Whole-genome resequencing reveals the single nucleotide polymorphisms associated with shell shape in Crassostrea gigas

Abstract Shell shape is an economically important trait in bivalves, as it can directly affect consumer behaviour. However, there have been few studies on the genes related to shell growth and shape. The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture species worldwide, and studies on its shell shape could significantly increase its economic value. In this study, the shell-length-to-shell-height ratio (SLSH) was defined as the phenotype of interest. Descriptive statistics and correlation analyses of shell-related traits in the long (low phenotypic) and round (high phenotypic) groups of Crassostrea gigas are presented. Whole-genome resequencing, using individuals from these two groups, was performed to screen candidate single nucleotide polymorphisms (SNPs) and genes. A total of 925 SNPs and 593 genes associated with shell shape were found. SNaPshot was used for genotyping validation in an independent population: two SNPs were significantly related to shell shape differences, and the minor C allele of SNP g26854_18684937 favoured the growth of round shells. Further, ten genes were identified as significantly differentially expressed in the extreme shell shape groups of the independent population using real-time PCR, and the results showed that different shell shape may vary in environmental stress responses. This is the first study to use whole-genome resequencing to identify shell shape-related sites in bivalves. These results not only provide a reference for genetic research on oyster shell shape but also contribute to the knowledge base for future selective breeding of bivalves.