Evaluation of fecal DNA preservation and extraction methods in Przewalski’s horse

Abstract

The study compares the effects of three preservation methods (ethanol, drying and freezing) and two extraction methods (commercial kit and manual) on the PCR success rate and genotyping errors with fecal DNA from Przewalski’s horse (Equus przewalskii). The interaction term between preservation and extraction was significant, and the highest amplification success rate (0.661) was obtained with samples stored in ethanol and extracted manually. The preservation method and time significantly impacted microsatellite amplification success rates. The method of preservation had an effect on the rate of allelic dropout (ADO), but the rate of false alleles (FA) varied nonsignificantly. Feces preserved in ethanol yielded the lowest ADO and FA, followed by drying and freezing. Our optimized preservation protocol probably have wide applicability to equids and rhinocerotids that produce large, high-fiber fecal pellets.