A refined panel of 42 microsatellite loci to universally genotype
catarrhine primates
Abstract
1. 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. 2. 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 faecal samples. 3. The final
panel of 42 microsatellite loci can efficiently be amplified with
primers distributed into three amplification pools. 4. 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.