The black-lipped pearl oyster in French Polynesia is one of the rare pearl oyster production based on wild spat collected from closed or semi-enclosed lagoons. The recent highly variable supply of wild spat and the perspectives to improve pearl quality using genetic selection encourages the development of hatcheries and the domestication of the species. As internationally recommended, the management of inbreeding in stocks in domestication is crucial to avoid potential negative effects but also to initially keep and conserve genetic variability. We report a first analysis in P. margaritifera of inbreeding risk by analyzing the conservation of genetic variability in commercial breeding practices of the Regahiga Pearls hatchery (Rikitea, Gambiers Archipelago) based of estimation of minimum effective size (Ne) and inbreeding coefficient indicators.
Two successive cohorts were analyzed using DNA from the parents and their progenies and the recent available 70k SNP array. Briefly, 18 sires and 13 dams (cohort B1) and 15 sires and 13 dams (cohort B2) were mated by mass spawning. Parents pooled in a maturation tank (MT) were thermally stimulated to spawn. Females emitting eggs were transferred after their cleaning in a spawning tank (SP) and aliquots of water and sperm from the MT tank were regularly added in the SP tank for fertilization, the duration between 1st male emission and the last spawn being less than 45’. Juveniles transferred in the lagoon were collected and phenotyped for growth and morphology in last summer 2022 and genotyped. After filtration, 1969 SNP were selected and used for DNA parentage assignment in using APIS genetic software.
The main results are that, inbreeding coefficient F estimated in cumulating data from the two cohorts are estimated to -2,05 % per generation when the pedigree is unknown (Ne = 24.4) and -1.09 % when the pedigree is traced by DNA parentage assignment (Ne = 46) allowing to not overrepresent some parents to create the next generation (Figure 1). It is concluded that at least 4 cohorts per generation (Ne = 92 et F = -0,54 %) is needed when using DNA parentage assignment and 8 cohorts should be needed when pedigree is unknown (Ne = 98 et F = -0,51 %) to follow FAO international recommendations to manage inbreeding in livestock.