Résumé
A great majority of modern apricot and peach varieties remain sensitive to the most problematic pests and diseases. To improve the capacity of varieties to deal with decreased levels of pesticide use, we need a better understanding of resistance and tolerance mechanisms in these crops. To serve this objective, we exposed large and diversified sets of apricot and peach accessions (so-called ‘core-collections’) to natural infections within a multi-environment trial. These core-collections consist in 150 apricot and 206 peach accessions, for which respectively 207,000 and 13,680 SNP data are available, and were observed from 2020 to 2023 at two to three environmentally contrasted locations in South-East of France. Respectively two and five pests and diseases were monitored in apricot and peach. After showing the impact of genetic and GxE effects on phenotypic variance via variance decompositions, we applied several GWAS models to identify associations (i) with conserved effects across environments, (ii), with interactive effects across environments, (iii) with environment-specific effects. We also explored non-additive mechanisms, yielding additional associations. This work led to the identification of 60 high confidence QTLs and 87 candidate genes involving both host-specific and basal resistance mechanisms. Interestingly, candidate regions were enriched for leucine-rich repeat containing receptors (LRR-CRs). We discuss the relevance of environment-dependant QTLs according to the different disease typologies found in this study. This work contributes to the establishment of marker assisted selection strategies to allow for a faster screening of the disease resilience capacity in peach and apricot breeding material.