUP was most accurate, often closely followed by RF-BLUP or LS-BLUP. In real datasets, involving metabolites in Arabidopsis and transcriptomics in maize, no method could substantially improve over univariate prediction when secondary traits were only available on the training set. LS-BLUP and RF-BLUP were most accurate when secondary traits were available also for the test set.
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Affiliation(s)
- Bader Arouisse
- Biometris, Wageningen University and Research, Wageningen, Netherlands
| | - Tom P J M Theeuwen
- Laboratory of Genetics, Wageningen University and Research, Wageningen, Netherlands
| | | | - Willem Kruijer
- Biometris, Wageningen University and Research, Wageningen, Netherlands
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Alonso-Díaz A, Satbhai SB, de Pedro-Jové R, Berry HM, Göschl C, Argueso CT, Novak O, Busch W, Valls M, Coll NS. A genome-wide association study reveals cytokinin as a major component in the root defense responses against Ralstonia solanacearum. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2727-2740. [PMID: 33475698 PMCID: PMC8006551 DOI: 10.1093/jxb/eraa610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/19/2021] [Indexed: 05/30/2023]
Abstract
Bacterial wilt caused by the soil-borne pathogen Ralstonia solancearum is economically devastating, with no effective methods to fight the disease. This pathogen invades plants through their roots and colonizes their xylem, clogging the vasculature and causing rapid wilting. Key to preventing colonization are the early defense responses triggered in the host's root upon infection, which remain mostly unknown. Here, we have taken advantage of a high-throughput in vitro infection system to screen natural variability associated with the root growth inhibition phenotype caused by R. solanacearum in Arabidopsis during the first hours of infection. To analyze the genetic determinants of this trait, we have performed a genome-wide association study, identifying allelic variation at several loci related to cytokinin metabolism, including genes responsible for biosynthesis and degradation of cytokinin. Further, our data clearly demonstrate that cytokinin signaling is induced early during the infection process and cytokinin contributes to immunity against R. solanacearum. This study highlights a new role for cytokinin in root immunity, paving the way for future research that will help in understanding the mechanisms underpinning root defenses.
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Affiliation(s)
- Alejandro Alonso-Díaz
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Santosh B Satbhai
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, Vienna 1030, Austria
- Salk Institute For Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Roger de Pedro-Jové
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Hannah M Berry
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Christian Göschl
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, Vienna 1030, Austria
| | - Cristiana T Argueso
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Ondrej Novak
- Laboratory of Growth Regulators, Olomouc, The Czech Republic
| | - Wolfgang Busch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr Bohr-Gasse 3, Vienna 1030, Austria
- Salk Institute For Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Marc Valls
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
- Genetics Department, University of Barcelona, Barcelona, Spain
| | - Núria S Coll
- Centre for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
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Montes N, Cobos A, Gil-Valle M, Caro E, Pagán I. Arabidopsis thaliana Genes Associated with Cucumber mosaic virus Virulence and Their Link to Virus Seed Transmission. Microorganisms 2021; 9:692. [PMID: 33801693 PMCID: PMC8067046 DOI: 10.3390/microorganisms9040692] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/27/2022] Open
Abstract
Virulence, the effect of pathogen infection on progeny production, is a major determinant of host and pathogen fitness as it affects host fecundity and pathogen transmission. In plant-virus interactions, ample evidence indicates that virulence is genetically controlled by both partners. However, the host genetic determinants are poorly understood. Through a genome-wide association study (GWAS) of 154 Arabidopsis thaliana genotypes infected by Cucumber mosaic virus (CMV), we identified eight host genes associated with virulence, most of them involved in response to biotic stresses and in cell wall biogenesis in plant reproductive structures. Given that virulence is a main determinant of the efficiency of plant virus seed transmission, we explored the link between this trait and the genetic regulation of virulence. Our results suggest that the same functions that control virulence are also important for CMV transmission through seeds. In sum, this work provides evidence of a novel role for some previously known plant defense genes and for the cell wall metabolism in plant virus interactions.
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Affiliation(s)
- Nuria Montes
- Unidad de Fisiología Vegetal, Departamento Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU Universities, Boadilla del Monte, 28003 Madrid, Spain;
- Servicio de Reumatología, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria (IIS-IP), 28006 Madrid, Spain
| | - Alberto Cobos
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Departamento de Biotecnología-Biología Vegetal, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28045 Madrid, Spain; (A.C.); (M.G.-V.); (E.C.)
| | - Miriam Gil-Valle
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Departamento de Biotecnología-Biología Vegetal, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28045 Madrid, Spain; (A.C.); (M.G.-V.); (E.C.)
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Departamento de Biotecnología-Biología Vegetal, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28045 Madrid, Spain; (A.C.); (M.G.-V.); (E.C.)
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Departamento de Biotecnología-Biología Vegetal, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28045 Madrid, Spain; (A.C.); (M.G.-V.); (E.C.)
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Ye J, Zhang L, Zhang X, Wu X, Fang R. Plant Defense Networks against Insect-Borne Pathogens. TRENDS IN PLANT SCIENCE 2021; 26:272-287. [PMID: 33277186 DOI: 10.1016/j.tplants.2020.10.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/19/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
Upon infection with insect-borne microbial pathogens, plants are exposed to two types of damage simultaneously. Over the past decade, numerous molecular studies have been conducted to understand how plants respond to pathogens or herbivores. However, investigations of host responses typically focus on a single stress and are performed under static laboratory conditions. In this review, we highlight research that sheds light on how plants deploy broad-spectrum mechanisms against both vector-borne pathogens and insect vectors. Among the host genes involved in multistress resistance, many are involved in innate immunity and phytohormone signaling (especially jasmonate and salicylic acid). The potential for genome editing or chemical modulators to fine-tune crop defensive signaling, to develop sustainable methods to control insect-borne diseases, is discussed.
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Affiliation(s)
- Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lili Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiujuan Wu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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Frontini M, Boisnard A, Frouin J, Ouikene M, Morel JB, Ballini E. Genome-wide association of rice response to blast fungus identifies loci for robust resistance under high nitrogen. BMC PLANT BIOLOGY 2021; 21:99. [PMID: 33602120 PMCID: PMC7893971 DOI: 10.1186/s12870-021-02864-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/01/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Nitrogen fertilization is known to increase disease susceptibility, a phenomenon called Nitrogen-Induced Susceptibility (NIS). In rice, this phenomenon has been observed in infections with the blast fungus Magnaporthe oryzae. A previous classical genetic study revealed a locus (NIS1) that enhances susceptibility to rice blast under high nitrogen fertilization. In order to further address the underlying genetics of plasticity in susceptibility to rice blast after fertilization, we analyzed NIS under greenhouse-controlled conditions in a panel of 139 temperate japonica rice strains. A genome-wide association analysis was conducted to identify loci potentially involved in NIS by comparing susceptibility loci identified under high and low nitrogen conditions, an approach allowing for the identification of loci validated across different nitrogen environments. We also used a novel NIS Index to identify loci potentially contributing to plasticity in susceptibility under different nitrogen fertilization regimes. RESULTS A global NIS effect was observed in the population, with the density of lesions increasing by 8%, on average, under high nitrogen fertilization. Three new QTL, other than NIS1, were identified. A rare allele of the RRobN1 locus on chromosome 6 provides robust resistance in high and low nitrogen environments. A frequent allele of the NIS2 locus, on chromosome 5, exacerbates blast susceptibility under the high nitrogen condition. Finally, an allele of NIS3, on chromosome 10, buffers the increase of susceptibility arising from nitrogen fertilization but increases global levels of susceptibility. This allele is almost fixed in temperate japonicas, as a probable consequence of genetic hitchhiking with a locus involved in cold stress adaptation. CONCLUSIONS Our results extend to an entire rice subspecies the initial finding that nitrogen increases rice blast susceptibility. We demonstrate the usefulness of estimating plasticity for the identification of novel loci involved in the response of rice to the blast fungus under different nitrogen regimes.
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Affiliation(s)
- Mathias Frontini
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Julien Frouin
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Malika Ouikene
- Groupe de Valorisation des Produits Agricoles (GVAPRO), Alger, Algeria
| | - Jean Benoit Morel
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Elsa Ballini
- BGPI, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Schueler S, George JP, Karanitsch-Ackerl S, Mayer K, Klumpp RT, Grabner M. Evolvability of Drought Response in Four Native and Non-native Conifers: Opportunities for Forest and Genetic Resource Management in Europe. FRONTIERS IN PLANT SCIENCE 2021; 12:648312. [PMID: 34305960 PMCID: PMC8295755 DOI: 10.3389/fpls.2021.648312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/07/2021] [Indexed: 05/05/2023]
Abstract
Intraspecific genetic variation in drought response is expected to play an important role in determining the persistence of tree populations in global change as it (1) allows for spontaneous selection and local adaptation of tree populations, (2) supports assisted seed transfer of less-drought-sensitive provenance, and (3) enables the integration of drought-sensitivity traits into tree breeding. Estimating the potential of such adaptation options requires quantitative genetic knowledge of drought sensitivity across significant parts of species distributions and a comparative assessment of genetic variation within economically and ecologically important tree species. We quantified genetic variation within and among populations of four conifers growing within common garden experiments in the drought-prone eastern Austria. This region experienced three strong drought periods between 1980 and 2010 that resulted in significant reductions in radial growth. Among the four tested species, Douglas-fir revealed the highest resistance during drought and silver fir the best recovery after drought, while European larch and Norway spruce showed the lowest resistance. High genetic variation among populations and phenotypic stability across all three drought events was found for Norway spruce and silver fir, but not for the other species. Heritability and evolvability of drought traits, both approximated via genetic repeatability, revealed strong differences among populations of all four species. Repeatability and evolvability for resistance were highest in Norway spruce and, for recovery, highest in European larch. Our comparison indicates that the mean drought sensitivity of a species is not related to the intraspecific genetic variation in drought response. Thus, also highly drought-sensitive species, such as Norway spruce and European larch, harbor significant genetic variation in drought response within and among populations to justify targeted tree breeding, assisted gene flow, and supportive forest management to foster local adaptations to future conditions.
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Affiliation(s)
- Silvio Schueler
- Department of Forest Growth, Silviculture and Genetics, Austrian Research Centre for Forests BFW, Vienna, Austria
- *Correspondence: Silvio Schueler
| | - Jan-Peter George
- Department of Forest Growth, Silviculture and Genetics, Austrian Research Centre for Forests BFW, Vienna, Austria
| | - Sandra Karanitsch-Ackerl
- Department of Material Sciences and Process Engineering, Institute of Wood Technology and Renewable Resources, University of Natural Resources and Life Sciences (BOKU), Tulln an der Donau, Austria
| | - Konrad Mayer
- Department of Material Sciences and Process Engineering, Institute of Wood Technology and Renewable Resources, University of Natural Resources and Life Sciences (BOKU), Tulln an der Donau, Austria
| | - Raphael Thomas Klumpp
- Department of Forest- and Soil Sciences, Institute of Silviculture, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Michael Grabner
- Department of Material Sciences and Process Engineering, Institute of Wood Technology and Renewable Resources, University of Natural Resources and Life Sciences (BOKU), Tulln an der Donau, Austria
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Cruz DF, De Meyer S, Ampe J, Sprenger H, Herman D, Van Hautegem T, De Block J, Inzé D, Nelissen H, Maere S. Using single-plant-omics in the field to link maize genes to functions and phenotypes. Mol Syst Biol 2020; 16:e9667. [PMID: 33346944 PMCID: PMC7751767 DOI: 10.15252/msb.20209667] [Citation(s) in RCA: 8] [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: 04/28/2020] [Revised: 10/29/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.
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Affiliation(s)
- Daniel Felipe Cruz
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Sam De Meyer
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Joke Ampe
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Heike Sprenger
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dorota Herman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Tom Van Hautegem
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Jolien De Block
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Steven Maere
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
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Deng M, Wang Y, Kuzma M, Chalifoux M, Tremblay L, Yang S, Ying J, Sample A, Wang HM, Griffiths R, Uchacz T, Tang X, Tian G, Joslin K, Dennis D, McCourt P, Huang Y, Wan J. Activation tagging identifies Arabidopsis transcription factor AtMYB68 for heat and drought tolerance at yield determining reproductive stages. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1535-1550. [PMID: 33048399 DOI: 10.1111/tpj.15019] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/13/2020] [Accepted: 09/23/2020] [Indexed: 05/23/2023]
Abstract
Heat stress occurring at reproductive stages can result in significant and permanent damage to crop yields. However, previous genetic studies in understanding heat stress response and signaling were performed mostly on seedling and plants at early vegetative stages. Here we identify, using a developmentally defined, gain-of-function genetic screen with approximately 18 000 Arabidopsis thaliana activation-tagged lines, a mutant that maintained productive seed set post-severe heat stress during flowering. Genome walking indicated this phenotype was caused by the insertion of 35S enhancers adjacent to a nuclear localized transcription factor AtMYB68. Subsequent overexpression analysis confirmed that AtMYB68 was responsible for the reproductive heat tolerance of the mutant. Furthermore, these transgenic Arabidopsis plants exhibited enhanced abscisic acid sensitivity at and post-germination, reduced transpirational water loss during a drought treatment, and enhanced seed yield under combined heat and drought stress during flowering. Ectopic expression of AtMYB68 in Brassica napus driven either by 35S or by heat-inducible promoter recapitulated the enhanced reproductive heat stress and drought tolerance phenotypes observed in the transgenic Arabidopsis. The improvement to heat stress is likely due to enhanced pollen viability observed in the transgenic plants. More importantly, the transgenic canola showed significant yield advantages over the non-transgenic controls in multiple locations, multiple season field trials under various drought and heat stress conditions. Together these results suggest that AtMYB68 regulate plant stress tolerance at the most important yield determining stage of plant development, and is an effective target for crop yield protection under current global climate volatility.
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Affiliation(s)
- Mingde Deng
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Yang Wang
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Monika Kuzma
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Maryse Chalifoux
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Linda Tremblay
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Shujun Yang
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Jifeng Ying
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Angela Sample
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Hung-Mei Wang
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Rebecca Griffiths
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Tina Uchacz
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Xurong Tang
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Gang Tian
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Katelyn Joslin
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - David Dennis
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Peter McCourt
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
| | - Yafan Huang
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
| | - Jiangxin Wan
- Performance Plants Inc., 1287 Gardiners Road, Kingston, Ontario, K7P 3J6, Canada
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45
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Marwal A, Gaur RK. Host Plant Strategies to Combat Against Viruses Effector Proteins. Curr Genomics 2020; 21:401-410. [PMID: 33093803 PMCID: PMC7536791 DOI: 10.2174/1389202921999200712135131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/02/2023] Open
Abstract
Viruses are obligate parasites that exist in an inactive state until they enter the host body. Upon entry, viruses become active and start replicating by using the host cell machinery. All plant viruses can augment their transmission, thus powering their detrimental effects on the host plant. To diminish infection and diseases caused by viruses, the plant has a defence mechanism known as pathogenesis-related biochemicals, which are metabolites and proteins. Proteins that ultimately prevent pathogenic diseases are called R proteins. Several plant R genes (that confirm resistance) and avirulence protein (Avr) (pathogen Avr gene-encoded proteins [effector/elicitor proteins involved in pathogenicity]) molecules have been identified. The recognition of such a factor results in the plant defence mechanism. During plant viral infection, the replication and expression of a viral molecule lead to a series of a hypersensitive response (HR) and affect the host plant's immunity (pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity). Avr protein renders the host RNA silencing mechanism and its innate immunity, chiefly known as silencing suppressors towards the plant defensive machinery. This is a strong reply to the plant defensive machinery by harmful plant viruses. In this review, we describe the plant pathogen resistance protein and how these proteins regulate host immunity during plant-virus interactions. Furthermore, we have discussed regarding ribosome-inactivating proteins, ubiquitin proteasome system, translation repression (nuclear shuttle protein interacting kinase 1), DNA methylation, dominant resistance genes, and autophagy-mediated protein degradation, which are crucial in antiviral defences.
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Affiliation(s)
- Avinash Marwal
- 1Department of Biotechnology, Vigyan Bhawan - Block B, New Campus, Mohanlal Sukhadia University, Udaipur, Rajasthan - 313001, India; 2Department of Biotechnology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh - 273009, India
| | - Rajarshi Kumar Gaur
- 1Department of Biotechnology, Vigyan Bhawan - Block B, New Campus, Mohanlal Sukhadia University, Udaipur, Rajasthan - 313001, India; 2Department of Biotechnology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh - 273009, India
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46
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Li B. Identification of Genes Conferring Plant Salt Tolerance using GWAS: Current Success and Perspectives. PLANT & CELL PHYSIOLOGY 2020; 61:1419-1426. [PMID: 32484868 DOI: 10.1093/pcp/pcaa073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/25/2020] [Indexed: 06/11/2023]
Abstract
An understanding of the molecular mechanisms that underlie plant salt tolerance is important for both economic and scientific interests. Genome-wide association study (GWAS) is a promising approach to pinpoint genes that confer plant salt tolerance. With the advancement of supporting technology and methodology, GWAS has enabled the discovery of genes that play central roles in regulating plant salt tolerance in the past decade. Here, I highlight recent successful GWAS work in unveiling the molecular factors underlying plant salt tolerance and discuss the concerns and opportunities in conducting such experiments. It is anticipated that GWAS will be increasingly successful in the identification of key genes that are useful for crop improvement.
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Affiliation(s)
- Bo Li
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou 730000, China
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47
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Prinzenberg AE, Campos‐Dominguez L, Kruijer W, Harbinson J, Aarts MGM. Natural variation of photosynthetic efficiency in Arabidopsis thaliana accessions under low temperature conditions. PLANT, CELL & ENVIRONMENT 2020; 43:2000-2013. [PMID: 32495939 PMCID: PMC7497054 DOI: 10.1111/pce.13811] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 03/29/2020] [Accepted: 05/18/2020] [Indexed: 05/18/2023]
Abstract
Low, but non-freezing, temperatures have negative effects on plant growth and development. Despite some molecular signalling pathways being known, the mechanisms causing different responses among genotypes are still poorly understood. Photosynthesis is one of the processes that are affected by low temperatures. Using an automated phenotyping platform for chlorophyll fluorescence imaging the steady state quantum yield of photosystem II (PSII) electron transport (ΦPSII ) was measured and used to quantify the effect of moderately low temperature on a population of Arabidopsis thaliana natural accessions. Observations were made over the course of several weeks in standard and low temperature conditions and a strong decrease in ΦPSII upon the cold treatment was found. A genome wide association study identified several quantitative trait loci (QTLs) that are associated with changes in ΦPSII in low temperature. One candidate for a cold specific QTL was validated with a mutant analysis to be one of the genes that is likely involved in the PSII response to the cold treatment. The gene encodes the PSII associated protein PSB27 which has already been implicated in the adaptation to fluctuating light.
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Affiliation(s)
- Aina E. Prinzenberg
- Horticulture and Product PhysiologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Plant BreedingWageningen University and ResearchPO Box 386Wageningen6700 AJThe Netherlands
| | - Lucia Campos‐Dominguez
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUnited Kingdom
| | - Willem Kruijer
- BiometrisWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
| | - Jeremy Harbinson
- Horticulture and Product PhysiologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Laboratory of BiophysicsWageningen University and ResearchWageningenThe Netherlands
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
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Elfstrand M, Baison J, Lundén K, Zhou L, Vos I, Capador HD, Åslund MS, Chen Z, Chaudhary R, Olson Å, Wu HX, Karlsson B, Stenlid J, García-Gil MR. Association genetics identifies a specifically regulated Norway spruce laccase gene, PaLAC5, linked to Heterobasidion parviporum resistance. PLANT, CELL & ENVIRONMENT 2020; 43:1779-1791. [PMID: 32276288 DOI: 10.1111/pce.13768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 03/21/2020] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
It is important to improve the understanding of the interactions between the trees and pathogens and integrate this knowledge about disease resistance into tree breeding programs. The conifer Norway spruce (Picea abies) is an important species for the forest industry in Europe. Its major pathogen is Heterobasidion parviporum, causing stem and root rot. In this study, we identified 11 Norway spruce QTLs (Quantitative trait loci) that correlate with variation in resistance to H. parviporum in a population of 466 trees by association genetics. Individual QTLs explained between 2.1 and 5.2% of the phenotypic variance. The expression of candidate genes associated with the QTLs was analysed in silico and in response to H. parviporum hypothesizing that (a) candidate genes linked to control of fungal sapwood growth are more commonly expressed in sapwood, and; (b) candidate genes associated with induced defences are respond to H. parviporum inoculation. The Norway spruce laccase PaLAC5 associated with control of lesion length development is likely to be involved in the induced defences. Expression analyses showed that PaLAC5 responds specifically and strongly in close proximity to the H. parviporum inoculation. Thus, PaLAC5 may be associated with the lignosuberized boundary zone formation in bark adjacent to the inoculation site.
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Affiliation(s)
- Malin Elfstrand
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - John Baison
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Karl Lundén
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Linghua Zhou
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - Hernan Dario Capador
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Matilda Stein Åslund
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Zhiqiang Chen
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Rajiv Chaudhary
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Åke Olson
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Harry X Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | - Jan Stenlid
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - María Rosario García-Gil
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Genetic Basis of Maize Resistance to Multiple Insect Pests: Integrated Genome-Wide Comparative Mapping and Candidate Gene Prioritization. Genes (Basel) 2020; 11:genes11060689. [PMID: 32599710 PMCID: PMC7349181 DOI: 10.3390/genes11060689] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 01/01/2023] Open
Abstract
Several species of herbivores feed on maize in field and storage setups, making the development of multiple insect resistance a critical breeding target. In this study, an association mapping panel of 341 tropical maize lines was evaluated in three field environments for resistance to fall armyworm (FAW), whilst bulked grains were subjected to a maize weevil (MW) bioassay and genotyped with Diversity Array Technology's single nucleotide polymorphisms (SNPs) markers. A multi-locus genome-wide association study (GWAS) revealed 62 quantitative trait nucleotides (QTNs) associated with FAW and MW resistance traits on all 10 maize chromosomes, of which, 47 and 31 were discovered at stringent Bonferroni genome-wide significance levels of 0.05 and 0.01, respectively, and located within or close to multiple insect resistance genomic regions (MIRGRs) concerning FAW, SB, and MW. Sixteen QTNs influenced multiple traits, of which, six were associated with resistance to both FAW and MW, suggesting a pleiotropic genetic control. Functional prioritization of candidate genes (CGs) located within 10-30 kb of the QTNs revealed 64 putative GWAS-based CGs (GbCGs) showing evidence of involvement in plant defense mechanisms. Only one GbCG was associated with each of the five of the six combined resistance QTNs, thus reinforcing the pleiotropy hypothesis. In addition, through in silico co-functional network inferences, an additional 107 network-based CGs (NbCGs), biologically connected to the 64 GbCGs, and differentially expressed under biotic or abiotic stress, were revealed within MIRGRs. The provided multiple insect resistance physical map should contribute to the development of combined insect resistance in maize.
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50
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Arouisse B, Korte A, van Eeuwijk F, Kruijer W. Imputation of 3 million SNPs in the Arabidopsis regional mapping population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:872-882. [PMID: 31856318 PMCID: PMC7318218 DOI: 10.1111/tpj.14659] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/02/2019] [Accepted: 12/05/2019] [Indexed: 06/01/2023]
Abstract
Natural variation has become a prime resource to identify genetic variants that contribute to phenotypic variation. The regional mapping (RegMap) population is one of the most important populations for studying natural variation in Arabidopsis thaliana, and has been used in a large number of association studies and in studies on climatic adaptation. However, only 413 RegMap accessions have been completely sequenced, as part of the 1001 Genomes (1001G) Project, while the remaining 894 accessions have only been genotyped with the Affymetrix 250k chip. As a consequence, most association studies involving the RegMap are either restricted to the sequenced accessions, reducing power, or rely on a limited set of SNPs. Here we impute millions of SNPs to the 894 accessions that are exclusive to the RegMap, using the 1135 accessions of the 1001G Project as the reference panel. We assess imputation accuracy using a novel cross-validation scheme, which we show provides a more reliable measure of accuracy than existing methods. After filtering out low accuracy SNPs, we obtain high-quality genotypic information for 2029 accessions and 3 million markers. To illustrate the benefits of these imputed data, we reconducted genome-wide association studies on five stress-related traits and could identify novel candidate genes.
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Affiliation(s)
- Bader Arouisse
- BiometrisWageningen University & ResearchWageningenNetherlands
| | - Arthur Korte
- Centre for Computational and Theoretical BiologyUniversity of WürzburgWürzburgGermany
| | | | - Willem Kruijer
- BiometrisWageningen University & ResearchWageningenNetherlands
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