Résumé
Coinfection by multiple pathogens is common in aquaculture. Since 2012, Pacific oysters in Europe have been affected by two main pathogens, with additive or cooperative pathogenicity: the ostreid herpes virus type 1 (OsHV-1) and bacterium Vibrio aestuarianus. In oysters, genetic improvement by selective breeding is effective in mitigating diseases caused by single pathogens, but little is known about resistance to coinfections. This study aimed to investigate the genetic parameters and genomic architecture of disease resistance in C. gigas by comparing experimental infections made with each of the two pathogens, as well as coinfection with both. One hundred families were produced using parents from three origins: two wild populations experiencing different pathogen pressures and oysters experimentally selected for their higher resistance to OsHV-1 and V. aestuarianus infections. The experimental infections were carried out on 7-month old juveniles, leading to survival rates of 52%, 55% and 43%, for the bacterial, the viral and dual infection, respectively. Individuals were genotyped using a 57k SNP array. Survival varied widely among families and parental origins. Heritability estimates for survival ranged from 0.20 to 0.50 for the three infections, and genetic correlations were low between V. aestuarianus and the two other experimental infections, but very high between OsHV-1 and coinfection. Genome-wide association study revealed a polygenic architecture for all traits. However, five quantitative trait loci (QTLs) were detected in the OsHV-1 treatment as well as for coinfection with one specific genomic region on linkage group 6 being related to higher survival. Prediction accuracy was higher using a genomic model than a pedigree-based model, particularly for OsHV-1 and coinfection, for which larger numbers of individuals were genotyped. Our results suggest that (1) geographic origin of oysters should be considered when establishing a breeding program for improved survival; (2) use of genomic selection (GS) and QTL mapping may lead to more efficient selection and faster genetic gain; and (3) the coinfection challenge used in this study, which is likely to be closer to field conditions than the other treatments, is practical and may be suitable for breeding programs. Our findings represent a significant step towards using genomic information to improve disease resistance in selective breeding programs for the Pacific oyster, and possibly other aquaculture species.