Genetic diversity and effective population size in successive mass selected generations of black shell strain Pacific oyster (Crassostrea gigas) based on microsatellites and mtDNA data

The Pacific oyster (Crassostrea gigas) is one of the highly fecund marine aquaculture species and has a large variance in reproductive success, these characteristics can result in loss of genetic diversity and inbreeding especially when conducting mass selection. In the current study, we investigated the level of genetic diversity and effective population size over three successive mass-selected generations in the black shell strain of C. gigas assessed by 11 microsatellites as well as mitochondrial COI region. The results showed that the genetic variation over three generations were maintained since no detectable depression of expected heterozygosity (He = 0.647–0.681), number of alleles (N = 5.6–6.0) and haplotypes (Nh = 2). The difference in alleles and haplotypes number between the base population (BP) and three mass selective generations (M5-M7) could be mainly due to the loss during preceding family selection process. Pair-wise FST values along with AMOVA analysis from both markers indicated unremarkable differentiation within each generation including BP. There was no deleterious effect on genetic diversity and population structure for mass selected generations imposed by our artificial breeding practice. The Neb estimation for M5, M6 and M7 was 29.8, 40.7 and 52.7, respectively. The different number of broodstocks used for each generation implied that using a balanced sex ratio and large size of broodstock as well as low selection pressure would help to increase the effective population size and avoid high level of inbreeding. The estimated linkage disequilibrium-based effective breeders size (Neb) was significantly lower than sex-ratio correction effective population size (Ne), which indicated high variance in family contribution. It is suggested during mass spawning to simply undertake several mini-spawn groups and then pool the embryos to produce next generation, which can be a hedge to the high variance in reproductive success, thus, the loss of effective populations size and diversity. Other practical strategies against the loss of genetic diversity were also discussed, however, it remains to be investigated how diverse selection and follow-up procedures will benefit retaining genetic variability. This study will provide an insight into the level of genetic diversity and effective population size within mass-selected black shell line and enable a better understanding of how efficient current breeding practices are at maintaining genetic variation. This information can be applied for future selective breeding program and in the design of suitable management guidelines for sustainable breeding of C. gigas.