Understanding resistance of key crop pests in Brazil

Lead Research Organisation: University of Exeter
Department Name: Biosciences

Abstract

Insect pests represent a major threat to current and future food security with an average of 20% of crops worldwide lost annually to herbivorous insects. This issue is particularly acute in Brazil where agriculture forms a key component of the economy accounting for 22% of gross domestic product (GDP). Synthetic insecticides are widely used by farmers and growers in Brazil in an attempt to reduce yield loss from insect pests. Unfortunately, the growing reliance on insecticides has resulted in the emergence of insect pest populations that are resistant to many of the chemicals used for control. Two of the most economically important species in this regard are the neotropical brown stink bug, Euschistus heros, and the fall armyworm, Spodoptera frugiperda. E. heros is a major pest of soybean and vegetable crops and causes severe damage to cotton and maize, while S. frugiperda feeds on more than 80 plant species but is particularly destructive on maize. Resistance to several important insecticides has now emerged in these species and threatens their sustainable control. Despite the seriousness of this issue very little research has been carried out to understand the evolution of resistance in E. heros and S. frugiperda and to use this knowledge to develop means to combat its emergence and spread. This is, in part, due to a lack of genomic resources for these key pest species - particularly in the case of E. heros.

This Stage 1 pump-prime project has two aims, firstly it will generate key 'omic' (genomic and transcriptomic) resources and data for E. heros and S. frugiperda that will be a valuable asset to the community studying these species. These will include the first annotated draft genome for E. heros, sequence characterization of the entire microbial community (the microbiome) in the gut of E. heros and S. frugiperda, and tissue-specific gene expression data for both species that can be used to determine where candidate genes (such as those involved in resistance) are expressed. In the context of this proposal these data will greatly facilitate future characterization of genes and DNA markers associated with insecticide resistance in these species that can be used to develop tools to prevent, slow or overcome the development of resistance.

To ensure that the knowledge gained in this and follow on projects can achieve applied impact the second main aim of this pump-prime project is to develop a network of key stakeholder groups in Brazilian agriculture. This will be achieved by holding workshops with members of growers associations, government and industry including representatives of Insecticide Resistance Action Committee Brazil (IRAC-BR), the Brazilian Cotton Growers Association (ABRAPA), the Soybean and Maize Growers Association (APROSOJA), the Brazilian Ministry of Agriculture and the Technical Advisory Committee of Pesticides (CTA). These meetings will define the priorities of future research and develop routes for translation of the science into tools and strategies for resistance management and rational control of these two important insect pests of Brazilian agri-ecosystems.

Planned Impact

The proposed research will be of direct and indirect benefit to several groups and end-users beyond the academic community. By providing underpinning resources and data to facilitate characterisation of the mechanisms of insecticide resistance in two highly damaging insect pests of some of the most economically important crops in Brazil, a primary beneficiary will be Brazilian agriculture. An improved understanding of the molecular basis of insecticide resistance (which detoxifying enzymes and target-site mutations confer insecticide resistance and to which chemical classes) will assist with anticipating resistance risks and cross-resistance profiles, and will thereby influence the design and monitoring of strategies for managing these pests while reducing selection pressure for specific resistance mechanisms. Furthermore the future translation of the knowledge generated in this project into tools that can be used to rapidly determine the frequency and distribution of resistance will help growers make rational control decisions. Farmers in other countries where these insects have recently emerged will also benefit from this work. For example the emergence of S. frugiperda in Africa represents a serious threat to maize, the most widely grown crop in Africa and a staple for around half the continent's people. The development of resistance management strategies in Brazil will provide a model that, with modification, would also assist stakeholders in affected African countries to prevent or slow the development of resistance.

The longer term goals of this proposal have additional benefits beyond those relating solely to the control of the target insect pests. Ineffective control due to resistance can result in the wasteful over-application of ineffective compounds leading to negative environmental and economic outcomes. The future development of diagnostics for specific resistance mechanisms will allow resistance to be detected at an early stage and avoid these off-target effects.

Another key beneficiary of our work is the agrochemical industry who recognise the responsibility of stewardship of current actives and are keen to prolong the life of these insecticides. The knowledge and deliverables derived from our study will inform the policy of IRAC (Insecticide Resistance Action Committee) international that works as a worldwide specialist technical group of the industry association CropLife providing a coordinated industry response to prevent or delay the development of resistance in insect and mite pests, and its national body in Brazil (IRAC-BR).

We envisage that a further impact of our research will be its potential influence on the policy and regulatory environment of insecticide registration and use. The ultimate outcomes of our work will be of direct relevance in defining which chemistry should be used for control of these species and how (i.e. how frequently, when and in combination with which other controls). A robust regulatory framework is extremely important in ensuring compliance with strategies that aim to manage resistance and extend the life-span of insecticides that retain efficacy.

The sequencing of a draft genome for E. heros and tissue-specific expression data for E. heros and S. frugiperda as part of this project has significant scope to result in wide ranging impacts beyond managing resistance. Many of the genes identified and annotated in the genome and transcriptomes represent potential targets for novel control strategies and their sequence characterisation is a prerequisite for strategies based on gene knockdown (RNAi) or genetic manipulation (i.e. gene drives). In the same way characterisation of the gut microbiome of these species and understanding the metabolic activity of these herbivore-associated microbes may assist in industrial development of novel pest-management strategies or may have application for biotechnological applications.

Publications

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Description This project aimed to generate genetic and biological resources for both the neotropical brown stink bug, Euschistus heros, and the fall armyworm, Spodoptera frugiperda, two economically important pests of agriculture in Brazil. These resources will accelerate subsequent investigation of the molecular mechanisms of insecticide resistance in these species.
A major outcome of the project was the sequencing and assembly of the transcriptome and genome of E. heros. Bioinformatic assessment of the genome sequence revealed it to be high quality with good representation of all of the genes of this species obtained. Annotation of the genes and other genomic features in this sequence assembly has also been completed. The genome sequence has been publicly available (pre-publication) at The National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/bioproject/489772) and a manuscript on the resource is in preparation. The genome sequence is currently being used by us in a follow on project to understand how insecticide resistance evolves in E. heros. In parallel, dissections of specific tissues from E. heros and S. frugiperda were performed and these have been sequenced in order to understand where genes, for example those involved in resistance, are expressed in these pest species. The data generated is currently being used in a follow-on project to develop user-friendly expression atlases for these species.
Sequencing was also used to characterise the gut microbiome (genetic material of all of the microbes in the insect gut) of insecticide resistant and susceptible strains of E. heros and S. frugiperda as an important first step in understanding the role of the microbiome in resistance. Analysis revealed marked variation in the distribution of microbes in the different parts of the gut of E. heros, providing reference information that will facilitate comparative analysis with resistant strains. We also sequenced the gut microbiota of strains of S. frugiperda that are resistant to several insecticides and showed that the gut microbial diversity was strongly influenced by the insecticide the insect sample was resistant. The data obtained is now being used in a follow on project to explore the role of the microbiome in resistance.
Finally we developed biological resources comprising insecticide resistant and susceptible lines of the two pest species that share a common genetic background. These make it much easier to identify the specific genes that confer insecticide resistance and are currently being used in a follow on project which aims to characterise resistance mechanisms and develop markers for resistance.
In order to ensure that the knowledge described above can achieve applied impact, the project also developed a network of key stakeholder groups. This was done by holding two workshops - the first in Gramado Brazil on 5th September 2018 included representatives of the Insecticide Resistance Action Committee Brazil (IRAC-BR) - http://www.irac-br.org/, Brazilian Cotton Growers Association (ABRAPA) - http://www.abrapa.com.br/, Soybean and Maize Growers Association (APROSOJA) - http://www.aprosoja.com.br/, and the Technical Advisory Committee of Pesticide (CTA). The second workshop was held on the 13th/14th March 2019 in central London and was attended by representatives of IRAC international and IRAC-BR. At both meetings the progress of the pump-prime project was presented and discussion held on how this project (and a potential stage 2 project) can inform and influence the policy and recommendations of global crop protection companies in order to most effectively promote resistance management. Thus, these activities help ensure the official development assistance (ODA) objectives of the project were met by ensuring the DAC list country (Brazil) can benefit from the research performed.
Exploitation Route We envisage the genome sequence we have generated (which is now freely available online) will be of significant value to other researchers working on this important pest. For example, many of the genes annotated in the genome represent potential targets for novel control strategies. Similarly the expression atlases will be made publicly available thus allowing researchers to understand the expression pattern of genes they are interested in to gain potential new insights into their function. Together these resources will accelerate research on E. heros and S. frugiperda. In the context of the aims of this project this will ensure that Brazilian agriculture will benefit by reducing yield lost to these pests. Beyond Brazil the research outcomes will also be of potential value to other DAC list countries as S. frugiperda has recently invaded several countries and recently appeared in Africa where it is rapidly spreading throughout the tropical and subtropical regions of the continent. It is likely that the founder populations in new territories carry resistance genes and thus work towards the characterization of resistance in populations in Brazil will be of direct relevance to scientists working on these species in Africa.
Sectors Agriculture, Food and Drink,Chemicals,Environment

 
Description Our findings have been used to inform several stakeholder groups which are working on the control of damaging crop pests in Brazil, in order to deliver economic and societal benefits in the Brazilian AgroEcosystems. These include the Insecticide Resistance Action Committee Brazil (IRAC-BR) - http://www.irac-br.org/, Brazilian Cotton Growers Association (ABRAPA) - http://www.abrapa.com.br/, Soybean and Maize Growers Association (APROSOJA) - http://www.aprosoja.com.br/, and the Technical Advisory Committee of Pesticide (CTA). These groups will use this knowledge to inform the development of strategies to slow, overcome or prevent resistance, and thus the project outputs will address several Sustainable Development Goals including Goal 2. To end hunger, achieve food security and improved nutrition and promote sustainable agriculture, and Goal 12. Ensure sustainable consumption and production patterns. As this was a small scale one year project the data generated in foundational and thus translation of the knowledge gained is at an early stage. However, the funding of a second stage project will enhance the impact prospects.
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Chemicals,Environment
Impact Types Economic

 
Description Understanding the evolution of insecticide resistance in Brazilian crop pests: Towards effective Insecticide Resistance Management (IRM)
Amount £505,297 (GBP)
Funding ID BB/S018719/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2019 
End 04/2021
 
Title Genome sequence of Neotropical Brown Stink Bug, Euschistus heros 
Description The draft genome of the Neotropical Brown Stink Bug, Euschistus heros was sequenced. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact This genomic resource has been used by ourselves to understand the evolution of resistance in Euschistus heros, but more broadly will accelerate a range of molecular studies on this species. 
URL https://www.ncbi.nlm.nih.gov/bioproject/489772
 
Title Genome assembly of the neotropical brown stink bug, Euschistus heros 
Description As part of BBSRC/FAPESP funded projects (Grant Refs: BB/S018719/1 and BB/R022623/1) we have created new genomic resources for the neotropical brown stink bug, Euschistus heros, an economically important pest of agriculture in Brazil (DAC country). These resources will accelerate subsequent investigation of the molecular mechanisms of insecticide resistance in this species. Bioinformatic assessment of the genome sequence revealed it to be high quality with good representation of all of the genes of this species obtained. Annotation of the genes and other genomic features in this sequence assembly has also been completed. The genome sequence has been publicly available (pre-publication) at The National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/bioproject/489772) and a manuscript on the resource is in preparation. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact The genome sequence is currently being used by us and our partners at the University of São Paulo in a project to understand how insecticide resistance evolves in E. heros as part of project BB/R022623/1. 
URL https://www.ncbi.nlm.nih.gov/bioproject/489772
 
Description Insecticide Resistance Action Committee Brazil (IRAC-BR) 
Organisation Insecticide Resistance Action Committee (IRAC)
Department Insecticide Resistance Action Committee Brazil (IRAC-BR)
Country Brazil 
Sector Charity/Non Profit 
PI Contribution We have provided information and knowledge on insecticide resistance in key crop pests of Brazilian Agri-Ecosystems and the development of tools and resources to combat it from two projects funded by the BBSRC/FAPESP (Grant Refs: BB/S018719/1 and BB/R022623/1).
Collaborator Contribution The collaborators have provided a route to disseminate the project results in order to enhance the impact from our projects (Grant Refs: BB/S018719/1 and BB/R022623/1).
Impact The Insecticide Resistance Action Committee Brazil (IRAC-BR) will consider our findings during the creation of recommendations for insecticide use targeted at growers/grower organisations. These will aim to reduce the loss of insecticides due to resistance, with associated economic and environmental benefits.
Start Year 2018
 
Description Insecticide Resistance Action Committee: IRAC have provided funds for research and have provided an excellent route to disseminate research findings and translate our science into practical recommendations for growers 
Organisation Insecticide Resistance Action Committee (IRAC)
Country Spain 
Sector Charity/Non Profit 
PI Contribution Our work on resistance has benefitted from forging strong links with the agrochemical industry. We have disseminated our research findings and translated out science into practical recommendations through our links to the Insecticide Resistance Action Committee (IRAC). IRAC is a global organisation that coordinates industry?s response to proven or perceived cases of insecticide resistance. Through this relationship we have co-authored IRAC alerts and recommendations for combating the emerging problem of neonicotinoid resistance in M. persicae. IRAC subsequently funded us to undertake a European-wide study to examine the frequency and distribution of neonicotinoid resistance mechanisms over the 2011 season. This study showed that the most potent levels of neonicotinoid resistance are spreading across southern Europe and show the potential to invade the UK in the near future.
Start Year 2009
 
Description The Brazilian Cotton Growers Association (ABRAPA) 
Organisation Brazilian Cotton Growers Association (ABRAPA)
Country Brazil 
Sector Charity/Non Profit 
PI Contribution We have provided information and knowledge on insecticide resistance in key crop pests of Brazilian Agri-Ecosystems and the development of tools and resources to combat it from two projects funded by the BBSRC/FAPESP (Grant Refs: BB/S018719/1 and BB/R022623/1).
Collaborator Contribution The collaborators have provided a route to disseminate the project results in order to enhance the impact from our projects (Grant Refs: BB/S018719/1 and BB/R022623/1).
Impact The Brazilian Cotton Growers Association (ABRAPA)will consider our findings during the creation of recommendations for insecticide use targeted at their growers. These will aim to reduce the loss of insecticides due to resistance, with associated economic and environmental benefits.
Start Year 2018
 
Description The Soybean and Maize Growers Association (APROSOJA) 
Organisation Mato Grosso Soy and Corn Producers Association (Aprosoja)
Country Brazil 
Sector Charity/Non Profit 
PI Contribution We have provided information and knowledge on insecticide resistance in key crop pests of Brazilian Agri-Ecosystems and the development of tools and resources to combat it from two projects funded by the BBSRC/FAPESP (Grant Refs: BB/S018719/1 and BB/R022623/1).
Collaborator Contribution The collaborators have provided a route to disseminate the project results in order to enhance the impact from our projects (Grant Refs: BB/S018719/1 and BB/R022623/1).
Impact The Soybean and Maize Growers Association (APROSOJA) will consider our findings during the creation of recommendations for insecticide use targeted at their growers. These will aim to reduce the loss of insecticides due to resistance, with associated economic and environmental benefits.
Start Year 2018
 
Description The Technical Advisory Committee of Pesticides (CTA) of the Brazilian Ministry of Agriculture 
Organisation Government of Brazil
Department Ministry of Agriculture, Livestock, and Food Supply
Country Brazil 
Sector Public 
PI Contribution We have provided information and knowledge on insecticide resistance in key crop pests of Brazilian Agri-Ecosystems and the development of tools and resources to combat it from two projects funded by the BBSRC/FAPESP (Grant Refs: BB/S018719/1 and BB/R022623/1).
Collaborator Contribution The collaborators have provided a route to disseminate the project results in order to enhance the impact from our projects (Grant Refs: BB/S018719/1 and BB/R022623/1).
Impact The Technical Advisory Committee of Pesticides (CTA) of the Brazilian Ministry of Agriculture will consider our findings during the creation of recommendations for insecticide use and regulation. These will aim to reduce the loss of insecticides due to resistance, with associated economic and environmental benefits.
Start Year 2018
 
Description University of Glasgow 
Organisation University of Glasgow
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaboration / partnership included as part of a grant application, (partnership between the UK and organisation in a DAC list country). This allowed joint funding between the the Biotechnology and Biological Sciences Research Council (BBSRC) and São Paulo Research Foundation (FAPESP) to be obtained (Grant Refs: BB/S018719/1 and BB/R022623/1). In the funded research we provided expertise in insect genomics to colleagues at the the University of Glasgow (most significantly insect genome assemblies). Together our research will facilitate the control of damaging crop pests of Brazilian Agri-ecoystems.
Collaborator Contribution Collaboration / partnership included as part of a grant application, (partnership between the UK and organisation in a DAC list country). This allowed joint funding between the the Biotechnology and Biological Sciences Research Council (BBSRC) and São Paulo Research Foundation (FAPESP) to be obtained (Grant Refs: BB/S018719/1 and BB/R022623/1). In the funded research our partners provided expertise in insect transcriptomics (most significantly insect gene expression atlases). Together our research will facilitate the control of damaging crop pests of Brazilian Agri-ecoystems.
Impact This collaboration allowed joint funding between the the Biotechnology and Biological Sciences Research Council (BBSRC) and São Paulo Research Foundation (FAPESP) to be obtained, Grant Refs: BB/S018719/1 and BB/R022623/1 (see relevant sections of the form for details).
Start Year 2018
 
Description University of São Paulo 
Organisation Universidade de São Paulo
Country Brazil 
Sector Academic/University 
PI Contribution Collaboration / partnership included as part of the original application, (partnership between the UK and organisation in a DAC list country). This allowed joint funding between the the Biotechnology and Biological Sciences Research Council (BBSRC) and São Paulo Research Foundation (FAPESP) to be obtained (Grant Refs: BB/S018719/1 and BB/R022623/1). In the funded research we provided expertise in insect genomics and transcriptomics to colleagues at the the University of São Paulo. Together our research will facilitate the control of damaging crop pests of Brazilian Agri-ecoystems.
Collaborator Contribution Collaboration / partnership included as part of the original application, (partnership between the UK and organisation in a DAC list country). This allowed joint funding between the the Biotechnology and Biological Sciences Research Council (BBSRC) and São Paulo Research Foundation (FAPESP) to be obtained (Grant Refs: BB/S018719/1 and BB/R022623/1). In the funded research our partners provided expertise in practical aspects of insecticide resistance (including the role of the microbiome in resistance) including (indirect) access to insect material. Together our research will facilitate the control of damaging crop pests of Brazilian Agri-ecoystems.
Impact This collaboration allowed joint funding between the Biotechnology and Biological Sciences Research Council (BBSRC) and São Paulo Research Foundation (FAPESP) to be obtained, Grant Refs: BB/S018719/1 and BB/R022623/1 (see relevant sections of the form for details).
Start Year 2018
 
Description Workshop on managing resistance in Brazilian Ari-ecosystems 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact A workshop on managing resistance in Brazilian Ari-ecosystems was held in Gramado Brazil on 5th September 2018. Attendees included representatives of the Insecticide Resistance Action Committee Brazil (IRAC-BR) - http://www.irac-br.org/, Brazilian Cotton Growers Association (ABRAPA) - http://www.abrapa.com.br/, Soybean and Maize Growers Association (APROSOJA) - http://www.aprosoja.com.br/, and the Technical Advisory Committee of Pesticide (CTA). The key outcomes of this workshop were: 1) Defining the infrastructure in Brazil for resistance management and monitoring and pathways to translation of the stage 1 and stage 2 projects. 2) Reaching agreement with IRAC-Brazil that project outcomes (such as DNA diagnostics) can be utilized in annual resistance monitoring programs conducted by IRAC for both species.
Year(s) Of Engagement Activity 2018
 
Description Workshop with Industry 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact A workshop was held on the topic of Insecticide Resistance in Brazilian AroEcosystems. The progress of the pump-prime project was presented and discussion held on how this project (and a potential stage 2 project) can inform and influence the policy and recommendations of global crop protection companies in order to most effectively promote resistance management. Representatives of IRAC international and IRAC-BR attended as well as project participants.
Year(s) Of Engagement Activity 2019