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Oliveira-Garcia E, Budot BO, Manangkil J, Lana FD, Angira B, Famoso A, Jia Y. An Efficient Method for Screening Rice Breeding Lines Against Races of Magnaporthe oryzae. PLANT DISEASE 2024; 108:1179-1187. [PMID: 37807096 DOI: 10.1094/pdis-05-23-0922-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Rice blast, caused by Magnaporthe oryzae, is the most destructive rice disease worldwide. The disease symptoms are usually expressed on the leaf and panicle. The leaf disease intensity in controlled environmental conditions is frequently quantified using a 0 to 5 scale, where 0 represents the absence of symptoms, and 5 represents large eyespot lesions. However, this scale restricts the qualitative classification of the varieties into intermediate resistant and susceptible categories. Here, we develop a 0 to 6 scale for blast disease that allows proper assignment of rice breeding lines and varieties into six resistance levels (highly resistant, resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible). We evaluated 40 common rice varieties against four major blast races (IB1, IB17, IB49, and IE1-K). Varieties carrying the Pi-ta gene were either highly resistant, resistant, or moderately resistant to IB17. The IE1-K race was able to break Pi-ta-mediated resistance of the rice varieties. The Pi-z gene conferred resistance to the IB17 and IE1-K races. The varieties M201, Cheniere, and Frontier were highly susceptible (score 6; 100% disease) to the race IE1-K. Moreover, varieties that were resistant or susceptible to all four blast races also showed similar levels of resistance/susceptibility to blast disease in the field. Taken together, our data proved that the 0 to 6 blast scale can efficiently determine the resistance levels of rice varieties against major blast races. This robust method will assist rice breeding programs to incorporate durable resistance against major and emerging blast races.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Ely Oliveira-Garcia
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Bernard Orense Budot
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
- University of the Philippines Los Baños, Los Baños, Philippines
| | - Jennifer Manangkil
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Felipe Dala Lana
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Brijesh Angira
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Yulin Jia
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR 72160, U.S.A
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Singh D, Mathur S, Ranjan R. Pattern recognition receptors as potential therapeutic targets for developing immunological engineered plants. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 140:525-555. [PMID: 38762279 DOI: 10.1016/bs.apcsb.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
There is an urgent need to combat pathogen infestations in crop plants to ensure food security worldwide. To counter this, plants have developed innate immunity mediated by Pattern Recognition Receptors (PRRs) that recognize pathogen-associated molecular patterns (PAMPs) and damage- associated molecular patterns (DAMPs). PRRs activate Pattern-Triggered Immunity (PTI), a defence mechanism involving intricate cell-surface and intracellular receptors. The diverse ligand-binding ectodomains of PRRs, including leucine-rich repeats (LRRs) and lectin domains, facilitate the recognition of MAMPs and DAMPs. Pathogen resistance is mediated by a variety of PTI responses, including membrane depolarization, ROS production, and the induction of defence genes. An integral part of intracellular immunity is the Nucleotide-binding Oligomerization Domain, Leucine-rich Repeat proteins (NLRs) which recognize and respond to effectors in a potent manner. Enhanced understanding of PRRs, their ligands, and downstream signalling pathways has contributed to the identification of potential targets for genetically modified plants. By transferring PRRs across plant species, it is possible to create broad-spectrum resistance, potentially offering innovative solutions for plant protection and global food security. The purpose of this chapter is to provide an update on PRRs involved in disease resistance, clarify the mechanisms by which PRRs recognize ligands to form active receptor complexes and present various applications of PRRs and PTI in disease resistance management for plants.
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Affiliation(s)
- Deeksha Singh
- Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra-282005, India
| | - Shivangi Mathur
- Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra-282005, India
| | - Rajiv Ranjan
- Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra-282005, India.
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Lee JH, Lee U, Yoo JH, Lee TS, Jung JH, Kim HS. AraDQ: an automated digital phenotyping software for quantifying disease symptoms of flood-inoculated Arabidopsis seedlings. PLANT METHODS 2024; 20:44. [PMID: 38493119 PMCID: PMC10943777 DOI: 10.1186/s13007-024-01171-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/09/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Plant scientists have largely relied on pathogen growth assays and/or transcript analysis of stress-responsive genes for quantification of disease severity and susceptibility. These methods are destructive to plants, labor-intensive, and time-consuming, thereby limiting their application in real-time, large-scale studies. Image-based plant phenotyping is an alternative approach that enables automated measurement of various symptoms. However, most of the currently available plant image analysis tools require specific hardware platform and vendor specific software packages, and thus, are not suited for researchers who are not primarily focused on plant phenotyping. In this study, we aimed to develop a digital phenotyping tool to enhance the speed, accuracy, and reliability of disease quantification in Arabidopsis. RESULTS Here, we present the Arabidopsis Disease Quantification (AraDQ) image analysis tool for examination of flood-inoculated Arabidopsis seedlings grown on plates containing plant growth media. It is a cross-platform application program with a user-friendly graphical interface that contains highly accurate deep neural networks for object detection and segmentation. The only prerequisite is that the input image should contain a fixed-sized 24-color balance card placed next to the objects of interest on a white background to ensure reliable and reproducible results, regardless of the image acquisition method. The image processing pipeline automatically calculates 10 different colors and morphological parameters for individual seedlings in the given image, and disease-associated phenotypic changes can be easily assessed by comparing plant images captured before and after infection. We conducted two case studies involving bacterial and plant mutants with reduced virulence and disease resistance capabilities, respectively, and thereby demonstrated that AraDQ can capture subtle changes in plant color and morphology with a high level of sensitivity. CONCLUSIONS AraDQ offers a simple, fast, and accurate approach for image-based quantification of plant disease symptoms using various parameters. Its fully automated pipeline neither requires prior image processing nor costly hardware setups, allowing easy implementation of the software by researchers interested in digital phenotyping of diseased plants.
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Grants
- Grant No. 2022R1C1C1012137 The National Research Foundation of Korea
- Grant No. 421002-04) The Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET) and Korea Smart Farm R&D (KosFarm) through the Smart Farm Innovation Technology Development Program, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) and Ministry of Science and ICT (MSIT), Rural Development Administration (RDA)
- The Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET) and Korea Smart Farm R&D (KosFarm) through the Smart Farm Innovation Technology Development Program, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) and Ministry of Science and ICT (MSIT), Rural Development Administration (RDA)
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Affiliation(s)
- Jae Hoon Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Unseok Lee
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Ji Hye Yoo
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Taek Sung Lee
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Je Hyeong Jung
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Hyoung Seok Kim
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea.
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Mohaimin AZ, Krishnamoorthy S, Shivanand P. A critical review on bioaerosols-dispersal of crop pathogenic microorganisms and their impact on crop yield. Braz J Microbiol 2024; 55:587-628. [PMID: 38001398 PMCID: PMC10920616 DOI: 10.1007/s42770-023-01179-9] [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: 11/25/2022] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Bioaerosols are potential sources of pathogenic microorganisms that can cause devastating outbreaks of global crop diseases. Various microorganisms, insects and viroids are known to cause severe crop diseases impeding global agro-economy. Such losses threaten global food security, as it is estimated that almost 821 million people are underfed due to global crisis in food production. It is estimated that global population would reach 10 billion by 2050. Hence, it is imperative to substantially increase global food production to about 60% more than the existing levels. To meet the increasing demand, it is essential to control crop diseases and increase yield. Better understanding of the dispersive nature of bioaerosols, seasonal variations, regional diversity and load would enable in formulating improved strategies to control disease severity, onset and spread. Further, insights on regional and global bioaerosol composition and dissemination would help in predicting and preventing endemic and epidemic outbreaks of crop diseases. Advanced knowledge of the factors influencing disease onset and progress, mechanism of pathogen attachment and penetration, dispersal of pathogens, life cycle and the mode of infection, aid the development and implementation of species-specific and region-specific preventive strategies to control crop diseases. Intriguingly, development of R gene-mediated resistant varieties has shown promising results in controlling crop diseases. Forthcoming studies on the development of an appropriately stacked R gene with a wide range of resistance to crop diseases would enable proper management and yield. The article reviews various aspects of pathogenic bioaerosols, pathogen invasion and infestation, crop diseases and yield.
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Affiliation(s)
- Abdul Zul'Adly Mohaimin
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Sarayu Krishnamoorthy
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam
| | - Pooja Shivanand
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Bandar Seri Begawan, BE1410, Brunei Darussalam.
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Vogel D, Hills P, Moore JP. Strigolactones GR-24 and Nijmegen Applications Result in Reduced Susceptibility of Tobacco and Grapevine Plantlets to Botrytis cinerea Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:3202. [PMID: 37765366 PMCID: PMC10535315 DOI: 10.3390/plants12183202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Priming agents are plant defence-inducing compounds which can prompt a state of protection but may also aid in plant growth and interactions with beneficial microbes. The synthetic strigolactones (±)-GR24 and Nijmegen-1 were evaluated as potential priming agents for induced resistance against Botrytis cinerea in tobacco and grapevine plants. The growth and stress response profiles of B. cinerea to strigolactones were also investigated. Soil drench treatment with strigolactones induced resistance in greenhouse-grown tobacco plants and restricted lesion development. The mode of action appeared to function by priming redox-associated compounds to produce an anti-oxidant protective response for limiting the infection. The results obtained in the in vitro assays mirrored that of the greenhouse-grown plants. Exposure of B. cinerea to the strigolactones resulted in increased hyphal branching, with (±)-GR24 stimulating a stronger effect than Nijmegen-1 by affecting colony diameter and radial growth. An oxidative stress response was observed, with B. cinerea exhibiting increased ROS and SOD levels when grown with strigolactones. This study identified the application of strigolactones as potential priming agents to induce disease resistance in both tobacco and grapevine plants. In addition, strigolactones may alter the ROS homeostasis of B. cinerea, resulting in both morphological and physiological changes, thereby reducing virulence.
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Affiliation(s)
- Dominic Vogel
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Paul Hills
- Institute for Plant Biotechnology, Department of Genetics, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7602, South Africa
| | - John P Moore
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch 7600, South Africa
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Chen L, Duan L, Sun M, Yang Z, Li H, Hu K, Yang H, Liu L. Current trends and insights on EMS mutagenesis application to studies on plant abiotic stress tolerance and development. FRONTIERS IN PLANT SCIENCE 2023; 13:1052569. [PMID: 36684716 PMCID: PMC9846265 DOI: 10.3389/fpls.2022.1052569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Ethyl methanesulfonate (EMS)-induced mutagenesis is a powerful tool to generate genetic resource for identifying untapped genes and characterizing the function of genes to understand the molecular basis of important agronomic traits. This review focuses on application of contemporary EMS mutagenesis in the field of plant development and abiotic stress tolerance research, with particular focuses on reviewing the mutation types, mutagenesis site, mutagen concentration, mutagenesis duration, the identification and characterization of mutations responsible for altered stress tolerance responses. The application of EMS mutation breeding combined with genetic engineering in the future plant breeding and fundamental research was also discussed. The collective information in this review will provide good insight on how EMS mutagenesis is efficiently applied to improve abiotic stress tolerance of crops with the utilization of Next-generation sequencing (NGS) for mutation identification.
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Affiliation(s)
- Liuzhu Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Liu Duan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Minghui Sun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Zhuo Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Hongyu Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Keming Hu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province/Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Yangzhou University, Yangzhou, China
| | - Hong Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
| | - Li Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, China
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Saxena H, Kulshreshtha A, Agarwal A, Kumar A, Singh N, Jain CK. LDRGDb - Legumes disease resistance genes database. FRONTIERS IN PLANT SCIENCE 2023; 14:1143111. [PMID: 37143876 PMCID: PMC10151526 DOI: 10.3389/fpls.2023.1143111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/22/2023] [Indexed: 05/06/2023]
Abstract
Legumes comprise one of the world's largest, most diverse, and economically important plant families, known for their nutritional and medicinal benefits. Legumes are susceptible to a wide range of diseases, similar to other agricultural crops. Diseases have a considerable impact on the production of legume crop species, resulting in large yield losses worldwide. Due to continuous interactions between plants and their pathogens in the environment and the evolution of new pathogens under high selection pressure; disease resistant genes emerge in plant cultivars in the field against those pathogens or disease. Thus, disease resistant genes play critical roles in plant resistance responses, and their discovery and subsequent use in breeding programmes aid in reducing yield loss. The genomic era, with its high-throughput and low-cost genomic tools, has revolutionised our understanding of the complex interactions between legumes and pathogens, resulting in the identification of several critical participants in both the resistant and susceptible relationships. However, a substantial amount of existing information about numerous legume species has been disseminated as text or is preserved across fractions in different databases, posing a challenge for researchers. As a result, the range, scope, and complexity of these resources pose challenges to those who manage and use them. Therefore, there is an urgent need to develop tools and a single conjugate database to manage genetic information for the world's plant genetic resources, allowing for the rapid incorporation of essential resistance genes into breeding strategies. Here, developed the first comprehensive database of disease resistance genes named as LDRGDb - LEGUMES DISEASE RESISTANCE GENES DATABASE comprises 10 legumes [Pigeon pea (Cajanus cajan), Chickpea (Cicer arietinum), Soybean (Glycine max), Lentil (Lens culinaris), Alfalfa (Medicago sativa), Barrelclover (Medicago truncatula), Common bean (Phaseolus vulgaris), Pea (Pisum sativum),Faba bean (Vicia faba), and Cowpea (Vigna unguiculata)]. The LDRGDb is a user-friendly database developed by integrating a variety of tools and software that combine knowledge about resistant genes, QTLs, and their loci, with proteomics, pathway interactions, and genomics (https://ldrgdb.in/).
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Affiliation(s)
- Harshita Saxena
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Aishani Kulshreshtha
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Avinav Agarwal
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Anuj Kumar
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Nisha Singh
- Department of Bioinformatics, Gujarat Biotechnology University, Gandhinagar, India
- *Correspondence: Chakresh Kumar Jain, ; Nisha Singh,
| | - Chakresh Kumar Jain
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
- *Correspondence: Chakresh Kumar Jain, ; Nisha Singh,
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Li M, Guo B, Liu F, Fu ZQ. Cross-kingdom vitamin B5 biosynthesis and cyst nematode susceptibility. Trends Parasitol 2023; 39:7-9. [PMID: 36443162 DOI: 10.1016/j.pt.2022.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
Abstract
Vitamin deficiencies are known to cause disorders in human beings. Siddique et al. discovered that vitamin B5 biosynthesis in cyst nematodes requires steps in their host plants. Disruption of an Arabidopsis thaliana 'susceptibility gene', which is involved in the production of vitamin B5 precursors, results in reduced parasitism.
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Affiliation(s)
- Min Li
- China-USA Citrus Huanglongbing Joint Laboratory (A Joint Laboratory of The University of Florida's Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Baodian Guo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China; School of Plant Protection, Hainan University, Haikou, Hainan 570228, China.
| | - Zheng Qing Fu
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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Abstract
In Darwin's and Mendel's times, researchers investigated a wealth of organisms, chosen to solve particular problems for which they seemed especially well suited. Later, a focus on a few organisms, which are accessible to systematic genetic investigations, resulted in larger repertoires of methods and applications in these few species. Genetic animal model organisms with large research communities are the nematode Caenorhabditis elegans, the fly Drosophila melanogaster, the zebrafish Danio rerio, and the mouse Mus musculus. Due to their specific strengths, these model organisms have their strongest impacts in rather different areas of biology. C. elegans is unbeatable in the analysis of cell-to-cell contacts by saturation mutagenesis, as worms can be grown very fast in very high numbers. In Drosophila, a rich pattern is generated in the embryo as well as in adults that is used to unravel the underlying mechanisms of morphogenesis. The transparent larvae of zebrafish are uniquely suited to study organ development in a vertebrate, and the superb versatility of reverse genetics in the mouse made it the model organism to study human physiology and diseases. The combination of these models allows the in-depth genetic analysis of many fundamental biological processes using a plethora of different methods, finally providing many specific approaches to combat human diseases. The plant model Arabidopsis thaliana provides an understanding of many aspects of plant biology that might ultimately be useful for breeding crops.
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Cheng C, Zhong Y, Wang B, Zhang Y, Wu H, Jiang N, Wu B, Lv Y, Jiang B. The Upregulated Expression of the Citrus RIN4 Gene in HLB Diseased Citrus Aids Candidatus Liberibacter Asiaticus Infection. Int J Mol Sci 2022; 23:ijms23136971. [PMID: 35805971 PMCID: PMC9266415 DOI: 10.3390/ijms23136971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 02/01/2023] Open
Abstract
The citrus industry has been threatened by Huanglongbing (HLB) for over a century. Here, an HLB-induced Arabidopsis RPM1-interacting protein 4 (RIN4) homologous gene was cloned from Citrus clementina, and its characteristics and function were analyzed to determine its role during citrus–Candidatus Liberibacter asiaticus (CLas) interactions. Quantitative real-time PCR showed that RIN4 was expressed in roots, stems, leaves and flowers, with the greatest expression level in leaves. Its expression was suppressed by gibberellic acid, indole-3-acetic acid, salicylic acid and jasmonic acid treatments, but was induced by abscisic acid and salt treatments, as well as wounding. The transient expression of a RIN4-GFP showed that RIN4 was localized in the cell membrane. RIN4-overexpressing transgenic C. maxima cv. ‘Shatianyou’ plants were obtained, and some transgenic plants showed greater sensitivity to CLas infection and earlier HLB symptoms appearance than non-transgenic controls. Results obtained in this study indicated that the upregulated expression of RIN4 in HLB diseased citrus may aid CLas infection.
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Affiliation(s)
- Chunzhen Cheng
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (C.C.); (B.W.); (Y.Z.); (H.W.)
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (N.J.); (B.W.); (B.J.)
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China;
| | - Yun Zhong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (N.J.); (B.W.); (B.J.)
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China;
- Correspondence:
| | - Bin Wang
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (C.C.); (B.W.); (Y.Z.); (H.W.)
| | - Yongyan Zhang
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (C.C.); (B.W.); (Y.Z.); (H.W.)
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (N.J.); (B.W.); (B.J.)
| | - Huan Wu
- College of Horticulture, Shanxi Agricultural University, Jinzhong 030801, China; (C.C.); (B.W.); (Y.Z.); (H.W.)
| | - Nonghui Jiang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (N.J.); (B.W.); (B.J.)
| | - Bo Wu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (N.J.); (B.W.); (B.J.)
| | - Yuanda Lv
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China;
- Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Bo Jiang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (N.J.); (B.W.); (B.J.)
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Omayio DO, Ndombi ST. Tool for determining levels and classifying; host plant resistance, tolerance to stress, vigour and pathogen virulence in plants. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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12
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Morphological characteristics of pollen from triploid watermelon and its fate on stigmas in a hybrid crop production system. Sci Rep 2022; 12:3222. [PMID: 35217699 PMCID: PMC8881623 DOI: 10.1038/s41598-022-06297-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/13/2022] [Indexed: 12/02/2022] Open
Abstract
Hybrid crop production is more reliant on pollinators compared to open-pollinated crops because they require cross-pollination between a male-fertile and a male-sterile line. Little is known about how stigma receipt of pollen from male-sterile genotypes affects reproduction in hybrids. Non-viable and non-compatible pollen cannot fertilise plant ovules, but may still interfere with pollination success. Here we used seedless watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) as a model hybrid plant, to evaluate the morphology, physiology, and movement of pollen from inter-planted genotypes (diploids and triploids). We found that pollen from triploids (‘Exclamation’ and ‘Royal Armada’) and diploids (‘SP-6’, ‘Summer Flavor 800’, and ‘Tiger’) was visually distinguishable. Pollen in triploids had more deformities (42.4–46%), tetrads (43–44%), and abnormal growth of callose plugs in pollen tubes. The amount of pollen in triploids to germinate on stigmas was low (8 ± 3%), and few pollen grains produced pollen tubes (6.5 ± 2%). Still, contrary to previous reports our results suggest that some viable pollen grains are produced by triploid watermelons. However, whilst honey bees can collect and deposit pollen from triploids onto stigmas, its effect on hybrid watermelon reproduction is likely to be minimal due to its low germination rate.
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Marwein R, Singh S, Maharana J, Kumar S, Arunkumar KP, Velmurugan N, Chikkaputtaiah C. Transcriptome-wide analysis of North-East Indian rice cultivars in response to Bipolaris oryzae infection revealed the importance of early response to the pathogen in suppressing the disease progression. Gene 2022; 809:146049. [PMID: 34743920 DOI: 10.1016/j.gene.2021.146049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022]
Abstract
Brown spot disease (BSD) of rice (Oryza sativa L.) caused by Bipolaris oryzae is one of the major and neglected fungal diseases worldwide affecting rice production. Despite its significance, very limited knowledge on genetics and genomics of rice in response to B. oryzae available. Our study firstly identified moderately resistant (Gitesh) and susceptible (Shahsarang) North-East Indian rice cultivars in response to a native Bipolaris oryzae isolate BO1. Secondly, a systematic comparative RNA seq was performed for both cultivars at four different time points viz. 12, 24, 48, and 72 hours post infestation (hpi). Differential gene expression analysis revealed the importance of early response to the pathogen in suppressing disease progression. The pathogen negatively regulates the expression of photosynthetic-related genes at early stages in both cultivars. Of the cell wall modification enzymes, cellulose synthase and callose synthase are important for signal transduction and defense. Cell wall receptors OsLYP6, OsWAK80 might positively and OsWAK25 negatively regulate disease resistance. Jasmonic acid and/or abscisic acid signaling pathways are presumably involved in disease resistance, whereas salicylic acid pathway, and an ethylene response gene OsEBP-89 in promoting disease. Surprisingly, pathogenesis-related proteins showed no antimicrobial impact on the pathogen. Additionally, transcription factors OsWRKY62 and OsWRKY45 together might negatively regulate resistance to the pathogen. Taken together, our study has identified and provide key regulatory genes involved in response to B. oryzae which serve as potential resources for functional genetic analysis to develop genetic tolerance to BSD of rice.
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Affiliation(s)
- Riwandahun Marwein
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Sanjay Singh
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India; Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Sanjeev Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Kallare P Arunkumar
- Central Muga Eri Research and Training Institute (CMER&TI), Lahdoigarh, Jorhat 785700, Assam, India
| | - Natarajan Velmurugan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India; Biological Sciences Division, Branch Laboratory-Itanagar, CSIR-NEIST, Naharlagun 791110, Arunachal Pradesh, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat 785006, Assam, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India.
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14
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Understanding the Various Strategies for the Management of Fungal Pathogens in Crop Plants in the Current Scenario. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Konovalova LN, Strelnikova SR, Zlobin NE, Kharchenko PN, Komakhin RA. Efficiency of Transient Expression in Protoplasts of Various Potato Cultivars. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821070048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Mores A, Borrelli GM, Laidò G, Petruzzino G, Pecchioni N, Amoroso LGM, Desiderio F, Mazzucotelli E, Mastrangelo AM, Marone D. Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies. Int J Mol Sci 2021; 22:5423. [PMID: 34063853 PMCID: PMC8196592 DOI: 10.3390/ijms22115423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 05/15/2021] [Indexed: 12/16/2022] Open
Abstract
Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.
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Affiliation(s)
- Antonia Mores
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Grazia Maria Borrelli
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | | | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (F.D.); (E.M.)
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy; (A.M.); (G.M.B.); (G.L.); (G.P.); (N.P.); (A.M.M.)
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17
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Pardal AJ, Piquerez SJM, Dominguez-Ferreras A, Frungillo L, Mastorakis E, Reilly E, Latrasse D, Concia L, Gimenez-Ibanez S, Spoel SH, Benhamed M, Ntoukakis V. Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis. PLoS Pathog 2021; 17:e1009572. [PMID: 34015058 PMCID: PMC8171942 DOI: 10.1371/journal.ppat.1009572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 06/02/2021] [Accepted: 04/19/2021] [Indexed: 01/23/2023] Open
Abstract
Perception of microbes by plants leads to dynamic reprogramming of the transcriptome, which is essential for plant health. The appropriate amplitude of this transcriptional response can be regulated at multiple levels, including chromatin. However, the mechanisms underlying the interplay between chromatin remodeling and transcription dynamics upon activation of plant immunity remain poorly understood. Here, we present evidence that activation of plant immunity by bacteria leads to nucleosome repositioning, which correlates with altered transcription. Nucleosome remodeling follows distinct patterns of nucleosome repositioning at different loci. Using a reverse genetic screen, we identify multiple chromatin remodeling ATPases with previously undescribed roles in immunity, including EMBRYO SAC DEVELOPMENT ARREST 16, EDA16. Functional characterization of the immune-inducible chromatin remodeling ATPase EDA16 revealed a mechanism to negatively regulate immunity activation and limit changes in redox homeostasis. Our transcriptomic data combined with MNase-seq data for EDA16 functional knock-out and over-expressor mutants show that EDA16 selectively regulates a defined subset of genes involved in redox signaling through nucleosome repositioning. Thus, collectively, chromatin remodeling ATPases fine-tune immune responses and provide a previously uncharacterized mechanism of immune regulation.
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Affiliation(s)
- Alonso J. Pardal
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sophie J. M. Piquerez
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | | | - Lucas Frungillo
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Emma Reilly
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Selena Gimenez-Ibanez
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, Spain
| | - Steven H. Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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18
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Zhang P, Berardini TZ, Ebert D, Li Q, Mi H, Muruganujan A, Prithvi T, Reiser L, Sawant S, Thomas PD, Huala E. PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference. PLANT DIRECT 2020; 4:e00293. [PMID: 33392435 PMCID: PMC7773024 DOI: 10.1002/pld3.293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 05/22/2023]
Abstract
We aim to enable the accurate and efficient transfer of knowledge about gene function gained from Arabidopsis thaliana and other model organisms to other plant species. This knowledge transfer is frequently challenging in plants due to duplications of individual genes and whole genomes in plant lineages. Such duplications result in complex evolutionary relationships between related genes, which may have similar sequences but highly divergent functions. In such cases, functional inference requires more than a simple sequence similarity calculation. We have developed an online resource, PhyloGenes (phylogenes.org), that displays precomputed phylogenetic trees for plant gene families along with experimentally validated function information for individual genes within the families. A total of 40 plant genomes and 10 non-plant model organisms are represented in over 8,000 gene families. Evolutionary events such as speciation and duplication are clearly labeled on gene trees to distinguish orthologs from paralogs. Nearly 6,000 families have at least one member with an experimentally supported annotation to a Gene Ontology (GO) molecular function or biological process term. By displaying experimentally validated gene functions associated to individual genes within a tree, PhyloGenes enables functional inference for genes of uncharacterized function, based on their evolutionary relationships to experimentally studied genes, in a visually traceable manner. For the many families containing genes that have evolved to perform different functions, PhyloGenes facilitates the use of evolutionary history to determine the most likely function of genes that have not been experimentally characterized. Future work will enrich the resource by incorporating additional gene function datasets such as plant gene expression atlas data.
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Affiliation(s)
| | | | - Dustin Ebert
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Qian Li
- Phoenix BioinformaticsFremontCAUSA
| | - Huaiyu Mi
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Anushya Muruganujan
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | | | | | | | - Paul D. Thomas
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
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19
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Lukan T, Pompe‐Novak M, Baebler Š, Tušek‐Žnidarič M, Kladnik A, Križnik M, Blejec A, Zagorščak M, Stare K, Dušak B, Coll A, Pollmann S, Morgiewicz K, Hennig J, Gruden K. Precision transcriptomics of viral foci reveals the spatial regulation of immune-signaling genes and identifies RBOHD as an important player in the incompatible interaction between potato virus Y and potato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:645-661. [PMID: 32772469 PMCID: PMC7692943 DOI: 10.1111/tpj.14953] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/21/2020] [Indexed: 05/18/2023]
Abstract
Whereas the activation of resistance (R) proteins has been intensively studied, the downstream signaling mechanisms leading to the restriction of the pathogen remain mostly unknown. We studied the immunity network response conditioned by the potato Ny-1 gene against potato virus Y. We analyzed the processes in the cell death zone and surrounding tissue on the biochemical and gene expression levels in order to reveal the spatiotemporal regulation of the immune response. We show that the transcriptional response in the cell death zone and surrounding tissue is dependent on salicylic acid (SA). For some genes the spatiotemporal regulation is completely lost in the SA-deficient line, whereas other genes show a different response, indicating multiple connections between hormonal signaling modules. The induction of NADPH oxidase RBOHD expression occurs specifically on the lesion border during the resistance response. In plants with silenced RBOHD, the functionality of the resistance response is perturbed and the spread of the virus is not arrested at the site of infection. RBOHD is required for the spatial accumulation of SA, and conversely RBOHD is under the transcriptional regulation of SA. Using spatially resolved RNA-seq, we also identified spatial regulation of an UDP-glucosyltransferase, another component in feedback activation of SA biosynthesis, thus deciphering a novel aspect of resistance signaling.
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Affiliation(s)
- Tjaša Lukan
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | | | - Špela Baebler
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | | | - Aleš Kladnik
- Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Maja Križnik
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Andrej Blejec
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Maja Zagorščak
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Katja Stare
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Barbara Dušak
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Anna Coll
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
| | - Stephan Pollmann
- Centre for Plant Biotechnology and GenomicsCampus de Montegancedo Crta M‐40, Km 38Pozuelo de Alarcón, Madrid28223UPM–INIA Spain
| | - Karolina Morgiewicz
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5aWarsaw02‐106Poland
| | - Jacek Hennig
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesPawińskiego 5aWarsaw02‐106Poland
| | - Kristina Gruden
- National Institute of BiologyVečna pot 111Ljubljana1000Slovenia
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20
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Bentham AR, De la Concepcion JC, Mukhi N, Zdrzałek R, Draeger M, Gorenkin D, Hughes RK, Banfield MJ. A molecular roadmap to the plant immune system. J Biol Chem 2020; 295:14916-14935. [PMID: 32816993 PMCID: PMC7606695 DOI: 10.1074/jbc.rev120.010852] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/17/2020] [Indexed: 12/15/2022] Open
Abstract
Plant diseases caused by pathogens and pests are a constant threat to global food security. Direct crop losses and the measures used to control disease (e.g. application of pesticides) have significant agricultural, economic, and societal impacts. Therefore, it is essential that we understand the molecular mechanisms of the plant immune system, a system that allows plants to resist attack from a wide variety of organisms ranging from viruses to insects. Here, we provide a roadmap to plant immunity, with a focus on cell-surface and intracellular immune receptors. We describe how these receptors perceive signatures of pathogens and pests and initiate immune pathways. We merge existing concepts with new insights gained from recent breakthroughs on the structure and function of plant immune receptors, which have generated a shift in our understanding of cell-surface and intracellular immunity and the interplay between the two. Finally, we use our current understanding of plant immunity as context to discuss the potential of engineering the plant immune system with the aim of bolstering plant defenses against disease.
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Affiliation(s)
- Adam R Bentham
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | | | - Nitika Mukhi
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Rafał Zdrzałek
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Markus Draeger
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Danylo Gorenkin
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Richard K Hughes
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom.
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21
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Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10091255] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.
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22
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Heterologous Expression of the Constitutive Disease Resistance 2 and 8 Genes from Poncirus trifoliata Restored the Hypersensitive Response and Resistance of Arabidopsis cdr1 Mutant to Bacterial Pathogen Pseudomonas syringae. PLANTS 2020; 9:plants9070821. [PMID: 32629813 PMCID: PMC7412121 DOI: 10.3390/plants9070821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/19/2020] [Accepted: 06/29/2020] [Indexed: 01/23/2023]
Abstract
Huanglongbing (HLB), also known as citrus greening, is the most destructive disease of citrus worldwide. In the United States, this disease is associated with a phloem-restricted bacterium, Candidatus Liberibacter asiaticus. Commercial citrus cultivars are susceptible to HLB, but Poncirus trifoliata, a close relative of Citrus, is highly tolerant of HLB. Isolating P. trifoliata gene(s) controlling its HLB tolerance followed by expressing the gene(s) in citrus is considered a potential cisgenic approach to engineering citrus for tolerance to HLB. Previous gene expression studies indicated that the constitutive disease resistance (CDR) genes in P. trifoliata (PtCDRs) may play a vital role in its HLB tolerance. This study was designed to use Arabidopsis mutants as a model system to confirm the function of PtCDRs in plant disease resistance. PtCDR2 and PtCDR8 were amplified from P. trifoliata cDNA and transferred into the Arabidopsis cdr1 mutant, whose resident CDR1 gene was disrupted by T-DNA insertion. The PtCDR2 and PtCDR8 transgenic Arabidopsis cdr1 mutant restored its hypersensitive response to the bacterial pathogen Pseudomonas syringae pv. tomato strain DC3000 (Pst DC3000) expressing avrRpt2. The defense marker gene PATHOGENESIS RELATED 1 (PR1) expressed at much higher levels in the PtCDR2 or PtCDR8 transgenic cdr1 mutant than in the non-transgenic cdr1 mutant with or without pathogen infection. Multiplication of Pst DC3000 bacteria in Arabidopsis was inhibited by the expression of PtCDR2 and PtCDR8. Our results showed that PtCDR2 and PtCDR8 were functional in Arabidopsis and played a positive role in disease resistance and demonstrated that Arabidopsis mutants can be a useful alternate system for screening Poncirus genes before making the time-consuming effort to transfer them into citrus, a perennial woody plant that is highly recalcitrant for Agrobacterium or biolistic-mediated transformation.
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23
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Adhikari P, Adhikari TB, Louws FJ, Panthee DR. Advances and Challenges in Bacterial Spot Resistance Breeding in Tomato ( Solanum lycopersicum L.). Int J Mol Sci 2020; 21:E1734. [PMID: 32138355 PMCID: PMC7084486 DOI: 10.3390/ijms21051734] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 12/21/2022] Open
Abstract
Bacterial spot is a serious disease of tomato caused by at least four species of Xanthomonas. These include X. euvesicatoria (race T1), X. vesicatoria (race T2), X. perforans (races T3 and T4), and X. gardneri, with the distinct geographical distribution of each group. Currently, X. gardneri and X. perforans are two major bacterial pathogens of tomato in North America, with X. perforans (race T4) dominating in east-coast while X. gardneri dominating in the Midwest. The disease causes up to 66% yield loss. Management of this disease is challenging due to the lack of useful chemical control measures and commercial resistant cultivars. Although major genes for resistance (R) and quantitative resistance have been identified, breeding tomato for resistance to bacterial spot has been impeded by multiple factors including the emergence of new races of the pathogen that overcome the resistance, multigenic control of the resistance, linkage drag, non-additive components of the resistance and a low correlation between seedling assays and field resistance. Transgenic tomato with Bs2 and EFR genes was effective against multiple races of Xanthomonas. However, it has not been commercialized because of public concerns and complex regulatory processes. The genomics-assisted breeding, effectors-based genomics breeding, and genome editing technology could be novel approaches to achieve durable resistance to bacterial spot in tomato. The main goal of this paper is to understand the current status of bacterial spot of tomato including its distribution and pathogen diversity, challenges in disease management, disease resistance sources, resistance genetics and breeding, and future prospectives with novel breeding approaches.
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Affiliation(s)
- Pragya Adhikari
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA; (P.A.); (F.J.L.)
| | - Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA;
| | - Frank J. Louws
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA; (P.A.); (F.J.L.)
| | - Dilip R. Panthee
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA; (P.A.); (F.J.L.)
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24
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Sathiyabama M, Muthukumar S. Chitosan guar nanoparticle preparation and its in vitro antimicrobial activity towards phytopathogens of rice. Int J Biol Macromol 2020; 153:297-304. [PMID: 32135260 DOI: 10.1016/j.ijbiomac.2020.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/21/2020] [Accepted: 03/01/2020] [Indexed: 01/09/2023]
Abstract
The aim of the present study was to prepare chitosan guar nanoparticle (CGNP) with high antimicrobial activity to use as a bioprotectant against rice phytopathogens. Nanoparticles were prepared using sodium tripolyphosphate by the ionic gelation method. The physico-chemical properties of nanoparticles were characterized through DLS, FTIR, TEM, SEM, AFM and XRD. The application of CGNP to rice seeds stimulated seed germination and seedling growth. CGNP showed growth inhibition towards rice pathogens P. grisea and X. oryzae under in-vitro condition. Excised rice leaves treated with CGNP and challenged with P. grisea showed no blast disease symptom whereas control leaves showed very high blast disease symptom. The results of this study indicate that CGNP can be used as an antimicrobial agent to control blast, blight disease of rice.
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Affiliation(s)
- M Sathiyabama
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu 24, India.
| | - S Muthukumar
- Department of Botany, Bharathidasan University, Tiruchirappalli, Tamil Nadu 24, India
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25
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Castro-Moretti FR, Gentzel IN, Mackey D, Alonso AP. Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions. Metabolites 2020; 10:E52. [PMID: 32013104 PMCID: PMC7074241 DOI: 10.3390/metabo10020052] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/16/2020] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant-microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed.
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Affiliation(s)
- Fernanda R. Castro-Moretti
- BioDiscovery Institute, University of North Texas, TX 76201, USA;
- Department of Biological Sciences, University of North Texas, TX 76201, USA
| | - Irene N. Gentzel
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA;
| | - David Mackey
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA;
| | - Ana P. Alonso
- BioDiscovery Institute, University of North Texas, TX 76201, USA;
- Department of Biological Sciences, University of North Texas, TX 76201, USA
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Stare T, Ramšak Ž, Križnik M, Gruden K. Multiomics analysis of tolerant interaction of potato with potato virus Y. Sci Data 2019; 6:250. [PMID: 31673114 PMCID: PMC6823367 DOI: 10.1038/s41597-019-0216-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/11/2019] [Indexed: 12/21/2022] Open
Abstract
Potato virus Y (PVY) is the most economically important viral pathogen of potato worldwide. Different potato cultivars react to the pathogen differently, resulting in resistant, tolerant or disease outcome of the interaction. Here we focus on tolerant interaction between potato cv. Désirée and PVYNTN. To capture the response in its full complexity, we analyzed the dynamic changes on multiple molecular levels, including transcriptomics, sRNAomics, degradomics, proteomics and hormonomics. The analysis was complemented by the measurements of viral accumulation, photosynthetic activity and phenotypisation of the symptoms. Besides cv. Désirée we also studied its transgenic counterpart depleted for the accumulation of salicylic acid (NahG-Désirée). This multiomics analysis provides better insights into the mechanisms leading to tolerant response of potato to viral infection and can be used as a base in further studies of plant immunity regulation.
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Affiliation(s)
- Tjaša Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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Ntoukakis V, Gifford ML. Plant-microbe interactions: tipping the balance. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4583-4586. [PMID: 31306482 PMCID: PMC6760295 DOI: 10.1093/jxb/erz321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- Vardis Ntoukakis
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Miriam L Gifford
- School of Life Sciences and Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
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28
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Moghaddam GA, Rezayatmand Z, Nasr Esfahani M, Khozaei M. Genetic defense analysis of tomatoes in response to early blight disease, Alternaria alternata. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:500-509. [PMID: 31445475 DOI: 10.1016/j.plaphy.2019.08.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
Early blight disease of tomato is one of the most devastating biotic stresses worldwide, and in Iran, Alternaria alternata is one of the most predominant species causing the disease. In the current study, a diverse collection of 35 tomato genotypes and implication of 5 SlWRKYs and 7 PR genes as well as enzymatic activity were evaluated on resistant and susceptible cultivars through real-time polymerase chain reaction at transplanting and maturing stages and by measuring product formation using spectrophotometry. The results indicated that the expression of these antifungal genes in 14 genotypes at two growth stages after inoculation with A. alternata highly enhanced by 1-50-fold. There was also significant upregulation of WRKYs and PRs genes among the resistant tomato varieties in comparison to susceptible and control varieties at both stages. These findings demonstrate the varieties that showed increased or decreased SlWRKY1 expression also displayed similar changes in the expression of PR1 and PR2 genes. Furthermore, the differential expression patterns of SlWRKY1 and SlWRKY11 were consistent with PR7 and PDF1.2 expression patterns. The analysis of enzymatic activity of PR2 and PR3 proteins, β-1,3-glucanase, and chitinase showed the highest level of activity in resistant inoculated genotypes against A. alternata. Therefore, the current findings suggest the possible involvement of these transcription factors in the increased expression of PR genes in response to A. alternata infection.
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Affiliation(s)
| | - Zahra Rezayatmand
- Department of Biology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran.
| | - Mehdi Nasr Esfahani
- Department of Biology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran; Plant Protection Research Division, Isfahan Center for Research and Education in Agricultural Science and Natural Resources, (AREEO), Isfahan, Iran.
| | - Mahdi Khozaei
- Plant Biotechnology, Department of Biology, University of Isfahan, Isfahan, Iran.
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29
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Osuna-Cruz CM, Paytuvi-Gallart A, Di Donato A, Sundesha V, Andolfo G, Aiese Cigliano R, Sanseverino W, Ercolano MR. PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes. Nucleic Acids Res 2019; 46:D1197-D1201. [PMID: 29156057 PMCID: PMC5753367 DOI: 10.1093/nar/gkx1119] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/25/2017] [Indexed: 11/28/2022] Open
Abstract
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user interface, new sections, new tools and new data for genetic improvement, allowing easy access not only to the plant science research community but also to breeders who want to improve plant disease resistance. The home page offers an overview of easy-to-read search boxes that streamline data queries and directly show plant species for which data from candidate or cloned genes have been collected. Bulk data files and curated resistance gene annotations are made available for each plant species hosted. The new Gene Model view offers detailed information on each cloned resistance gene structure to highlight shared attributes with other genes. PRGdb 3.0 offers 153 reference resistance genes and 177 072 annotated candidate Pathogen Receptor Genes (PRGs). Compared to the previous release, the number of putative genes has been increased from 106 to 177 K from 76 sequenced Viridiplantae and algae genomes. The DRAGO 2 tool, which automatically annotates and predicts (PRGs) from DNA and amino acid with high accuracy and sensitivity, has been added. BLAST search has been implemented to offer users the opportunity to annotate and compare their own sequences. The improved section on plant diseases displays useful information linked to genes and genomes to connect complementary data and better address specific needs. Through, a revised and enlarged collection of data, the development of new tools and a renewed portal, PRGdb 3.0 engages the plant science community in developing a consensus plan to improve knowledge and strategies to fight diseases that afflict main crops and other plants.
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Affiliation(s)
| | | | - Antimo Di Donato
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | - Vicky Sundesha
- Sequentia Biotech SL, Calle Comte D'Urgell 240, 08036 Barcelona, Spain
| | - Giuseppe Andolfo
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | | | | | - Maria R Ercolano
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
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30
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Page MT, Parry MA, Carmo‐Silva E. A high-throughput transient expression system for rice. PLANT, CELL & ENVIRONMENT 2019; 42:2057-2064. [PMID: 30938460 PMCID: PMC6618034 DOI: 10.1111/pce.13542] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/11/2019] [Accepted: 02/24/2019] [Indexed: 05/18/2023]
Abstract
Rice is an important global crop and represents a vital source of calories for many food insecure regions. Efforts to improve this crop by improving yield, nutritional content, stress tolerance, or resilience to climate change are certain to include biotechnological approaches, which rely on the expression of transgenes in planta. The throughput and cost of currently available transgenic expression systems is frequently incompatible with modern, high-throughput molecular cloning methods. Here, we present a protocol for isolating high yields of green rice protoplasts and for PEG-mediated transformation of isolated protoplasts. Factors affecting transformation efficiency were investigated, and the resulting protocol is fast, cheap, robust, high-throughput, and does not require specialist equipment. When coupled to a high-throughput modular cloning system such as Golden Gate, this transient expression system provides a valuable resource to help break the "design-build-test" bottleneck by permitting the rapid screening of large numbers of transgenic expression cassettes prior to stable plant transformation. We used this system to rapidly assess the expression level, subcellular localisation, and protein aggregation pattern of nine single-gene expression cassettes, which represent the essential component parts of the β-cyanobacterial carboxysome.
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Affiliation(s)
- Mike T. Page
- Lancaster Environment CentreLancaster UniversityLancasterUK
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31
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Pinheiro C, Dickinson E, Marriott A, Ribeiro IC, Pintó-Marijuan M, António C, Zarrouk O, Chaves MM, Dodd IC, Munné-Bosch S, Thomas-Oates J, Wilson J. Distinctive phytohormonal and metabolic profiles of Arabidopsis thaliana and Eutrema salsugineum under similar soil drying. PLANTA 2019; 249:1417-1433. [PMID: 30684038 DOI: 10.1007/s00425-019-03095-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
Arabidopsis and Eutrema show similar stomatal sensitivity to drying soil. In Arabidopsis, larger metabolic adjustments than in Eutrema occurred, with considerable differences in the phytohormonal responses of the two species. Although plants respond to soil drying via a series of concurrent physiological and molecular events, drought tolerance differs greatly within the plant kingdom. While Eutrema salsugineum (formerly Thellungiella salsuginea) is regarded as more stress tolerant than its close relative Arabidopsis thaliana, their responses to soil water deficit have not previously been directly compared. To ensure a similar rate of soil drying for the two species, daily soil water depletion was controlled to 5-10% of the soil water content. While partial stomatal closure occurred earlier in Arabidopsis (Day 4) than Eutrema (from Day 6 onwards), thereafter both species showed similar stomatal sensitivity to drying soil. However, both targeted and untargeted metabolite analysis revealed greater response to drought in Arabidopsis than Eutrema. Early peaks in foliar phytohormone concentrations and different sugar profiles between species were accompanied by opposing patterns in the bioactive cytokinin profiles. Untargeted analysis showed greater metabolic adjustment in Arabidopsis with more statistically significant changes in both early and severe drought stress. The distinct metabolic responses of each species during early drought, which occurred prior to leaf water status declining, seemed independent of later stomatal closure in response to drought. The two species also showed distinct water usage, with earlier reduction in water consumption in Eutrema (Day 3) than Arabidopsis (Day 6), likely reflecting temporal differences in growth responses. We propose Arabidopsis as a promising model to evaluate the mechanisms responsible for stress-induced growth inhibition under the mild/moderate soil drying that crop plants are typically exposed to.
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Affiliation(s)
- Carla Pinheiro
- Instituto de Tecnologia Química E Biológica, Universidade NOVA de Lisboa, Av. da República, EAN, 2781-901, Oeiras, Portugal.
- DCV-Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| | - Elizabeth Dickinson
- Department of Mathematics, University of York, Heslington, York, YO10 5DD, UK
| | - Andrew Marriott
- Department of Mathematics, University of York, Heslington, York, YO10 5DD, UK
| | - Isa C Ribeiro
- Instituto de Tecnologia Química E Biológica, Universidade NOVA de Lisboa, Av. da República, EAN, 2781-901, Oeiras, Portugal
| | - Marta Pintó-Marijuan
- Instituto de Tecnologia Química E Biológica, Universidade NOVA de Lisboa, Av. da República, EAN, 2781-901, Oeiras, Portugal
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
| | - Carla António
- Instituto de Tecnologia Química E Biológica, Universidade NOVA de Lisboa, Av. da República, EAN, 2781-901, Oeiras, Portugal
- Department of Mathematics, University of York, Heslington, York, YO10 5DD, UK
| | - Olfa Zarrouk
- Instituto de Tecnologia Química E Biológica, Universidade NOVA de Lisboa, Av. da República, EAN, 2781-901, Oeiras, Portugal
| | - Maria Manuela Chaves
- Instituto de Tecnologia Química E Biológica, Universidade NOVA de Lisboa, Av. da República, EAN, 2781-901, Oeiras, Portugal
| | - Ian C Dodd
- The Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Sergi Munné-Bosch
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 643, 08028, Barcelona, Spain
| | - Jane Thomas-Oates
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Julie Wilson
- Department of Mathematics, University of York, Heslington, York, YO10 5DD, UK.
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32
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Brulé D, Villano C, Davies LJ, Trdá L, Claverie J, Héloir M, Chiltz A, Adrian M, Darblade B, Tornero P, Stransfeld L, Boutrot F, Zipfel C, Dry IB, Poinssot B. The grapevine (Vitis vinifera) LysM receptor kinases VvLYK1-1 and VvLYK1-2 mediate chitooligosaccharide-triggered immunity. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:812-825. [PMID: 30256508 PMCID: PMC6419575 DOI: 10.1111/pbi.13017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/23/2018] [Indexed: 05/05/2023]
Abstract
Chitin, a major component of fungal cell walls, is a well-known pathogen-associated molecular pattern (PAMP) that triggers defense responses in several mammal and plant species. Here, we show that two chitooligosaccharides, chitin and chitosan, act as PAMPs in grapevine (Vitis vinifera) as they elicit immune signalling events, defense gene expression and resistance against fungal diseases. To identify their cognate receptors, the grapevine family of LysM receptor kinases (LysM-RKs) was annotated and their gene expression profiles were characterized. Phylogenetic analysis clearly distinguished three V. vinifera LysM-RKs (VvLYKs) located in the same clade as the Arabidopsis CHITIN ELICITOR RECEPTOR KINASE1 (AtCERK1), which mediates chitin-induced immune responses. The Arabidopsis mutant Atcerk1, impaired in chitin perception, was transformed with these three putative orthologous genes encoding VvLYK1-1, -2, or -3 to determine if they would complement the loss of AtCERK1 function. Our results provide evidence that VvLYK1-1 and VvLYK1-2, but not VvLYK1-3, functionally complement the Atcerk1 mutant by restoring chitooligosaccharide-induced MAPK activation and immune gene expression. Moreover, expression of VvLYK1-1 in Atcerk1 restored penetration resistance to the non-adapted grapevine powdery mildew (Erysiphe necator). On the whole, our results indicate that the grapevine VvLYK1-1 and VvLYK1-2 participate in chitin- and chitosan-triggered immunity and that VvLYK1-1 plays an important role in basal resistance against E. necator.
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Affiliation(s)
- Daphnée Brulé
- AgroécologieAgrosup DijonINRAUniversité Bourgogne Franche‐ComtéCNRS ERL 6003DijonFrance
| | | | - Laura J. Davies
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)AdelaideSAAustralia
| | - Lucie Trdá
- AgroécologieAgrosup DijonINRAUniversité Bourgogne Franche‐ComtéCNRS ERL 6003DijonFrance
| | - Justine Claverie
- AgroécologieAgrosup DijonINRAUniversité Bourgogne Franche‐ComtéCNRS ERL 6003DijonFrance
| | - Marie‐Claire Héloir
- AgroécologieAgrosup DijonINRAUniversité Bourgogne Franche‐ComtéCNRS ERL 6003DijonFrance
| | - Annick Chiltz
- AgroécologieAgrosup DijonINRAUniversité Bourgogne Franche‐ComtéCNRS ERL 6003DijonFrance
| | - Marielle Adrian
- AgroécologieAgrosup DijonINRAUniversité Bourgogne Franche‐ComtéCNRS ERL 6003DijonFrance
| | | | - Pablo Tornero
- Instituto de Biología Molecular y Celular de PlantasUniversitat Politècnica de ValènciaConsejo Superior de Investigaciones CientíficasValenciaSpain
| | | | | | - Cyril Zipfel
- The Sainsbury LaboratoryNorwich Research ParkNorwichUK
| | - Ian B. Dry
- Commonwealth Scientific and Industrial Research Organisation (CSIRO)AdelaideSAAustralia
| | - Benoit Poinssot
- AgroécologieAgrosup DijonINRAUniversité Bourgogne Franche‐ComtéCNRS ERL 6003DijonFrance
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Abstract
Bacterial spot (BS), caused by four species of Xanthomonas: X. euvesicatoria, X. vesicatoria, X. perforans and X. gardneri in tomato (Solanum lycopersicum L.) results in severe loss in yield and quality by defoliation and the appearance of lesions on fruits, respectively. The combined industry standard for BS control (foliar applications Actigard® rotated with copper plus mancozeb) does not offer sufficient protection, especially when weather conditions favor disease spread. Development of tomato cultivars with BS resistance is thus an important measure to minimize losses. Hypersensitive and non-hypersensitive resistance has been identified in different wild accessions and cultivated tomato relatives and has been transferred to cultivated tomato. However, complete resistance is yet to be obtained. With the advent of next generation sequencing and precise genome editing tools, the genetic regions that confer resistance to bacterial spot can be targeted and enriched through gene pyramiding in a new commercial cultivar which may confer higher degree of horizontal resistance to multiple strains of Xanthomonas causing bacterial spot in tomato.
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Aman R, Mahas A, Butt H, Aljedaani F, Mahfouz M. Engineering RNA Virus Interference via the CRISPR/Cas13 Machinery in Arabidopsis. Viruses 2018; 10:E732. [PMID: 30572690 PMCID: PMC6315463 DOI: 10.3390/v10120732] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/09/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems are key immune mechanisms helping prokaryotic species fend off RNA and DNA viruses. CRISPR/Cas9 has broad applications in basic research and biotechnology and has been widely used across eukaryotic species for genome engineering and functional analysis of genes. The recently developed CRISPR/Cas13 systems target RNA rather than DNA and thus offer new potential for transcriptome engineering and combatting RNA viruses. Here, we used CRISPR/LshCas13a to stably engineer Arabidopsis thaliana for interference against the RNA genome of Turnip mosaic virus (TuMV). Our data demonstrate that CRISPR RNAs (crRNAs) guiding Cas13a to the sequences encoding helper component proteinase silencing suppressor (HC-Pro) or GFP target 2 (GFP-T2) provide better interference compared to crRNAs targeting other regions of the TuMV RNA genome. This work demonstrates the exciting potential of CRISPR/Cas13 to be used as an antiviral strategy to obstruct RNA viruses, and encourages the search for more robust and effective Cas13 variants or CRISPR systems that can target RNA.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Ahmed Mahas
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Fatimah Aljedaani
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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35
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Pereira JA, Yu F, Zhang Y, Jones JB, Mou Z. The Arabidopsis Elongator Subunit ELP3 and ELP4 Confer Resistance to Bacterial Speck in Tomato. FRONTIERS IN PLANT SCIENCE 2018; 9:1066. [PMID: 30087688 PMCID: PMC6066517 DOI: 10.3389/fpls.2018.01066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/29/2018] [Indexed: 06/08/2023]
Abstract
Although production of tomato (Solanum lycopersicum) is threatened by a number of major diseases worldwide, it has been difficult to identify effective and durable management measures against these diseases. In this study, we attempted to improve tomato disease resistance by transgenic overexpression of genes encoding the Arabidopsis thaliana Elongator (AtELP) complex subunits AtELP3 and AtELP4. We show that overexpression of AtELP3 and AtELP4 significantly enhanced resistance to tomato bacterial speck caused by the Pseudomonas syringae pv. tomato strain J4 (Pst J4) without clear detrimental effects on plant growth and development. Interestingly, the transgenic plants exhibited resistance to Pst J4 only when inoculated through foliar sprays but not through infiltration into the leaf apoplast. Although this result suggested possible involvement of stomatal immunity, we found that Pst J4 inoculation did not induce stomatal closure and there were no differences in stomatal apertures and conductance between the transgenic and control plants. Further RNA sequencing and real-time quantitative PCR analyses revealed a group of defense-related genes to be induced to higher levels after infection in the AtELP4 transgenic tomato plants than in the control, suggesting that the enhanced disease resistance of the transgenic plants may be attributed to elevated induction of defense responses. Additionally, we show that the tomato genome contains single-copy genes encoding all six Elongator subunits (SlELPs), which share high identities with the AtELP proteins, and that SlELP3 and SlELP4 complemented the Arabidopsis Atelp3 and Atelp4 mutants, respectively, indicating that the function of tomato Elongator is probably conserved. Taken together, our results not only shed new light on the tomato Elongator complex, but also revealed potential candidate genes for engineering disease resistance in tomato.
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Affiliation(s)
- Juliana A. Pereira
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Fahong Yu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, United States
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Zhonglin Mou
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
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Samad AFA, Nazaruddin N, Murad AMA, Jani J, Zainal Z, Ismail I. Deep sequencing and in silico analysis of small RNA library reveals novel miRNA from leaf Persicaria minor transcriptome. 3 Biotech 2018; 8:136. [PMID: 29479512 DOI: 10.1007/s13205-018-1164-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/08/2018] [Indexed: 01/25/2023] Open
Abstract
In current era, majority of microRNA (miRNA) are being discovered through computational approaches which are more confined towards model plants. Here, for the first time, we have described the identification and characterization of novel miRNA in a non-model plant, Persicaria minor (P. minor) using computational approach. Unannotated sequences from deep sequencing were analyzed based on previous well-established parameters. Around 24 putative novel miRNAs were identified from 6,417,780 reads of the unannotated sequence which represented 11 unique putative miRNA sequences. PsRobot target prediction tool was deployed to identify the target transcripts of putative novel miRNAs. Most of the predicted target transcripts (mRNAs) were known to be involved in plant development and stress responses. Gene ontology showed that majority of the putative novel miRNA targets involved in cellular component (69.07%), followed by molecular function (30.08%) and biological process (0.85%). Out of 11 unique putative miRNAs, 7 miRNAs were validated through semi-quantitative PCR. These novel miRNAs discoveries in P. minor may develop and update the current public miRNA database.
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Affiliation(s)
- Abdul Fatah A Samad
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Nazaruddin Nazaruddin
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
- 3Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Syiah Kuala, Darussalam, Banda Aceh, 23111 Indonesia
| | - Abdul Munir Abdul Murad
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Jaeyres Jani
- BioEasy Sdn. Bhd. and ScienceVision Sdn. Bhd., Setia Alam, Seksyen U13, 40170 Shah Alam, Selangor Malaysia
| | - Zamri Zainal
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
- 2Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Ismanizan Ismail
- 1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
- 2Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
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37
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Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol 2018; 19:1. [PMID: 29301551 PMCID: PMC5755456 DOI: 10.1186/s13059-017-1381-1] [Citation(s) in RCA: 372] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/13/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome. Here, we employ CRISPR/Cas13a to engineer interference with an RNA virus, Turnip Mosaic Virus (TuMV), in plants. RESULTS CRISPR/Cas13a produces interference against green fluorescent protein (GFP)-expressing TuMV in transient assays and stable overexpression lines of Nicotiana benthamiana. CRISPR RNA (crRNAs) targeting the HC-Pro and GFP sequences exhibit better interference than those targeting other regions such as coat protein (CP) sequence. Cas13a can also process pre-crRNAs into functional crRNAs. CONCLUSIONS Our data indicate that CRISPR/Cas13a can be used for engineering interference against RNA viruses, providing a potential novel mechanism for RNA-guided immunity against RNA viruses and for other RNA manipulations in plants.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Fatimah Aljedaani
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Zuhaib Khan
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shouwei Ding
- Center for Plant Cell Biology, Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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GIBSON AMANDAK, MORRAN LEVIT. A Model for Evolutionary Ecology of Disease: The Case for Caenorhabditis Nematodes and Their Natural Parasites. J Nematol 2018. [DOI: 10.21307/jofnem-2017-083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Gibson AK, Morran LT. A Model for Evolutionary Ecology of Disease: The Case for Caenorhabditis Nematodes and Their Natural Parasites. J Nematol 2017; 49:357-372. [PMID: 29353923 PMCID: PMC5770282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 06/07/2023] Open
Abstract
Many of the outstanding questions in disease ecology and evolution call for combining observation of natural host-parasite populations with experimental dissection of interactions in the field and the laboratory. The "rewilding" of model systems holds great promise for this endeavor. Here, we highlight the potential for development of the nematode Caenorhabditis elegans and its close relatives as a model for the study of disease ecology and evolution. This powerful laboratory model was disassociated from its natural habitat in the 1960s. Today, studies are uncovering that lost natural history, with several natural parasites described since 2008. Studies of these natural Caenorhabditis-parasite interactions can reap the benefits of the vast array of experimental and genetic tools developed for this laboratory model. In this review, we introduce the natural parasites of C. elegans characterized thus far and discuss resources available to study them, including experimental (co)evolution, cryopreservation, behavioral assays, and genomic tools. Throughout, we present avenues of research that are interesting and feasible to address with caenorhabditid nematodes and their natural parasites, ranging from the maintenance of outcrossing to the community dynamics of host-associated microbes. In combining natural relevance with the experimental power of a laboratory supermodel, these fledgling host-parasite systems can take on fundamental questions in evolutionary ecology of disease.
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Affiliation(s)
| | - Levi T Morran
- Department of Biology, Emory University, Atlanta, GA 30322
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40
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Stare T, Stare K, Weckwerth W, Wienkoop S, Gruden K. Comparison between Proteome and Transcriptome Response in Potato (Solanum tuberosum L.) Leaves Following Potato Virus Y (PVY) Infection. Proteomes 2017; 5:proteomes5030014. [PMID: 28684682 PMCID: PMC5620531 DOI: 10.3390/proteomes5030014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/27/2017] [Accepted: 07/01/2017] [Indexed: 12/17/2022] Open
Abstract
Plant diseases caused by viral infection are affecting all major crops. Being an obligate intracellular organisms, chemical control of these pathogens is so far not applied in the field except to control the insect vectors of the viruses. Understanding of molecular responses of plant immunity is therefore economically important, guiding the enforcement of crop resistance. To disentangle complex regulatory mechanisms of the plant immune responses, understanding system as a whole is a must. However, integrating data from different molecular analysis (transcriptomics, proteomics, metabolomics, smallRNA regulation etc.) is not straightforward. We evaluated the response of potato (Solanum tuberosum L.) following the infection with potato virus Y (PVY). The response has been analyzed on two molecular levels, with microarray transcriptome analysis and mass spectroscopy-based proteomics. Within this report, we performed detailed analysis of the results on both levels and compared two different approaches for analysis of proteomic data (spectral count versus MaxQuant). To link the data on different molecular levels, each protein was mapped to the corresponding potato transcript according to StNIB paralogue grouping. Only 33% of the proteins mapped to microarray probes in a one-to-one relation and additionally many showed discordance in detected levels of proteins with corresponding transcripts. We discussed functional importance of true biological differences between both levels and showed that the reason for the discordance between transcript and protein abundance lies partly in complexity and structure of biological regulation of proteome and transcriptome and partly in technical issues contributing to it.
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Affiliation(s)
- Tjaša Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia.
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia.
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, 1010 Wien, Austria.
| | - Stefanie Wienkoop
- Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, 1010 Wien, Austria.
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia.
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van Hove L, Gillund F. Is it only the regulatory status? Broadening the debate on cisgenic plants. ENVIRONMENTAL SCIENCES EUROPE 2017; 29:22. [PMID: 28680789 PMCID: PMC5487859 DOI: 10.1186/s12302-017-0120-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/12/2017] [Indexed: 05/30/2023]
Abstract
In current debates on emerging technologies for plant breeding in Europe, much attention has been given to the regulatory status of these techniques and their public acceptance. At present, both genetically modified plants with cisgenic approaches-using genes from crossable species-as well as transgenic approaches-using genes from different species-fall under GMO regulation in the EU and both are mandatorily labelled as GMOs. Researchers involved in the early development of cisgenic GM plants convey the message that the potential use and acceptance of cisgenic approaches will be seriously hindered if GMO regulations are not adjusted. Although the similar treatment and labelling of transgenic and cisgenic plants may be a legitimate concern for the marketability of a cisgenic GM plant, there are concerns around their commercialization that reach beyond the current focus on (de)regulation. In this paper, we will use the development of the cisgenic GM potato that aims to overcome 'late blight'-the most devastating potato disease worldwide-as a case to argue that it is important to recognize, reflect and respond to broader concerns than the dominant focus on the regulatory 'burden' and consumer acceptance. Based on insights we gained from discussing this case with diverse stakeholders within the agricultural sector and potato production in Norway during a series of workshops, we elaborate on additional issues such as the (technical) solution offered; different understandings of the late blight problem; the durability of the potato plant resistance; and patenting and ownership. Hence, this paper contributes to empirical knowledge on stakeholder perspectives on emerging plant breeding technologies, underscoring the importance to broaden the scope of the debate on the opportunities and challenges of agricultural biotechnologies, such as cisgenic GM plants. The paper offers policy-relevant input to ongoing efforts to broaden the scope of risk assessments of agricultural biotechnologies. We aim to contribute to the recognition of the complex socio-ecological, legal and political dimensions in which these technological developments are entangled as a means to acknowledge, discuss and respond to these concerns and thereby contribute to more comprehensive and responsible developments within agricultural biotechnology.
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Affiliation(s)
- Lilian van Hove
- Society, Ecology and Ethics Department, GenØk Centre for Biosafety, SIVA Innovation Centre, 9294 Tromsø, Norway
| | - Frøydis Gillund
- Society, Ecology and Ethics Department, GenØk Centre for Biosafety, SIVA Innovation Centre, 9294 Tromsø, Norway
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Richa K, Tiwari IM, Devanna BN, Botella JR, Sharma V, Sharma TR. Novel Chitinase Gene LOC_Os11g47510 from Indica Rice Tetep Provides Enhanced Resistance against Sheath Blight Pathogen Rhizoctonia solani in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:596. [PMID: 28487708 PMCID: PMC5403933 DOI: 10.3389/fpls.2017.00596] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/03/2017] [Indexed: 05/20/2023]
Abstract
Sheath blight disease (ShB), caused by the fungus Rhizoctonia solani Kühn, is one of the most destructive diseases of rice (Oryza sativa L.), causing substantial yield loss in rice. In the present study, a novel rice chitinase gene, LOC_Os11g47510 was cloned from QTL region of R. solani tolerant rice line Tetep and used for functional validation by genetic transformation of ShB susceptible japonica rice line Taipei 309 (TP309). The transformants were characterized using molecular and functional approaches. Molecular analysis by PCR using a set of primers specific to CaMv 35S promoter, chitinase and HptII genes confirmed the presence of transgene in transgenic plants which was further validated by Southern hybridization. Further, qRT-PCR analysis of transgenic plants showed good correlation between transgene expression and the level of sheath blight resistance among transformants. Functional complementation assays confirmed the effectiveness of the chitinase mediated resistance in all the transgenic TP309 plants with varying levels of enhanced resistance against R. solani. Therefore, the novel chitinase gene cloned and characterized in the present study from the QTL region of rice will be of significant use in molecular plant breeding program for developing sheath blight resistance in rice.
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Affiliation(s)
- Kamboj Richa
- National Research Centre on Plant BiotechnologyNew Delhi, India
- Department of Bioscience and Biotechnology, Banasthali UniversityBanasthali, India
| | - Ila M. Tiwari
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - B. N. Devanna
- National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Jose R. Botella
- School of Agriculture and Food Sciences, The University of Queensland, St LuciaQLD, Australia
| | - Vinay Sharma
- Department of Bioscience and Biotechnology, Banasthali UniversityBanasthali, India
| | - Tilak R. Sharma
- National Research Centre on Plant BiotechnologyNew Delhi, India
- National Agri-Food Biotechnology InstituteMohali, India
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43
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Rigault M, Buellet A, Masclaux-Daubresse C, Fagard M, Chardon F, Dellagi A. Quantitative Methods to Assess Differential Susceptibility of Arabidopsis thaliana Natural Accessions to Dickeya dadantii. FRONTIERS IN PLANT SCIENCE 2017; 8:394. [PMID: 28400777 PMCID: PMC5368239 DOI: 10.3389/fpls.2017.00394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/07/2017] [Indexed: 05/29/2023]
Abstract
Among the most devastating bacterial diseases of plants, soft rot provoked by Dickeya spp. cause crop yield losses on a large range of species with potato being the most economically important. The use of antibiotics being prohibited in most countries in the field, identifying tolerance genes is expected to be one of the most effective alternate disease control approaches. A prerequisite for the identification of tolerance genes is to develop robust disease quantification methods and to identify tolerant plant genotypes. In this work, we investigate the feasibility of the exploitation of Arabidopsis thaliana natural variation to find tolerant genotypes and to develop robust quantification methods. We compared different quantification methods that score either symptom development or bacterial populations in planta. An easy to set up and reliable bacterial quantification method based on qPCR amplification of bacterial DNA was validated. This study demonstrates that it is possible to conduct a robust phenotyping of soft rot disease, and that Arabidopsis natural accessions are a relevant source of tolerance genes.
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Field Guide to Plant Model Systems. Cell 2017; 167:325-339. [PMID: 27716506 DOI: 10.1016/j.cell.2016.08.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/28/2016] [Accepted: 08/15/2016] [Indexed: 12/20/2022]
Abstract
For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.
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45
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Andolfo G, Iovieno P, Frusciante L, Ercolano MR. Genome-Editing Technologies for Enhancing Plant Disease Resistance. FRONTIERS IN PLANT SCIENCE 2016; 7:1813. [PMID: 27990151 PMCID: PMC5130979 DOI: 10.3389/fpls.2016.01813] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/16/2016] [Indexed: 05/23/2023]
Abstract
One of the greatest challenges for agricultural science in the 21st century is to improve yield stability through the progressive development of superior cultivars. The increasing numbers of infectious plant diseases that are caused by plant-pathogens make it ever more necessary to develop new strategies for plant disease resistance breeding. Targeted genome engineering allows the introduction of precise modifications directly into a commercial variety, offering a viable alternative to traditional breeding methods. Genome editing is a powerful tool for modifying crucial players in the plant immunity system. In this work, we propose and discuss genome-editing strategies and targets for improving resistance to phytopathogens. First of all, we present the opportunities to rewrite the effector-target sequence for avoiding effector-target molecular interaction and also to modify effector-target promoters for increasing the expression of target genes involved in the resistance process. In addition, we describe potential approaches for obtaining synthetic R-genes through genome-editing technologies (GETs). Finally, we illustrate a genome editing flowchart to modify the pathogen recognition sites and engineer an R-gene that mounts resistance to some phylogenetically divergent pathogens. GETs potentially mark the beginning of a new era, in which synthetic biology affords a basis for obtaining a reinforced plant defense system. Nowadays it is conceivable that by modulating the function of the major plant immunity players, we will be able to improve crop performance for a sustainable agriculture.
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Affiliation(s)
| | | | | | - Maria R. Ercolano
- Department of Agricultural Sciences, University of Naples ‘Federico II’Portici, Italy
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Herrera Diaz A, Kovacs I, Lindermayr C. Inducible Expression of the De-Novo Designed Antimicrobial Peptide SP1-1 in Tomato Confers Resistance to Xanthomonas campestris pv. vesicatoria. PLoS One 2016; 11:e0164097. [PMID: 27706237 PMCID: PMC5051901 DOI: 10.1371/journal.pone.0164097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 09/20/2016] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial peptides (AMPs) are small peptides with less than 50 amino acids and are part of the innate immune response in almost all organisms, including bacteria, vertebrates, invertebrates and plants. AMPs are active against a broad-spectrum of pathogens. The inducible expression of AMPs in plants is a promising approach to combat plant pathogens with minimal negative side effects, such as phytotoxicity or infertility. In this study, inducible expression of the de-novo designed AMP SP1-1 in Micro Tom tomato protected tomato fruits against bacterial spot disease caused by Xanthomonas campestris pv. vesicatoria. The peptide SP1-1 was targeted to the apoplast which is the primary infection site for plant pathogens, by fusing SP1-1 peptide to the signal peptide RsAFP1 of radish (Raphanus sativus). The pathogen inducibility of the expression was enabled by using an optimized inducible 4XW2/4XS promoter. As a result, the tomato fruits of independently generated SP1-1 transgenic lines were significantly more resistant to X. campestris pv. vesicatoria than WT tomato fruits. In transgenic lines, bacterial infection was reduced up to 65% in comparison to the infection of WT plants. Our study demonstrates that the combination of the 4XW2/4XS cis-element from parsley with the synthetic antimicrobial peptide SP1-1 is a good alternative to protect tomato fruits against infections with X. campestris pv. vesicatoria.
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Affiliation(s)
- Areli Herrera Diaz
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764, München/Neuherberg, Germany
| | - Izabella Kovacs
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764, München/Neuherberg, Germany
| | - Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764, München/Neuherberg, Germany
- * E-mail:
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47
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Dessaux Y, Grandclément C, Faure D. Engineering the Rhizosphere. TRENDS IN PLANT SCIENCE 2016; 21:266-278. [PMID: 26818718 DOI: 10.1016/j.tplants.2016.01.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/14/2015] [Accepted: 01/04/2016] [Indexed: 05/25/2023]
Abstract
All components of the rhizosphere can be engineered to promote plant health and growth, two features that strongly depend upon the interactions of living organisms with their environment. This review describes the progress in plant and microbial molecular genetics and ecology that has led to a wealth of potential applications. Recent efforts especially deal with the plant defense machinery that is instrumental in engineering plant resistance to biotic stresses. Another approach involves microbial population engineering rather than single strain engineering. More generally, the plants (and the associated microbes) are no longer seen as 'individual' but rather as a holobiont, in other words a unit of selection in evolution, a concept that holds great promise for future plant breeding programs.
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Affiliation(s)
- Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
| | - Catherine Grandclément
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France
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48
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Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P. 50 years of Arabidopsis research: highlights and future directions. THE NEW PHYTOLOGIST 2016; 209:921-44. [PMID: 26465351 DOI: 10.1111/nph.13687] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/24/2015] [Indexed: 05/14/2023]
Abstract
922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jose Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Vincent Colot
- Departement de Biologie École Normale Supérieure, Biologie Moleculaire des Organismes Photosynthetiques, F-75230, Paris, France
| | - Sean Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Jeff Dangl
- Department of Biology and Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Joanna D Friesner
- Department of Plant Biology, Agricultural Sustainability Institute, University of California, Davis, CA, 95616, USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Erich Grotewold
- Center for Applied Plant Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Elliot Meyerowitz
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jennifer Nemhauser
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, A-1030, Vienna, Austria
| | - Craig Pikaard
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Chris Somerville
- Energy Biosciences Institute, University of California, Berkeley, CA, 94704, USA
| | - Mark Stitt
- Metabolic Networks Department, Max Planck Institute for Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Keiko U Torii
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Jamie Waese
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter McCourt
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
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Brewer HC, Hammond-Kosack KE. Host to a Stranger: Arabidopsis and Fusarium Ear Blight. TRENDS IN PLANT SCIENCE 2015; 20:651-663. [PMID: 26440434 DOI: 10.1016/j.tplants.2015.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/23/2015] [Accepted: 06/29/2015] [Indexed: 06/05/2023]
Abstract
Fusarium ear blight (FEB) is a devastating fungal disease of cereal crops. Outbreaks are sporadic and current control strategies are severely limited. This review highlights the use of Arabidopsis to study plant-FEB interactions. Use of this pathosystem has identified natural variation in Fusarium susceptibility in Arabidopsis, and native plant genes and signalling processes modulating the interaction. Recent breakthroughs include the identification of plant- and insect-derived small molecules which increase disease resistance, and the use of a host-induced gene silencing (HIGS) construct to silence an important Fusarium gene to prevent infection. Arabidopsis has also been used to study other fungi that cause cereal diseases. These findings offer the potential for translational research in cereals which could yield much-needed novel control strategies.
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Affiliation(s)
- Helen C Brewer
- Plant Biology and Crop Science, Rothamsted Research, Harpenden AL5 2JQ, UK
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50
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Figueroa M, Castell-Miller CV, Li F, Hulbert SH, Bradeen JM. Pushing the boundaries of resistance: insights from Brachypodium-rust interactions. FRONTIERS IN PLANT SCIENCE 2015; 6:558. [PMID: 26284085 PMCID: PMC4519692 DOI: 10.3389/fpls.2015.00558] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/07/2015] [Indexed: 05/20/2023]
Abstract
The implications of global population growth urge transformation of current food and bioenergy production systems to sustainability. Members of the family Poaceae are of particular importance both in food security and for their applications as biofuel substrates. For centuries, rust fungi have threatened the production of valuable crops such as wheat, barley, oat, and other small grains; similarly, biofuel crops can also be susceptible to these pathogens. Emerging rust pathogenic races with increased virulence and recurrent rust epidemics around the world point out the vulnerability of monocultures. Basic research in plant immunity, especially in model plants, can make contributions to understanding plant resistance mechanisms and improve disease management strategies. The development of the grass Brachypodium distachyon as a genetically tractable model for monocots, especially temperate cereals and grasses, offers the possibility to overcome the experimental challenges presented by the genetic and genomic complexities of economically valuable crop plants. The numerous resources and tools available in Brachypodium have opened new doors to investigate the underlying molecular and genetic bases of plant-microbe interactions in grasses and evidence demonstrating the applicability and advantages of working with B. distachyon is increasing. Importantly, several interactions between B. distachyon and devastating plant pathogens, such rust fungi, have been examined in the context of non-host resistance. Here, we discuss the use of B. distachyon in these various pathosystems. Exploiting B. distachyon to understand the mechanisms underpinning disease resistance to non-adapted rust fungi may provide effective and durable approaches to fend off these pathogens. The close phylogenetic relationship among Brachypodium spp. and grasses with industrial and agronomic value support harnessing this model plant to improve cropping systems and encourage its use in translational research.
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Affiliation(s)
- Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Claudia V. Castell-Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - James M. Bradeen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, MN, USA
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