Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single-nucleotide Polymorphism Markers

The level and extent of linkage disequilibrium (LD) and effective population size (Ne) were studied in three selected lines and a wild population of Pacific oyster, Crassostrea gigas, using 61 single-nucleotide polymorphisms. Significant differences were detected in the average r(2) between the selected lines and wild population for both syntenic and nonsyntenic loci with LD beyond population-specific critical values (P<0.05). Moreover, the proportions of syntenic and nonsyntenic loci with the expected LD level in the wild population were lower than that in the selected lines. Taken together, the LD level of the selected lines was higher than that of the wild population. The extent of LD analysis showed that a short range of LD (0-0.23 cM) was detected in the four populations, and the decay distance was lower in the wild population than in the selected lines. Ne values ranged from 47.6 to 58.5 in the selected lines and ranged from 527.9 to 709.6 with infinite upper limits in the wild population. Further variance analysis of LD demonstrated that genetic drift and epistatic selection might account for the increased LD levels in selected lines. The LD information will be valuable for further association study and marker-assisted selection in oysters.