Abstract
The utilization of insect pest pathogens as biocontrol agents can serve as an effective alternative to chemical pesticides. However, pests can develop resistance to these pathogens, similar to resistance observed with chemicals. Identifying the genetic bases of resistance is a crucial step in comprehending the co-evolution mechanisms between insect hosts and their pathogens, thereby enhancing the durability of these biocontrol methods. Cydia pomonella, a major pest of apple and pear trees found across all continents, can be effectively controlled in commercial orchards through the use of the granulovirus, CpGV. However, since 2005, resistance to the CpGV-M isolate has been reported in Europe, leading to significant challenges in managing C. pomonella in organic orchards. Studies conducted on CPGV-M resistance have revealed that viral replication is blocked in resistant phenotypes, and resistance is linked to a major gene located on the Z sex chromosome. Nevertheless, this major gene appears to be insufficient in explaining resistance to CPGV-M, as other forms of resistance involving autosomal genes have been identified subsequently. The objective of this study was to gain insights into the genetic architecture of C. pomonella resistance to CpGV-M by conducting a genome-wide association study using newly generated whole-genome resequencing data from pools of individuals (Pool-Seq) sampled from 13 susceptible and resistant populations across four regions in France and Italy. Through this analysis, eight candidate regions were identified, including one located on the Z sex chromosome. These eight regions encompass a total of 27 lncRNAs (long non-coding RNAs) and 40 genes, of which three are known to be involved in insects immune pathways.