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The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera
Microsatellite markers are difficult to apply within lepidopteran studies due to the lack of locus-specific PCR amplification and the high proportion of “null” alleles, such that erroneous estimations of population genetic parameters often result. Herein single nucleotide polymorphism (SNP) markers...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Research Foundation
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268592/ https://www.ncbi.nlm.nih.gov/pubmed/22303334 http://dx.doi.org/10.3389/fgene.2011.00038 |
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author | Coates, Brad Steven Bayles, Darrell O. Wanner, Kevin W. Robertson, Hugh M. Hellmich, Richard L. Sappington, Thomas W. |
author_facet | Coates, Brad Steven Bayles, Darrell O. Wanner, Kevin W. Robertson, Hugh M. Hellmich, Richard L. Sappington, Thomas W. |
author_sort | Coates, Brad Steven |
collection | PubMed |
description | Microsatellite markers are difficult to apply within lepidopteran studies due to the lack of locus-specific PCR amplification and the high proportion of “null” alleles, such that erroneous estimations of population genetic parameters often result. Herein single nucleotide polymorphism (SNP) markers are developed from Ostrinia nubilalis (Lepidoptera: Crambidae) using next generation expressed sequence tag (EST) data. A total of 2742 SNPs were predicted within a reference assembly of 7414 EST contigs, and a subset of 763 were incorporated into 24 multiplex PCR reactions. To validate this pipeline, 5 European and North American sample sites were genotyped at 178 SNP loci, which indicated 84 (47.2%) were in Hardy–Weinberg equilibrium. Locus-by-locus F(ST), analysis of molecular variance, and STRUCTURE analyses indicate significant genetic differentiation may exist between European and North American O. nubilalis. The observed genetic diversity was significantly lower among European sites, which may result from genetic drift, natural selection, a genetic bottleneck, or ascertainment bias due to North American origin of EST sequence data. SNPs are an abundant source of mutation data for molecular genetic marker development in non-model species, with shared ancestral SNPs showing application within closely related species. These markers offer advantages over microsatellite markers for genetic and genomic analyses of Lepidoptera, but the source of mutation data may affect the estimation of population parameters and likely need to be considered in the interpretation of empirical data. |
format | Online Article Text |
id | pubmed-3268592 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Frontiers Research Foundation |
record_format | MEDLINE/PubMed |
spelling | pubmed-32685922012-02-02 The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera Coates, Brad Steven Bayles, Darrell O. Wanner, Kevin W. Robertson, Hugh M. Hellmich, Richard L. Sappington, Thomas W. Front Genet Genetics Microsatellite markers are difficult to apply within lepidopteran studies due to the lack of locus-specific PCR amplification and the high proportion of “null” alleles, such that erroneous estimations of population genetic parameters often result. Herein single nucleotide polymorphism (SNP) markers are developed from Ostrinia nubilalis (Lepidoptera: Crambidae) using next generation expressed sequence tag (EST) data. A total of 2742 SNPs were predicted within a reference assembly of 7414 EST contigs, and a subset of 763 were incorporated into 24 multiplex PCR reactions. To validate this pipeline, 5 European and North American sample sites were genotyped at 178 SNP loci, which indicated 84 (47.2%) were in Hardy–Weinberg equilibrium. Locus-by-locus F(ST), analysis of molecular variance, and STRUCTURE analyses indicate significant genetic differentiation may exist between European and North American O. nubilalis. The observed genetic diversity was significantly lower among European sites, which may result from genetic drift, natural selection, a genetic bottleneck, or ascertainment bias due to North American origin of EST sequence data. SNPs are an abundant source of mutation data for molecular genetic marker development in non-model species, with shared ancestral SNPs showing application within closely related species. These markers offer advantages over microsatellite markers for genetic and genomic analyses of Lepidoptera, but the source of mutation data may affect the estimation of population parameters and likely need to be considered in the interpretation of empirical data. Frontiers Research Foundation 2011-06-29 /pmc/articles/PMC3268592/ /pubmed/22303334 http://dx.doi.org/10.3389/fgene.2011.00038 Text en Copyright © 2011 Coates, Bayles, Wanner, Robertson, Hellmich and Sappington. http://www.frontiersin.org/licenseagreement This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and other Frontiers conditions are complied with. |
spellingShingle | Genetics Coates, Brad Steven Bayles, Darrell O. Wanner, Kevin W. Robertson, Hugh M. Hellmich, Richard L. Sappington, Thomas W. The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera |
title | The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera |
title_full | The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera |
title_fullStr | The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera |
title_full_unstemmed | The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera |
title_short | The Application and Performance of Single Nucleotide Polymorphism Markers for Population Genetic Analyses of Lepidoptera |
title_sort | application and performance of single nucleotide polymorphism markers for population genetic analyses of lepidoptera |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268592/ https://www.ncbi.nlm.nih.gov/pubmed/22303334 http://dx.doi.org/10.3389/fgene.2011.00038 |
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