Genetic signatures of domestication found in pigs and chickens

As wild boars and red junglefowl gave rise to common pigs and chickens, these animals’ genes evolved to express themselves differently, leading to signatures of domestication such as weaker bones and better viral resistance.

That’s according to a new study from Hiroshima University, which could provide insight into the genetic changes of the domestication process and highlight target genes for healthier and more productive livestock breeding. The team’s results were published in the journal Animals.

As explained by corresponding author Professor Hidemasa Bono, who is associated with Hiroshima’s Laboratory of Genome Informatics and Laboratory of Bio-DX, pigs and chickens have been selectively bred for specific traits useful to humans, such as faster growth rates, improved meat quality and increased litter size. “This process has significantly altered the animals’ behaviour, morphology and physiological functions,” he said.

“While the selection for traits beneficial to humans has occurred, excessive selective breeding has led to health issues in domesticated animals and decreased their reproductive capacity. To address these issues, it is crucial to understand the changes in gene expression between domesticated animals and their wild ancestors.”

By comparing how genes are expressed in pairs of pigs and wild boars, as well as pairs of chickens and red junglefowl, the researchers aimed to elucidate common patterns of such changes. Using data from publicly available databases, they compared 240 genes in pigs and 206 in chickens and found 10 were upregulated — meaning they were expressed more compared to their wild ancestor partners. They also found seven genes were upregulated in wild boars and red junglefowl, which have a total of 206 genes and 200 genes, respectively.

“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,” said first author Motoki Uno, a graduate student in the Laboratory of Genome Informatics.

“Our analysis revealed that genes commonly upregulated in pigs and chickens are involved in the immune response, olfactory learning, epigenetic regulation, cell division and the extracellular matrix, which is the molecular structure that gives support to cells and tissues in an organism. In contrast, genes upregulated in wild boar and red junglefowl are related to stress response, cell proliferation, cardiovascular function, neural regulation and energy metabolism.”

According to the researchers, these changes may have come about because domesticated animals are typically kept at high densities in confined spaces, such as chickens in a coop. This closeness can foster more vulnerability to infection as viruses spread, compared to their wild ancestor counterparts. In contrast, wild boars and red junglefowl are exposed to more stressors in nature, such as avoiding predators and finding food, which could account for the upregulated genes related to 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,” Bono said. “Moving forward, we aim to contribute to sustainable breeding through the improvement of analytical methods and the integration of various biological data.”

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