The adaptive potential of clonality in aphid crop pests

Lead Research Organisation: UNIVERSITY OF EXETER
Department Name: Biosciences

Abstract

Aphids are among the world's most damaging group of insect pests, causing billions of US dollars of yield loss per annum to a wide range of food and commodity crops. The control of pest aphids has relied heavily on the use of chemical insecticides, however, the evolution of resistance poses a growing threat to their sustainable control.

Aphids are in part so successful because of their remarkable capacity to rapidly increase in number under favourable conditions, indeed, it has been estimated that without predation or disease a single aphid could produce 600 billion descendants in just one season. This incredible reproductive output is achieved by asexual reproduction (parthenogenesis) - with adult female aphids giving birth to daughters that are clones of themselves for most of the growing season. For most aphid species this mode of reproduction alternates with a yearly cycle of sexual reproduction, however, in some countries such as the UK certain species, including important pests such as Myzus persicae, reproduce exclusively by parthenogenesis.

Because aphid clonal lineages have been assumed to be genetically identical they have been referred to as 'evolutionary dead ends' with little or no capacity to evolve. However, we have recently shown that aphid clonal populations derived from a single female aphid can evolve heritable resistance to insecticides. Although this clearly demonstrates that aphid clonal lineages have adaptive potential the mechanisms by which aphid clones evolve are completely unknown.

The aim of this project is to understand the adaptive potential of aphid clonal lineages and the molecular mechanisms underpinning clonal evolution in aphids. We will use the global aphid pest M. persicae as a model and exploit recent advances in genomics, transcriptomics and epigenetics to address a range of key knowledge gaps on this topic. These include understanding how quickly mutations accumulate in aphid clonal lineages, how this is affected by pesticide stress, and how clones adapt at the phenotypic and molecular level in the absence of sex. In the first objective of the proposal we will calculate the frequency and spectrum of mutations that spontaneously arise in clones of M. persicae using an experimental approach called mutation accumulation (which overcomes the difficulty of directly studying how rare mutations arise by allowing them to build up over several generations in lines propagated by single progeny descent). In this objective we will also test the hypothesis that sub-lethal insecticide exposure increases mutation rate by comparing how mutations accumulate in lines exposed to insecticide with insecticide unexposed lines. In the second objective we will use an approach called experimental evolution (the use of experimental populations exposed to specific conditions in the laboratory to study evolutionary processes) to examine the response of large clonal populations of M. persicae to insecticide selection. We will combine this approach with three different sequencing approaches to explore the molecular mechanisms underpinning evolved resistance, which will be validated in Objective 3 using functional approaches.

The data from these experiments will fundamentally advance our understanding of how insects evolve in the absence of sex. Furthermore, the knowledge generated will be of considerable applied importance in relation to the sustainable control of aphid pests. For example, it will allow us to anticipate resistance risk development in countries where aphids reproduce asexually and optimise pesticide dosing strategies to avoid accelerating the evolution of mutations that might lead to resistance. Finally, understanding how clonal pest populations evolve resistance at the molecular level may provide opportunities to exploit and counter this process by developing strategies against the underpinning mechanisms involved.

Technical Summary

Aphids contain some of the world's most economically important agricultural pests. Their pest status is enhanced by their remarkable adaptability and their extraordinary reproductive output. The latter is achieved by parthenogenesis with females giving birth to live daughters that have been assumed to be genetically identical clones of themselves. Because of the perceived lack of genetic variation generated during this process such clonal lineages have been referred to as 'evolutionary dead ends'. However, we have recently shown that aphid populations established from a single foundress can evolve transgenerational resistance to insecticides, strongly suggesting their adaptive potential has been underestimated. Surprisingly, we know almost nothing about the evolutionary and molecular properties of adaptation in aphid clones, despite the fact that key aphid crop pests reproduce exclusively by parthenogenesis in many temperate countries like the UK. In this project we will use the global aphid pest Myzus persicae as a model to understand the adaptive potential of aphid clones and the molecular mechanisms underpinning clonal evolution. Mutation accumulation and experimental evolution experiments will be used in combination with (epi)genome and transcriptome sequencing and functional approaches to: a) Characterise the genetic fidelity of aphid clones for the first time (i.e. what is the rate, spectrum and potential impact of (epi)mutations arising in clonal lineages of M. persicae?), b) investigate if sub-lethal pesticide stress increases mutation frequency and, c) characterise how clonal lineages adapt to pesticide exposure at the phenotypic and molecular level in the absence of sex. The data generated will fundamentally advance our understanding of evolution in asexually reproducing insects and has clear application in terms of controlling a global, highly damaging group of crop pests.

Planned Impact

The data generated in our study will ultimately inform the development of strategies that aim to prevent, slow or overcome resistance in aphid clonal populations. As such, the long-term primary economic impact of our research is to UK and global agriculture through the prevention or reduction of crop yield loss. Key beneficiaries within this sector will include UK and European farmers and growers (and associated grower associations), advisers/agronomists, industry and regulatory authorities. Aphids cause billions of US dollars of crop yield loss per annum worldwide and thus the economic impact of leveraging our results to improve control of these pest species has the potential to be substantial. The model used in our study, Myzus persicae, is globally distributed and highly polyphagous, feeding on more than 400 plant species including a range of food and commodity crops. In the UK, the economic and operational impact of resistance is exemplified particularly well by challenges with controlling M. persicae on sugar beet. The British Beet Research Organisation (BBRO) has estimated that failure to forestall the widespread development of resistance in this species could result in yield reductions of up to 50% in sugar beet, rendering the industry uneconomic. The sugar beet industry currently generates >£250 million in revenue to UK farms per annum and supports around 20,000 jobs. Similar scenarios of economic threat unquestionably apply to other crops attacked by M. persicae or other aphid pest species. We have previously used our research to inform European farmers and growers of the resistance status in M. persicae (see Case for Support), and are well placed to exploit these links to ensure the impact from our study is maximised (see Pathways to Impact).

The longer term impact of this proposal has 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. Thus the development of control strategies based on judicious and informed use of insecticides has clear environmental and societal benefits. In relation to this we envisage that a further longer term impact of our research will be its potential influence on the policy and regulatory environment of insecticide registration and use. 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. Beneficiaries within this sector are policy makers, such as the Chemicals Regulation Division of the Health and Safety Executive of the UK, who define how chemistry should be used for control.

Ultimately the only solution to resistance that has become unmanageable is to substitute other compounds with novel modes of action, but these are in extremely short supply and hugely expensive to develop and bring to the marketplace. A recent study by CropLife America and the European Crop Protection Association calculated that the cost of bringing a new pesticide to market is now 260 million US$. Thus a significant beneficiary of the proposed study is the agrochemical industry who recognise the responsibility of stewardship of current actives and are keen to prolong the life of these insecticides. This is clearly demonstrated by the financial and in-kind support of Bayer CropScience AG in this proposal. The knowledge and deliverables of this study will inform policy of the Insecticide Resistance Action Group (IRAG) that aims to develop and implement recommendations for conserving the effectiveness of insecticides in the UK and IRAC (Insecticide Resistance Action Committee) 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.
 
Description As part of the research funded by this project we have created a new genomic resource for the aphid Myzus persicae (the species used as a model pest in this project). Specifically, we generated a chromosome-level genome assembly of the M. persicae s.s. clone G006. This new G006 assembly (G006v2) represents a near complete and highly contiguous assembly and a significant improvement on the existing short read assembly of this clone (G006v1). This genomic resource has been made publicly available at the National Center for Biotechnology Information (NCBI) under the Bio Project ID: PRJNA574571, and at AphidBase https://bipaa.genouest.org/is/aphidbase/. Furthermore we were able to use aphid cultures maintained with funding from the grant in a collaboration with Australian scientists to investigate the molecular basis of resistance to the insecticide spirotetramat. Specifically, we uncovered evidence of spirotetramat resistance in populations of M. persicae from Australia. We showed that this was associated with cross-resistance to other insecticides within the same chemical group, namely spiromesifen and spirodiclofen. We also demonstrated that resistance is associated with a mutation, A2226V in the target site of spirotetramat, acetyl-CoA carboxylase.
Exploitation Route The high-quality chromosome-scale assembly of M. persicae generated in this study represents a powerful resource for further research on aphids. We envisage this resource has strong potential to provide researchers in academia and industry with a range of insights into the evolution and genetic basis of many of the biological traits exhibited by aphids. For example, together with aphidologists from around the world, we have recently leveraged this resource to advance understanding of the evolution of insecticide resistance in an important insect pest at a global scale, uncovering both mechanisms underpinning resistance and ecological factors that influence its emergence and spread. Furthermore, this resource will also be of significant utility to researchers working on the control of this highly damaging aphid pest. Specifically, many of the genes identified and annotated in the genome 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).

Our findings on resistance to spirotetramat provide new insight into the resistance conferred by the A2226V mutation and have implications for the control of M. persicae in Australia and worldwide. A diagnostic assay developed in this study should serve as a valuable tool for future resistance monitoring and to support the implementation of pest management strategies.
Sectors Agriculture

Food and Drink

Chemicals

Environment

 
Description Our discovery that resistance to spirotetramat in populations of the aphid Myzus persicae is conferred by the A2226V mutation has implications for the control of M. persicae in Australia and worldwide. This knowledge was leveraged to develop a diagnostic assay, this is being used in resistance monitoring and to support the implementation of pest management strategies in Australia.
First Year Of Impact 2022
Sector Agriculture, Food and Drink
 
Description Bayer CropScience 
Organisation Bayer
Department Bayer CropScience Ltd
Country United Kingdom 
Sector Private 
PI Contribution We have collaborated with Bayer CropScience on a number of projects and brought our expertise in insect molecular biology and particularly insect transcriptomics and genomics to joint projects.
Collaborator Contribution Bayer CropScience contributed their expertise in the field of insecticide resistance and the functional expression and characterisation of insect detoxification enzymes. They have also contributed financially to joint research projects.
Impact doi: 10.1111/j.1365-2583.2011.01105.x. doi: 10.1073/pnas.1314122110 doi:10.1016/j.ibmb.2014.05.003
Start Year 2010
 
Description Return to Learning, Widening Participation through Skills 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other audiences
Results and Impact I presented an interactive talk at a Return to Learning, Widening Participation through Skills event. This was an outreach activity enabling those who have never studied at degree level to gain an insight into what's on offer at university and the research we do. The event was open to the general public and gave a sense of what university study and research is like, with the aim that some individuals may be interest in pursuing further studies and developing their careers. The response from the attendees was enthusiastic and raised a lot of questions. Some of the participants indicated they planned to give serious thought to pursuing further education linked to this topic.
Year(s) Of Engagement Activity 2019
 
Description School visit - Science at Christmas 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact More than 150 year six and seven students from primary schools attended for a school visit to the University for a series of talks on research conducted at the University. I delivered an interactive lecture including several activities for the children to inspire (which also included research from this BBSRC funded project) and enthuse them on both the topic of insects and science generally. Following the event the teachers in attendance provided very positive feedback and increased interest in insects and research.
Year(s) Of Engagement Activity 2019
 
Description Visit to St Francis School Falmouth 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I visited St Francis School in Falmouth and conducted an interactive workshop on insects (covering in very general terms current BBSRC research) to >60 primary school children. Their teachers at the school reported significsant increased interest in this topic and appreciation for insects following my visit.
Year(s) Of Engagement Activity 2020