Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays
Although single nucleotide polymorphisms (SNPs) are commonly used in human genetics, they have only recently been incorporated into genetic studies of non-model organisms, including cetaceans. SNPs have several advantages over other molecular markers for studies of population genetics: they are quic...
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ftdryad:oai:v1.datadryad.org:10255/dryad.41235 2023-05-15T17:35:05+02:00 Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays Vollmer, Nicole L. Rosel, Patricia E. Gulf of Mexico western North Atlantic 2012-08-11T19:00:53Z http://hdl.handle.net/10255/dryad.41235 https://doi.org/10.5061/dryad.29ds0 unknown doi:10.5061/dryad.29ds0/1 doi:10.5061/dryad.29ds0/2 doi:10.5061/dryad.29ds0/3 doi:10.1111/1755-0998.12008 PMID:22978635 doi:10.5061/dryad.29ds0 Vollmer NL, Rosel PE (2012) Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays. Molecular Ecology Resources 12(6): 1124–1132. http://hdl.handle.net/10255/dryad.41235 CATS loci cetacean Conservation Genetics SNP discovery TaqMan® Assays targeted gene approach Article 2012 ftdryad https://doi.org/10.5061/dryad.29ds0 https://doi.org/10.5061/dryad.29ds0/1 https://doi.org/10.5061/dryad.29ds0/2 https://doi.org/10.5061/dryad.29ds0/3 https://doi.org/10.1111/1755-0998.12008 2020-01-01T14:57:19Z Although single nucleotide polymorphisms (SNPs) are commonly used in human genetics, they have only recently been incorporated into genetic studies of non-model organisms, including cetaceans. SNPs have several advantages over other molecular markers for studies of population genetics: they are quicker and more straightforward to score, cross-laboratory comparisons of data are less complicated, and they can be used successfully with low-quality DNA. We screened portions of the genome of one of the most abundant cetaceans in U.S. waters, the common bottlenose dolphin (Tursiops truncatus), and identified 153 SNPs resulting in an overall average of one SNP every 463 base pairs. Custom TaqMan® Assays were designed for 53 of these SNPs and their performance was tested by genotyping a set of bottlenose dolphin samples, including some with low quality DNA. We found that in 19% of the loci examined, the minor allele frequency (MAF) estimated during initial SNP ascertainment using a DNA pool of 10 individuals differed significantly from the final MAF after genotyping over 100 individuals, suggesting caution when making inferences about MAF values based on small data sets. For two assays, we also characterised the basis for unusual clustering patterns to determine whether their data could still be utilised for further genetic studies. Overall results support the use of these SNPs for accurate analysis of both poor and good quality DNA. We report the first SNP markers and genotyping assays for use in population and conservation genetic studies of bottlenose dolphins. Article in Journal/Newspaper North Atlantic Dryad Digital Repository (Duke University) |
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Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
CATS loci cetacean Conservation Genetics SNP discovery TaqMan® Assays targeted gene approach |
spellingShingle |
CATS loci cetacean Conservation Genetics SNP discovery TaqMan® Assays targeted gene approach Vollmer, Nicole L. Rosel, Patricia E. Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays |
topic_facet |
CATS loci cetacean Conservation Genetics SNP discovery TaqMan® Assays targeted gene approach |
description |
Although single nucleotide polymorphisms (SNPs) are commonly used in human genetics, they have only recently been incorporated into genetic studies of non-model organisms, including cetaceans. SNPs have several advantages over other molecular markers for studies of population genetics: they are quicker and more straightforward to score, cross-laboratory comparisons of data are less complicated, and they can be used successfully with low-quality DNA. We screened portions of the genome of one of the most abundant cetaceans in U.S. waters, the common bottlenose dolphin (Tursiops truncatus), and identified 153 SNPs resulting in an overall average of one SNP every 463 base pairs. Custom TaqMan® Assays were designed for 53 of these SNPs and their performance was tested by genotyping a set of bottlenose dolphin samples, including some with low quality DNA. We found that in 19% of the loci examined, the minor allele frequency (MAF) estimated during initial SNP ascertainment using a DNA pool of 10 individuals differed significantly from the final MAF after genotyping over 100 individuals, suggesting caution when making inferences about MAF values based on small data sets. For two assays, we also characterised the basis for unusual clustering patterns to determine whether their data could still be utilised for further genetic studies. Overall results support the use of these SNPs for accurate analysis of both poor and good quality DNA. We report the first SNP markers and genotyping assays for use in population and conservation genetic studies of bottlenose dolphins. |
format |
Article in Journal/Newspaper |
author |
Vollmer, Nicole L. Rosel, Patricia E. |
author_facet |
Vollmer, Nicole L. Rosel, Patricia E. |
author_sort |
Vollmer, Nicole L. |
title |
Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays |
title_short |
Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays |
title_full |
Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays |
title_fullStr |
Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays |
title_full_unstemmed |
Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays |
title_sort |
data from: developing genomic resources for the common bottlenose dolphin (tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays |
publishDate |
2012 |
url |
http://hdl.handle.net/10255/dryad.41235 https://doi.org/10.5061/dryad.29ds0 |
op_coverage |
Gulf of Mexico western North Atlantic |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_relation |
doi:10.5061/dryad.29ds0/1 doi:10.5061/dryad.29ds0/2 doi:10.5061/dryad.29ds0/3 doi:10.1111/1755-0998.12008 PMID:22978635 doi:10.5061/dryad.29ds0 Vollmer NL, Rosel PE (2012) Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays. Molecular Ecology Resources 12(6): 1124–1132. http://hdl.handle.net/10255/dryad.41235 |
op_doi |
https://doi.org/10.5061/dryad.29ds0 https://doi.org/10.5061/dryad.29ds0/1 https://doi.org/10.5061/dryad.29ds0/2 https://doi.org/10.5061/dryad.29ds0/3 https://doi.org/10.1111/1755-0998.12008 |
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1766134128725458944 |