DAP assisted in field evaluation, conducted data analysis, and wrote the manuscript. BTV confirmed propriety of statistical analysis, conducted the mixed effects analysis and assisted in writing the manuscript. RJC and JP conducted field evaluation at RI sites, collected disease acquisition data, and assisted with data analysis. SKA Jr. coordinated activities in VA (e.g. production of southern lines, field evaluation at the VA site) and assisted in writing the manuscript. JMS assisted in coordinating activities in VA. XG, CL, ML, and GD conducted field evaluation in NJ. PR coordinated activities in ME (production of northern lines, field evaluation at the ME site). MGC coordinated the entire project, and assisted in writing the manuscript.

Incubation Parameters Impact Heart Methylome expression, and suggests increased cell proliferation in broiler hatchlings incubated at higher temperatures. Overall, these results identified numerous epigenetic associations between chick incubation factors and heart development that may manifest in long-term differences in animal performance.

Background Genetics studies in the porcine immune system have enhanced selection practices for disease resistance phenotypes and increased the efficacy of porcine models in biomedical research; however limited functional annotation of the porcine immunome has hindered progress on both fronts. Among epigenetic mechanisms that regulate gene expression, DNA methylation is the most ubiquitous modification made to the DNA molecule and influences transcription factor binding as well as gene and phenotype expression. Human and mouse DNA methylation studies have improved mapping of regulatory elements in these species, but comparable studies in the pig have been limited in scope. Results We performed whole-genome bisulfite sequencing to assess DNA methylation patterns in nine pig immune cell populations: CD21+ and CD21− B cells, four T cell fractions (CD4+, CD8+, CD8+CD4+, and SWC6γδ+), natural killer and myeloid cells, and neutrophils. We identified 54,391 cell differentially methylated regions (cDMRs), and clustering by cDMR methylation rate grouped samples by cell lineage. 32,737 cDMRs were classified as cell lowly methylated regions (cLMRs) in at least one cell type, and cLMRs were broadly enriched in genes and regions of intermediate CpG density. We observed strong correlations between differential methylation and expression across immune cell populations, with cell-specific low methylation disproportionately impacting genes exhibiting enriched gene expression in the same cell type. Motif analysis of cLMRs revealed cell type-specific enrichment of transcription factor binding motifs, indicating that cell-specific methylation patterns may influence accessibility by trans-acting factors. Lastly, cDMRs were enriched for immune capacity GWAS SNPs, and many such overlaps occurred within genes known to influence immune cell development and function (CD8B, NDRG1). Conclusion Our DNA methylation data improve functional annotation of the porcine genome through characterization of epigenomic regulatory patterns that contribute to immune cell identity and function, and increase the potential for identifying mechanistic links between genotype and phenotype.

Changes to the epigenome, including those to DNA methylation, have been proposed as mechanisms by which stress can induce long-term physiological changes in livestock species. Pig weaning is associated with dietary and social stress, both of which elicit an immune response and changes to the hypothalamic–pituitary–adrenal (HPA) axis. While differential methylation following stress has been assessed in model organisms, it remains poorly understood how the pig methylome is altered by stressors in production settings. We quantified changes in CpG methylation and transcript abundance in piglet peripheral blood mononuclear cells (PBMCs) following weaning and also assessed differential patterns in pigs exhibiting high and low stress response as measured by cortisol concentration and lesion scores. Blood was collected from nine gilt piglets 24 h before and after weaning, and whole-genome bisulfite sequencing (WGBS) and RNA-sequencing were performed on six and nine animals, respectively, at both time points. We identified 2,674 differentially methylated regions (DMRs) that were enriched within promoters of genes associated with lymphocyte stimulation and transcriptional regulation. Stress groups displayed unique differential methylation and expression patterns associated with activation and suppression of T cell immunity in low and high stress animals, respectively. Differential methylation was strongly associated with differential expression; specifically, upregulated genes were enriched among hypomethylated genes. We observed post-weaning hypermethylation of the glucocorticoid receptor (NR3C1) promoter and a significant decrease in NR3C1 expression (n = 9, p = 6.1 × 10–3). Our results indicate that weaning-associated stress elicits genome-wide methylation changes associated with differential gene expression, reduced T cell activation, and an altered HPA axis response.

Perkinsus marinus, the causative agent of Dermo disease, is responsible for mass mortalities and negatively impacts aquaculture production of the eastern oyster, Crassostrea virginica. Selective breeding is a viable option for Dermo disease management; however, fluctuations in natural selection pressure and environmental noise hinder accumulation of genetic gains acquired through field performance trials. The purpose of this study was to adapt and apply laboratory disease challenge methods to eastern oysters, better characterize resistance‐specific traits and assess the potential for genetic variation in Dermo resistance among distinct families within a breeding population. Two challenge experiments were conducted, one in 2014 and the other in 2015. Significant treatment (control vs. challenged) and family effects on survival (measured as per cent survival and days to death) were detected in the 2014 challenge, while overall high survival precluded the detection of a significant family effect in the 2015 challenge. An alternate measure of resistance, parasite elimination rate, was also measured in the 2015 challenge, and this varied significantly among families. Thus, both survival and the change in parasite concentration in oyster tissues over time represent Dermo resistance phenotypes that can be measured accurately with the adapted laboratory disease challenge protocol described here. The obvious next step is to incorporate the challenge protocol in eastern oyster breeding programmes to assess whether well‐defined, accurately measured, Dermo‐resistant phenotypes result in enhanced genetic improvement for this commercially important trait.