Development of High‐Throughput Genomic Resources to Inform White‐Tailed Deer Population and Disease Management

White-tailed deer (Odocoileus virginianus) are the most abundant and widespread cervid in North America. Genetic data are used as a tool to monitor populations and make management decisions for this game species. However, the development and use of genomic tools that can generate a set of markers suitable for longitudinal genomic data collection, whether for management purposes or to study the demographic and evolutionary processes of widely distributed species, have been challenging. This is mainly due to the cost required to fully implement and interpret the data produced. Here, we generated whole genome resequencing data for 44 free-ranging deer from three regions in their central and eastern North American range and identified over 89 million single nucleotide polymorphisms (SNPs). We used a subset of these SNPs to develop two nested SNP tools, a high-density array (702,183 SNPs) and a medium-density array (72,723 SNPs) to support deer and chronic wasting disease (CWD) management and research. SNPs were selected to ensure an even distribution across scaffolds of the reference genome and include SNPs associated with CWD susceptibility. Using genotyping results for 469 deer from 15 states in the US and Mexico generated by the high-density array and 1335 deer from 18 states generated by the medium-density array, we assessed genotyping success across different populations and explored some insights into population structure. These genomic tools offer a standard set of markers that will enable researchers and managers to address important questions related to white-tailed deer and CWD management. Our SNP arrays also offer the opportunity to examine aspects of white-tailed deer ecology and evolutionary history that were previously difficult to address.

Authors

Institutions

Publication Details

Journal
Molecular Ecology Resources
Published
2025-11-26
DOI
https://doi.org/10.1111/1755-0998.70085
Citations
1
Primary Topic
Prion Diseases and Protein Misfolding
Type
article
Field-Weighted Citation Impact
0.81

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Development of High‐Throughput Genomic Resources to Inform White‐Tailed Deer Population and Disease Management

Emily K. Latch, Caitlin N. Ott‐Conn, Julie A. Blanchong, Arun S. Seetharam et al.
1 citations
Molecular Ecology Resources
Prion Diseases and Protein Misfolding
0.81
article

Development of High‐Throughput Genomic Resources to Inform White‐Tailed Deer Population and Disease Management

Emily K. Latch, Caitlin N. Ott‐Conn, Julie A. Blanchong, Arun S. Seetharam, Peter T. Euclide, William T. McKinley, Mitch L. Lockwood, Joe N. Caudell, Jay Cantrell, Wesley A. Larson, W. David Walter, James M. Reecy, Charlie H. Killmaster, Jason A. Sumners, R. G. Chandika, Daniel J. Storm, Andrew Josef Severin, Krysten L. Schuler, Zhi‐Liang Hu, Anaïs K. Tallon, Daniel P. Walsh, Andrew S. Norton, Randy W. DeYoung, David Navarro, Michelle Carstensen
article en
1 citations

Abstract

White-tailed deer (Odocoileus virginianus) are the most abundant and widespread cervid in North America. Genetic data are used as a tool to monitor populations and make management decisions for this game species. However, the development and use of genomic tools that can generate a set of markers suitable for longitudinal genomic data collection, whether for management purposes or to study the demographic and evolutionary processes of widely distributed species, have been challenging. This is mainly due to the cost required to fully implement and interpret the data produced. Here, we generated whole genome resequencing data for 44 free-ranging deer from three regions in their central and eastern North American range and identified over 89 million single nucleotide polymorphisms (SNPs). We used a subset of these SNPs to develop two nested SNP tools, a high-density array (702,183 SNPs) and a medium-density array (72,723 SNPs) to support deer and chronic wasting disease (CWD) management and research. SNPs were selected to ensure an even distribution across scaffolds of the reference genome and include SNPs associated with CWD susceptibility. Using genotyping results for 469 deer from 15 states in the US and Mexico generated by the high-density array and 1335 deer from 18 states generated by the medium-density array, we assessed genotyping success across different populations and explored some insights into population structure. These genomic tools offer a standard set of markers that will enable researchers and managers to address important questions related to white-tailed deer and CWD management. Our SNP arrays also offer the opportunity to examine aspects of white-tailed deer ecology and evolutionary history that were previously difficult to address.

Molecular Ecology ResourcesVol. 26(1)
Indiana Department of Natural Resources (US), United States Geological Survey (US), Georgia Department of Natural Resources (US), Michigan Department of Natural Resources (US), Pennsylvania State University (US), South Carolina Department of Natural Resources (US), Missouri Department of Conservation (US), Minnesota Department of Natural Resources (US), Texas Parks and Wildlife Department (US), Iowa State University (US), Texas A&M University – Kingsville (US), Cornell University (US), Purdue University West Lafayette (US), Wisconsin Department of Natural Resources (US), Illinois Indiana Sea Grant (US), North Dakota Game and Fish Department (US), NOAA National Marine Fisheries Service Alaska Fisheries Science Center (US), Montana Fish, Wildlife & Parks (US), Mississippi Department of Wildlife Fisheries and Parks (US), New York State College of Veterinary Medicine (US), University of Wisconsin–Milwaukee (US), University of Montana (US)
Michigan State University, Iowa State University, Michigan Department of Natural Resources, Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation, Maryland Department of Natural Resources, U.S. Fish and Wildlife Service, College of Engineering, Michigan State University
Openalex Percentile: Top 21%
Prion Diseases and Protein Misfolding
0.81
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.