Identification of robust microsatellite markers for wild pig fecal DNA
Abstract
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 ( C t ) 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, C t 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 exposuremore »
- Authors:
-
- University of Georgia Savannah River Ecology Laboratory Aiken SC 29802 USA
- University of Georgia, Savannah River Ecology Laboratory Warnell School of Forestry and Natural Resources Aiken SC 29802 USA
- U.S. Department of Agriculture, Mississippi Field Station, National Wildlife Research Center Wildlife Services PO Box 6099 Mississippi State MS 39762 USA
- U.S. Department of Agriculture, National Wildlife Research Center Wildlife Services 4101 LaPorte Avenue Fort Collins CO 80521 USA
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1401690
- Grant/Contract Number:
- DE‐FC09‐07SR22506
- Resource Type:
- Publisher's Accepted Manuscript
- Journal Name:
- Journal of Wildlife Management
- Additional Journal Information:
- Journal Name: Journal of Wildlife Management Journal Volume: 80 Journal Issue: 6; Journal ID: ISSN 0022-541X
- Publisher:
- Wiley Blackwell (John Wiley & Sons)
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Kierepka, Elizabeth M., Unger, Shem D., Keiter, David A., Beasley, James C., Rhodes, Jr, Olin E., Cunningham, Fred L., and Piaggio, Antoinette J. Identification of robust microsatellite markers for wild pig fecal DNA. United States: N. p., 2016.
Web. doi:10.1002/jwmg.21102.
Kierepka, Elizabeth M., Unger, Shem D., Keiter, David A., Beasley, James C., Rhodes, Jr, Olin E., Cunningham, Fred L., & Piaggio, Antoinette J. Identification of robust microsatellite markers for wild pig fecal DNA. United States. https://doi.org/10.1002/jwmg.21102
Kierepka, Elizabeth M., Unger, Shem D., Keiter, David A., Beasley, James C., Rhodes, Jr, Olin E., Cunningham, Fred L., and Piaggio, Antoinette J. Fri .
"Identification of robust microsatellite markers for wild pig fecal DNA". United States. https://doi.org/10.1002/jwmg.21102.
@article{osti_1401690,
title = {Identification of robust microsatellite markers for wild pig fecal DNA},
author = {Kierepka, Elizabeth M. and Unger, Shem D. and Keiter, David A. and Beasley, James C. and Rhodes, Jr, Olin E. and Cunningham, Fred L. and Piaggio, Antoinette J.},
abstractNote = {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 ( C t ) 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, C t 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. © 2016 The Wildlife Society.},
doi = {10.1002/jwmg.21102},
journal = {Journal of Wildlife Management},
number = 6,
volume = 80,
place = {United States},
year = {Fri Jun 10 00:00:00 EDT 2016},
month = {Fri Jun 10 00:00:00 EDT 2016}
}
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