Identification of growth-related SNPs and genes in the genome of the pearl oyster (Pinctada fucata) using GWAS

Pinctada fucata is one of the most important pearl production and mariculture shellfish in China, and enhancing growth rate has become a vital task of the P.fataca farming industry. At present, there is a lack of systematic screening of growth-related genes and loci in the P.fataca. Foot tissue was extracted DNA and sequenced. Clean readings of high-quality is obtained by filtering and quality control. According the genocme-wide association study (GWAS) gained the annotation of the associated region and locate genes. In this study, six growth-related traits in P.fataca were analyzed by the genocme-wide association study (GWAS) utilizing 4,349,618 single nucleotide polymorphism (SNP) markers. Population structure and phylogenetic analysis of the study population showed that PC1, PC2, and PC3 accounted for 13.8% of the total phenotypic variation . PC1 explained 5.61% of the total genetic variation and was divided into two clusters. PC2 explained 4.29% of the total genetic variation and PC3 explained 3.9% of it, consistent with pedigree records A total of 52 SNPs and 165 genes associated with growth traits were identified. Additionally, Pma_10012812 and Pma_10015664 were regarded as candidate genes, that may influence growth-related traits by some biological processes (cell growth, cell functions, cellular adhesion, survival, migration, and structural integrity). In summary, the results could promote the marker-assisted choice associated with the improved growth, and provide a theoretical basis to further develop and utilize the genomic resources of P. fataca.