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Crassostrea nippona has recently been identified as a potential aquaculture species for its high glycogen content and delicate flavor in summer when Crassostrea gigas suffer from low meat quality. In 2014, we initiated the selective breeding program to improve growth traits of C. nippona through successive generations of mass selection, yet the genetic impact of an intense artificial selection on the genetic variability of C. nippona was not fully understood. In this study, the genetic diversity and genetic structure of three generations of mass-selected lines (G1-G3) and three wild populations were investigated using both 15 microsatellite loci and mitochondrial COI sequences (mtCOI). The selected lines exhibited no significant decrease in the average number of alleles (N a : 7.53–9.87), observed heterozygosity (H o : 0.58–0.64), expected heterozygosity (H e : 0.67–0.71) and alleles richness (A r : 6.35–7.75), compared with those of the wild populations. The abundant genetic diversity of selected lines was successfully maintained during three generations of mass selection due to no detectable loss. The effective population sizes (N e − lin) estimated by linkage disequilibrium methods for G1, G2 and G3 were 64.1, 25.3 and 47.4, respectively. Moreover, little genetic differentiation within the selected lines was observed in AMOVA analysis (global F ST : 0.005, P > 0.05) and significant genetic differentiation among the wild populations was revealed by global F ST (0.15, P < 0.01), pairwise F ST (0.095–0.211), Nei's D (0.260–0.730) and clustering results, which might suggest genetically isolated populations occurring in these sampling locations. To maximize future selective breeding efforts, a larger scale of broodstock and multi-line breeding strategy along with alleviating selection intensity is recommended against the reduction in the genetic diversity and effective population size in subsequent breeding practices. This study contributes to an increasing understanding of the efficiency of current breeding procedures in maintaining genetic variation and provides insight into future genetic improvement programs of C. nippona. • This study is the first to investigate the genetic diversity of C. nippona using both microsatellites and mtCOI. • Microsatellite analysis revealed no significant difference in genetic diversity between selected and wild populations. • The genetic diversity of the selected lines was successfully maintained over successive generations of mass selection. • Little genetic differentiation among the selected lines was observed based on the microsatellite result. [ABSTRACT FROM AUTHOR]

The Iwagaki oyster (Crassostrea nippona) is a potential aquaculture species with delicious taste and edibility in summer when the Pacific oyster (Crassostrea gigas) suffer from low meat quality. Although there is an increasing interest in hatchery mass production and field grow-out among farmers, large-scale expansion of C. nippona aquaculture has been compromised by unimproved growth performance. To improve the growth rate of C. nippona , we initiated the mass selective breeding program for fast growth in 2014 and estimated the genetic parameters of growth traits in the first three successive mass-selected generations. Each selected line exhibited better growth performance than the corresponding control group at all sampling dates. At grow-out stage, the average selection response (SR), realized heritability (h R 2) and genetic gain (GG) for shell height was 0.45–0.56, 0.27–0.42 and 9.20–11.12% in the three mass selected lines, respectively. A significant increase in GG for shell height was observed in the third-generation selected line compared with that in the first-generation (P < 0.05). Meanwhile, the average SR (0.44–0.49) and GG (11.07–12.46%) for body weight of C. nippona were observed in the selective breeding program after three successive generations of mass selection. The encouraging results obtained in this study suggest that genetic variances still remain at a relatively high level in the breeding populations of C. nippona , and demonstrate the feasibility of improving the growth traits by selective breeding for C. nippona. • Mass selection for fast growth of Crassostrea nippona obtained considerable selection responses. • Continuous and stable genetic gains for growth were observed during an intense mass selection. • Realized heritability of growth traits proved to possess great potential for genetic improvements. [ABSTRACT FROM AUTHOR]