Analysis of the genetic basis of inbreeding depression in the Pacific oyster Crassostrea gigas

The genetic basis of inbreeding depression and its converse heterosis, may be attributable to recessive deleterious mutations, epistatic interactions between loci, or overdominant gene action. Over the last century, the relative contribution of these models has been debated. We take a multi-generational approach to analyze the genetic basis of viability selection in the Pacific oyster, Crassostrea gigas. Viability selection in 2–3-month-old oysters is evidenced by segregation ratio distortion of IBD homozygotes at microsatellite loci in F₂–F₃ hybrid lines. We test the F₃–F₄ progeny generation for segregation ratio distortion at loci deficient in their parents. Deficient genotypes in the F₂–F₃ were predictably transmitted to the progeny F₃–F₄ generation in 10/12 explicit tests, and six new cases of segregation ratio distortion were observed for genotypes becoming IBD homozygous for the first time. The mutation-selection hypothesis was supported in 22 out of 25 cases, with no evidence for overdominance or synergistic epistasis. To quantify viability genes contributing to inbreeding depression, we take a map-based approach covering 56% of the total 880 cM C. gigas linkage map. In one line, we estimate 2 I unique segregation distorting loci (SDL) across three F₄ families, nearly double the estimate in the previous generation, suggesting that the Load in this species is higher than previously reported. We attribute the increase to a rise in the inbreeding coefficient, f of 0.09, and greater genome coverage, though actual Load is likely larger, because 1/3 of the loci tested, were fixed by inbreeding. The estimation of genetic load is also influenced by the life-stages over which selection acts. We investigate the timing of selection, by sampling 20-day-old, post-metamorphic spat, and test whether loci showing segregation distortion have significantly different 95% confidence intervals at earlier, and later life stages. We determined that 1/3 of the genes contributing to viability reductions were expressed in larvae between day 2 and day 11, while the remaining 2/3 are expressed at or just prior to metamorphosis. There was no evidence that selection against IBD homozygotes continued to the 3-month juvenile stage, suggesting that early-acting inbreeding depression is correlated with physiological changes brought about by metamorphosis.