title: 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.
authors.affiliation: National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China; University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Zhicai
authors.initials: Z
authors.lastname: She
authors.affiliation: National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Li
authors.initials: L
authors.lastname: Li
authors.affiliation: National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Haigang
authors.initials: H
authors.lastname: Qi
authors.affiliation: National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Song
authors.affiliation: National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Huayong
authors.initials: H
authors.lastname: Que
authors.affiliation: National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.
authors.forename: Guofan
authors.initials: G
authors.lastname: Zhang
mesh_terms: D000818:Animals; D049896:Crassostrea / Q000737:chemistry / Q000235:genetics*; D020869:Gene Expression Profiling; D056726:Genetic Association Studies; D005838:Genotype; D006003:Glycogen / Q000378:metabolism*; D006004:Glycogen Debranching Enzyme System / Q000235:genetics*; D024981:Glycogen Phosphorylase / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D006004:Glycogen Debranching Enzyme System; D006003:Glycogen; D024981:Glycogen Phosphorylase