Understanding the evolution of insecticide resistance in Brazilian crop pests: Towards effective Insecticide Resistance Management (IRM)

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 26% 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 project builds on key 'omic' (genomic and transcriptomic) and biological resources for E. heros and S. frugiperda generated in a stage 1 pump-prime project to understand the molecular basis of resistance in the two pest species. Specifically, we generated a high quality draft genome sequence of E. heros and strains of E. heros and S. frugiperda that share a common genetic background but differ in their susceptibility to several insecticides. These resources will be exploited in the stage 2 project to identify candidate genes and genetic variation associated with resistance and their causal role validated using transgenic approaches. Understanding the role of these genes in resistance will be facilitated by the generation of gene expression atlases for both species which will comprise databases and user-friendly web applications for studying the expression of genes in different tissues of adults or larvae. These resources will be used in the project to identify where candidate resistance genes are expressed in order to understand how they confer resistance. More broadly their publication will accelerate broad functional genomic research in these pest species beyond the scope of this project. Another key output of the stage 1 project was characterisation of the microbial community (the microbiome) present in the gut of both pest species and the identification of gut bacteria that degrade pesticides. The genomic and biological material generated will be used in the stage 2 project to understand how and to what extent these microbes contribute to resistance, and how they might be disrupted in order to overcome resistance.

The data from these experiments will fundamentally advance our understanding of how insects evolve resistance to insecticides. Furthermore, the knowledge generated will be of direct applied importance in relation to the sustainable control of both pest species. To translate the knowledge gained in this project to combat resistance we will develop simple DNA-based diagnostics, and use these to determine the frequency and distribution of resistance in the field in order to inform rational control decisions and develop insecticide resistance management strategies. Furthermore, we will develop screening tools (recombinant enzyme assays or transgenic insect lines) that can be used by academia and industry to develop resistance-breaking chemistry.

The proposed research will be of direct and indirect benefit to several groups and end-users beyond the academic community. By characterising 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 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 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 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 genomic and transcriptomic data generated 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.