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Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)
Qi, Haigang1,2,3; Song, Kai1,3,4; Li, Chunyan1,2,3; Wang, Wei1,2,3; Li, Busu1,2,3; Li, Li1,3,4; Zhang, Guofan1,2,3
2017-03-22
Source PublicationPLOS ONE
Volume12Issue:3
SubtypeArticle
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 similar to 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, similar to 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.
DOI10.1371/journal.pone.0174007
Indexed BySCI
Language英语
WOS IDWOS:000399094700042
Citation statistics
Cited Times:12[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Version出版稿
Identifierhttp://ir.qdio.ac.cn/handle/337002/136695
Collection海洋生物技术研发中心
实验海洋生物学重点实验室
Affiliation1.Chinese Acad Sci, Key Lab Expt Marine Biol, Inst Oceanol, Qingdao, Peoples R China
2.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Biol & Biotechnol, Qingdao, Peoples R China
3.Chinese Acad Sci, Natl & Local Joint Engn Lab Ecol Mariculture, Inst Oceanol, Qingdao, Peoples R China
4.Qingdao Natl Lab Marine Sci & Technol, Lab Marine Fisheries & Aquaculture, Qingdao, Shandong, Peoples R China
First Author AffilicationInstitute of Oceanology, Chinese Academy of Sciences
Recommended Citation
GB/T 7714
Qi, Haigang,Song, Kai,Li, Chunyan,et al. Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)[J]. PLOS ONE,2017,12(3).
APA Qi, Haigang.,Song, Kai.,Li, Chunyan.,Wang, Wei.,Li, Busu.,...&Zhang, Guofan.(2017).Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas).PLOS ONE,12(3).
MLA Qi, Haigang,et al."Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas)".PLOS ONE 12.3(2017).
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