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Developing genomic resources for the common bottlenose dolphin ( Tursiops truncatus ): isolation and characterization of 153 single nucleotide polymorphisms and 53 genotyping assays
Author(s) -
Vollmer N. L.,
Rosel P. E.
Publication year - 2012
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12008
Subject(s) - biology , genotyping , snp genotyping , snp , genetics , single nucleotide polymorphism , molecular inversion probe , snp array , population , bottlenose dolphin , allele frequency , genotype , evolutionary biology , gene , fishery , demography , sociology
Abstract Although single nucleotide polymorphisms ( SNP s) are commonly used in human genetics, they have only recently been incorporated into genetic studies of non‐model organisms, including cetaceans. SNP s 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 SNP s resulting in an overall average of one SNP every 463 base pairs. Custom TaqMan ® Assays were designed for 53 of these SNP s, 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 characterized the basis for unusual clustering patterns to determine whether their data could still be utilized for further genetic studies. Overall results support the use of these SNP s 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.