Abstract
BackgroundOyster is rich in glycogen and free amino acids and is called “the milk of sea”. To understand the main genetic effects of these traits and the genetic networks underlying their correlation, we have conducted the whole genome resequencing with 427 oysters collected from the world-wide scale.ResultsAfter association analysis, 168 clustered significant single nucleotide polymorphism (SNP) loci were identified for glycogen content and 17 SNPs were verified with 288 oyster individuals in another wide populations. These were the most important candidate loci for oyster breeding. Among 24 genes in the 100-kb regions of the leading SNP loci, cytochrome P450 17A1 (CYP17A1) contained a non-synonymous SNP and displayed higher expressions in high glycogen content individuals. This might enhance the gluconeogenesis process by the transcriptionally regulating the expression of phosphoenolpyruvate carboxykinase (PEPCK) and glucose 6-phosphatase (G6Pase). Also, for amino acids content, 417 clustered significant SNPs were identified. After genetic network analysis, three node SNP regions were identified to be associated with glycogen, protein, and Asp content, which might explain their significant correlation.ConclusionOverall, this study provides insights into the genetic correlation among complex traits, which will facilitate future oyster functional studies and breeding through molecular design.
Highlights
Oyster is rich in glycogen and free amino acids and is called “the milk of sea”
Resequencing and population structure analysis of 371 wild oysters collected in China have been conducted by us previously [33]
We mainly focused on the single nucleotide polymorphism (SNP) located on candidate regions which obtained from the Genome wide association analysis (GWAS) results
Summary
Oyster is rich in glycogen and free amino acids and is called “the milk of sea”. To understand the main genetic effects of these traits and the genetic networks underlying their correlation, we have conducted the whole genome resequencing with 427 oysters collected from the world-wide scale. Oyster is rich in taurine (50 μmol/g wet weight), amino acids (45–57% of dry weight), and glycogen (20–40% of the dry weight), Meng et al BMC Genomics (2019) 20:625 breeding traits [6, 7]. The genetic studies of oyster nutrient traits, such as glycogen, protein and amino acids, is necessary for the development of molecular breeding inoysters. An effective haplotype of glycogen synthase is found in C. gigas, which is significantly related to the glycogen content [20]. These analyses mainly focused on several genes involved in glycogen synthesis and degradation pathways. With respect to complex regulation mechanisms, this analysis cannot detect the major loci and genes
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