ArticlePloS one2017
Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas).
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 79 citations in OpenAlex.
- Genome-wide association mapping for heat shock tolerance in Mercenaria mercenaria through SNP microarray analysis.BMC genomics · 2025Article
- Genetic Diversity and Population Structure in Farmed and Wild Pacific Oysters (International journal of molecular sciences · 2025Article
- Weak genetic divergence and signals of adaptation obscured by high gene flow in an economically important aquaculture species.BMC genomics · 2025Article
- Development and validation of a 66K SNP array for the hard clam (Mercenaria mercenaria).BMC genomics · 2024Article
- An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster.G3 (Bethesda, Md.) · 2024Article
- Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila ClamAnimals : an open access journal from MDPI · 2024Article
- Genomic selection for resistance to one pathogenic strain ofFrontiers in genetics · 2024Article
- Design and validation of a high-density single nucleotide polymorphism array for the Eastern oyster (Crassostrea virginica).G3 (Bethesda, Md.) · 2023Article
- SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array.Evolutionary applications · 2023Article
- Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica.Marine biotechnology (New York, N.Y.) · 2023Article
- Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Frontiers in genetics · 2022Article
- Article
- The Negative Relationship between Fouling Organisms and the Content of Eicosapentaenoic Acid and Docosahexaenoic Acid in Cultivated Pacific Oysters,Marine drugs · 2021Article
- Potential of genomic technologies to improve disease resistance in molluscan aquaculture.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021Review
- Genetic Dissection of a Precocious Phenotype in Male Tiger Pufferfish (Takifugu rubripes) using Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di).Marine biotechnology (New York, N.Y.) · 2021Article
- Article
- Development and Validation of an Open Access SNP Array for Nile Tilapia (G3 (Bethesda, Md.) · 2020Article
- Article
- Development and Evaluation of a High-Throughput Single-Nucleotide Polymorphism Array for Large Yellow Croaker (Frontiers in genetics · 2020Article
- Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 oyster 190K SNP array using Affymetrix Axiom genotyping technology. We designed 190,420 SNPs on the chip; these SNPs were selected from 54 million SNPs identified through re-sequencing of 472 Pacific oysters collected in China, Japan, Korea, and Canada. Our genotyping results indicated that 133,984 (70.4%) SNPs were polymorphic and successfully converted on the chip. The SNPs were distributed evenly throughout the oyster genome, located in 3,595 scaffolds with a length of ~509.4 million; the average interval spacing was 4,210 bp. In addition, 111,158 SNPs were distributed in 21,050 coding genes, with an average of 5.3 SNPs per gene. In comparison with genotypes obtained through re-sequencing, ~69% of the converted SNPs had a concordance rate of >0.971; the mean concordance rate was 0.966. Evaluation based on genotypes of full-sib family individuals revealed that the average genotyping accuracy rate was 0.975. Carrying 133 K polymorphic SNPs, our oyster 190K SNP array is the first commercially available high-density SNP chip for mollusks, with the highest throughput. It represents a valuable tool for oyster genome-wide association studies, fine linkage mapping, and population genetics.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.