An inversion on chromosome 8 is associated with individual resistance to Bonamia ostreae in the European flat oyster

The European flat oyster (Ostrea edulis) has experienced severe population declines across Europe, largely due to infection by Bonamia ostreae. Previous studies identified a chromosomal inversion on chromosome 8 (C8) associated with resistance to this parasite at population level, but its association at individual level has not yet been demonstrated. Here, we investigated three Irish shellfish beds (Lough Swilly, Galway, and Rossmore) with contrasting bonamiosis histories combining smear/microscopy diagnosis and qualitative PCR detection to evaluate parasite presence/load in heart and gill on a sample of 436 oysters. A medium-density SNP array was used for genotyping the three large flat oyster inversions to check for karyotype association both using binary (uninfected vs infected) and semi-quantitative (infection level) traits. We found a strong association at individual level between the C8 inversion and B. ostreae infection in heart tissue but not in gill, suggesting a resistance mechanism hampering the entrance of the parasite to infect haemocytes. An additive model of association was the best fitted to data and an overdominant model was fully discarded. No association was detected for the two other large inversions of flat oyster on C2 and C5. Based on these findings, a cost-effective five-SNP MassARRAY panel was developed to genotype the C8 inversion efficiently using as reference the whole SNP panel. Our results confirm that the C8 inversion holds a key mechanism of resistance to B. ostreae and provide a practical tool for marker-assisted selection in O. edulis to enhance resistance in restoration and breeding programs.