A genome-wide association study to identify the genes associated with shell growth and shape-related traits in Crassostrea gigas

Oyster shell traits are economically important for commercial trade, and can directly reflect the quality of oysters, and thus affect consumer purchasing decisions. However, few studies have been conducted on the molecular mechanisms of oyster shell growth and shaping. For the Pacific oyster, Crassostrea gigas, we measured shell related traits of F1 individuals from 427 half-sib families at four growth stages. We defined shell height (SH), shell length (SL), and shell width (SW) as shell growth-related traits, while secondary traits of shell length to shell height ratio (SLSH) and shell width-to-shell height ratio (SWSH) were defined as shell shape-related traits. Further, we identified the genes associated with these traits using genome-wide association studies (GWAS). A total of 212 candidate single nucleotide polymorphism (SNP) markers were found to be associated with related traits. Then, 66 candidate genes that may relate to oyster shell growth within 100 kb upstream and downstream of these SNPs were selected for further study. We validated these genes in the extreme phenotypic groups of another independent population. Finally, we obtained seven genes (Rpsa, Trim3, Tnn, Ky, Fndc2, SLC7A9, and Ankrd44) with significantly different expressions in these groups, six of which were associated with secondary shell shape-related traits. Our results fill a research gap in oyster shell shaping and may serve as a reference for future selective breeding.