Risks involved in fecal DNA-based genotyping of microsatellite loci in the Amur tiger Panthera tigris altaica: a pilot study

Abstract

In modern wildlife ecological research, feces is the most common non-invasive source of DNA obtained in the field and polymerase chain reaction (PCR) technology based on microsatellite markers is used to mine genetic information contained within. This is especially the case for endangered species. However, there are risks associated with this genotyping method because of the poor quality of fecal DNA. In this study, we assessed genotyping risk across 12 microsatellite loci commonly used in previous tiger studies using blood and fecal DNA from captive Amur tigers (Panthera tigris altaica). To begin, we developed an index termed the accumulated matching rate of genotypes (R m ) between positive DNA (blood samples) and fecal DNA to explore the correct genotyping probability of a certain microsatellite locus. We found that different microsatellite loci had different genotyping risks and required different PCR amplification protocols. The genotyping errors we detected altered population genetic parameters and potentially impact subsequent analyses. Based on these findings, we recommend that: (1) four loci (E7, Fca094, Pti007 and Pti010) of 12 loci are not suitable for Amur tiger genetic research because of a low R m and difficulty reaching a stable status; (2) the R m of the 12 microsatellite loci plateaued differently, and considering limited budgets, amplification times of some loci could be increased when using fecal samples; and (3) future genetic analysis of wild Amur tigers should be corrected by genotyping error rates (1 − R m ).