Data from: Developing genomic resources for the common bottlenose dolphin (Tursiops truncatus): isolation and characterisation of 153 single nucleotide polymorphisms and 53 genotyping assays

• Main Authors: Vollmer, Nicole L., Rosel, Patricia E., Vollmer, N. L., Rosel, P. E.
• Format: Dataset
• Language: unknown
• Published: Dryad Digital Repository 2012
• Subjects: conservation genetics; CATS loci; TaqMan® Assays; SNP discovery; targeted gene approach; cetacean; Tursiops truncatus; Gulf of Mexico; western North Atlantic; Life sciences; medicine and health care; envir; geo; North Atlantic
• Online Access: https://doi.org/10.5061/dryad.29ds0

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. T.truncatus COL3A1-like geneSequence alignment file (.fasta) presenting sequencing results of five T. truncatus individuals of the DNA pool for the collagen type III alpha 1-like gene (COL3A1). There is one SNP in this fragment. Four individuals were sampled in the Gulf of Mexico and one in the western North Atlantic. Sequences were derived using an ABI 3130 and aligned in the program Se-Al. All work was completed at the Southeast Fisheries Science Center ...