Transcriptional Signatures of Domestication Revealed by Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data

Domesticated animals have undergone significant changes in their behavior, morphology, and physiological functions during domestication. To identify the changes in gene expression associated with domestication, we collected RNA-seq data of pigs, chickens, wild boars, and red junglefowl from public databases and performed a meta-analysis. Gene expression was quantified and the expression ratio between domesticated animals and their wild ancestors (DW-ratio) was calculated. Genes were classified as "upregulated," "downregulated," or "unchanged" based on their DW-ratio, and DW-score was calculated for each gene. Gene set enrichment analysis revealed that genes upregulated in pigs were related to defense from viral infection, whereas those upregulated in chickens were associated with aminoglycan and carbohydrate derivative catabolic processes. Genes commonly upregulated in pigs and chickens are involved in the immune response, olfactory learning, epigenetic regulation, cell division, and extracellular matrix. In contrast, genes upregulated in wild boar and red junglefowl are related to stress response, cell proliferation, cardiovascular function, neural regulation, and energy metabolism. These findings provide valuable insights into the genetic basis of the domestication process and highlight potential candidate genes for breeding applications. Simple SummaryDomesticated animals, such as pigs and chickens, have undergone significant genetic changes compared to their wild ancestors. We collected gene expression data from pigs, chickens, wild boars, and red junglefowl, and performed a comprehensive analysis. We identified differentially expressed genes by comparing the gene expression patterns of domesticated animals and their wild counterparts. These genes are involved in various biological processes, including immune response, metabolism, and stress response. Notably, domesticated animals exhibited higher expression of genes related to viral resistance and bone weakness, whereas their wild ancestors showed higher expression of genes associated with stress response and energy metabolism. Identifying these differentially expressed genes provides valuable insights into the genetic changes that occurred during the domestication process. Furthermore, these findings have highlighted potential candidate genes that could be targeted in breeding programs to improve the health and productivity of domesticated animals, ultimately contributing to the development of sustainable livestock production and addressing the growing global food demand.