Methylome and transcriptome responses to feed stress induced by low-energy diet in liver and blood of laying hens

Background Poultry farming provides an important source of protein for human consumption around the world. Improving chicken adaptation to changing environmental conditions and feed constraints resulting from climate change is required to tackle the challenge of a growing human population. The production conditions for laying hens may differ from the controlled environments used for pure-bred selection, particularly in terms of temperature and dietary energy content. To investigate the response of laying hens to a suboptimal diet, molecular data have been generated from liver and blood of hens exposed or not to a high fiber and low-energy diet. Results We combined RNA sequencing (RNA-Seq) and Reduced Representation Bisulfite Sequencing (RRBS) on the same samples to profile the transcriptome and genome-wide single base resolution DNA methylation map. Whereas we identified 1705 and 71 differentially expressed genes (DEGs) in blood and liver, respectively, we only detected 11 and 10 significant differentially methylated CpG sites (DMCs) in blood and liver respectively. These DMCs were associated with a total of 16 and 14 differentially methylated genes (DMGs) in blood and liver respectively, with 2 DMCs associated to a DEG. Conclusions These results show that changes in the feed resource of hens can lead to changes in gene expression, especially in blood, however very few of these changes could be explained by a change in methylation of a local CpG observed by RRBS.