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 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.

尽管单核苷酸多态性（single nucleotide polymorphisms, SNPs）已广泛应用于人类遗传学研究，但直到近年才被纳入包括鲸类（cetaceans）在内的非模式生物的遗传学研究。相较于其他群体遗传学研究所用的分子标记，SNPs具备多项优势：分型更为快捷简便、实验室间的数据比对难度更低，且可成功应用于低质量DNA样本的检测。我们对美国水域中数量最多的鲸类之一——宽吻海豚（Tursiops truncatus）的部分基因组区域进行了筛选，共鉴定出153个SNPs，整体平均每463个碱基对即存在1个SNP。针对其中53个SNPs设计了定制TaqMan®检测试剂盒，并通过对一组宽吻海豚样本（包含部分低质量DNA样本）进行基因分型，验证了其检测性能。研究发现，在19%的检测位点中，基于10个个体的DNA混合池进行初始SNP筛选时估算的次要等位基因频率（minor allele frequency, MAF），与对超过100个个体进行基因分型后得到的最终MAF存在显著差异，这提示基于小样本数据集推断MAF值时需谨慎。针对2个检测试剂盒，我们还对其异常聚类模式的成因进行了分析，以确认其数据是否仍可用于后续遗传学研究。整体研究结果证实，这些SNPs可精准应用于高质量与低质量DNA样本的遗传分析。本研究报道了首个可用于宽吻海豚群体遗传学与保护遗传学研究的SNP标记及基因分型检测方法。