Genomic architecture of phenotypic extremes in a wild cervid

• Published in: BMC genomics Vol. 23; no. 1; pp. 126 - 13
• Main Authors: Anderson, S. J., Côté, S. D., Richard, J. H., Shafer, A. B. A.
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 12.02.2022; BioMed Central; BMC
• Subjects: Analysis; Animals; Annotations; Antlers; Body size; Cell death; Datasets; Deer; Deer - genetics; Divergence; Evolutionary genetics; Extreme phenotypes; Gene enrichment; Gene frequency; Gene sequencing; Genes; Genetic aspects; Genomes; Genomics; Genotype & phenotype; Growth; Humans; Male; Males; Methods; Multifactorial traits; Observations; Odocoileus virginianus; Oncogenes; Outliers (statistics); Phenotype; Phenotypes; Pool-seq; Population; Population genetics; Protein metabolism; Protein turnover; Proteins; Quantitative genetics; Quantitative traits; Simulation; Single-nucleotide polymorphism; Software; White-tailed deer; Canada; Anticosti Island; Gene enrichment; Extreme phenotypes; Quantitative traits; Pool-seq; Population genetics
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-022-08333-x

Identifying the genes underlying fitness-related traits such as body size and male ornamentation can provide tools for conservation and management and are often subject to various selective pressures. Here we performed high-depth whole genome re-sequencing of pools of individuals representing the phenotypic extremes 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 after controlling for age. Our results revealed a largely homogenous population but detected highly divergent windows between pools for both traits, with the mean allele frequency difference of 14% for and 13% for antler and body SNPs in outlier windows, respectively. Genes in outlier antler windows were enriched for pathways associated with cell death and protein metabolism and some of the most differentiated windows included genes associated with oncogenic pathways and reproduction, processes consistent with antler evolution and growth. Genes associated with body size were more nuanced, suggestive of a highly complex trait. Overall, this study revealed the complex genomic make-up of both antler morphology and body size in free-ranging white-tailed deer and identified target loci for additional analyses.