Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array
Various salmonid species are cultivated in cold water aquaculture. However, due to limited genomic data resources, specific high-throughput genotyping tools are not available to many of the salmonid species. In this study, a 57K single nucleotide polymorphism (SNP) array for rainbow trout (Oncorhync...
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ftpubmed:oai:pubmedcentral.nih.gov:6097679 2023-05-15T16:34:58+02:00 Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array Zhang, Han-Yuan Zhao, Zi-Xia Xu, Jian Xu, Peng Bai, Qing-Li Yang, Shi-Yong Jiang, Li-Kun Chen, Bao-Hua 2018-08-17 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097679/ http://www.ncbi.nlm.nih.gov/pubmed/30118517 https://doi.org/10.1371/journal.pone.0202582 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097679/ http://www.ncbi.nlm.nih.gov/pubmed/30118517 http://dx.doi.org/10.1371/journal.pone.0202582 © 2018 Zhang et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2018 ftpubmed https://doi.org/10.1371/journal.pone.0202582 2018-09-02T00:40:22Z Various salmonid species are cultivated in cold water aquaculture. However, due to limited genomic data resources, specific high-throughput genotyping tools are not available to many of the salmonid species. In this study, a 57K single nucleotide polymorphism (SNP) array for rainbow trout (Oncorhynchus mykiss) was utilized to detect polymorphisms in seven salmonid species, including Hucho taimen, Oncorhynchus masou, Salvelinus fontinalis, Brachymystax lenok, Salvelinus leucomaenis, O. kisutch, and O. mykiss. The number of polymorphic markers per population ranged from 3,844 (O. kisutch) to 53,734 (O. mykiss), indicating that the rainbow trout SNP array was applicable as a universal genotyping tool for other salmonid species. Among the six other salmonid populations from four genera, 28,882 SNPs were shared, whereas 525 SNPs were polymorphic in all four genera. The genetic diversity and population relationships of the seven salmonid species were studied by principal component analysis (PCA). The phylogenetic relationships among populations were analyzed using the maximum likelihood method, which indicated that the shared SNP markers provide reliable genomic information for population genetic analyses in common aquaculture salmonid fishes. Furthermore, this obtained genomic information may be applicable for population genetic evaluation, marker-assisted breeding, and propagative parent selection in fry production. Text Hucho taimen PubMed Central (PMC) PLOS ONE 13 8 e0202582 |
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Research Article Zhang, Han-Yuan Zhao, Zi-Xia Xu, Jian Xu, Peng Bai, Qing-Li Yang, Shi-Yong Jiang, Li-Kun Chen, Bao-Hua Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array |
topic_facet |
Research Article |
description |
Various salmonid species are cultivated in cold water aquaculture. However, due to limited genomic data resources, specific high-throughput genotyping tools are not available to many of the salmonid species. In this study, a 57K single nucleotide polymorphism (SNP) array for rainbow trout (Oncorhynchus mykiss) was utilized to detect polymorphisms in seven salmonid species, including Hucho taimen, Oncorhynchus masou, Salvelinus fontinalis, Brachymystax lenok, Salvelinus leucomaenis, O. kisutch, and O. mykiss. The number of polymorphic markers per population ranged from 3,844 (O. kisutch) to 53,734 (O. mykiss), indicating that the rainbow trout SNP array was applicable as a universal genotyping tool for other salmonid species. Among the six other salmonid populations from four genera, 28,882 SNPs were shared, whereas 525 SNPs were polymorphic in all four genera. The genetic diversity and population relationships of the seven salmonid species were studied by principal component analysis (PCA). The phylogenetic relationships among populations were analyzed using the maximum likelihood method, which indicated that the shared SNP markers provide reliable genomic information for population genetic analyses in common aquaculture salmonid fishes. Furthermore, this obtained genomic information may be applicable for population genetic evaluation, marker-assisted breeding, and propagative parent selection in fry production. |
format |
Text |
author |
Zhang, Han-Yuan Zhao, Zi-Xia Xu, Jian Xu, Peng Bai, Qing-Li Yang, Shi-Yong Jiang, Li-Kun Chen, Bao-Hua |
author_facet |
Zhang, Han-Yuan Zhao, Zi-Xia Xu, Jian Xu, Peng Bai, Qing-Li Yang, Shi-Yong Jiang, Li-Kun Chen, Bao-Hua |
author_sort |
Zhang, Han-Yuan |
title |
Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array |
title_short |
Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array |
title_full |
Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array |
title_fullStr |
Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array |
title_full_unstemmed |
Population genetic analysis of aquaculture salmonid populations in China using a 57K rainbow trout SNP array |
title_sort |
population genetic analysis of aquaculture salmonid populations in china using a 57k rainbow trout snp array |
publisher |
Public Library of Science |
publishDate |
2018 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097679/ http://www.ncbi.nlm.nih.gov/pubmed/30118517 https://doi.org/10.1371/journal.pone.0202582 |
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Hucho taimen |
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Hucho taimen |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097679/ http://www.ncbi.nlm.nih.gov/pubmed/30118517 http://dx.doi.org/10.1371/journal.pone.0202582 |
op_rights |
© 2018 Zhang et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
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CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0202582 |
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PLOS ONE |
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13 |
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