The pig genome is mapped

(14.11.2012) In a major international study, the pig genome is now mapped. Researchers from Uppsala University and the Swedish University of Agricultural Sciences (SLU) have contributed to the study by analysing genes that played a key role in the evolution of the domesticated pig and by mapping endogenous retroviruses (ERV), retroviruses whose genes have become part of the host organism’s genome. The findings are now being published in the journals Nature and PNAS.

Together with an international team of geneticists and retrovirologists, Uppsala University researchers have charted the pig genome.

“The pig is one of our most important domesticated animals, and it was high time for its genome to be mapped,” says Professor Leif Andersson, who participated in the project.

The major project to chart the pig genome shows that the wild boar originated in Southeast Asia about 4 million years ago. The findings also reveal that domestication started nearly 10,000 years ago, taking place in several independent locations all over the European and Asian land mass. It was also common that wild boar mixed with domesticated pigs, especially in Europe during early agriculturalisation, with free-ranging animals.

Uppsala researchers Patric Jern, Alexander Hayward, Göran Sperber, and Jonas Blomberg used the computer program RetroTector and detailed sequence comparisons in so-called phylogenetic studies to map the retrovirus part of the pig genome. What all retroviruses, such as HIV in humans, have in common is that they need to become part of the host cell’s genome in order to produce new viruses.

When a germ line-cell is infected there is a chance for the virus to be passed on to the host organism’s offspring, and for millions of years retroviruses remotely related to HIV have colonised vertebrates, leaving traces in their genetic make-up as endogenous retroviruses (ERV).

The researchers were able to see that pigs have fewer ERVs than humans, however, unlike human ERVs, some pig ERVs have the capacity to reproduce and infect, which might pose a risk when transplanting pig organs to humans. The article constitutes a baseline for assessing that risk, but it also provides an enhanced understanding of how retroviruses have spread among vertebrates in the course of their evolution.

Carl-Johan Rubin, Leif Andersson, and their associates have been in charge of looking for the genes that have had the greatest importance in the evolution of the domesticated pig. One of the most striking differences between the wild boar and the domesticated pig is that the latter has a considerably longer back, including more vertebrae.

The researchers have now identified three gene regions that are critical for understanding this difference. Two of them correspond to genes that explain variation in body length in humans, another instance of genes having a very similar function across different species.

Domesticated animals constitute excellent models for evolution, and the new study shows how white colour developed. The gene variant for white colour in pigs differs from the gene variant found in wild boar, with at least five different mutations, four of which are duplications of DNA sequences.

This is the most striking example of two key discoveries the Uppsala scientists have made in recent years, that:

  • structural changes in the genome (e.g. duplications) have contributed significantly to the evolution of domesticated animals.
  • the evolution of domesticated animals has been underway for so long that we can now see the evolution of gene variants, that is, genes in which several successive mutations gradually changed the function of the gene.

The findings are now being published in Nature and PNAS:

Groenen et al. (2012) Pig genomes provide insight into porcine demography and evolution, Nature, DOI: 10.1038/nature11622

Rubin et al. (2012) Strong signatures of selection in the domestic pig genome. Proceedings of the National Academy of Sciences (USA), DOI: 10.1073/pnas.1217149109



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