• Research

DNA methylation in aphids

DNA methylation and the evolution of pesticide-resistance genes in aphids

Project summary.

Led by: Swarbreck Group

Start date: July 2018

End date: Dec 2021

Duration: 30 months

Grants: UKRI / BBSRC

Value: £962,887

The green peach aphid (GPA) Myzus persicae is unusual among plant pests in that it can colonize over 400 different plant species and transmit more than 100 different plant viruses. Moreover, GPA has evolved resistance to 71 different pesticides. The rapid evolution of pesticide resistance, coupled with changes in the regulatory landscape on pesticide usage, has resulted in a lack of control methods for this insect.

Research so far has focused on the identification of genes that are involved in stable pesticide resistance of aphids. However, little is known about how stable resistance evolves and what mechanisms underlie GPA’s extraordinary ability to adjust to diverse environments, including exposure to exogenous chemicals from diverse plant species and pesticides. In this project, we will focus on epigenetic mechanisms, specifically the role of de novo DNA methylation in pesticide resistance.

Details.

To analyze aphid responses to pesticide treatment, Green peach aphid (GPA) clones O ( pesticide susceptible) and FRC (pesticide resistant) will be reared on A.thaliana dsGFP/ds3A/ds3B (methyltransferase knockdown lines). These plants will be treated with different doses of pesticide. We will harvest wild type, 3A-RNAi and 3B-RNAi aphids for both clone O and FRC and RNA-seq will be performed.

We wish to investigate which genes are directly regulated by DNMT3A/B de novo gene body methylation in GPA. There is evidence that DNMT3A/B is involved in splicing in insects. Hence, we will use strand-specific RNA-seq data generated to identify splice variants and see whether they are altered in the 3A-RNAi and/or 3B-RNAi variant.

We have generated whole-genome bisulfite sequencing of GPA clone O transferred to nine different plant species. We will use this data to determine if there is association between differential methylation, splicing and expression.

Our hypothesis is that DNMT3A/B response genes are under strong positive selection in GPA. So far, genotyping of GPA field populations has been mainly conducted via microsatellite analysis, but with the availability of whole genome sequencing (WGS) of two GPA clones and advanced WGS technologies, we will re-sequence whole genomes. We will re-sequence the genomes of at least 100 single field collected aphids with different genotypes. This will be used to test our hypothesis that genes in the DNMT3 response pathway show the fastest rate of evolution, comparing this to the evolutionary rate of the other genes.

Collaborators.

Professor Saskia Hogenhout

John Innes Centre

Professor Cock van Oosterhout

University of East Anglia

Impact statement.

In this project we will identify genes and genetic variants that enable the green peach aphid (GPA) to rapidly evolve resistance to pesticides and adapt to new host plants. More specifically, we will have revealed how DNA methylation regulates genes responsible for GPA colonization of diverse plant species and how these relate to those involved in pesticide resistance.

We will also compare gene networks affected by adaptive DNA methylation to a closely related aphid with limited host range. Taken together these data will help us understand how the development of insecticide resistance initiates and evolves, and, in turn, is expected to lead to new control strategies for GPA and related insect pests.