Grant: Discovery Grants Program - Individual

Quantitative genetics (QG) is the study of complex traits like height and body mass; QG relies on a simple model that assume many genes influence the measured phenotype, which allows for estimating important parameters like heritability (h2). Traditionally, QG methods needed to integrate pedigree information into the model, but genomic data circumvent this by generating accurate relatedness matrices. This advancement has made QG approaches more accessible to wild populations; but despite now being able to estimate h2, the problem of `missing heritability' remains, meaning most heritable variation remains un-explained when conducting genotypic associations. Epigenetic variation and epistatic interactions have remained largely unexplored in this context, even though laboratory experiments and human datasets show they contribute to both additive and environmental variance components of h2 estimates. Further, identifying genomic signals linked to traits and population health (i.e. genetic load) with novel tools can provide better population assessments and guide management strategies. For example, epigenetic clocks - defined as methylation patterns predictive of chronological age - appear elevated in inbred populations; meaning, the genetic aging of individuals is more advanced when inbred. Combining genomic and epigenome signatures can provide a novel lens for evaluating population health and understanding trait variation in wild populations. The long-term objective of my research program is to quantify the drivers of phenotypic change and predict responses to selection. To accomplish this I will focus white-tailed deer (WTD; Odocoileus virginianus) as it has become an ideal system to address quantitative and population genomics questions, and the species play a vital role in ecosystems across North America. Harvest of WTD also generates billions of dollars annually, and they are an important cultural component of many Indigenous communities. My lab annotated a high-quality WTD genome and continues to build upon an extensive tissue and phenotypic database consisting of thousands of samples. The goal of my DG proposal is to use genomic and epigenomic markers, along with novel analytical approaches to quantify h2 and elucidate the genomic architecture of antlers and body size, and inbreeding depression in WTD. I will address this with three research objectives: 1) in-silico assessment and validation of heritability estimates without pedigrees in free-ranging populations; 2) quantitative epigenomics of trait variation ; 3) epigenomic assessment of inbreeding depression in island populations. The research objectives address fundamental questions in Evolution and Ecology with broader management applications stemming from quantifying h2, selection, and inbreeding in natural populations. This work contributes to the training of HQP in highly transferrable skills, and will produce high quality open-access articles, analytical pipelines, and data.