Assessment of germplasm resource and detection of genomic signature under artificial selection of Zhikong scallop (Chlamys farreri)

Zhikong scallop (Chlamys farreri) is an economically important bivalve species and a major contributor to aquaculture in China as it is nutrient-dense and has a large adductor muscle. Farming and artificial breeding of this species mainly have relied mainly upon natural collected seed to be moved onto farms or be artificially bred. Hence, it is vital to determine the current status of C. farreri germplasm resources. In the present study, we genotyped six natural populations around the Shandong Peninsula in Northern China as well as populations of the artificially selected PR and ZY strains characterized by rapid growth and high survival. We identified 19,438 high-quality single-nucleotide polymorphisms (SNPs) that evenly distributed across the C. farreri genome. All populations exhibited high levels of genetic diversity, including high heterozygosity (Ho: 0.280-0.311) and low inbreeding (Fis: - 0.087-0.019). They also displayed a high frequency of rare alleles (13.80%-23.63%). Hence, these germplasms could be applied toward the genetic improvement of this species. A population analysis revealed no obvious genetic differentiation among natural populations. In contrast, the artificially selected populations in general, and the ZY strain in particular, significantly differed from the natural ones (Fst > 0.05). A selective sweep analysis indicated that 95 regions containing 76 genes, and 118 regions containing 99 genes, showed significant selection signatures in PR and ZY, respectively. These candidate genes may regulate various biological processes including growth, reproduction, and stress resistance, and account for the rapid growth and stress-resistance characteristic ZY and PR. The results of this work provide valuable information for resource management and germplasm improvement in C. farreri, and contribute to understand the genetic basis of selective breeding in scallop.