FACCE ERA-NET+ New generation sustainable tools to control emerging mite pests under climate change
Lead Research Organisation:
East Malling Research (United Kingdom)
Department Name: Science
Abstract
Climate change will have serious and profound impacts on pests and diseases of agricultural crops in Europe and it is vital that new tools and management methods are developed to tackle the problems that will increasingly threaten EU food production as a result.
* In this project, for the first time, comprehensive state-of-the-art genomic, metabolomic and modelling methods will be used to develop the necessary tools and management methods for tackling spider mites that are increasingly serious pests of many important crops throughout the EU.
* This will not only be an outstanding contribution to spider mite management under climate change but crucially be an example, demonstrating how the best and most advanced methods can be applied to the vast array of other important pests and diseases that will develop because of climate change.
* Spider mite outbreaks and crop damage are strongly favoured by high temperatures and drought stress caused by climate change (especially in combination) that will have a serious impact not only in southern Europe and the Mediterranean basin but also throughout Europe because of more extreme weather events including heat waves and droughts. The two-spotted spider mite, Tetranychus urticae (TSSM), is a highly polyphagous species which attacks many crops and is adapting to attack several important new crops including grape vines and corn. Tetranychus evansi (TE) is a recently arrived alien invasive pest that is spreading through Europe and attacks important solanacious crops including tomato and potato.
* Phytoseiid predatory mites are the main naturally occurring predators that help regulate spider mite populations and are introduced as biocontrol agents for control of spider mites in commercial crops. They are sensitive to broad-spectrum insecticides and the increasing use of these insecticides to control other alien invasive pests, e.g. spotted wing Drosophila and brown marmorated stink bug, are harming them and causing more serious outbreaks of spider mites.
* In this project, teams from 7 EU countries and Canada will model the performance of each organism in plant-spider mite-predators tritrophic interaction under changing climatic (CC) conditions. This will be accompanied by determination of reciprocal transcriptional and metabolomics changes in plants (tomato and strawberry) and spider mites (TSSM and TE) upon their interactions under normal and CC scenarios. In addition, we will search for elicitors and effectors of TSSM and TE that are capable of modulating plant defences. Using Systems biology approaches, we will link performance of plants and mites with genome-wide changes in their responses. Thus, our study will not only model performance of organisms involve in tritrophic interaction, but will also model processes whose changes lead to modulated performance under CC. This comprehensive knowledge can then be used to develop new tools and methods for climate-smart pest control.
* In this project, for the first time, comprehensive state-of-the-art genomic, metabolomic and modelling methods will be used to develop the necessary tools and management methods for tackling spider mites that are increasingly serious pests of many important crops throughout the EU.
* This will not only be an outstanding contribution to spider mite management under climate change but crucially be an example, demonstrating how the best and most advanced methods can be applied to the vast array of other important pests and diseases that will develop because of climate change.
* Spider mite outbreaks and crop damage are strongly favoured by high temperatures and drought stress caused by climate change (especially in combination) that will have a serious impact not only in southern Europe and the Mediterranean basin but also throughout Europe because of more extreme weather events including heat waves and droughts. The two-spotted spider mite, Tetranychus urticae (TSSM), is a highly polyphagous species which attacks many crops and is adapting to attack several important new crops including grape vines and corn. Tetranychus evansi (TE) is a recently arrived alien invasive pest that is spreading through Europe and attacks important solanacious crops including tomato and potato.
* Phytoseiid predatory mites are the main naturally occurring predators that help regulate spider mite populations and are introduced as biocontrol agents for control of spider mites in commercial crops. They are sensitive to broad-spectrum insecticides and the increasing use of these insecticides to control other alien invasive pests, e.g. spotted wing Drosophila and brown marmorated stink bug, are harming them and causing more serious outbreaks of spider mites.
* In this project, teams from 7 EU countries and Canada will model the performance of each organism in plant-spider mite-predators tritrophic interaction under changing climatic (CC) conditions. This will be accompanied by determination of reciprocal transcriptional and metabolomics changes in plants (tomato and strawberry) and spider mites (TSSM and TE) upon their interactions under normal and CC scenarios. In addition, we will search for elicitors and effectors of TSSM and TE that are capable of modulating plant defences. Using Systems biology approaches, we will link performance of plants and mites with genome-wide changes in their responses. Thus, our study will not only model performance of organisms involve in tritrophic interaction, but will also model processes whose changes lead to modulated performance under CC. This comprehensive knowledge can then be used to develop new tools and methods for climate-smart pest control.
Technical Summary
WP1: Species distribution models and tritrophic interactions under CC scenarios in Europe
The combined effects of abiotic and biotic stress on the development and distribution of two mite pests, T. urticae (TSSM) and T. evansi (TE), and their predatory mite natural enemies, Neoseiulus californicus and Euseius gallicus under CC scenarios will be investigated through experimental and modelling approaches.
WP2: Reciprocal transcriptional responses of mites and plants under CC
The aim of this WP is to determine tomato and strawberry transcriptional responses to mite herbivory under varying CC (drought stress, high temperature).
WP3: Identification of plant and mite metabolites upon herbivory and CC
The objective of this work package is to comprehensively analyse the effect of CC (increasing temperature and reduced water availability) on the metabolome/lipidome of tomato and strawberry plants for both the non-infected and the mite-infected state.
WP4: Identification of mite elicitors/effectors and their activities
We aim to uncover mite elicitors/effectors and the interacting pathways in the plant. Modulation of plant defences by herbivorous arthropods has been shown to be meditated by salivary secretions and therefore mite saliva is a primary source to uncover potential elicitors/effectors.
WP5: Systems biology: Correlation of plant transcriptomics and metabolomic responses with tritrophic performance and mite transcriptome responses
Data from WPs 1-3 will be integrated with the aim to correlate transcriptional and metabolic changes (WPs 2 and 3) in different plant species subjected to the herbivory and adaptations of spider mites. To ultimately integrate gene expression and metabolite screens, we will have to map the current gene annotations of mites, strawberry and tomato on pathways.
The combined effects of abiotic and biotic stress on the development and distribution of two mite pests, T. urticae (TSSM) and T. evansi (TE), and their predatory mite natural enemies, Neoseiulus californicus and Euseius gallicus under CC scenarios will be investigated through experimental and modelling approaches.
WP2: Reciprocal transcriptional responses of mites and plants under CC
The aim of this WP is to determine tomato and strawberry transcriptional responses to mite herbivory under varying CC (drought stress, high temperature).
WP3: Identification of plant and mite metabolites upon herbivory and CC
The objective of this work package is to comprehensively analyse the effect of CC (increasing temperature and reduced water availability) on the metabolome/lipidome of tomato and strawberry plants for both the non-infected and the mite-infected state.
WP4: Identification of mite elicitors/effectors and their activities
We aim to uncover mite elicitors/effectors and the interacting pathways in the plant. Modulation of plant defences by herbivorous arthropods has been shown to be meditated by salivary secretions and therefore mite saliva is a primary source to uncover potential elicitors/effectors.
WP5: Systems biology: Correlation of plant transcriptomics and metabolomic responses with tritrophic performance and mite transcriptome responses
Data from WPs 1-3 will be integrated with the aim to correlate transcriptional and metabolic changes (WPs 2 and 3) in different plant species subjected to the herbivory and adaptations of spider mites. To ultimately integrate gene expression and metabolite screens, we will have to map the current gene annotations of mites, strawberry and tomato on pathways.
Planned Impact
The GENOMITE research will produce knowledge with broad impacts on climate smart agriculture and pest control, basic science, development of tools and agricultural practices and agricultural industry, policy-making and society at large.
* Development of basic knowledge for climate smart agriculture
Our multidisciplinary consortium aims to produce basic understanding and fundamental knowledge on interactions between crop plants, pests and climate. The understanding of the holistic interaction between these 3 systems is currently lacking and prevents development of climate-smart agriculture and pest control concepts.
* Development of technologies and applications: agricultural industry
Our basic discoveries represent a novel avenue for development of climate-smart pest control technologies. Therefore, commercialization plan and experience of the GENOMITE consortium is critical for the development of the novel technologies.
* Impact on climate smart agriculture practices and approaches
The GENOMITE discoveries have a potential to introduce climate-smart spider mite control practices in agriculture.
* Societal impact: education and dissemination
The GENOMITE consortium has an ambitious plan to disseminate and educate broader public on scientific approaches to develop climate-smart pest control.
* Impact on policy development:
Our studies will have an important impact on EU policy development. Our project focuses on understanding and management of pests induced by climate change (T. urticae) and management of invasive introduces species (T. evansi). These case studies have a potential to influence development of agricultural policies.
In conclusion, the GENOMITE project has potential for development of broad impact including creation of new knowledge, technologies and approaches for climate-smart agriculture and sustainable pest control. In addition, impacts at the societal and policy-making level have potential to develop measures that equip policy makers with new tools to efficiently tackle the impact of climate change on agriculture and to educate general society on scientific potentials for sustainable agricultural development. The novelty of this approach, the international and trans-continental composition of our group and its critical mass of researchers puts us in a position to develop this ambitious program with relatively limited financial input but with broad impact in area of climate-smart agriculture.
* Development of basic knowledge for climate smart agriculture
Our multidisciplinary consortium aims to produce basic understanding and fundamental knowledge on interactions between crop plants, pests and climate. The understanding of the holistic interaction between these 3 systems is currently lacking and prevents development of climate-smart agriculture and pest control concepts.
* Development of technologies and applications: agricultural industry
Our basic discoveries represent a novel avenue for development of climate-smart pest control technologies. Therefore, commercialization plan and experience of the GENOMITE consortium is critical for the development of the novel technologies.
* Impact on climate smart agriculture practices and approaches
The GENOMITE discoveries have a potential to introduce climate-smart spider mite control practices in agriculture.
* Societal impact: education and dissemination
The GENOMITE consortium has an ambitious plan to disseminate and educate broader public on scientific approaches to develop climate-smart pest control.
* Impact on policy development:
Our studies will have an important impact on EU policy development. Our project focuses on understanding and management of pests induced by climate change (T. urticae) and management of invasive introduces species (T. evansi). These case studies have a potential to influence development of agricultural policies.
In conclusion, the GENOMITE project has potential for development of broad impact including creation of new knowledge, technologies and approaches for climate-smart agriculture and sustainable pest control. In addition, impacts at the societal and policy-making level have potential to develop measures that equip policy makers with new tools to efficiently tackle the impact of climate change on agriculture and to educate general society on scientific potentials for sustainable agricultural development. The novelty of this approach, the international and trans-continental composition of our group and its critical mass of researchers puts us in a position to develop this ambitious program with relatively limited financial input but with broad impact in area of climate-smart agriculture.
Organisations
- East Malling Research (United Kingdom) (Lead Research Organisation)
- Western University (Collaboration)
- University of Amsterdam (Collaboration)
- Spanish National Research Council (CSIC) (Collaboration)
- University of Ghent (Collaboration)
- Technical University of Madrid (Collaboration)
- Cyprus University of Technology (Collaboration)
- MetaSysx Gmbh (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
| Description | See responses for BB/M018121/2 |
| Exploitation Route | See responses for BB/M018121/2 |
| Sectors | Agriculture, Food and Drink,Environment,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Description | GENOMITE: New generation sustainable tools to control emerging mite pests |
| Organisation | Cyprus University of Technology |
| Department | Department of Agricultural Sciences, Biotechnology and Food Science |
| Country | Cyprus |
| Sector | Academic/University |
| PI Contribution | Prof Jerry Cross, EMR, is overall leader and coordinator of this project. EMR is responsible for 3 research areas in the project: 1) studying the behaviour and interactions between mites and their natural enemies under simulated CC conditions which will generate the data necessary for developing models to predict the effect of different CC scenarios on biocontrol outcomes; 2) EMR will collaborate with other modelling groups in the consortium to develop models predicting the distribution and population size of mites and their natural enemies using published and new data generated in this project. In particular EMRs contribution will be on using network theory to model the spread of the mites and natural enemies across the EU. The network theory will consider the physical distance, geographical barriers and environmental conditions when modelling the spatial spread; 3) Finally, EMR will be responsible for characterising early host responses to pest attack. This will include the characterisation of transcriptomes at several intervals after mite attack. The data will be mined (analysed) against the diploid strawberry and the recently published octoploid strawberry draft genome to identify particular genes in host response. This will identify candidate resistance genes which can be deployed for combating climate change. |
| Collaborator Contribution | INRA INRA is responsible for work on spider mite/predatory mite species distribution models and tritrophic interactions under CC scenarios in Europe:1) Recording occurrences of pests and predators in the EU 2) Mite-plant interactions under varying climatic conditions 3) Assessing demographic parameters and dispersion of mite pests and predators under climate change conditions 4) Predation capacity of predators and tritrophic interactions under simulated climate change conditions 5) Predicting distributions of mites and effectiveness of predator control under CC 6) Field validating the pest-natural enemy distribution model and effectiveness of biological control. Provision of glasshouse experimental facilities for large scale collaborative experiment for other work areas. MetaSysx Gmbh Responsible for the (coordination of the) metabolome/lipidome analysis of the biological samples which will be generated by the different experimental groups. Plant material of plants kept at different environmental conditions with and without challenge to spider mites as well as mites fed on different plant materials will be subjected to three different analytical platforms: Lipidomics primary metabolites and secondary metabolites resulting in several hundred up to thousand metabolites. Cyprus University of Technology (CUT) The group at CUT is recording the current distribution of pests and natural enemies, modelling the distribution of pest and natural enemies in response to climate change and validating the predictions of models intensive field sampling and experimentation in farmer's fields in Cyprus. University of Amsterdam (UvA) The UvA research in this proposal covers two distinct areas. UvA is in charge of effector identification and characterization. 1) We will perform LC-MS analysis on saliva of Tetranychus urticae and T evansi with previously validated methods devised in our group and construct a strand-specific and quantitative transcriptome of the mite gnathosoma. We will further prioritize candidates with our expertise in genome analysis and via in planta expression tools. Candidate effectors will be tested after infiltration of plants with peptides or Agrobactrium tumefaciens transient assays (ATTA) in collaboration with the plant physiology group (prof. dr. Haring), phytopathology group (prof. dr. Cornelissen) and other partners of this project. 2) UvA will identify differentially expressed genes in mites feeding on tomato and strawberry under the described conditions (Task 2.5) to be further linked with plant transcriptomics and metabolomic profiles. VIB VIB work is to link the annotation that we produced on tomato, Tetranychus evansi and Tetranychus urticae with the results from the project. This will involve handling the RNAseq to provide expression values for the genes from all 3 listed genomes. For the strawberry genome VIB will rely on an assembled transcriptome (from public data (35 sets available)) that might have to be complemented for the specific strain to be used in the project. In order to be able to compare the genome's expressed genes upon mite infection table of orthological relationships will be established between strawberry and tomato. The same is true for the mites. This orthology will allow us to compare comparable trends in gene expression across species. To build a bridge between metabolites and genes we plan to investigate and setup a framework that would allow VIB to store reactions from pathways and link those with the genes from the genomes included in this study. Several pathway databases and platforms exist from which we could start to implement or adapt to the project's needs. The publically available pathway data will then also serve as a starting material to link what is generally known. From the results from the other WPs we hope to be able to add more reactions and complement pathways. Besides enzymatic pathways, in this project, we also have an interest for regulatory networks, mainly in the mites aiming at identifying the genes regulated and secreted in the salivary glands. Goal here is to find the peptides that might influence the host plant upon feeding. For this we will analyze the RNAseq data. The regulators and their target genes will be identified from LeMoNe analyses and potential regulatory target sites will be predicted. Universidad Politecnica de Madrid (UPM) UPM work focusses on the analysis of transcriptional tomato responses to mites under varying drought stress and high temperature which will generate the data necessary to identify genes/proteins in different CC scenarios and to correlate them with specific metabolic pathways involved in the defense response. The UPM team will collaborate in the analysis of interactions of putative mite effectors with plant physiology through infiltration of peptides or transient expression of effectors in plants and in the identification of candidate transcription factors responsible for reprograming/suppression of induced defense response and in the study of generated plant pathway databases to finally build an orthologous gene-set between tomato and strawberry. This will identify and validate candidate resistance genes which can be deployed for combating pests under the climate change scenario. Consejo Superior de Investigaciones (CSIC) CSIC research in this project focuses on determining which varying environmental conditions (temperature and water stress) have a measurable effect on the performance of Tetranychus urticae and T. evansi on tomato. CSIC are also participating in the analysis of the transcriptome of mites and in the integration of these results with the plant transcriptomics and metabolomic responses. University of Western Ontario (UWO) Dr Mike Grbic, UWO, is the scientific leader of this research project. UWO is together with UPM team analysing tomato transcriptional responses to drought and mite stress. UWO will then functionally characterize candidate tomato DEGs to establish their requirements for the tomato stress resistance. In addition, UWO will work with UvA to identify differentially expressed genes in mites feeding on tomato under the described conditions to be further linked with plant transcriptomics and metabolomic profiles. |
| Impact | International conferences and project meetings |
| Start Year | 2015 |
| Description | GENOMITE: New generation sustainable tools to control emerging mite pests |
| Organisation | French National Institute of Agricultural Research |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Prof Jerry Cross, EMR, is overall leader and coordinator of this project. EMR is responsible for 3 research areas in the project: 1) studying the behaviour and interactions between mites and their natural enemies under simulated CC conditions which will generate the data necessary for developing models to predict the effect of different CC scenarios on biocontrol outcomes; 2) EMR will collaborate with other modelling groups in the consortium to develop models predicting the distribution and population size of mites and their natural enemies using published and new data generated in this project. In particular EMRs contribution will be on using network theory to model the spread of the mites and natural enemies across the EU. The network theory will consider the physical distance, geographical barriers and environmental conditions when modelling the spatial spread; 3) Finally, EMR will be responsible for characterising early host responses to pest attack. This will include the characterisation of transcriptomes at several intervals after mite attack. The data will be mined (analysed) against the diploid strawberry and the recently published octoploid strawberry draft genome to identify particular genes in host response. This will identify candidate resistance genes which can be deployed for combating climate change. |
| Collaborator Contribution | INRA INRA is responsible for work on spider mite/predatory mite species distribution models and tritrophic interactions under CC scenarios in Europe:1) Recording occurrences of pests and predators in the EU 2) Mite-plant interactions under varying climatic conditions 3) Assessing demographic parameters and dispersion of mite pests and predators under climate change conditions 4) Predation capacity of predators and tritrophic interactions under simulated climate change conditions 5) Predicting distributions of mites and effectiveness of predator control under CC 6) Field validating the pest-natural enemy distribution model and effectiveness of biological control. Provision of glasshouse experimental facilities for large scale collaborative experiment for other work areas. MetaSysx Gmbh Responsible for the (coordination of the) metabolome/lipidome analysis of the biological samples which will be generated by the different experimental groups. Plant material of plants kept at different environmental conditions with and without challenge to spider mites as well as mites fed on different plant materials will be subjected to three different analytical platforms: Lipidomics primary metabolites and secondary metabolites resulting in several hundred up to thousand metabolites. Cyprus University of Technology (CUT) The group at CUT is recording the current distribution of pests and natural enemies, modelling the distribution of pest and natural enemies in response to climate change and validating the predictions of models intensive field sampling and experimentation in farmer's fields in Cyprus. University of Amsterdam (UvA) The UvA research in this proposal covers two distinct areas. UvA is in charge of effector identification and characterization. 1) We will perform LC-MS analysis on saliva of Tetranychus urticae and T evansi with previously validated methods devised in our group and construct a strand-specific and quantitative transcriptome of the mite gnathosoma. We will further prioritize candidates with our expertise in genome analysis and via in planta expression tools. Candidate effectors will be tested after infiltration of plants with peptides or Agrobactrium tumefaciens transient assays (ATTA) in collaboration with the plant physiology group (prof. dr. Haring), phytopathology group (prof. dr. Cornelissen) and other partners of this project. 2) UvA will identify differentially expressed genes in mites feeding on tomato and strawberry under the described conditions (Task 2.5) to be further linked with plant transcriptomics and metabolomic profiles. VIB VIB work is to link the annotation that we produced on tomato, Tetranychus evansi and Tetranychus urticae with the results from the project. This will involve handling the RNAseq to provide expression values for the genes from all 3 listed genomes. For the strawberry genome VIB will rely on an assembled transcriptome (from public data (35 sets available)) that might have to be complemented for the specific strain to be used in the project. In order to be able to compare the genome's expressed genes upon mite infection table of orthological relationships will be established between strawberry and tomato. The same is true for the mites. This orthology will allow us to compare comparable trends in gene expression across species. To build a bridge between metabolites and genes we plan to investigate and setup a framework that would allow VIB to store reactions from pathways and link those with the genes from the genomes included in this study. Several pathway databases and platforms exist from which we could start to implement or adapt to the project's needs. The publically available pathway data will then also serve as a starting material to link what is generally known. From the results from the other WPs we hope to be able to add more reactions and complement pathways. Besides enzymatic pathways, in this project, we also have an interest for regulatory networks, mainly in the mites aiming at identifying the genes regulated and secreted in the salivary glands. Goal here is to find the peptides that might influence the host plant upon feeding. For this we will analyze the RNAseq data. The regulators and their target genes will be identified from LeMoNe analyses and potential regulatory target sites will be predicted. Universidad Politecnica de Madrid (UPM) UPM work focusses on the analysis of transcriptional tomato responses to mites under varying drought stress and high temperature which will generate the data necessary to identify genes/proteins in different CC scenarios and to correlate them with specific metabolic pathways involved in the defense response. The UPM team will collaborate in the analysis of interactions of putative mite effectors with plant physiology through infiltration of peptides or transient expression of effectors in plants and in the identification of candidate transcription factors responsible for reprograming/suppression of induced defense response and in the study of generated plant pathway databases to finally build an orthologous gene-set between tomato and strawberry. This will identify and validate candidate resistance genes which can be deployed for combating pests under the climate change scenario. Consejo Superior de Investigaciones (CSIC) CSIC research in this project focuses on determining which varying environmental conditions (temperature and water stress) have a measurable effect on the performance of Tetranychus urticae and T. evansi on tomato. CSIC are also participating in the analysis of the transcriptome of mites and in the integration of these results with the plant transcriptomics and metabolomic responses. University of Western Ontario (UWO) Dr Mike Grbic, UWO, is the scientific leader of this research project. UWO is together with UPM team analysing tomato transcriptional responses to drought and mite stress. UWO will then functionally characterize candidate tomato DEGs to establish their requirements for the tomato stress resistance. In addition, UWO will work with UvA to identify differentially expressed genes in mites feeding on tomato under the described conditions to be further linked with plant transcriptomics and metabolomic profiles. |
| Impact | International conferences and project meetings |
| Start Year | 2015 |
| Description | GENOMITE: New generation sustainable tools to control emerging mite pests |
| Organisation | MetaSysx Gmbh |
| Country | Germany |
| Sector | Private |
| PI Contribution | Prof Jerry Cross, EMR, is overall leader and coordinator of this project. EMR is responsible for 3 research areas in the project: 1) studying the behaviour and interactions between mites and their natural enemies under simulated CC conditions which will generate the data necessary for developing models to predict the effect of different CC scenarios on biocontrol outcomes; 2) EMR will collaborate with other modelling groups in the consortium to develop models predicting the distribution and population size of mites and their natural enemies using published and new data generated in this project. In particular EMRs contribution will be on using network theory to model the spread of the mites and natural enemies across the EU. The network theory will consider the physical distance, geographical barriers and environmental conditions when modelling the spatial spread; 3) Finally, EMR will be responsible for characterising early host responses to pest attack. This will include the characterisation of transcriptomes at several intervals after mite attack. The data will be mined (analysed) against the diploid strawberry and the recently published octoploid strawberry draft genome to identify particular genes in host response. This will identify candidate resistance genes which can be deployed for combating climate change. |
| Collaborator Contribution | INRA INRA is responsible for work on spider mite/predatory mite species distribution models and tritrophic interactions under CC scenarios in Europe:1) Recording occurrences of pests and predators in the EU 2) Mite-plant interactions under varying climatic conditions 3) Assessing demographic parameters and dispersion of mite pests and predators under climate change conditions 4) Predation capacity of predators and tritrophic interactions under simulated climate change conditions 5) Predicting distributions of mites and effectiveness of predator control under CC 6) Field validating the pest-natural enemy distribution model and effectiveness of biological control. Provision of glasshouse experimental facilities for large scale collaborative experiment for other work areas. MetaSysx Gmbh Responsible for the (coordination of the) metabolome/lipidome analysis of the biological samples which will be generated by the different experimental groups. Plant material of plants kept at different environmental conditions with and without challenge to spider mites as well as mites fed on different plant materials will be subjected to three different analytical platforms: Lipidomics primary metabolites and secondary metabolites resulting in several hundred up to thousand metabolites. Cyprus University of Technology (CUT) The group at CUT is recording the current distribution of pests and natural enemies, modelling the distribution of pest and natural enemies in response to climate change and validating the predictions of models intensive field sampling and experimentation in farmer's fields in Cyprus. University of Amsterdam (UvA) The UvA research in this proposal covers two distinct areas. UvA is in charge of effector identification and characterization. 1) We will perform LC-MS analysis on saliva of Tetranychus urticae and T evansi with previously validated methods devised in our group and construct a strand-specific and quantitative transcriptome of the mite gnathosoma. We will further prioritize candidates with our expertise in genome analysis and via in planta expression tools. Candidate effectors will be tested after infiltration of plants with peptides or Agrobactrium tumefaciens transient assays (ATTA) in collaboration with the plant physiology group (prof. dr. Haring), phytopathology group (prof. dr. Cornelissen) and other partners of this project. 2) UvA will identify differentially expressed genes in mites feeding on tomato and strawberry under the described conditions (Task 2.5) to be further linked with plant transcriptomics and metabolomic profiles. VIB VIB work is to link the annotation that we produced on tomato, Tetranychus evansi and Tetranychus urticae with the results from the project. This will involve handling the RNAseq to provide expression values for the genes from all 3 listed genomes. For the strawberry genome VIB will rely on an assembled transcriptome (from public data (35 sets available)) that might have to be complemented for the specific strain to be used in the project. In order to be able to compare the genome's expressed genes upon mite infection table of orthological relationships will be established between strawberry and tomato. The same is true for the mites. This orthology will allow us to compare comparable trends in gene expression across species. To build a bridge between metabolites and genes we plan to investigate and setup a framework that would allow VIB to store reactions from pathways and link those with the genes from the genomes included in this study. Several pathway databases and platforms exist from which we could start to implement or adapt to the project's needs. The publically available pathway data will then also serve as a starting material to link what is generally known. From the results from the other WPs we hope to be able to add more reactions and complement pathways. Besides enzymatic pathways, in this project, we also have an interest for regulatory networks, mainly in the mites aiming at identifying the genes regulated and secreted in the salivary glands. Goal here is to find the peptides that might influence the host plant upon feeding. For this we will analyze the RNAseq data. The regulators and their target genes will be identified from LeMoNe analyses and potential regulatory target sites will be predicted. Universidad Politecnica de Madrid (UPM) UPM work focusses on the analysis of transcriptional tomato responses to mites under varying drought stress and high temperature which will generate the data necessary to identify genes/proteins in different CC scenarios and to correlate them with specific metabolic pathways involved in the defense response. The UPM team will collaborate in the analysis of interactions of putative mite effectors with plant physiology through infiltration of peptides or transient expression of effectors in plants and in the identification of candidate transcription factors responsible for reprograming/suppression of induced defense response and in the study of generated plant pathway databases to finally build an orthologous gene-set between tomato and strawberry. This will identify and validate candidate resistance genes which can be deployed for combating pests under the climate change scenario. Consejo Superior de Investigaciones (CSIC) CSIC research in this project focuses on determining which varying environmental conditions (temperature and water stress) have a measurable effect on the performance of Tetranychus urticae and T. evansi on tomato. CSIC are also participating in the analysis of the transcriptome of mites and in the integration of these results with the plant transcriptomics and metabolomic responses. University of Western Ontario (UWO) Dr Mike Grbic, UWO, is the scientific leader of this research project. UWO is together with UPM team analysing tomato transcriptional responses to drought and mite stress. UWO will then functionally characterize candidate tomato DEGs to establish their requirements for the tomato stress resistance. In addition, UWO will work with UvA to identify differentially expressed genes in mites feeding on tomato under the described conditions to be further linked with plant transcriptomics and metabolomic profiles. |
| Impact | International conferences and project meetings |
| Start Year | 2015 |
| Description | GENOMITE: New generation sustainable tools to control emerging mite pests |
| Organisation | Spanish National Research Council (CSIC) |
| Department | Biological Research Center |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Prof Jerry Cross, EMR, is overall leader and coordinator of this project. EMR is responsible for 3 research areas in the project: 1) studying the behaviour and interactions between mites and their natural enemies under simulated CC conditions which will generate the data necessary for developing models to predict the effect of different CC scenarios on biocontrol outcomes; 2) EMR will collaborate with other modelling groups in the consortium to develop models predicting the distribution and population size of mites and their natural enemies using published and new data generated in this project. In particular EMRs contribution will be on using network theory to model the spread of the mites and natural enemies across the EU. The network theory will consider the physical distance, geographical barriers and environmental conditions when modelling the spatial spread; 3) Finally, EMR will be responsible for characterising early host responses to pest attack. This will include the characterisation of transcriptomes at several intervals after mite attack. The data will be mined (analysed) against the diploid strawberry and the recently published octoploid strawberry draft genome to identify particular genes in host response. This will identify candidate resistance genes which can be deployed for combating climate change. |
| Collaborator Contribution | INRA INRA is responsible for work on spider mite/predatory mite species distribution models and tritrophic interactions under CC scenarios in Europe:1) Recording occurrences of pests and predators in the EU 2) Mite-plant interactions under varying climatic conditions 3) Assessing demographic parameters and dispersion of mite pests and predators under climate change conditions 4) Predation capacity of predators and tritrophic interactions under simulated climate change conditions 5) Predicting distributions of mites and effectiveness of predator control under CC 6) Field validating the pest-natural enemy distribution model and effectiveness of biological control. Provision of glasshouse experimental facilities for large scale collaborative experiment for other work areas. MetaSysx Gmbh Responsible for the (coordination of the) metabolome/lipidome analysis of the biological samples which will be generated by the different experimental groups. Plant material of plants kept at different environmental conditions with and without challenge to spider mites as well as mites fed on different plant materials will be subjected to three different analytical platforms: Lipidomics primary metabolites and secondary metabolites resulting in several hundred up to thousand metabolites. Cyprus University of Technology (CUT) The group at CUT is recording the current distribution of pests and natural enemies, modelling the distribution of pest and natural enemies in response to climate change and validating the predictions of models intensive field sampling and experimentation in farmer's fields in Cyprus. University of Amsterdam (UvA) The UvA research in this proposal covers two distinct areas. UvA is in charge of effector identification and characterization. 1) We will perform LC-MS analysis on saliva of Tetranychus urticae and T evansi with previously validated methods devised in our group and construct a strand-specific and quantitative transcriptome of the mite gnathosoma. We will further prioritize candidates with our expertise in genome analysis and via in planta expression tools. Candidate effectors will be tested after infiltration of plants with peptides or Agrobactrium tumefaciens transient assays (ATTA) in collaboration with the plant physiology group (prof. dr. Haring), phytopathology group (prof. dr. Cornelissen) and other partners of this project. 2) UvA will identify differentially expressed genes in mites feeding on tomato and strawberry under the described conditions (Task 2.5) to be further linked with plant transcriptomics and metabolomic profiles. VIB VIB work is to link the annotation that we produced on tomato, Tetranychus evansi and Tetranychus urticae with the results from the project. This will involve handling the RNAseq to provide expression values for the genes from all 3 listed genomes. For the strawberry genome VIB will rely on an assembled transcriptome (from public data (35 sets available)) that might have to be complemented for the specific strain to be used in the project. In order to be able to compare the genome's expressed genes upon mite infection table of orthological relationships will be established between strawberry and tomato. The same is true for the mites. This orthology will allow us to compare comparable trends in gene expression across species. To build a bridge between metabolites and genes we plan to investigate and setup a framework that would allow VIB to store reactions from pathways and link those with the genes from the genomes included in this study. Several pathway databases and platforms exist from which we could start to implement or adapt to the project's needs. The publically available pathway data will then also serve as a starting material to link what is generally known. From the results from the other WPs we hope to be able to add more reactions and complement pathways. Besides enzymatic pathways, in this project, we also have an interest for regulatory networks, mainly in the mites aiming at identifying the genes regulated and secreted in the salivary glands. Goal here is to find the peptides that might influence the host plant upon feeding. For this we will analyze the RNAseq data. The regulators and their target genes will be identified from LeMoNe analyses and potential regulatory target sites will be predicted. Universidad Politecnica de Madrid (UPM) UPM work focusses on the analysis of transcriptional tomato responses to mites under varying drought stress and high temperature which will generate the data necessary to identify genes/proteins in different CC scenarios and to correlate them with specific metabolic pathways involved in the defense response. The UPM team will collaborate in the analysis of interactions of putative mite effectors with plant physiology through infiltration of peptides or transient expression of effectors in plants and in the identification of candidate transcription factors responsible for reprograming/suppression of induced defense response and in the study of generated plant pathway databases to finally build an orthologous gene-set between tomato and strawberry. This will identify and validate candidate resistance genes which can be deployed for combating pests under the climate change scenario. Consejo Superior de Investigaciones (CSIC) CSIC research in this project focuses on determining which varying environmental conditions (temperature and water stress) have a measurable effect on the performance of Tetranychus urticae and T. evansi on tomato. CSIC are also participating in the analysis of the transcriptome of mites and in the integration of these results with the plant transcriptomics and metabolomic responses. University of Western Ontario (UWO) Dr Mike Grbic, UWO, is the scientific leader of this research project. UWO is together with UPM team analysing tomato transcriptional responses to drought and mite stress. UWO will then functionally characterize candidate tomato DEGs to establish their requirements for the tomato stress resistance. In addition, UWO will work with UvA to identify differentially expressed genes in mites feeding on tomato under the described conditions to be further linked with plant transcriptomics and metabolomic profiles. |
| Impact | International conferences and project meetings |
| Start Year | 2015 |
| Description | GENOMITE: New generation sustainable tools to control emerging mite pests |
| Organisation | Technical University of Madrid |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Prof Jerry Cross, EMR, is overall leader and coordinator of this project. EMR is responsible for 3 research areas in the project: 1) studying the behaviour and interactions between mites and their natural enemies under simulated CC conditions which will generate the data necessary for developing models to predict the effect of different CC scenarios on biocontrol outcomes; 2) EMR will collaborate with other modelling groups in the consortium to develop models predicting the distribution and population size of mites and their natural enemies using published and new data generated in this project. In particular EMRs contribution will be on using network theory to model the spread of the mites and natural enemies across the EU. The network theory will consider the physical distance, geographical barriers and environmental conditions when modelling the spatial spread; 3) Finally, EMR will be responsible for characterising early host responses to pest attack. This will include the characterisation of transcriptomes at several intervals after mite attack. The data will be mined (analysed) against the diploid strawberry and the recently published octoploid strawberry draft genome to identify particular genes in host response. This will identify candidate resistance genes which can be deployed for combating climate change. |
| Collaborator Contribution | INRA INRA is responsible for work on spider mite/predatory mite species distribution models and tritrophic interactions under CC scenarios in Europe:1) Recording occurrences of pests and predators in the EU 2) Mite-plant interactions under varying climatic conditions 3) Assessing demographic parameters and dispersion of mite pests and predators under climate change conditions 4) Predation capacity of predators and tritrophic interactions under simulated climate change conditions 5) Predicting distributions of mites and effectiveness of predator control under CC 6) Field validating the pest-natural enemy distribution model and effectiveness of biological control. Provision of glasshouse experimental facilities for large scale collaborative experiment for other work areas. MetaSysx Gmbh Responsible for the (coordination of the) metabolome/lipidome analysis of the biological samples which will be generated by the different experimental groups. Plant material of plants kept at different environmental conditions with and without challenge to spider mites as well as mites fed on different plant materials will be subjected to three different analytical platforms: Lipidomics primary metabolites and secondary metabolites resulting in several hundred up to thousand metabolites. Cyprus University of Technology (CUT) The group at CUT is recording the current distribution of pests and natural enemies, modelling the distribution of pest and natural enemies in response to climate change and validating the predictions of models intensive field sampling and experimentation in farmer's fields in Cyprus. University of Amsterdam (UvA) The UvA research in this proposal covers two distinct areas. UvA is in charge of effector identification and characterization. 1) We will perform LC-MS analysis on saliva of Tetranychus urticae and T evansi with previously validated methods devised in our group and construct a strand-specific and quantitative transcriptome of the mite gnathosoma. We will further prioritize candidates with our expertise in genome analysis and via in planta expression tools. Candidate effectors will be tested after infiltration of plants with peptides or Agrobactrium tumefaciens transient assays (ATTA) in collaboration with the plant physiology group (prof. dr. Haring), phytopathology group (prof. dr. Cornelissen) and other partners of this project. 2) UvA will identify differentially expressed genes in mites feeding on tomato and strawberry under the described conditions (Task 2.5) to be further linked with plant transcriptomics and metabolomic profiles. VIB VIB work is to link the annotation that we produced on tomato, Tetranychus evansi and Tetranychus urticae with the results from the project. This will involve handling the RNAseq to provide expression values for the genes from all 3 listed genomes. For the strawberry genome VIB will rely on an assembled transcriptome (from public data (35 sets available)) that might have to be complemented for the specific strain to be used in the project. In order to be able to compare the genome's expressed genes upon mite infection table of orthological relationships will be established between strawberry and tomato. The same is true for the mites. This orthology will allow us to compare comparable trends in gene expression across species. To build a bridge between metabolites and genes we plan to investigate and setup a framework that would allow VIB to store reactions from pathways and link those with the genes from the genomes included in this study. Several pathway databases and platforms exist from which we could start to implement or adapt to the project's needs. The publically available pathway data will then also serve as a starting material to link what is generally known. From the results from the other WPs we hope to be able to add more reactions and complement pathways. Besides enzymatic pathways, in this project, we also have an interest for regulatory networks, mainly in the mites aiming at identifying the genes regulated and secreted in the salivary glands. Goal here is to find the peptides that might influence the host plant upon feeding. For this we will analyze the RNAseq data. The regulators and their target genes will be identified from LeMoNe analyses and potential regulatory target sites will be predicted. Universidad Politecnica de Madrid (UPM) UPM work focusses on the analysis of transcriptional tomato responses to mites under varying drought stress and high temperature which will generate the data necessary to identify genes/proteins in different CC scenarios and to correlate them with specific metabolic pathways involved in the defense response. The UPM team will collaborate in the analysis of interactions of putative mite effectors with plant physiology through infiltration of peptides or transient expression of effectors in plants and in the identification of candidate transcription factors responsible for reprograming/suppression of induced defense response and in the study of generated plant pathway databases to finally build an orthologous gene-set between tomato and strawberry. This will identify and validate candidate resistance genes which can be deployed for combating pests under the climate change scenario. Consejo Superior de Investigaciones (CSIC) CSIC research in this project focuses on determining which varying environmental conditions (temperature and water stress) have a measurable effect on the performance of Tetranychus urticae and T. evansi on tomato. CSIC are also participating in the analysis of the transcriptome of mites and in the integration of these results with the plant transcriptomics and metabolomic responses. University of Western Ontario (UWO) Dr Mike Grbic, UWO, is the scientific leader of this research project. UWO is together with UPM team analysing tomato transcriptional responses to drought and mite stress. UWO will then functionally characterize candidate tomato DEGs to establish their requirements for the tomato stress resistance. In addition, UWO will work with UvA to identify differentially expressed genes in mites feeding on tomato under the described conditions to be further linked with plant transcriptomics and metabolomic profiles. |
| Impact | International conferences and project meetings |
| Start Year | 2015 |
| Description | GENOMITE: New generation sustainable tools to control emerging mite pests |
| Organisation | University of Amsterdam |
| Department | Institute for Biodiversity and Ecosystem Dynamics (IBED) |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | Prof Jerry Cross, EMR, is overall leader and coordinator of this project. EMR is responsible for 3 research areas in the project: 1) studying the behaviour and interactions between mites and their natural enemies under simulated CC conditions which will generate the data necessary for developing models to predict the effect of different CC scenarios on biocontrol outcomes; 2) EMR will collaborate with other modelling groups in the consortium to develop models predicting the distribution and population size of mites and their natural enemies using published and new data generated in this project. In particular EMRs contribution will be on using network theory to model the spread of the mites and natural enemies across the EU. The network theory will consider the physical distance, geographical barriers and environmental conditions when modelling the spatial spread; 3) Finally, EMR will be responsible for characterising early host responses to pest attack. This will include the characterisation of transcriptomes at several intervals after mite attack. The data will be mined (analysed) against the diploid strawberry and the recently published octoploid strawberry draft genome to identify particular genes in host response. This will identify candidate resistance genes which can be deployed for combating climate change. |
| Collaborator Contribution | INRA INRA is responsible for work on spider mite/predatory mite species distribution models and tritrophic interactions under CC scenarios in Europe:1) Recording occurrences of pests and predators in the EU 2) Mite-plant interactions under varying climatic conditions 3) Assessing demographic parameters and dispersion of mite pests and predators under climate change conditions 4) Predation capacity of predators and tritrophic interactions under simulated climate change conditions 5) Predicting distributions of mites and effectiveness of predator control under CC 6) Field validating the pest-natural enemy distribution model and effectiveness of biological control. Provision of glasshouse experimental facilities for large scale collaborative experiment for other work areas. MetaSysx Gmbh Responsible for the (coordination of the) metabolome/lipidome analysis of the biological samples which will be generated by the different experimental groups. Plant material of plants kept at different environmental conditions with and without challenge to spider mites as well as mites fed on different plant materials will be subjected to three different analytical platforms: Lipidomics primary metabolites and secondary metabolites resulting in several hundred up to thousand metabolites. Cyprus University of Technology (CUT) The group at CUT is recording the current distribution of pests and natural enemies, modelling the distribution of pest and natural enemies in response to climate change and validating the predictions of models intensive field sampling and experimentation in farmer's fields in Cyprus. University of Amsterdam (UvA) The UvA research in this proposal covers two distinct areas. UvA is in charge of effector identification and characterization. 1) We will perform LC-MS analysis on saliva of Tetranychus urticae and T evansi with previously validated methods devised in our group and construct a strand-specific and quantitative transcriptome of the mite gnathosoma. We will further prioritize candidates with our expertise in genome analysis and via in planta expression tools. Candidate effectors will be tested after infiltration of plants with peptides or Agrobactrium tumefaciens transient assays (ATTA) in collaboration with the plant physiology group (prof. dr. Haring), phytopathology group (prof. dr. Cornelissen) and other partners of this project. 2) UvA will identify differentially expressed genes in mites feeding on tomato and strawberry under the described conditions (Task 2.5) to be further linked with plant transcriptomics and metabolomic profiles. VIB VIB work is to link the annotation that we produced on tomato, Tetranychus evansi and Tetranychus urticae with the results from the project. This will involve handling the RNAseq to provide expression values for the genes from all 3 listed genomes. For the strawberry genome VIB will rely on an assembled transcriptome (from public data (35 sets available)) that might have to be complemented for the specific strain to be used in the project. In order to be able to compare the genome's expressed genes upon mite infection table of orthological relationships will be established between strawberry and tomato. The same is true for the mites. This orthology will allow us to compare comparable trends in gene expression across species. To build a bridge between metabolites and genes we plan to investigate and setup a framework that would allow VIB to store reactions from pathways and link those with the genes from the genomes included in this study. Several pathway databases and platforms exist from which we could start to implement or adapt to the project's needs. The publically available pathway data will then also serve as a starting material to link what is generally known. From the results from the other WPs we hope to be able to add more reactions and complement pathways. Besides enzymatic pathways, in this project, we also have an interest for regulatory networks, mainly in the mites aiming at identifying the genes regulated and secreted in the salivary glands. Goal here is to find the peptides that might influence the host plant upon feeding. For this we will analyze the RNAseq data. The regulators and their target genes will be identified from LeMoNe analyses and potential regulatory target sites will be predicted. Universidad Politecnica de Madrid (UPM) UPM work focusses on the analysis of transcriptional tomato responses to mites under varying drought stress and high temperature which will generate the data necessary to identify genes/proteins in different CC scenarios and to correlate them with specific metabolic pathways involved in the defense response. The UPM team will collaborate in the analysis of interactions of putative mite effectors with plant physiology through infiltration of peptides or transient expression of effectors in plants and in the identification of candidate transcription factors responsible for reprograming/suppression of induced defense response and in the study of generated plant pathway databases to finally build an orthologous gene-set between tomato and strawberry. This will identify and validate candidate resistance genes which can be deployed for combating pests under the climate change scenario. Consejo Superior de Investigaciones (CSIC) CSIC research in this project focuses on determining which varying environmental conditions (temperature and water stress) have a measurable effect on the performance of Tetranychus urticae and T. evansi on tomato. CSIC are also participating in the analysis of the transcriptome of mites and in the integration of these results with the plant transcriptomics and metabolomic responses. University of Western Ontario (UWO) Dr Mike Grbic, UWO, is the scientific leader of this research project. UWO is together with UPM team analysing tomato transcriptional responses to drought and mite stress. UWO will then functionally characterize candidate tomato DEGs to establish their requirements for the tomato stress resistance. In addition, UWO will work with UvA to identify differentially expressed genes in mites feeding on tomato under the described conditions to be further linked with plant transcriptomics and metabolomic profiles. |
| Impact | International conferences and project meetings |
| Start Year | 2015 |
| Description | GENOMITE: New generation sustainable tools to control emerging mite pests |
| Organisation | University of Ghent |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | Prof Jerry Cross, EMR, is overall leader and coordinator of this project. EMR is responsible for 3 research areas in the project: 1) studying the behaviour and interactions between mites and their natural enemies under simulated CC conditions which will generate the data necessary for developing models to predict the effect of different CC scenarios on biocontrol outcomes; 2) EMR will collaborate with other modelling groups in the consortium to develop models predicting the distribution and population size of mites and their natural enemies using published and new data generated in this project. In particular EMRs contribution will be on using network theory to model the spread of the mites and natural enemies across the EU. The network theory will consider the physical distance, geographical barriers and environmental conditions when modelling the spatial spread; 3) Finally, EMR will be responsible for characterising early host responses to pest attack. This will include the characterisation of transcriptomes at several intervals after mite attack. The data will be mined (analysed) against the diploid strawberry and the recently published octoploid strawberry draft genome to identify particular genes in host response. This will identify candidate resistance genes which can be deployed for combating climate change. |
| Collaborator Contribution | INRA INRA is responsible for work on spider mite/predatory mite species distribution models and tritrophic interactions under CC scenarios in Europe:1) Recording occurrences of pests and predators in the EU 2) Mite-plant interactions under varying climatic conditions 3) Assessing demographic parameters and dispersion of mite pests and predators under climate change conditions 4) Predation capacity of predators and tritrophic interactions under simulated climate change conditions 5) Predicting distributions of mites and effectiveness of predator control under CC 6) Field validating the pest-natural enemy distribution model and effectiveness of biological control. Provision of glasshouse experimental facilities for large scale collaborative experiment for other work areas. MetaSysx Gmbh Responsible for the (coordination of the) metabolome/lipidome analysis of the biological samples which will be generated by the different experimental groups. Plant material of plants kept at different environmental conditions with and without challenge to spider mites as well as mites fed on different plant materials will be subjected to three different analytical platforms: Lipidomics primary metabolites and secondary metabolites resulting in several hundred up to thousand metabolites. Cyprus University of Technology (CUT) The group at CUT is recording the current distribution of pests and natural enemies, modelling the distribution of pest and natural enemies in response to climate change and validating the predictions of models intensive field sampling and experimentation in farmer's fields in Cyprus. University of Amsterdam (UvA) The UvA research in this proposal covers two distinct areas. UvA is in charge of effector identification and characterization. 1) We will perform LC-MS analysis on saliva of Tetranychus urticae and T evansi with previously validated methods devised in our group and construct a strand-specific and quantitative transcriptome of the mite gnathosoma. We will further prioritize candidates with our expertise in genome analysis and via in planta expression tools. Candidate effectors will be tested after infiltration of plants with peptides or Agrobactrium tumefaciens transient assays (ATTA) in collaboration with the plant physiology group (prof. dr. Haring), phytopathology group (prof. dr. Cornelissen) and other partners of this project. 2) UvA will identify differentially expressed genes in mites feeding on tomato and strawberry under the described conditions (Task 2.5) to be further linked with plant transcriptomics and metabolomic profiles. VIB VIB work is to link the annotation that we produced on tomato, Tetranychus evansi and Tetranychus urticae with the results from the project. This will involve handling the RNAseq to provide expression values for the genes from all 3 listed genomes. For the strawberry genome VIB will rely on an assembled transcriptome (from public data (35 sets available)) that might have to be complemented for the specific strain to be used in the project. In order to be able to compare the genome's expressed genes upon mite infection table of orthological relationships will be established between strawberry and tomato. The same is true for the mites. This orthology will allow us to compare comparable trends in gene expression across species. To build a bridge between metabolites and genes we plan to investigate and setup a framework that would allow VIB to store reactions from pathways and link those with the genes from the genomes included in this study. Several pathway databases and platforms exist from which we could start to implement or adapt to the project's needs. The publically available pathway data will then also serve as a starting material to link what is generally known. From the results from the other WPs we hope to be able to add more reactions and complement pathways. Besides enzymatic pathways, in this project, we also have an interest for regulatory networks, mainly in the mites aiming at identifying the genes regulated and secreted in the salivary glands. Goal here is to find the peptides that might influence the host plant upon feeding. For this we will analyze the RNAseq data. The regulators and their target genes will be identified from LeMoNe analyses and potential regulatory target sites will be predicted. Universidad Politecnica de Madrid (UPM) UPM work focusses on the analysis of transcriptional tomato responses to mites under varying drought stress and high temperature which will generate the data necessary to identify genes/proteins in different CC scenarios and to correlate them with specific metabolic pathways involved in the defense response. The UPM team will collaborate in the analysis of interactions of putative mite effectors with plant physiology through infiltration of peptides or transient expression of effectors in plants and in the identification of candidate transcription factors responsible for reprograming/suppression of induced defense response and in the study of generated plant pathway databases to finally build an orthologous gene-set between tomato and strawberry. This will identify and validate candidate resistance genes which can be deployed for combating pests under the climate change scenario. Consejo Superior de Investigaciones (CSIC) CSIC research in this project focuses on determining which varying environmental conditions (temperature and water stress) have a measurable effect on the performance of Tetranychus urticae and T. evansi on tomato. CSIC are also participating in the analysis of the transcriptome of mites and in the integration of these results with the plant transcriptomics and metabolomic responses. University of Western Ontario (UWO) Dr Mike Grbic, UWO, is the scientific leader of this research project. UWO is together with UPM team analysing tomato transcriptional responses to drought and mite stress. UWO will then functionally characterize candidate tomato DEGs to establish their requirements for the tomato stress resistance. In addition, UWO will work with UvA to identify differentially expressed genes in mites feeding on tomato under the described conditions to be further linked with plant transcriptomics and metabolomic profiles. |
| Impact | International conferences and project meetings |
| Start Year | 2015 |
| Description | GENOMITE: New generation sustainable tools to control emerging mite pests |
| Organisation | Western University |
| Department | Department of Biology |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | Prof Jerry Cross, EMR, is overall leader and coordinator of this project. EMR is responsible for 3 research areas in the project: 1) studying the behaviour and interactions between mites and their natural enemies under simulated CC conditions which will generate the data necessary for developing models to predict the effect of different CC scenarios on biocontrol outcomes; 2) EMR will collaborate with other modelling groups in the consortium to develop models predicting the distribution and population size of mites and their natural enemies using published and new data generated in this project. In particular EMRs contribution will be on using network theory to model the spread of the mites and natural enemies across the EU. The network theory will consider the physical distance, geographical barriers and environmental conditions when modelling the spatial spread; 3) Finally, EMR will be responsible for characterising early host responses to pest attack. This will include the characterisation of transcriptomes at several intervals after mite attack. The data will be mined (analysed) against the diploid strawberry and the recently published octoploid strawberry draft genome to identify particular genes in host response. This will identify candidate resistance genes which can be deployed for combating climate change. |
| Collaborator Contribution | INRA INRA is responsible for work on spider mite/predatory mite species distribution models and tritrophic interactions under CC scenarios in Europe:1) Recording occurrences of pests and predators in the EU 2) Mite-plant interactions under varying climatic conditions 3) Assessing demographic parameters and dispersion of mite pests and predators under climate change conditions 4) Predation capacity of predators and tritrophic interactions under simulated climate change conditions 5) Predicting distributions of mites and effectiveness of predator control under CC 6) Field validating the pest-natural enemy distribution model and effectiveness of biological control. Provision of glasshouse experimental facilities for large scale collaborative experiment for other work areas. MetaSysx Gmbh Responsible for the (coordination of the) metabolome/lipidome analysis of the biological samples which will be generated by the different experimental groups. Plant material of plants kept at different environmental conditions with and without challenge to spider mites as well as mites fed on different plant materials will be subjected to three different analytical platforms: Lipidomics primary metabolites and secondary metabolites resulting in several hundred up to thousand metabolites. Cyprus University of Technology (CUT) The group at CUT is recording the current distribution of pests and natural enemies, modelling the distribution of pest and natural enemies in response to climate change and validating the predictions of models intensive field sampling and experimentation in farmer's fields in Cyprus. University of Amsterdam (UvA) The UvA research in this proposal covers two distinct areas. UvA is in charge of effector identification and characterization. 1) We will perform LC-MS analysis on saliva of Tetranychus urticae and T evansi with previously validated methods devised in our group and construct a strand-specific and quantitative transcriptome of the mite gnathosoma. We will further prioritize candidates with our expertise in genome analysis and via in planta expression tools. Candidate effectors will be tested after infiltration of plants with peptides or Agrobactrium tumefaciens transient assays (ATTA) in collaboration with the plant physiology group (prof. dr. Haring), phytopathology group (prof. dr. Cornelissen) and other partners of this project. 2) UvA will identify differentially expressed genes in mites feeding on tomato and strawberry under the described conditions (Task 2.5) to be further linked with plant transcriptomics and metabolomic profiles. VIB VIB work is to link the annotation that we produced on tomato, Tetranychus evansi and Tetranychus urticae with the results from the project. This will involve handling the RNAseq to provide expression values for the genes from all 3 listed genomes. For the strawberry genome VIB will rely on an assembled transcriptome (from public data (35 sets available)) that might have to be complemented for the specific strain to be used in the project. In order to be able to compare the genome's expressed genes upon mite infection table of orthological relationships will be established between strawberry and tomato. The same is true for the mites. This orthology will allow us to compare comparable trends in gene expression across species. To build a bridge between metabolites and genes we plan to investigate and setup a framework that would allow VIB to store reactions from pathways and link those with the genes from the genomes included in this study. Several pathway databases and platforms exist from which we could start to implement or adapt to the project's needs. The publically available pathway data will then also serve as a starting material to link what is generally known. From the results from the other WPs we hope to be able to add more reactions and complement pathways. Besides enzymatic pathways, in this project, we also have an interest for regulatory networks, mainly in the mites aiming at identifying the genes regulated and secreted in the salivary glands. Goal here is to find the peptides that might influence the host plant upon feeding. For this we will analyze the RNAseq data. The regulators and their target genes will be identified from LeMoNe analyses and potential regulatory target sites will be predicted. Universidad Politecnica de Madrid (UPM) UPM work focusses on the analysis of transcriptional tomato responses to mites under varying drought stress and high temperature which will generate the data necessary to identify genes/proteins in different CC scenarios and to correlate them with specific metabolic pathways involved in the defense response. The UPM team will collaborate in the analysis of interactions of putative mite effectors with plant physiology through infiltration of peptides or transient expression of effectors in plants and in the identification of candidate transcription factors responsible for reprograming/suppression of induced defense response and in the study of generated plant pathway databases to finally build an orthologous gene-set between tomato and strawberry. This will identify and validate candidate resistance genes which can be deployed for combating pests under the climate change scenario. Consejo Superior de Investigaciones (CSIC) CSIC research in this project focuses on determining which varying environmental conditions (temperature and water stress) have a measurable effect on the performance of Tetranychus urticae and T. evansi on tomato. CSIC are also participating in the analysis of the transcriptome of mites and in the integration of these results with the plant transcriptomics and metabolomic responses. University of Western Ontario (UWO) Dr Mike Grbic, UWO, is the scientific leader of this research project. UWO is together with UPM team analysing tomato transcriptional responses to drought and mite stress. UWO will then functionally characterize candidate tomato DEGs to establish their requirements for the tomato stress resistance. In addition, UWO will work with UvA to identify differentially expressed genes in mites feeding on tomato under the described conditions to be further linked with plant transcriptomics and metabolomic profiles. |
| Impact | International conferences and project meetings |
| Start Year | 2015 |
| Description | 7th spider mite genome conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | 3 day international conference about spider mite genomes and related molecular and applied biology |
| Year(s) Of Engagement Activity | 2015 |
| Description | FACCE - ERA-NET Plus on Climate Smart Agriculture project meeting 21 Sep 15 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Launch meeting for the projects funded under the FACCE - ERA-NET Plus on Climate Smart Agriculture |
| Year(s) Of Engagement Activity | 2015 |
| Description | GENOMITE General Assembly 1-2 Oct 15 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Second General Assembly meeting for the project |
| Year(s) Of Engagement Activity | 2015 |
| Description | GENOMITE General Assembly and project launch 10 Oct 14 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | First general assembly meeting for the project |
| Year(s) Of Engagement Activity | 2014 |