On the epigenetic basis of semen traits

Several studies have shown that epigenetic factors contribute to variation in quantitative traits. However, the biological mechanisms that regulate the variation and establishment of these factors and their contributions to many of these traits are not yet fully understood, including for semen quality traits. This is of particular importance considering that semen quality and fertility traits are important factors in pig breeding. Previous studies have addressed semen quality traits and their seasonal variation in porcine semen using transcriptome data. However, the link between the methylome, the transcriptome and environmental variation and their role in shaping the phenotype of semen traits has not been fully elucidated. This project aims to estimate the contribution of the genome, epigenome, and transcriptome to phenotypic variation in semen traits in pigs and measure the extent to which environmental changes affect the epigenetic landscape of sperm cells. To accomplish this task, a large collection of semen samples will be characterized at different levels, including DNA polymorphism, methylation, gene expression, and phenotypic data. Semen quality will be assessed with the CASA system; an equipment routinely used in breeding companies to assess semen quality and record several parameters that can be used as semen quality traits. A recently developed method - GBS-MeDIP (Genotype by Sequencing – Methylated DNA Immunoprecipitation) will be used, allowing for a feasible epigenomic assessment of 2 repeated samples from 500 boars. Bioinformatics pipelines will be used to analyze these high-throughput data. These pipelines will be used to identify genetic (GWAS) and epigenetic (EWAS) loci associated with phenotypic variation in semen traits and to estimate the proportion of (Epi)genetic variation attributing to phenotypic variation in these traits. Finally, these data will be used to determine the effects of season and age on epigenetic variation and transcript content.