The monitoring of resistance to plant protection products (PPP) in pest populations (frequency and spatial distribution) is a major objective of phytopharmacovigilance. The efficiency and resolution of this monitoring can allow the development of strategies that, together with recommendations, can minimise the use of PPPs and maximise their sustainability. While the phenotyping approaches (biotests) currently used to monitor pest resistance are necessary for initial characterisation, the number of samples tested is often limited by the heaviness of this method. In order to improve monitoring, better assess risks and develop strategies in a reactive manner (almost in real time) on a coherent territorial scale for a given pathosystem, it is essential to have "high throughput" tests that can rapidly analyse a large number of samples at a reduced cost. Such tools are now within reach thanks to the development of new sequencing techniques (NGS). Indeed, it is now possible to develop molecular tests to detect resistance at "high throughput" based on the knowledge of mutations, genes or portions of genes involved in these resistances, especially since the genome of certain pests is now sequenced.

This project will consider a particularly problematic insect pest with regard to resistance, the codling moth, Cydia pomonella. This lepidopteran is the main pest of apple trees in the world and is responsible for 2/3 of the insecticide treatments carried out in France in orchards, making this crop one of the most treated. Today, most of the insecticides used against C. pomonella are resistant, including two biopesticide, the granulosis virus (CpGV), and spinosad. The main families of insecticide molecules derived from synthetic chemistry encounter specific resistance via mutations in target proteins (target-linked resistance, TLR), which affect the direct interaction between the insecticide and its biochemical target (Brun-Barale et al. 2005, Cassanelli et al. 2006). There are other, so-called non-specific resistance mechanisms (non-target resistance, NTR), the most important of which is the detoxification mechanism that confers cross-resistance to almost all chemical families used (Reyes et al. 2009). The basis and genetic architecture of RNLCs are complex (involving families of genes) and are only partially known in C. pomonella as in many other pests (Rodriguez et al. 2010). The mutations at the base of the RNLC can cause overexpression (regulatory mutations, gene duplication) or increased activity (structural mutations) of enzymes or metabolic pathways involved in the neutralisation of pesticides. They are therefore more complex to identify.

 Objectives

The main objective of this project is to organise the conditions for a change of scale in the monitoring of resistance in C. pomonella: from national to territorial and from individual to collective. This will involve (i) completing the identification of the genetic bases of resistances already identified by biotest in France, and (ii) carrying out large-scale sampling in the main production basins in France to make a complete inventory of the distribution and frequency of resistances by high-speed sequencing. Such an advance is made possible by new genomic technologies and the recent sequencing of the C. pomonella genome (753 MB), annotated and assembled into 29 chromosomes.