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Thorat YE, Dutta TK, Jain PK, Subramaniam K, Sirohi A. A nematode-inducible promoter can effectively drives RNAi construct to confer Meloidogyne incognita resistance in tomato. PLANT CELL REPORTS 2023; 43:3. [PMID: 38117317 DOI: 10.1007/s00299-023-03114-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/30/2023] [Indexed: 12/21/2023]
Abstract
KEY MESSAGE Heterologous expression of a nematode-responsive promoter in tomato successfully driven the RNAi constructs to impart root-knot nematode resistance. The root-knot nematode Meloidogyne incognita seriously afflicts the global productivity of tomatoes. Nematode management options are extremely reliant on chemical methods, however, only a handful of nematicides are commercially available. Additionally, nematodes have developed resistance-breaking phenotypes against the commercially available Mi gene-expressing tomatoes. Nematode resistance in crop plants can be enhanced using the bio-safe RNAi technology, in which plants are genetically modified to express nematode gene-specific dsRNA/siRNA molecules. However, the majority of the RNAi crops conferring nematode tolerance have used constitutive promoters, which have many limitations. In the present study, using promoter-GUS fusion, we functionally validated two nematode-inducible root-specific promoters (pAt1g74770 and pAt2g18140, identified from Arabidopsis thaliana) in the Solanum lycopersicum-M. incognita pathosystem. pAt2g18140 was found to be nematode-responsive during 10-21 days post-inoculation (dpi) and became non-responsive during the late infection stage (28 dpi). In contrast, pAt1g74770 remained nematode-responsive for a longer duration (10-28 dpi). Next, a number of transgenic lines were developed that expressed RNAi constructs (independently targeting the M. incognita integrase and splicing factor genes) driven by the pAt1g74770 promoter. M. incognita parasitic success (measured by multiplication factor ratio) in pAt1g74770:integrase and pAt1g74770:splicing factor RNAi lines were significantly reduced by 60.83-74.93% and 69.34-75.31%, respectively, compared to the control. These data were comparable with the RNAi lines having CaMV35S as the promoter. Further, a long-term RNAi effect was evident, because females extracted from transgenic lines were of deformed shape with depleted transcripts of integrase and splicing factor genes. We conclude that pAt1g74770 can be an attractive alternative to drive localized expression of RNAi constructs rather than using a constitutive promoter. The pAt1g74770-driven gene silencing system can be expanded into different plant-nematode interaction models.
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Affiliation(s)
- Yogesh E Thorat
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Biological Control Centre, ICAR-Indian Institute of Sugarcane Research, Ahmednagar, Maharashtra, 413712, India
| | - Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Pradeep K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | | | - Anil Sirohi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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2
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Dutta TK, Ray S, Phani V. The status of the CRISPR/Cas9 research in plant-nematode interactions. PLANTA 2023; 258:103. [PMID: 37874380 DOI: 10.1007/s00425-023-04259-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/01/2023] [Indexed: 10/25/2023]
Abstract
MAIN CONCLUSION As an important biotic stressor, plant-parasitic nematodes afflict global crop productivity. Deployment of CRISPR/Cas9 system that selectively knock out host susceptibility genes conferred improved nematode tolerance in crop plants. As an important biotic stressor, plant-parasitic nematodes cause a considerable yield decline in crop plants that eventually contributes to a negative impact on global food security. Being obligate plant parasites, the root-knot and cyst nematodes maintain an intricate and sophisticated relationship with their host plants by hijacking the host's physiological and metabolic pathways for their own benefit. Significant progress has been made toward developing RNAi-based transgenic crops that confer nematode resistance. However, the strategy of host-induced gene silencing that targets nematode effectors is likely to fail because the induced silencing of effectors (which interact with plant R genes) may lead to the development of nematode phenotypes that break resistance. Lately, the CRISPR/Cas9-based genome editing system has been deployed to achieve host resistance against bacteria, fungi, and viruses. In these studies, host susceptibility (S) genes were knocked out to achieve resistance via loss of susceptibility. As the S genes are recessively inherited in plants, induced mutations of the S genes are likely to be long-lasting and confer broad-spectrum resistance. A number of S genes contributing to plant susceptibility to nematodes have been identified in Arabidopsis thaliana, rice, tomato, cucumber, and soybean. A few of these S genes were targeted for CRISPR/Cas9-based knockout experiments to improve nematode tolerance in crop plants. Nevertheless, the CRISPR/Cas9 system was mostly utilized to interrogate the molecular basis of plant-nematode interactions rather than direct research toward achieving tolerance in crop plants. The current standalone article summarizes the progress made so far on CRISPR/Cas9 research in plant-nematode interactions.
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Affiliation(s)
- Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Soham Ray
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Victor Phani
- Department of Agricultural Entomology, College of Agriculture, Uttar Banga Krishi Viswavidyalaya, Dakshin Dinajpur, West Bengal, 733133, India
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3
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Chou WC, Jha S, Linhoff MW, Ting JPY. The NLR gene family: from discovery to present day. Nat Rev Immunol 2023; 23:635-654. [PMID: 36973360 PMCID: PMC11171412 DOI: 10.1038/s41577-023-00849-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2023] [Indexed: 03/29/2023]
Abstract
The mammalian NLR gene family was first reported over 20 years ago, although several genes that were later grouped into the family were already known at that time. Although it is widely known that NLRs include inflammasome receptors and/or sensors that promote the maturation of caspase 1, IL-1β, IL-18 and gasdermin D to drive inflammation and cell death, the other functions of NLR family members are less well appreciated by the scientific community. Examples include MHC class II transactivator (CIITA), a master transcriptional activator of MHC class II genes, which was the first mammalian NBD-LRR-containing protein to be identified, and NLRC5, which regulates the expression of MHC class I genes. Other NLRs govern key inflammatory signalling pathways or interferon responses, and several NLR family members serve as negative regulators of innate immune responses. Multiple NLRs regulate the balance of cell death, cell survival, autophagy, mitophagy and even cellular metabolism. Perhaps the least discussed group of NLRs are those with functions in the mammalian reproductive system. The focus of this Review is to provide a synopsis of the NLR family, including both the intensively studied and the underappreciated members. We focus on the function, structure and disease relevance of NLRs and highlight issues that have received less attention in the NLR field. We hope this may serve as an impetus for future research on the conventional and non-conventional roles of NLRs within and beyond the immune system.
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Affiliation(s)
- Wei-Chun Chou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sushmita Jha
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Jodhpur, India
| | - Michael W Linhoff
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jenny P-Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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4
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Xu S, Tian P, Jiang Z, Chen X, Li B, Sun J, Zhang Z. Transcriptome analysis of two tobacco varieties with contrast resistance to Meloidogyne incognita in response to PVY M SN R infection. FRONTIERS IN PLANT SCIENCE 2023; 14:1213494. [PMID: 37701805 PMCID: PMC10493397 DOI: 10.3389/fpls.2023.1213494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023]
Abstract
Root-knot nematode (RKN) disease is a major disease of tobacco worldwide, which seriously hinders the improvement of tobacco yield and quality. Obvious veinal necrosis-hypersensitive responses are observed only in RKN-resistant lines infected by Potyvirus Y (PVY) MSNR, making this an effective approach to screen for RKN-resistant tobacco. RNA-seq analysis, real-time quantitative PCR (qRT-PCR) and functional enrichment analysis were conducted to gain insight into the transcription dynamics difference between G28 (RKN-resistant) and CBH (RKN-susceptible) varieties infected with PVY MSNR. Results showed that a total of 7900, 10576, 9921, 11530 and 12531 differentially expressed genes (DEGs) were identified between the two varieties at 0, 1, 3, 5, and 7 d after infection, respectively. DEGs were associated with plant hormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, and photosynthesis-related metabolic pathways. Additional DEGs related to starch and sucrose metabolism, energy production, and the indole-3-acetic acid signaling pathway were induced in CBH plants after infection. DEGs related to phenylpropanoid biosynthesis, abscisic acid, salicylic acid, brassinosteroids, and jasmonic acid signaling pathway were induced in G28 after infection. Our findings reveal DEGs that may contribute to differences in PVY MSNR resistance among tobacco varieties. These results help us to understand the differences in transcriptional dynamics and metabolic processes between RKN-resistant and RKN-susceptible varieties involved in tobacco-PVY MSNR interaction.
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Affiliation(s)
- Shixiao Xu
- College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, China
| | - Pei Tian
- China Tobacco Jiangsu Industry Co, Ltd. Xuzhou Cigarette Factory, Xuzhou, China
| | - Zhimin Jiang
- China Tobacco Zhejiang Industry Co, Ltd., Hangzhou, China
| | - Xiaoxiang Chen
- China Tobacco Zhejiang Industry Co, Ltd., Hangzhou, China
| | - Bo Li
- China Tobacco Zhejiang Industry Co, Ltd., Hangzhou, China
| | - Jutao Sun
- College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, China
| | - Zhiqiang Zhang
- College of Tobacco Science, Henan Agricultural University, National Tobacco Cultivation & Physiology & Biochemistry Research Centre, Scientific Observation and Experiment Station of Henan, Ministry of Agriculture, Zhengzhou, China
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5
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Understanding Molecular Plant–Nematode Interactions to Develop Alternative Approaches for Nematode Control. PLANTS 2022; 11:plants11162141. [PMID: 36015444 PMCID: PMC9415668 DOI: 10.3390/plants11162141] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/26/2022]
Abstract
Developing control measures of plant-parasitic nematodes (PPNs) rank high as they cause big crop losses globally. The growing awareness of numerous unsafe chemical nematicides and the defects found in their alternatives are calling for rational molecular control of the nematodes. This control focuses on using genetically based plant resistance and exploiting molecular mechanisms underlying plant–nematode interactions. Rapid and significant advances in molecular techniques such as high-quality genome sequencing, interfering RNA (RNAi) and gene editing can offer a better grasp of these interactions. Efficient tools and resources emanating from such interactions are highlighted herein while issues in using them are summarized. Their revision clearly indicates the dire need to further upgrade knowledge about the mechanisms involved in host-specific susceptibility/resistance mediated by PPN effectors, resistance genes, or quantitative trait loci to boost their effective and sustainable use in economically important plant species. Therefore, it is suggested herein to employ the impacts of these techniques on a case-by-case basis. This will allow us to track and optimize PPN control according to the actual variables. It would enable us to precisely fix the factors governing the gene functions and expressions and combine them with other PPN control tactics into integrated management.
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Marquez J, Hajihassani A, Davis RF. Evaluation of summer and winter cover crops for variations in host suitability for Meloidogyne incognita, M. arenaria and M. javanica. NEMATOLOGY 2022. [DOI: 10.1163/15685411-bja10172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Root-knot nematode (RKN) is an important pathogen on vegetables; therefore, planting a non- or poor host cover crop following a susceptible vegetable crop is a promising management option. This study builds upon previous studies and evaluates the variations in host status of cover crop candidates for reducing the reproduction of RKN populations (Meloidogyne incognita, M. arenaria and M. javanica) in Georgia, USA, to shed light on previous inconsistencies regarding the host status of cover crops and effectiveness in the field. Two glasshouse trials tested the host status of 14 plant species and 18 cultivars plus susceptible tomato ‘Rutgers’. Sixty days after inoculation, roots were evaluated for galling (GI) and egg mass index (EI). Gall formation was not a reliable indication of RKN reproduction for many cover crops, which had higher EI than GI. Based on GI, all cover crops were either non-hosts, ranging from non-hosts to poor hosts or poor hosts to all three RKN species, except blue lupine and hairy vetch, which were susceptible to all three RKN species and had a GI and EI equal to the susceptible tomato control. Based on EI, only bahiagrass, bermudagrass, marigold, millet and velvetbean were either non-hosts or ranged from non-hosts to poor hosts. Eleven cover crops varied in host status to the three RKN species screened, ranging from either non-host to poor hosts or poor hosts to susceptible, which could explain inconsistencies in glasshouse and field trials.
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Affiliation(s)
- Josiah Marquez
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
| | - Abolfazl Hajihassani
- Department of Entomology and Nematology, Fort Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Davie, FL 33314, USA
| | - Richard F. Davis
- Crop Genetics and Breeding Research Unit, United States Department of Agriculture – Agricultural Research Service, Tifton, GA 31793, USA
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Nguyen HT, Mantelin S, Ha CV, Lorieux M, Jones JT, Mai CD, Bellafiore S. Insights Into the Genetics of the Zhonghua 11 Resistance to Meloidogyne graminicola and Its Molecular Determinism in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:854961. [PMID: 35599898 PMCID: PMC9116194 DOI: 10.3389/fpls.2022.854961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Meloidogyne graminicola is a widely spread nematode pest of rice that reduces crop yield up to 20% on average in Asia, with devastating consequences for local and global rice production. Due to the ban on many chemical nematicides and the recent changes in water management practices in rice agriculture, an even greater impact of M. graminicola can be expected in the future, stressing the demand for the development of new sustainable nematode management solutions. Recently, a source of resistance to M. graminicola was identified in the Oryza sativa japonica rice variety Zhonghua 11 (Zh11). In the present study, we examine the genetics of the Zh11 resistance to M. graminicola and provide new insights into its cellular and molecular mechanisms. The segregation of the resistance in F2 hybrid populations indicated that two dominant genes may be contributing to the resistance. The incompatible interaction of M. graminicola in Zh11 was distinguished by a lack of swelling of the root tips normally observed in compatible interactions. At the cellular level, the incompatible interaction was characterised by a rapid accumulation of reactive oxygen species in the vicinity of the nematodes, accompanied by extensive necrosis of neighbouring cells. The expression profiles of several genes involved in plant immunity were analysed at the early stages of infection during compatible (susceptible plant) and incompatible (resistant plant) interactions. Notably, the expression of OsAtg4 and OsAtg7, significantly increased in roots of resistant plants in parallel with the cell death response, suggesting that autophagy is activated and may contribute to the resistance-mediated hypersensitive response. Similarly, transcriptional regulation of genes involved in hormonal pathways in Zh11 indicated that salicylate signalling may be important in the resistance response towards M. graminicola. Finally, the nature of the resistance to M. graminicola and the potential exploitation of the Zh11 resistance for breeding are discussed.
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Affiliation(s)
- Hue Thi Nguyen
- LMI RICE-2, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
- Department of Life Sciences, University of Science and Technology of Hanoi (USTH), Hanoi, Vietnam
| | - Sophie Mantelin
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) UMR 1355 Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Cuong Viet Ha
- Research Center of Tropical Plant Disease, Vietnam National University of Agriculture (VNUA), Hanoi, Vietnam
| | - Mathias Lorieux
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - John T. Jones
- The James Hutton Institute, Dundee, United Kingdom
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Chung Duc Mai
- LMI RICE-2, Agricultural Genetics Institute (AGI), Hanoi, Vietnam
| | - Stéphane Bellafiore
- PHIM Plant Health Institute, University of Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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8
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Palomares-Rius JE, Hasegawa K, Siddique S, Vicente CSL. Editorial: Protecting Our Crops - Approaches for Plant Parasitic Nematode Control. FRONTIERS IN PLANT SCIENCE 2021; 12:726057. [PMID: 34539718 PMCID: PMC8440992 DOI: 10.3389/fpls.2021.726057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Juan E. Palomares-Rius
- Institute for Sustainable Agriculture-Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Koichi Hasegawa
- Department of Environmental Biology, Chubu University, Kasugai, Japan
| | - Shahid Siddique
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States
| | - Claudia S. L. Vicente
- MED-Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research, University of Évora, Évora, Portugal
- INIAV, I.P. – Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, Portugal
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9
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Kozlowski DKL, Hassanaly‐Goulamhoussen R, Da Rocha M, Koutsovoulos GD, Bailly‐Bechet M, Danchin EGJ. Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest. Evol Appl 2021; 14:1844-1866. [PMID: 34295368 PMCID: PMC8288018 DOI: 10.1111/eva.13246] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022] Open
Abstract
Despite reproducing without sexual recombination, Meloidogyne incognita is an adaptive and versatile phytoparasitic nematode. This species displays a global distribution, can parasitize a large range of plants, and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability remain poorly known. At the whole-genome level, only a few single nucleotide variations have been observed across different geographical isolates with distinct ranges of compatible hosts. Exploring other factors possibly involved in genomic plasticity is thus important. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M. incognita. Here, we have annotated the TE content of M. incognita, analyzed the statistical properties of this TE landscape, and used whole-genome pool-seq data to estimate the mobility of these TEs across twelve geographical isolates, presenting variations in ranges of compatible host plants. DNA transposons are more abundant than retrotransposons, and the high similarity of TE copies to their consensus sequences suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed substantial variations across the different isolates. Overall, variations in TE frequencies across isolates followed their phylogenetic divergence, suggesting TEs participate in the species diversification. Compared with the M. incognita reference genome, we detected isolate and lineage-specific de novo insertion of some TEs, including within genic regions or in the upstream regulatory regions. We validated by PCR the insertion of some of these TEs inside genic regions, confirming TE movements have possible functional impacts. Overall, we show DNA transposons can drive genomic plasticity in M. incognita and their role in genome evolution of other parthenogenetic animal deserves further investigation.
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10
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Sharma M, Saini I, Kaushik P, Aldawsari MM, Balawi TA, Alam P. Mycorrhizal fungi and Pseudomonas fluorescens application reduces root-knot nematode ( Meloidogyne javanica) infestation in eggplant. Saudi J Biol Sci 2021; 28:3685-3691. [PMID: 34220219 PMCID: PMC8241595 DOI: 10.1016/j.sjbs.2021.05.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 10/26/2022] Open
Abstract
Eggplant cultivation is subjected to attacks by numbers of pests and diseases from the nursery stage until harvest. Root-knot nematode (M. javanica) is one of the most significant restrictions in the successful cultivation of eggplant as it damages the crop year-round. One of the most essential classes of plant symbionts is arbuscular mycorrhizal fungi (AMF) and phosphate solubilizing bacteria (PSB), which significantly impact plant development, feeding, disease tolerance, and resistance to M. javanica. Eggplant seedlings were inoculated with two mycorrhizal fungi, Glomus mosseae (Gm) and Gigaspora gigantea (Gg), together with the phosphate-solubilizing bacteria (PSB) Pseudomonas fluorescens (Pf; ATCC-17400) under the presence of nematodes inoculation of Meloidogyne javanica as 1000 eggs of M. javanica in each pot. Observations were recorded for 9 morphological traits, 6 fruit morphometric traits using Tomato Analyzer (version 4) software program, and 4 fruit biochemical traits. Along with the data recorded for mycorrhization (%), number of galls and reaction to RKN. Plants inoculated with the consortium (Pf + Gm + Gg) performed substantially better for most traits. Furthermore, the eggplant plants treated with consortium developed the highest levels of fruit biochemical content along with the highest level of mycorrhization (68.20%). Except for certain fruit morphometric traits, the treatment containing Pf + Gg outperformed the treatment containing Pf + Gm. Overall, this research showed that AM fungi could be a sustainable solution to the eggplant RKN problem.
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Affiliation(s)
- Meenakshi Sharma
- Department of Botany, Kurukshetra University, Kurukshetra 136118, Haryana, India
| | - Ishan Saini
- Department of Botany, Kurukshetra University, Kurukshetra 136118, Haryana, India
| | - Prashant Kaushik
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Mona Mohammed Aldawsari
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Thamer Al Balawi
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
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11
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Nilusmas S, Mercat M, Perrot T, Djian‐Caporalino C, Castagnone‐Sereno P, Touzeau S, Calcagno V, Mailleret L. Multi-seasonal modelling of plant-nematode interactions reveals efficient plant resistance deployment strategies. Evol Appl 2020; 13:2206-2221. [PMID: 33005219 PMCID: PMC7513734 DOI: 10.1111/eva.12989] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023] Open
Abstract
Root-knot nematodes, Meloidogyne spp., are soil-borne polyphagous pests with major impact on crop yield worldwide. Resistant crops efficiently control avirulent root-knot nematodes, but favour the emergence of virulent forms. Since virulence is associated with fitness costs, susceptible crops counter-select virulent root-knot nematodes. In this study, we identify optimal rotation strategies between susceptible and resistant crops to control root-knot nematodes and maximize crop yield. We developed an epidemiological model describing the within-season dynamics of avirulent and virulent root-knot nematodes on susceptible or resistant plant root-systems, and their between-season survival. The model was fitted to experimental data and used to predict yield-maximizing rotation strategies, with special attention to the impact of epidemic severity and genetic parameters. Crop rotations were found to be efficient under realistic parameter ranges. They were characterized by low ratios of resistant plants and were robust to parameter uncertainty. Rotations provide significant gain over resistant-only strategies, especially under intermediate fitness costs and severe epidemic contexts. Switching from the current general deployment of resistant crops to custom rotation strategies could not only maintain or increase crop yield, but also preserve the few and valuable R-genes available.
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Affiliation(s)
- Samuel Nilusmas
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
| | - Mathilde Mercat
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
| | - Thomas Perrot
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
| | | | | | - Suzanne Touzeau
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
| | | | - Ludovic Mailleret
- Université Côte d'Azur, INRAE, CNRS, ISASophia AntipolisFrance
- Université Côte d'Azur, INRIA, INRAE, CNRS, Sorbonne Université, BIOCORESophia AntipolisFrance
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12
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Parisi M, Alioto D, Tripodi P. Overview of Biotic Stresses in Pepper ( Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics. Int J Mol Sci 2020; 21:E2587. [PMID: 32276403 PMCID: PMC7177692 DOI: 10.3390/ijms21072587] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 12/16/2022] Open
Abstract
Pepper (Capsicum spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant. The genus includes over 30 species, five of which (C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens) are domesticated and mainly grown for consumption as food and for non-food purposes (e.g., cosmetics). The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security, the growing consumers' demand for food. Furthermore, demographic trends and changes to climate require more efficient use of plant genetic resources in breeding programs. Increases in pepper consumption have been observed in the past 20 years, and for maintaining this trend, the development of new resistant and high yielding varieties is demanded. The range of pathogens afflicting peppers is very broad and includes fungi, viruses, bacteria, and insects. In this context, the large number of accessions of domesticated and wild species stored in the world seed banks represents a valuable resource for breeding in order to transfer traits related to resistance mechanisms to various biotic stresses. In the present review, we report comprehensive information on sources of resistance to a broad range of pathogens in pepper, revisiting the classical genetic studies and showing the contribution of genomics for the understanding of the molecular basis of resistance.
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Affiliation(s)
- Mario Parisi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, Italy;
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici, Naples, Italy;
| | - Pasquale Tripodi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, Italy;
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Koutsovoulos GD, Marques E, Arguel M, Duret L, Machado ACZ, Carneiro RMDG, Kozlowski DK, Bailly‐Bechet M, Castagnone‐Sereno P, Albuquerque EVS, Danchin EGJ. Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest. Evol Appl 2020; 13:442-457. [PMID: 31993088 PMCID: PMC6976969 DOI: 10.1111/eva.12881] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
The root-knot nematodes are the most devastating worms to worldwide agriculture with Meloidogyne incognita being the most widely distributed and damaging species. This parasitic and ecological success seems surprising given its supposed obligatory clonal reproduction. Clonal reproduction has been suspected based on cytological observations but, so far, never confirmed by population genomics data. As a species, M. incognita is highly polyphagous with thousands of host plants. However, different M. incognita isolates present distinct and overlapping patterns of host compatibilities. Historically, four "host races" had been defined as a function of ranges of compatible and incompatible plants. In this study, we used population genomics to assess whether (a) reproduction is actually clonal in this species, (b) the host races follow an underlying phylogenetic signal or, rather represent multiple independent transitions, and (c) how genome variations associate with other important biological traits such as the affected crops and geographical distribution. We sequenced the genomes of 11 M. incognita isolates across Brazil that covered the four host races in replicates. By aligning the genomic reads of these isolates to the M. incognita reference genome assembly, we identified point variations. Analysis of linkage disequilibrium and 4-gametes test showed no evidence for recombination, corroborating the clonal reproduction of M. incognita. The few point variations between the isolates showed no significant association with the host races, the geographical origin of the samples, or the crop on which they have been collected. Addition of isolates from other locations around the world confirmed this lack of underlying phylogenetic signal. This suggests multiple gains and losses of parasitic abilities and adaptations to different environments account for the broad host spectrum and wide geographical distribution of M. incognita and thus to its high economic impact. This surprising adaptability without sex poses both evolutionary and agro-economic challenges.
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Affiliation(s)
| | - Eder Marques
- Embrapa Recursos Genéticos e BiotecnologiaBrasíliaBrazil
| | | | - Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558CNRSUniversité Lyon 1Université de LyonVilleurbanneFrance
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Tomato Natural Resistance Genes in Controlling the Root-Knot Nematode. Genes (Basel) 2019; 10:genes10110925. [PMID: 31739481 PMCID: PMC6896013 DOI: 10.3390/genes10110925] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 02/01/2023] Open
Abstract
The root-knot nematode (RKN) is one of the most dangerous and widespread types of nematodes affecting tomatoes. There are few methods for controlling nematodes in tomatoes. Nature resistance genes (R-genes) are important in conferring resistance against nematodes. These genes that confer resistance to the RKN have already been identified as Mi-1, Mi-2, Mi-3, Mi-4, Mi-5, Mi-6, Mi-7, Mi-8, Mi-9, and Mi-HT. Only five of these genes have been mapped. The major problem is that their resistance breaks down at high temperatures. Some of these genes still work at high temperatures. In this paper, the mechanism and characteristics of these natural resistance genes are summarized. Other difficulties in using these genes in the resistance and how to improve them are also mentioned.
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Vieira P, Gleason C. Plant-parasitic nematode effectors - insights into their diversity and new tools for their identification. CURRENT OPINION IN PLANT BIOLOGY 2019; 50:37-43. [PMID: 30921686 DOI: 10.1016/j.pbi.2019.02.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 05/20/2023]
Abstract
Plant-parasitic nematodes (PPNs) are a large group of obligate biotrophic pathogens that secrete molecules, called effectors, involved in parasitism. The majority of work in molecular phytonematology has focused on the root-knot and cyst nematodes, which are both sedentary endoparasitic nematodes. More recently, inexpensive sequencing technology has facilitated effector searches in PPNs with different parasitic lifestyles. Work in different PPN species suggests that effectors are diverse, and selection pressure from plant hosts has contributed to the presence of large, expanded effector gene families. The identification of promoter elements/motifs preceding effector gene sequences suggests that promoter analysis can computationally predict new putative effectors. However, until a method of genetic transformation is available for PPNs, work on characterizing effectors will be hindered.
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Affiliation(s)
- Paulo Vieira
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, United States
| | - Cynthia Gleason
- Dept. of Plant Pathology, Washington State University, Pullman, WA 99164, United States.
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16
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Expósito A, García S, Giné A, Escudero N, Sorribas FJ. Cucumis metuliferus reduces Meloidogyne incognita virulence against the Mi1.2 resistance gene in a tomato-melon rotation sequence. PEST MANAGEMENT SCIENCE 2019; 75:1902-1910. [PMID: 30536835 DOI: 10.1002/ps.5297] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Susceptible tomato cv. Durinta, ungrafted or grafted onto cv. Aligator resistant rootstock, both followed by the susceptible melon cv. Paloma, ungrafted or grafted onto Cucumis metuliferus BGV11135, and in the reverse order, were cultivated from 2015 to 2017 in the same plots in a plastic greenhouse, infested or not with Meloidogyne incognita. For each crop, soil nematode densities, galling index, number of eggs per plant and crop yield were determined. Virulence selection was evaluated in pot experiments. RESULTS In the tomato-melon rotation, nematode densities increased progressively for the grafted tomato, being higher than for ungrafted plants at the end of the study; this was not the case in the melon-tomato rotation. Grafted crops yielded more than ungrafted crops in the infested plots. Virulence against the Mi1.2 gene was detected, but not against C. metuliferus. Reproduction of M. incognita on the resistant tomato was ∼ 120% that on the susceptible cultivar after the first grafted tomato crop, but this decreased to just 25% at the end of the experiment. CONCLUSION Alternating different resistant plant species suppresses nematode population growth rate and yield losses. Although this strategy does not prevent virulence selection, the level was reduced. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Alejandro Expósito
- Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Sergi García
- Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Ariadna Giné
- Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Nuria Escudero
- Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Francisco Javier Sorribas
- Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Barcelona, Spain
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Castagnone‐Sereno P, Mulet K, Danchin EGJ, Koutsovoulos GD, Karaulic M, Da Rocha M, Bailly‐Bechet M, Pratx L, Perfus‐Barbeoch L, Abad P. Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant‐parasitic nematode
Meloidogyne incognita. Mol Ecol 2019; 28:2559-2572. [DOI: 10.1111/mec.15095] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 03/11/2019] [Accepted: 04/01/2019] [Indexed: 01/05/2023]
Affiliation(s)
| | - Karine Mulet
- INRAUniversité Côte d'AzurCNRSISA Sophia Antipolis France
| | | | | | | | | | | | - Loris Pratx
- INRAUniversité Côte d'AzurCNRSISA Sophia Antipolis France
| | | | - Pierre Abad
- INRAUniversité Côte d'AzurCNRSISA Sophia Antipolis France
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18
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Abdelsamad N, Regmi H, Desaeger J, DiGennaro P. Nicotinamide adenine dinucleotide induced resistance against root-knot nematode Meloidogyne hapla is based on increased tomato basal defense. J Nematol 2019; 51:1-10. [PMID: 31088034 PMCID: PMC6930958 DOI: 10.21307/jofnem-2019-022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Indexed: 11/11/2022] Open
Abstract
Root-knot nematodes (RKN; Meloidogyne spp.) are among the most damaging pests to tomato production in the USA and worldwide, with yield losses ranging from 25 to 100%. Host resistance conferred by the Mi gene in tomato is effective against some species of RKN (e.g. M. incognita, M. javanica, and M. arenaria); however, there are virulent species and lines including M. hapla and M. eterolobii that break Mi-mediated resistance. Plant innate immunity is another possible form of defense against pathogen attack and is known to be induced by chemical elicitors. Nicotinamide adenine dinucleotide (NAD) is one such chemical elicitor that regulates plant defense responses to multiple biotic stresses. In this study, we investigated the role of NAD in the context of induced tomato innate immunity and RKN pathogenicity in two tomato cultivars; VFN and Rutgers, with and without Mi, respectively. Single soil drench application of NAD 24 hr before nematode inoculation significantly induced defense response pathways, reduced infective-juveniles penetration, number of galls, and increased plant mass in both cultivars. Importantly, we observed no direct toxic effects of NAD on nematode viability and infectivity. The results presented here suggest that NAD induces resistance against RKN pathogenicity likely through the accumulation of tomato basal defense responses rather than the direct effect on the infective-juveniles behavior.
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Affiliation(s)
- Noor Abdelsamad
- Department of Entomology and Nematology, College of Agriculture and Animal Science, University of Florida , Gainesville
| | - H Regmi
- Department of Entomology and Nematology, College of Agriculture and Animal Science, University of Florida , Gainesville ; Gulf Coast Research and Education Center, University of Florida , Wimauma
| | - J Desaeger
- Gulf Coast Research and Education Center, University of Florida , Wimauma
| | - P DiGennaro
- Department of Entomology and Nematology, College of Agriculture and Animal Science, University of Florida , Gainesville
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19
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Sobkowiak R, Bojarska N, Krzyżaniak E, Wągiel K, Ntalli N. Chemoreception of botanical nematicides by Meloidogyne incognita and Caenorhabditis elegans. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2018; 53:493-502. [PMID: 29708833 DOI: 10.1080/03601234.2018.1462936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Plant-parasitic nematodes, such as Meloidogyne incognita, cause serious damage to various agricultural crops worldwide, and their control necessitates environmentally safe measures. We have studied the effects of plant secondary metabolites on M. incognita locomotion, as it is an important factor affecting host inoculation inside the soil. We compared the effects to the respective behavioral responses of the model saprophytic nematode Caenorhabditis elegans. The tested botanical nematicides, all reported to be active against Meloidogyne sp. in our previous works, are small molecular weight molecules (acids, alcohols, aldehydes, and ketones). Here, we specifically report on the attractant or repellent properties of trans-anethole, (E,E)-2,4-decadienal, (E)-2-decenal, fosthiazate, and 2-undecanone. The treatments for both nematode species were made at sublethal concentration levels, namely, 1 mM (<EC50), and the chemical controls used for the experiments were the commercial nematicides fosthiazate and oxamyl. According to our results, trans-anethole, decenal, and oxamyl attract C. elegans, while 2-undecanone strongly attracts M. incognita. These findings can be of use in the development of nematicidal formulations, contributing to the disruption of nematode chemotaxis to root systems.
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Affiliation(s)
- Robert Sobkowiak
- a Department of Cell Biology , Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University , Poznań , Poland
| | - Natalia Bojarska
- a Department of Cell Biology , Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University , Poznań , Poland
| | - Emilia Krzyżaniak
- a Department of Cell Biology , Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University , Poznań , Poland
| | - Karolina Wągiel
- a Department of Cell Biology , Faculty of Biology, Institute of Experimental Biology, Adam Mickiewicz University , Poznań , Poland
| | - Nikoletta Ntalli
- b Department of Pesticides Control & Phytopharmacy , Benaki Phytopathological Institute, Laboratory of Biological Control of Pesticides , Kifissia , Athens , Greece
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20
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Eoche-Bosy D, Gautier M, Esquibet M, Legeai F, Bretaudeau A, Bouchez O, Fournet S, Grenier E, Montarry J. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida. Mol Ecol 2017; 26:4700-4711. [PMID: 28734070 DOI: 10.1111/mec.14240] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 12/30/2022]
Abstract
Improving resistance durability involves to be able to predict the adaptation speed of pathogen populations. Identifying the genetic bases of pathogen adaptation to plant resistances is a useful step to better understand and anticipate this phenomenon. Globodera pallida is a major pest of potato crop for which a resistance QTL, GpaVvrn , has been identified in Solanum vernei. However, its durability is threatened as G. pallida populations are able to adapt to the resistance in few generations. The aim of this study was to investigate the genomic regions involved in the resistance breakdown by coupling experimental evolution and high-density genome scan. We performed a whole-genome resequencing of pools of individuals (Pool-Seq) belonging to G. pallida lineages derived from two independent populations having experimentally evolved on susceptible and resistant potato cultivars. About 1.6 million SNPs were used to perform the genome scan using a recent model testing for adaptive differentiation and association to population-specific covariables. We identified 275 outliers and 31 of them, which also showed a significant reduction in diversity in adapted lineages, were investigated for their genic environment. Some candidate genomic regions contained genes putatively encoding effectors and were enriched in SPRYSECs, known in cyst nematodes to be involved in pathogenicity and in (a)virulence. Validated candidate SNPs will provide a useful molecular tool to follow frequencies of virulence alleles in natural G. pallida populations and define efficient strategies of use of potato resistances maximizing their durability.
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Affiliation(s)
- D Eoche-Bosy
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - M Gautier
- CBGP, INRA, IRD, CIRAD, Montpellier SupAgro, Montferrier-sur-Lez, France.,IBC, Montpellier, France
| | - M Esquibet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - F Legeai
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenScale, INRIA, Rennes, France
| | - A Bretaudeau
- IGEPP, BIPAA, INRA, Agrocampus Ouest, Université de Rennes 1, Rennes, France.,IRISA, GenOuest COre Facility, INRIA, Rennes, France
| | - O Bouchez
- GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France.,GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - S Fournet
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - E Grenier
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
| | - J Montarry
- IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, Le Rheu, France
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21
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Duke SO. Summing up 2015. PEST MANAGEMENT SCIENCE 2016; 72:5-7. [PMID: 26769292 DOI: 10.1002/ps.4176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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