Cargando…

Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness

While Simple Sequence Repeats (SSRs) are extremely useful genetic markers, recent advances in technology have produced a shift toward use of single nucleotide polymorphisms (SNPs). The different mutational properties of these two classes of markers result in differences in heterozygosities and allel...

Descripción completa

Detalles Bibliográficos
Autores principales: Hamblin, Martha T., Warburton, Marilyn L., Buckler, Edward S.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2137949/
https://www.ncbi.nlm.nih.gov/pubmed/18159250
http://dx.doi.org/10.1371/journal.pone.0001367
_version_ 1782143449073451008
author Hamblin, Martha T.
Warburton, Marilyn L.
Buckler, Edward S.
author_facet Hamblin, Martha T.
Warburton, Marilyn L.
Buckler, Edward S.
author_sort Hamblin, Martha T.
collection PubMed
description While Simple Sequence Repeats (SSRs) are extremely useful genetic markers, recent advances in technology have produced a shift toward use of single nucleotide polymorphisms (SNPs). The different mutational properties of these two classes of markers result in differences in heterozygosities and allele frequencies that may have implications for their use in assessing relatedness and evaluation of genetic diversity. We compared analyses based on 89 SSRs (primarily dinucleotide repeats) to analyses based on 847 SNPs in individuals from the same 259 inbred maize lines, which had been chosen to represent the diversity available among current and historic lines used in breeding. The SSRs performed better at clustering germplasm into populations than did a set of 847 SNPs or 554 SNP haplotypes, and SSRs provided more resolution in measuring genetic distance based on allele-sharing. Except for closely related pairs of individuals, measures of distance based on SSRs were only weakly correlated with measures of distance based on SNPs. Our results suggest that 1) large numbers of SNP loci will be required to replace highly polymorphic SSRs in studies of diversity and relatedness and 2) relatedness among highly-diverged maize lines is difficult to measure accurately regardless of the marker system.
format Text
id pubmed-2137949
institution National Center for Biotechnology Information
language English
publishDate 2007
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-21379492007-12-26 Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness Hamblin, Martha T. Warburton, Marilyn L. Buckler, Edward S. PLoS One Research Article While Simple Sequence Repeats (SSRs) are extremely useful genetic markers, recent advances in technology have produced a shift toward use of single nucleotide polymorphisms (SNPs). The different mutational properties of these two classes of markers result in differences in heterozygosities and allele frequencies that may have implications for their use in assessing relatedness and evaluation of genetic diversity. We compared analyses based on 89 SSRs (primarily dinucleotide repeats) to analyses based on 847 SNPs in individuals from the same 259 inbred maize lines, which had been chosen to represent the diversity available among current and historic lines used in breeding. The SSRs performed better at clustering germplasm into populations than did a set of 847 SNPs or 554 SNP haplotypes, and SSRs provided more resolution in measuring genetic distance based on allele-sharing. Except for closely related pairs of individuals, measures of distance based on SSRs were only weakly correlated with measures of distance based on SNPs. Our results suggest that 1) large numbers of SNP loci will be required to replace highly polymorphic SSRs in studies of diversity and relatedness and 2) relatedness among highly-diverged maize lines is difficult to measure accurately regardless of the marker system. Public Library of Science 2007-12-26 /pmc/articles/PMC2137949/ /pubmed/18159250 http://dx.doi.org/10.1371/journal.pone.0001367 Text en This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
spellingShingle Research Article
Hamblin, Martha T.
Warburton, Marilyn L.
Buckler, Edward S.
Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness
title Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness
title_full Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness
title_fullStr Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness
title_full_unstemmed Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness
title_short Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and Relatedness
title_sort empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2137949/
https://www.ncbi.nlm.nih.gov/pubmed/18159250
http://dx.doi.org/10.1371/journal.pone.0001367
work_keys_str_mv AT hamblinmarthat empiricalcomparisonofsimplesequencerepeatsandsinglenucleotidepolymorphismsinassessmentofmaizediversityandrelatedness
AT warburtonmarilynl empiricalcomparisonofsimplesequencerepeatsandsinglenucleotidepolymorphismsinassessmentofmaizediversityandrelatedness
AT buckleredwards empiricalcomparisonofsimplesequencerepeatsandsinglenucleotidepolymorphismsinassessmentofmaizediversityandrelatedness