Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas

The Pacific oyster, Crassostrea gigas, is an important aquaculture shellfish around the world with great economic and ecological value. Selective breeding programs have been carried out globally to improve production and performance traits, while genomic signatures of artificial selection remain largely unexplored. In China, we performed selective breeding of C. gigas for over a decade, leading to production of several fast-growing strains. In the present study, we conducted whole-genome resequencing of 20 oysters from two fast-growing strains that have been successively selected for 10 generations, and 20 oysters from the two corresponding wild populations. Sequencing depth of >10x was achieved for each sample, leading to identification of over 12.20 million SNPs. The population structures investigated with three independent methods (principal component analysis, phylogenetic tree, and structure) suggested distinct patterns among selected and wild oyster populations. Assessment of the linkage disequilibrium (LD) decay clearly indicated the changes in genetic diversity during selection. Fixation index (F-st) combined with cross-population composite likelihood ratio (XP-CLR) allowed for identification of 768 and 664 selective sweeps (encompassing 1042 and 872 genes) tightly linked to selection in the two fast-growing strains. KEGG enrichment and functional analyses revealed that 33 genes are important for growth regulation, which act as key components of various signaling pathways with close connection and further take part in regulating the process of cell cycle. This work provides valuable information for the understanding of genomic signatures for long-term selective breeding and will also be important for growth study and genome-assisted breeding of the Pacific oyster in the future.

Automated summary

This study investigated the genomic signatures of long-term selective breeding in Pacific oysters, revealing the impact of artificial selection on genetic diversity and genomic features. Population structure analysis and identification of selective sweeps highlighted the genetic differences between fast-growing oyster strains and wild populations. The findings provide valuable insights for understanding the genetic basis of growth regulation in Pacific oysters and will be beneficial for future genome-assisted breeding programs.