In the footsteps of Darwin: pigs DNA sheds light on evolution and selection


The pig and its cousin the wild boar share a lot with humans. They are world travellers and they are easy to seduce (with food). But there is more: a new analysis of their DNA reveals some unexpected and potentially beneficial similarities with humans, further supporting the pig as a valuable biomedical model. Prof. Martien Groenen – who received a € 2.5 million Advanced Grant from the European Research Council (ERC) in 2009 – conducted this unprecedented genomic study with scientists from twelve countries. Prof. Groenen also analysed pigs DNA evolution since humans started to domesticate these animals some 10,000 years ago. The latest analysis was conducted in collaboration with another ERC Advanced grantee, Prof. Leif Andersson. Both studies are featured this week in two renowned scientific journals: Nature and the Proceedings of the National Academy of Sciences (PNAS).
Written in collaboration with the University of Wageningen, The Netherlands
Image©Prof M. A.M. Groenen

“These two research studies demonstrate the benefits of basic genomic research on agricultural animals and their closest living relatives. The new analysis has important implications for agriculture, and also contributes to our understanding of evolution and to the advancement of human medicine”, explains ERC grantee Prof. Groenen from the University of Wageningen, The Netherlands.

Published in Nature, the first study focuses on the changes that have accumulated in the genome of the pig during its speciation in Eurasia and during its subsequent domestication and selection by humans. An international team of researchers compared the genome of a common farm pig, Sus scrofa domesticus, with those of ten wild boars – all from different parts of Europe and Asia. They also analysed the pig genome in parallel with those of the human, mouse, dog, horse and cow. Comparisons of Asian and European wild boars revealed significant genetic differences, which are the result of their separating from one another roughly one million years ago.

Some gene families are undergoing relatively fast evolution in the pig, with immune genes and olfactory genes quickly expanding. The pig has more unique olfactory genes than humans, mice or dogs, the researchers report. While pigs can smell a world of things humans and many other animals can’t (e.g. truffles), their sense of taste is somewhat impaired.

The new analysis also supports the use of the pig as a model in studies of human diseases such as e.g. obesity, diabetes, dyslexia, Parkinson’s disease and Alzheimer’s disease. In total, the team found 112 positions where the porcine protein has the same amino acid that is implicated in a disease in humans. “By also sequencing the genomes of another 48 pigs, we identified many more gene variants implicated in human disease, further supporting the pig as a valuable biomedical model”, adds Prof. Groenen.

How the European domestic pig became longer and got its white colour

The study published in PNAS analyses more specifically what genes and regions of the porcine genome have been changed during the 10,000 years of domestication and selection of this animal. The European team of researchers identified three loci that affect one of the most striking morphological changes in the domestic pig – the elongation of the back and the increased number of vertebrae. This important change had already been observed and described by Charles Darwin in his book The variation of animals and plants under domestication.

The researchers have identified three genes that are strong candidates for the observed changes in the European domestic pig. Interestingly two of these genes have been associated with variation in size in other species including humans. The researchers also showed that structural variation of certain genes is more common than usually thought. They identified a complex pattern resulting in a variety of coat colours including the dominant white, patched and belted phenotypes (physical characteristics). “The gene variant causing dominant white colour in pigs is the most striking example of an emerging picture that structural variants (duplications, deletions and inversions) have contributed significantly to phenotypic evolution of domestic animals”, concludes ERC grantee Prof. Andersson from Uppsala University, Sweden.

Project details

© Prof M. A.M. Groenen
Principal investigator: Martien Groenen
Host institution: Wageningen Universiteit (Netherlands)
Project: Molecular characterization of genetic factors in the pig under selection during speciation, domestication and breeding (SELSWEEP)
ERC call: Advanced Grant 2009
ERC funding: € 2.5 million for five years The research published in Nature today was also funded by FP6 “SABRE” and FP7 “Quantomics” collaborative projects.
Wageningen Universiteit

Project details

© Erik Bongcam-Rudloff

Principal investigator: Leif Andersson
Host institution: Uppsala Universitet (Sweden)
Project: Dissecting genotype-phenotype relationships using high-throughput genomics and carefully selected study populations (BATESON)
ERC call: Advanced Grant 2011
ERC funding: € 2.3 million for five years
Uppsala Universitet

Read more

Article in Nature: Analyses of pig genomes provide insight into porcine demography and evolution ( table of content)
Article in PNAS: Strong signatures of selection in the domestic pig genome