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.Supplementary Table1 - Pig and Wild Boar Sample metadataSupplementary Table2 - Chicken and Red Junglefowl sample metadataSupplementary Table3 - TPM Data of Pig and Wild BoarSupplementary Table4 - TPM Data of Chicken and Red JunglefowlSupplementary Table5 - DW-Score Data for Gene Expression of Pig and Wild BoarSupplementary Table6 - DW-Score Data for Gene Expression of Chicken and Red JunglefowlSupplementary Table7 - Lists of upregulated genes in PigSupplementary Table8 - Lists of upregulated genes in Wild BoarSupplementary Table9 - Result and lists of enrichment analysis of PigSupplementary Table10 - Result and lists of enrichment analysis of Wild BoarSupplementary Table11 - Lists of upregulated genes in ChickenSupplementary Table12 - Lists of upregulated genes in Red JunglefowlSupplementary Table13 - Result and lists of enrichment analysis of chickenSupplementary Table14 - Result and lists of enrichment analysis of Red JunglefowlSupplementary Table15 - DW-Score data for pig and wild boar converted to human gene IDsSupplementary Table16 - Lists of upregulated genes in Pig converted to human gene IDsSupplementary Table17 - Lists of upregulated genes in Wild Boar converted to human gene IDs