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The adaptive potential of clonality in aphid crop pests

Reference	BB/S006060/1
Principal Investigator / Supervisor	Professor Christopher Bass
Co-Investigators / Co-Supervisors
Institution	University of Exeter
Department	Biosciences
Funding type	Research
Value (£)	545,416
Status	Current
Type	Research Grant
Start date	01/07/2019
End date	30/06/2024
Duration	60 months

Abstract

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.

Summary

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.

Impact Summary

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.

Committee	Research Committee B (Plants, microbes, food & sustainability)
Research Topics	Crop Science, Plant Science
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	Industrial Partnership Award (IPA)

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