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...
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ftchinacasciocas:oai:ir.qdio.ac.cn:337002/136695 2023-05-15T15:58:17+02:00 Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas) Qi, Haigang Song, Kai Li, Chunyan Wang, Wei Li, Busu Li, Li Zhang, Guofan 2017-03-22 http://ir.qdio.ac.cn/handle/337002/136695 https://doi.org/10.1371/journal.pone.0174007 英语 eng PLOS ONE 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). http://ir.qdio.ac.cn/handle/337002/136695 doi:10.1371/journal.pone.0174007 Article 期刊论文 2017 ftchinacasciocas https://doi.org/10.1371/journal.pone.0174007 2022-06-27T05:37:57Z 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 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. Article in Journal/Newspaper Crassostrea gigas Pacific oyster Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR Canada Pacific PLOS ONE 12 3 e0174007 |
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Open Polar |
collection |
Institute of Oceanology, Chinese Academy of Sciences: IOCAS-IR |
op_collection_id |
ftchinacasciocas |
language |
English |
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 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. |
format |
Article in Journal/Newspaper |
author |
Qi, Haigang Song, Kai Li, Chunyan Wang, Wei Li, Busu Li, Li Zhang, Guofan |
spellingShingle |
Qi, Haigang Song, Kai Li, Chunyan Wang, Wei Li, Busu Li, Li Zhang, Guofan Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas) |
author_facet |
Qi, Haigang Song, Kai Li, Chunyan Wang, Wei Li, Busu Li, Li Zhang, Guofan |
author_sort |
Qi, Haigang |
title |
Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas) |
title_short |
Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas) |
title_full |
Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas) |
title_fullStr |
Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas) |
title_full_unstemmed |
Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas) |
title_sort |
construction and evaluation of a high-density snp array for the pacific oyster (crassostrea gigas) |
publishDate |
2017 |
url |
http://ir.qdio.ac.cn/handle/337002/136695 https://doi.org/10.1371/journal.pone.0174007 |
geographic |
Canada Pacific |
geographic_facet |
Canada Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_relation |
PLOS ONE 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). http://ir.qdio.ac.cn/handle/337002/136695 doi:10.1371/journal.pone.0174007 |
op_doi |
https://doi.org/10.1371/journal.pone.0174007 |
container_title |
PLOS ONE |
container_volume |
12 |
container_issue |
3 |
container_start_page |
e0174007 |
_version_ |
1766394006656253952 |