The project investigates epigenetic and transcriptomic changes occurring in multiple regions of the brain of chickens, and other organs related to stress response, during development. The project will contribute to the understanding of molecular mechanisms of stress response in farmed chickens to improve their animal welfare in production settings. In this project, the data from 16 on-farm hatched hens and transported hens will be collected. In experiment 2 the effect of the housing system on 1200 chickens (layers sire line) will be investigated. Within each pen, 30 animals will be selected as focal animals for longitudinal assessment at 50,120, 175, 245, and 420 days of age. red blood cells from blood sampling will be used to investigate potential methylome and genomic marks that would be associated with different traits. At 420 days of age, we will collect adrenal and hypothalamus to build a cumulative stress index in combination with tracking data and health assessments. In experiment 3, the impact of seasonality on pig reproductive performance on endometrial tissue collected by biopsy will be investigated. The methods consist of the DNA/RNA extraction from tissues, and application of the GBS-MeDIP method (Genotype by sequencing integrated with methylated DNA immunoprecipitation) to assess DNA methylation changes in the reduced genome. Briefly, after DNA extraction, this new approach starts with an enzymatic cleavage of the genome to produce fragments with overhangs, followed by the ligation of barcodes and Illumina adapters. Then, sample pooling is performed, and a fraction of this pool is subjected to MeDIP. Two libraries are produced after PCR amplification, one that was not subjected to MeDIP (Genomic) and one that was subjected to MeDIP (methylomic). After PCR, the libraries are purified and will be sent for sequencing (SciLifeLab).