Comparative analysis of genetic diversity and structure among four shell color strains of the Pacific oyster Crassostrea gigas based on the mitochondrial COI gene and microsatellites

Abstract

Shell color is one of the major determinants in the popularity of shelled seafood. To enhance the commercial value of the Pacific oyster (Crassostrea gigas), four shell color strains of black (SB), white (SW), gold (SG), and orange (SO) were bred purposefully for 11–12 generations. In this study, CIELAB colorimetric analysis was used to evaluate the effectiveness of shell color selection of C. gigas. The color parameters (L⁎, a⁎, b⁎) by statistical analysis differed significantly across black, white, gold, and orange shell strains (P < 0.05), and the principal component analysis characterized the considerable improvement in shell color uniformity. Further, we carried out genetic analysis by 15 microsatellites and mitochondrial cytochrome oxidase I sequences (mtCOI). A total of 121 alleles were detected at all 15 microsatellite loci, with the average number of alleles per locus ranging from 4.07 in SO to 7.67 in SW. Compared with wild populations, the shell color strains had significantly fewer alleles and mtCOI haplotypes, but the average heterozygosity, including Ho from 0.52 to 0.66 and He from 0.59 to 0.75, was not statistically different (P < 0.05). The SO samples suffered the greatest loss of diversity and occupied the lowest value of all genetic diversity indices, which is likely due to the smaller size of founding stock resulting in a stronger bottleneck. Population simulation analysis showed that the genetic background of four shell color strains was completely separated, confirming the consistency of phenotypically defined and genetically differentiated populations. Pairwise FST calculated by microsatellites with a range of 0.267 to 0.121 revealed high levels of genetic differentiation among strains, which has far exceeded the divergence between different geographical populations of C. gigas (FST: 0.012–0.034). The results obtained in the study provide valuable information for further genetic improvement of shell color variants through selective breeding.