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

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... Full description

Journal Title: PLoS One Mar 2017, Vol.12(3), p.e0174007
Main Author: Qi, Haigang
Other Authors: Song, Kai , Li, Chunyan , Wang, Wei , Li, Busu , Li, Li , Zhang, Guofan
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: E-ISSN: 19326203 ; DOI: 10.1371/journal.pone.0174007
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recordid: proquest1879964608
title: Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)
format: Article
creator:
  • Qi, Haigang
  • Song, Kai
  • Li, Chunyan
  • Wang, Wei
  • Li, Busu
  • Li, Li
  • Zhang, Guofan
subjects:
  • Crassostrea Gigas
  • Mollusca
  • Oncorhynchus Mykiss
  • Bivalvia
  • Glycine Max
  • Cyprinus Carpio
  • Oryza
  • Mollusks
  • Aquaculture
  • Laboratories
  • Science
  • Fisheries
  • Bioinformatics
  • Marine Ecology
  • Gene Mapping
  • Population Genetics
  • Oysters
  • Genomes
  • Genomics
  • Genetics
ispartof: PLoS One, Mar 2017, Vol.12(3), p.e0174007
description: 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...
language: eng
source:
identifier: E-ISSN: 19326203 ; DOI: 10.1371/journal.pone.0174007
fulltext: fulltext_linktorsrc
issn:
  • 19326203
  • 1932-6203
url: Link


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titleConstruction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)
creatorQi, Haigang ; Song, Kai ; Li, Chunyan ; Wang, Wei ; Li, Busu ; Li, Li ; Zhang, Guofan
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identifierE-ISSN: 19326203 ; DOI: 10.1371/journal.pone.0174007
subjectCrassostrea Gigas ; Mollusca ; Oncorhynchus Mykiss ; Bivalvia ; Glycine Max ; Cyprinus Carpio ; Oryza ; Mollusks ; Aquaculture ; Laboratories ; Science ; Fisheries ; Bioinformatics ; Marine Ecology ; Gene Mapping ; Population Genetics ; Oysters ; Genomes ; Genomics ; Genetics
descriptionSingle 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...
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titleConstruction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)
descriptionSingle 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...
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titleConstruction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)
authorQi, Haigang ; Song, Kai ; Li, Chunyan ; Wang, Wei ; Li, Busu ; Li, Li ; Zhang, Guofan
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8Aquaculture
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abstractSingle 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...
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urlhttp://search.proquest.com/docview/1879964608/
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date2017-03-01