A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment
Abstract 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...
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ftbiomed:oai:biomedcentral.com:1471-2156-11-2 2023-05-15T15:32:42+02:00 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 2010-01-06 http://www.biomedcentral.com/1471-2156/11/2 en eng BioMed Central Ltd. http://www.biomedcentral.com/1471-2156/11/2 Copyright 2010 Glover et al; licensee BioMed Central Ltd. Research article 2010 ftbiomed 2010-02-14T00:25:55Z Abstract 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. Article in Journal/Newspaper Atlantic salmon BioMed Central |
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Open Polar |
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BioMed Central |
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ftbiomed |
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English |
description |
Abstract 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. |
format |
Article in Journal/Newspaper |
author |
Glover, Kevin A Hansen, Michael M Lien, Sigbjørn Als, Thomas D Høyheim, Bjørn Skaala, Øystein |
spellingShingle |
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 |
author_facet |
Glover, Kevin A Hansen, Michael M Lien, Sigbjørn Als, Thomas D Høyheim, Bjørn Skaala, Øystein |
author_sort |
Glover, Kevin A |
title |
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_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_sort |
comparison of snp and str loci for delineating population structure and performing individual genetic assignment |
publisher |
BioMed Central Ltd. |
publishDate |
2010 |
url |
http://www.biomedcentral.com/1471-2156/11/2 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
http://www.biomedcentral.com/1471-2156/11/2 |
op_rights |
Copyright 2010 Glover et al; licensee BioMed Central Ltd. |
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