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Rare breeds represent a valuable resource for current or future market demands, but their low census compromises the genetic variability and future utilization of these breeds. Whether genetic variability of rare breeds with low initial genetic variation can be maintained during an intense mass selection becomes the key to applying mass selection to the genetic improvement of these breeds. The genetic variability among three generations of successive mass selection of the orange-shell line of Crassostrea gigas (MS1–MS3) were evaluated by both 20 nuclear microsatellite loci and mitochondrial cytochrome oxidase I sequences (mtCOI) compared to four wild populations. In this study, the orange-shell line exhibited very low genetic variability. Only one mtCOI haplotype was detected in all individuals of MS1–MS3. Significant reductions in average number of alleles (N a : 69.55–76.92%), allelic richness (A r : 68.17–74.91%) and expected heterozygosity (H e : 34.21–39.24%) as well as increased mean pairwise genetic relatedness (R : 6.87–25.79 times) were observed in MS1–MS3 when compared to wild populations. However, the genetic variability of orange-shell line with very low initial variation successfully maintained during three generations of mass selection. No significant difference in N a (3.60–4.40), A r (3.51–4.08) and H e (0.48–0.50) occurred among MS1–MS3. Pedigree reconstructions (no full-sib group from MS1–MS3 was larger than 16% of the whole group) revealed artificial spawning used in this study has a better control over contribution of gametes than traditional mass spawning. In addition, effective population size of MS1–MS3 calculated by linkage disequilibrium methods increased from 29.3 to 67.0 indicating the linkage disequilibrium decays over time. This study provides important insights in the genetic consequences of a rare variant line of C. gigas with very low genetic variation over generations of mass selection. This will provide a reference for carrying out genetic improvement programs on rare breeds where small populations are inevitable. • This study is the first to report genetic change of rare variant of oysters over several generations of mass selection. • The initial variation of orange-shell line was lower than that of most other strains of mollusk in previous studies. • The genetic variability of orange-shell line successfully maintained during three generations of intense mass selection. • This will provide a reference for carrying out genetic improvement programs on rare breeds. [ABSTRACT FROM AUTHOR]

Abstract 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 (H e = 0.647–0.681), number of alleles (N = 5.6–6.0) and haplotypes (N h = 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 F ST 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 N eb 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 (N eb) was significantly lower than sex-ratio correction effective population size (N e), 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. Highlights • Genetic diversity and effective population size over successive mass-selected generations in the black shell strain were assessed. • There was no detectable loss of genetic diversity revealed by 11 microsatellites and mtDNA COI region. • A large size and balanced sex-ration of broodstock and lower selection pressure would alleviate effective population size loss. • It is suggested to simply undertake mini-spawning during mass spawning to against high variance in reproductive success. [ABSTRACT FROM AUTHOR]