Genetic variability of mass-selected and wild populations of Iwagaki oyster (Crassostrea nippona) revealed by microsatellites and mitochondrial COI sequences

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 (Nₐ: 7.53–9.87), observed heterozygosity (Hₒ: 0.58–0.64), expected heterozygosity (Hₑ: 0.67–0.71) and alleles richness (Aᵣ: 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 (Nₑ₋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 FST: 0.005, P > 0.05) and significant genetic differentiation among the wild populations was revealed by global FST (0.15, P < 0.01), pairwise FST (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.