Genome-Wide Analysis of Inbreeding Depression in the Pacific Oyster

Discovery of a large number of deleterious recessive mutations (genetic load) in the Pacific oyster explains distorted marker segregation ratios, seen widely in bivalves, and supports the dominance theory of heterosis and inbreeding depression.  Up to this point however, analysis of segregation data in F₂ families has been constrained by single locus models which lack genomic perspective.   We report advances in our analyses of these data using a ‘viability-selection model’ that applies quantitative trait locus (QTL) mapping techniques to the characterization of deleterious mutations (viability loci) across the genome.  With this approach we can better address a number of questions in inbred families such as the interaction of genetic load with the environment (diet) and the developmental timing of selection against viability loci.  We find a large number of viability loci (14-15), half of which are expressed during metamorphosis.  We find that selection increases at viability loci in harsher (nutrient poor) diets, but also that dominance is increased, exposing more of the population to selection than expected from recessive mutations alone.   Genetic load may be responsible for most of the early mortality (Type-III survivorship) in inbred Pacific oyster families, which has implications for threatened populations of highly fecund marine animals.