Trede Franziska, Kil Niels, Stranks James, Connell Andrew Jesse, Fischer Julia, Ostner Julia, Schülke Oliver, Zinner Dietmar, Roos Christian
Cognitive Ethology Laboratory German Primate Center Leibniz Institute for Primate Research Göttingen Germany.
Primate Genetics Laboratory German Primate Center Leibniz Institute for Primate Research Göttingen Germany.
Ecol Evol. 2020 Dec 13;11(1):498-505. doi: 10.1002/ece3.7069. eCollection 2021 Jan.
Microsatellite genotyping is an important genetic method for a number of research questions in biology. Given that the traditional fragment length analysis using polyacrylamide gel or capillary electrophoresis has several drawbacks, microsatellite genotyping-by-sequencing (GBS) has arisen as a promising alternative. Although GBS mitigates many of the problems of fragment length analysis, issues with allelic dropout and null alleles often remain due to mismatches in primer binding sites and unnecessarily long PCR products. This is also true for GBS in catarrhine primates where cross-species amplification of loci (often human derived) is common.We therefore redesigned primers for 45 microsatellite loci based on 17 available catarrhine reference genomes. Next, we tested them in singleplex and different multiplex settings in a panel of species representing all major lineages of Catarrhini and further validated them in wild Guinea baboons () using fecal samples.The final panel of 42 microsatellite loci can efficiently be amplified with primers distributed into three amplification pools.With our microsatellite panel, we provide a tool to universally genotype catarrhine primates via GBS from different sample sources in a cost- and time-efficient way, with higher resolution, and comparability among laboratories and species.
微卫星基因分型是生物学中许多研究问题的重要遗传方法。鉴于使用聚丙烯酰胺凝胶或毛细管电泳的传统片段长度分析存在若干缺点，微卫星测序基因分型（GBS）已成为一种有前景的替代方法。尽管GBS减轻了片段长度分析的许多问题，但由于引物结合位点不匹配和不必要的长PCR产物，等位基因缺失和无效等位基因问题仍然经常存在。在狭鼻猿灵长类动物中进行GBS时也是如此，在那里位点的跨物种扩增（通常是人类来源）很常见。因此，我们基于17个可用的狭鼻猿参考基因组重新设计了45个微卫星位点的引物。接下来，我们在代表狭鼻猿所有主要谱系的一组物种中，以单重和不同的多重组合设置对它们进行了测试，并使用粪便样本在野生几内亚狒狒中进一步验证了它们。最终的42个微卫星位点组合可以用分布在三个扩增池中的引物有效地进行扩增。通过我们的微卫星组合，我们提供了一种工具，能够以经济高效的方式，从不同样本来源通过GBS对狭鼻猿灵长类动物进行通用基因分型，具有更高的分辨率，并且在不同实验室和物种之间具有可比性。
