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.