SREL Reprint #3375

Identification of robust microsatellite markers for wild pig fecal DNA

Elizabeth M. Kierepka1, Shem D. Unger1, David A. Keiter1,2, James C. Beasley1,2, Olin E. Rhodes, Jr1,
Fred L. Cunningham3, and Antoinette J. Piaggio4

1University of Georgia, Savannah River Ecology Laboratory, Aiken, SC 29802, USA
2Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA USA
3U.S. Department of Agriculture, Mississippi Field Station, National Wildlife Research Center,
Wildlife Services, PO Box 6099, Mississippi State, MS 39762, USA
4U.S. Department of Agriculture, National Wildlife Research Center, Wildlife Services,
4101 LaPorte Avenue, Fort Collins, CO 80521, USA

Abstract: Collection of fecal samples for use in a genetic capture-mark-recapture framework has become popular as a noninvasive method of monitoring wildlife populations. A major caveat to this process, however, is that fecal samples often yield low quality DNA that is prone to genotyping errors, potentially leading to biases in population parameter estimation. Therefore, considerable care is required to identify robust genetic markers, especially in hot or humid conditions that may accelerate DNA degradation. We identified microsatellite loci in wild pig (Sus scrofa) fecal samples that were robust and informative within warm, humid ecosystems. To examine how degradation affected genotyping success, we sampled pig feces across 5 days and calculated how the number of quantitative polymerase chain reaction (qPCR) cycles required to reach the fluorescent threshold (Ct) changed over time. We identified 17 microsatellite loci that had high polymorphism and amplification success and low genotyping error rates (0–0.050 per locus). In the degradation experiment, Ct increased over the 5 days, but in the absence of rain, the majority of samples produced accurate genotypes after 5 days (2,211/2,550 genotypes). Based on the high amplification success and low error rates, even after 5 days of exposure to warm, humid conditions, these loci are useful for estimating population parameters in pig fecal samples.

Keywords: degradation, feces, microsatellites, noninvasive, South Carolina, Sus scrofa, wild pigs

SREL Reprint #3375

Kierepka, E. M., S. D. Unger, D. A. Keiter, J. C. Beasley, O. E. Rhodes Jr., F. L. Cunningham, and A. J. Piaggio. 2016. Identification of robust microsatellite markers for wild pig fecal DNA. Journal of Wildlife Management 80(6): 1120-1128.

This information was provided by the University of Georgia's Savannah River Ecology Laboratory (srel.uga.edu).