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

Abstract

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 the 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 the 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.

Keywords: Gallus gallus; Sus scrofa; Sus scrofa domesticus; breeding; domesticated animals; gene set enrichment analysis.

Figure 1

The workflow of this study. The gene expression data of domesticated animals and their wild ancestors were obtained from public databases. The datasets were processed to quantify gene expression and calculate the expression ratio between domesticated animals and wild ancestors (DW-ratio). Genes were classified based on their DW-ratio, and a DW-score was calculated for each gene. Gene set enrichment analysis was performed using top-ranked genes for each domesticated–wild pair. Gene IDs were converted to human gene IDs to identify commonly differentially expressed genes across species. DEG, differentially expressed gene; DW, domestic–wild.

Figure 2

Tissue distribution of the curated RNA-seq data pairs. A total of 46 pig–wild boar pairs and 59 chicken–red junglefowl pairs of RNA-seq data were obtained. The left pie chart shows the proportion of pairs for each tissue type in the pig–wild boar pairs, with muscle tissue having the highest proportion. The right pie chart represents the tissue distribution in the chicken–red junglefowl pairs, with brain tissue having the highest proportion.

Figure 3

A scatter plot of the DW-score and gene set enrichment analysis of genes upregulated in pigs and wild boars. (A) The scatter plot shows the DW-score of each gene, with red dots representing genes upregulated in pigs (positive DW-score values) and blue dots representing genes upregulated in wild boars (negative DW-score values). (B) Gene set enrichment analysis for genes upregulated in pigs. The analysis was performed using the top 218 genes based on their DW-scores. (C) Gene set enrichment analysis for genes upregulated in wild boars. The analysis was performed the top 239 genes based on their DW-scores.

Figure 4

Scatter plot of the DW-score and gene set enrichment analysis of upregulated genes in chickens and red junglefowl. (A) The scatter plot shows the DW-score of each gene, with red dots representing genes upregulated in chickens (positive DW-score values) and blue dots representing genes upregulated in red junglefowl (negative DW-score values). (B) Gene set enrichment analysis for genes upregulated in chickens. The analysis was performed using the top 206 genes based on their DW-scores. (C) Gene set enrichment analysis for genes upregulated in red junglefowl. The analysis was performed with the top 200 genes based on their DW-scores.

Figure 5

Upregulated genes in common among domesticated animals (pig and chicken) and their wild ancestors (wild boar and red junglefowl). (A) A Venn diagram showing the overlap between the top upregulated genes in pigs (240 genes) and chickens (206 genes). Ten genes were found to be upregulated in both domesticated animals. (B) A Venn diagram showing the overlap between the top upregulated genes in wild boars (206 genes) and red junglefowl (RJF) (200 genes). Seven genes were found to be upregulated in both wild ancestors.