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A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment

BACKGROUND: Technological advances have lead to the rapid increase in availability of single nucleotide polymorphisms (SNPs) in a range of organisms, and there is a general optimism that SNPs will become the marker of choice for a range of evolutionary applications. Here, comparisons between 300 pol...

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Autores principales: Glover, Kevin A, Hansen, Michael M, Lien, Sigbjørn, Als, Thomas D, Høyheim, Bjørn, Skaala, Øystein
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818610/
https://www.ncbi.nlm.nih.gov/pubmed/20051144
http://dx.doi.org/10.1186/1471-2156-11-2
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author Glover, Kevin A
Hansen, Michael M
Lien, Sigbjørn
Als, Thomas D
Høyheim, Bjørn
Skaala, Øystein
author_facet Glover, Kevin A
Hansen, Michael M
Lien, Sigbjørn
Als, Thomas D
Høyheim, Bjørn
Skaala, Øystein
author_sort Glover, Kevin A
collection PubMed
description BACKGROUND: Technological advances have lead to the rapid increase in availability of single nucleotide polymorphisms (SNPs) in a range of organisms, and there is a general optimism that SNPs will become the marker of choice for a range of evolutionary applications. Here, comparisons between 300 polymorphic SNPs and 14 short tandem repeats (STRs) were conducted on a data set consisting of approximately 500 Atlantic salmon arranged in 10 samples/populations. RESULTS: Global F(ST )ranged from 0.033-0.115 and -0.002-0.316 for the 14 STR and 300 SNP loci respectively. Global F(ST )was similar among 28 linkage groups when averaging data from mapped SNPs. With the exception of selecting a panel of SNPs taking the locus displaying the highest global F(ST )for each of the 28 linkage groups, which inflated estimation of genetic differentiation among the samples, inferred genetic relationships were highly similar between SNP and STR data sets and variants thereof. The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment. CONCLUSION: Whilst the optimal combinations of SNPs identified in this study are linked to the samples from which they were selected, this study demonstrates that identification of highly informative SNP loci from larger panels will provide researchers with a powerful approach to delineate genetic relationships at the individual and population levels.
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spelling pubmed-28186102010-02-10 A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment Glover, Kevin A Hansen, Michael M Lien, Sigbjørn Als, Thomas D Høyheim, Bjørn Skaala, Øystein BMC Genet Research article BACKGROUND: Technological advances have lead to the rapid increase in availability of single nucleotide polymorphisms (SNPs) in a range of organisms, and there is a general optimism that SNPs will become the marker of choice for a range of evolutionary applications. Here, comparisons between 300 polymorphic SNPs and 14 short tandem repeats (STRs) were conducted on a data set consisting of approximately 500 Atlantic salmon arranged in 10 samples/populations. RESULTS: Global F(ST )ranged from 0.033-0.115 and -0.002-0.316 for the 14 STR and 300 SNP loci respectively. Global F(ST )was similar among 28 linkage groups when averaging data from mapped SNPs. With the exception of selecting a panel of SNPs taking the locus displaying the highest global F(ST )for each of the 28 linkage groups, which inflated estimation of genetic differentiation among the samples, inferred genetic relationships were highly similar between SNP and STR data sets and variants thereof. The best 15 SNPs (30 alleles) gave a similar level of self-assignment to the best 4 STR loci (83 alleles), however, addition of further STR loci did not lead to a notable increase assignment whereas addition of up to 100 SNP loci increased assignment. CONCLUSION: Whilst the optimal combinations of SNPs identified in this study are linked to the samples from which they were selected, this study demonstrates that identification of highly informative SNP loci from larger panels will provide researchers with a powerful approach to delineate genetic relationships at the individual and population levels. BioMed Central 2010-01-06 /pmc/articles/PMC2818610/ /pubmed/20051144 http://dx.doi.org/10.1186/1471-2156-11-2 Text en Copyright ©2010 Glover et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research article
Glover, Kevin A
Hansen, Michael M
Lien, Sigbjørn
Als, Thomas D
Høyheim, Bjørn
Skaala, Øystein
A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment
title A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment
title_full A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment
title_fullStr A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment
title_full_unstemmed A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment
title_short A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment
title_sort comparison of snp and str loci for delineating population structure and performing individual genetic assignment
topic Research article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818610/
https://www.ncbi.nlm.nih.gov/pubmed/20051144
http://dx.doi.org/10.1186/1471-2156-11-2
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