A refined panel of 42 microsatellite loci to universally genotype catarrhine primates. Issue 1 (13th December 2020)

• Record Type: Journal Article
• Authors: Trede, Franziska; Kil, Niels; Stranks, James; Connell, Andrew Jesse; Fischer, Julia; Ostner, Julia; Schülke, Oliver; Zinner, Dietmar; Roos, Christian
• Is Part Of: Ecology and evolution. Volume 11:Issue 1(2021)
• Page Start: 498
• Page End: 505
• Publication Date: 2020-12-13
• Subjects: apes -- genotyping‐by‐sequencing -- high‐throughput sequencing -- Old World monkeys -- simple tandem repeats; Ecology -- Periodicals; Evolution -- Periodicals; 577.05
• DOI: 10.1002/ece3.7069
• Languages: English
• ISSNs: 2045-7758

Abstract

Abstract: 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 ( Papio papio ) 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. Abstract : Even with genotyping‐by‐sequencing (GBS) of microsatellites issues with allelic dropout, null alleles and off‐target amplifications often remain due to poor primer design or using primers for cross‐species amplification. We re‐designed and validated a panel of 42 microsatellites providing 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.