Understanding Porcine Welfare: Transcriptome Differences in the Brain between Two Husbandry Systems and Different Allostatic Load

In modern pig husbandry, the well-being of animals is becoming of paramount importance, particularly in the face of various stressors such as weaning, transport, and regrouping as this can have an effect on animal’s welfare, production, immunity and disease resistance. This study investigates the combined effects of (i) divergent environmental conditions and (ii) repeated mixing to create allostatic load on the transcriptome of the brain tissue in pigs. Pigs were exposed to either standard barren housing conditions or enriched environments featuring sawdust, toys, regular access to a a play arena, and positive human contact. Half of the pigs from each environment underwent repeated mixing, a common stressor in commercial pig production. We aimed to provide a holistic perspective on the physiological as well as the behavioural outcomes of the study set-up. For this, we generated RNA-seq data from three brain sections (hypothalamus, hippocampus and prefrontal cortex) in 48 animals. More than 40 M reads were obtained on average across samples and tissue types, and 85-98% were mapped to the porcine genome (Scrofa11.1). On average over 15,000 genes (> 1 CPM) were obtained for the brain tissues. Interestingly, differential expression (DE) analyses on the effect of different farm systems showed no DE genes in brain tissues. DE analyses on the effect of repeated mixing revealed no DE genes in cortex. In hypothalamus a single gene was upregulated in the high allostatic load group: MPZ, previously associated to weaning stress in pigs. Hippocampus resulted in 38 DE genes, including TTR, TRH, BLK and CORT, related to the release of neuropeptide hormones as thyrotropin and corticotropin, as well as immune responses. This study aims to offer a comprehensive exploration of the intricate relationship between environmental conditions, allostatic load, and gene expression in pigs to enhance our understanding on animal welfare and husbandry practices.