Candidate gene polymorphisms and their association with glycogen content in the Pacific Oyster Crassostrea gigas

Abstract

Background: The Pacific oyster Crassostrea gigas is an important cultivated shellfish that is rich in nutrients. It contains high levels of glycogen, which is of high nutritional value. To investigate the genetic basis of this high glycogen content and its variation, we conducted a candidate gene association analysis using a wild population, and confirmed our results using an independent population, via targeted gene resequencing and mRNA expression analysis. Results: We validated 295 SNPs in the 90 candidate genes surveyed for association with glycogen content, 86 of were ultimately genotyped in all 144 experimental individuals from Jiaonan (JN). In addition, 732 SNPs were genotyped via targeted gene resequencing. Two SNPs (Cg-SNP-TY202 and Cg-SNP-3021) in Cg-GD1 (glycogen debranching enzyme) and one SNP (Cg-SNP-4) in Cg-GP1 (glycogen phosphorylase) were identified as being associated with glycogen content. The glycogen content of individuals with genotypes TT and TC in Cg-SNP-TY202 was higher than that of individuals with genotype CC. The transcript abundance of both glycogen-associated genes was differentially expressed in high glycogen content and low glycogen content individuals. Conclusions: This study identified three polymorphisms in two genes associated with oyster glycogen content, via candidate gene association analysis. The transcript abundance differences in Cg-GD1 and Cg-GP1 between low- and the high-glycogen content individuals suggests that it is possible that transcript regulation is mediated by variations of Cg-SNP-TY202, Cg-SNP-3021, and Cg-SNP-4. These findings will not only provide insights into the genetic basis of oyster quality, but also promote research into the molecular breeding of oysters.