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Pearce, D.L., J.E. Edson, C.S. Jennelle, and W.D. Walter. 2024. Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels. Scientific Reports 14, 11340. https://doi.org/10.1038/s41598-024-56128-9
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Abstract
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May 2024
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Genetics studies are used by wildlife managers and researchers to gain inference into a population of a species of interest. To gain these insights, microsatellites have been the primary method, however, there currently is a shift from microsatellites to single nucleotide polymorphisms (SNPs). With the DNA requirements between microsatellites and SNPs being different, an investigation into which samples can provide adequate DNA yield is warranted. Using samples that were collected from previous genetic projects from regions in the USA from 2014 to 2021, we investigated the DNA yield of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed SNP panels. We found four sample categories that met the DNA requirements for use in all three panels, three sample categories that only met the DNA requirements for two panels, and one sample category that did not meet any of the three panels requirements. Additionally, we used linear random-effects models to determine which covariates would have the greatest influence on DNA yield. We determined that all covariates, tissue type, storage method, preservative, DNA quality, time until DNA extraction and time after DNA extraction could influence DNA yield.
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Miller, W.M., C.M. Miller-Butterworth, D.R. Diefenbach, and W.D. Walter. 2020. Assessment of spatial genetic structure to identify populations at risk for infection of an emerging epizootic disease. Ecology and Evolution 10(9):3977–3990;
https://doi.org/10.1002/ece3.6161
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May 2020
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Miller, W.L., J. Edson, P. Pietrandrea, C. Miller-Butterworth, and W. David Walter. 2019. Identification and evaluation of a core microsatellite panel for use in white-tailed deer (Odocoileus virginianus). BMC Genetics 20:49.
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June 2019
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Miller, W.L. and W.D. Walter. 2020. Can genetic assignment tests provide insight on the influence of captive egression on the epizootiology of chronic wasting disease? Evolutionary Applications. 13:715–726; https://doi.org/10.1111/eva.12895.
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Publisher Website
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March 2020
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Miller, W.L. and W. D. Walter. 2019. Spatial heterogeneity of prion gene polymorphisms in an area recently infected by chronic wasting disease. Prion 13: 65-76.
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Abstract
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February 2019
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Genetic variability in the prion protein (PRNP) gene influences host susceptibility to many pathogenic prion diseases. Understanding the distribution of susceptible PRNP variants and determining factors influencing spatial genetic patterns are important components of many chronic wasting disease mitigation strategies. Here, we describe PRNP variability in white-tailed deer (Odocoileus virginianus) from the Mid-Atlantic region of the United States of America, an area with a recent history of infection and low disease incidence. This population is characterized by lower rates of polymorphism and significantly higher frequencies of the more susceptible 96GG genotype compared to previously surveyed populations. The prevalence of the most susceptible genotypes at disease-associated loci did vary among subregions, indicating that populations have innate differences in genotype-dictated susceptibility.
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Edson, J., J. Brown, W.L. Miller, and W. D. Walter. 2021. Comparison of sample types from white-tailed deer (Odocoileus virginianus) for DNA extraction and analyses. Scientific Reports 11, 10003. https://doi.org/10.1038/s41598-021-89390-2
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Abstract
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May 2021
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Collection of biological samples for DNA is necessary in a variety of disciplines including disease epidemiology, landscape genetics, and forensics. Quantity and quality of DNA varies depending on the method of collection or media available for collection (e.g., blood, tissue, fecal). Blood is the most common sample collected in vials or on Whatman FTA cards with short- and long-term storage providing adequate DNA for study objectives. The focus of this study was to determine if biological samples other than blood stored on Whatman FTA Elute cards were a reasonable alternative to traditional DNA sample collection, storage and extraction. Tissue, nasal swabs, and ocular fluid were collected from white-tailed deer (<i>Odocoileus virginianus</i>). Tissue samples acted as a control to compare extraction and DNA suitability for microsatellite analysis for nasal swabs and nasal swabs and ocular fluid extracted from FTA Elute cards. We determined that FTA Elute cards improved the extraction time and storage of samples and that nasal swabs and ocular fluid containing pigmented fluid were reasonable alternatives to traditional tissue DNA extractions. Also, DNA extractions from nasal swabs provided ample DNA but did not improve extraction time or storage of samples.
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