Genomics

Dataset Information

54

Affymetrix SNP array data for the Pacific oyster


ABSTRACT: The Pacific oyster (Crassostrea gigas) is a kind of marine bivalve of great economic and ecological importance and is among the animals possessing the highest level of genome DNA variations. Despite large efforts made for the discovery of Pacific oyster SNPs in many research groups, challenge still remains as how to utilize SNPs in a high-throughput, transferable and economical manner. In the study, we constructed an oyster 190K SNP array with Affymetrix Axiom genotyping technology. A total of 190,420 SNPs were designed on the chip, which were selected from 54 M SNPs identified by re-sequencing of more than 400 Pacific oysters. Genotyping results from 96 wild oysters indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. Carrying 133K polymorphic SNPs, the oyster 190K SNP array is the first high density SNP chip with the largest throughput currently in mollusc and is commercially available to the worldwide research community. Overall design: A total of 96 Pacific oysters were genotyped according to the manufacturer's directions to assess the performance of the oyster SNP array. All DNA were extracted from mantle tissues using a standard phenol-chloroform method.

INSTRUMENT(S): [Axiom_CgiSNP] Affymetrix Oyster SNP

SUBMITTER: Haigang Qi  

PROVIDER: GSE94633 | GEO | 2017-03-22

SECONDARY ACCESSION(S): PRJNA371639

REPOSITORIES: GEO

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Publications

Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas).

Qi Haigang H   Song Kai K   Li Chunyan C   Wang Wei W   Li Busu B   Li Li L   Zhang Guofan G  

PloS one 20170322 3


Single nucleotide polymorphisms (SNPs) are widely used in genetics and genomics research. The Pacific oyster (Crassostrea gigas) is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an  ...[more]

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