Genomic architecture of artificially and sexually selected traits in a wild cervid

Characterization of the genomic architecture of fitness-related traits such as body size and male ornamentation in mammals provides tools for conservation and management: as both indicators of quality and health, these traits are often subject to sexual and artificial selective pressures. Here we performed high-depth whole genome re-sequencing on pools of individuals representing the phenotypic extremes in our study system for antler and body size in white-tailed deer (Odocoileus virginianus). Samples were selected from a tissue repository containing phenotypic data for 4,466 male white-tailed deer from Anticosti Island, Quebec, with four pools representing the extreme phenotypes for antler and body size in the population, after controlling for age. Our results revealed a largely panmictic population, but detected highly diverged windows between pools for both traits with high shifts in allele frequency (mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows). These regions often contained putative genes of small-to-moderate effect consistent with a polygenic model of quantitative traits. Genes in outlier antler windows had known direct or indirect effects on growth and pathogen defence, while body genes, overall GO terms, and transposable element analyses were more varied and nuanced. Through qPCR analysis we validated both a body and antler gene. Overall, this study revealed the polygenic nature of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.