Genetic differentiation and selection signatures in two bay scallop (Argopecten irradians) breeds revealed by whole-genome resequencing analysis

Abstract

Abstract Bay scallop is an economically important bivalve species in aquaculture industry. Due to its rapid growth rate and short reproduction cycle, bay scallop possesses the highest annual yield in Chinese scallop production and serves as a good model species to study the genetic effects of population differentiation and selective breeding. Via whole genomic resequencing analysis of two artificially selective breeds (Haiyifeng12 and Zhongkehong) and a hatchery reference population (Jiaonan), we acquired a total of 3,885,213 high quality SNPs and 22,312 SSRs. A lower level of genomic polymorphism and increased linkage disequilibrium were detected in the two selective breeds compared with the hatchery reference population. Selective sweep analysis revealed that 104 and 223 genes are under selection in the two breeds respectively, which may be the causal factors for the improved performance in growth and immunity. Our study provides insight into the genetic differentiation and selection signatures of bay scallop selective breeds. Together with the generated genome wide SNP and SSR data, these findings are an important addition to the scallop genomic resources and have practical implications for breeding programs in scallop aquaculture.