Experimental design and population data. Credit: Carneiro et al., Science/AAAS DOI: 10.1126/science.1253714

How exercise animals go domesticated?

08 September 2014
Past Bronwen Aken

The domestication of plants and animals many thousands of years ago revolutionised human societies and changed the course of history.

Take you always wondered how this domestication occurs? What changes happen at a genetic level to make one animal tamer than some other?

Rabbits were domesticated only 1,400 years ago at monasteries in southern France. They're an excellent model for studying domestication because we know when and where they were domesticated, and also because wild populations still exist in the region.

I'm a bioinformatician at the EMBL-European Bioinformatics Institute (EBI) working as part of the Ensembl team. My team and I collaborated with researchers to sympathise what genetic changes took identify when wild rabbits were domesticated.

The results of the consortium's research, published in Science, evidence that rabbit domestication occurred due to small changes in many genes, and not due to large changes in a few genes.

These pocket-size changes, known equally genetic variants, take contradistinct frequencies in domesticated rabbits when compared to wild populations. Many of these genes are involved in the development of the encephalon and nervous system, which may explain the behavioural changes that we see in domestic rabbits such equally a weaker flight response.

In addition, we observed more genetic changes to the genome in regions that do not code for proteins. This finding is especially interesting in low-cal of projects such as the ENCyclopedia of Deoxyribonucleic acid Elements (ENCODE), which accept collected copious information illuminating how regions of the genome outside of protein-coding genes play a vital role in gene regulation. This not-coding genetic variation could therefore control which genes are switched on or off or human activity like a volume control to adapt the level to which a gene is switched on or expressed.

Comparing wild and domesticated rabbits

Get-go, Deoxyribonucleic acid from one domestic rabbit was sequenced to build a high-quality reference genome associates. Having a reference genome associates is a critical outset step in whatever genome assay because it provides a basis against which other genetic data tin can be compared.

Next, the genomes of other rabbits were sequenced: six domestic breeds, and wild rabbits from 14 different places too. This provided a fantastic opportunity for comparing the genetic changes that occurred when wild rabbits were domesticated because genetic changes that are more or less frequently observed in the domesticated breeds compared to wild populations are more probable to contribute to domestication.

Ensembl'due south part

In add-on to having a reference genome assembly, researchers also need a well-characterised cistron fix. This was the function of the project that I was involved with. I co-managed the Ensembl cistron notation project for the rabbit.

Magali Ruffier in the Ensembl Genebuild squad predicted the location of protein-coding genes for the rabbit by mapping known poly peptide sequences from rabbit other animals to the rabbit genome. This is a computationally expensive job and tin can take several months to consummate. Daniel Barrell likewise mapped the consortium'due south gene expression (transcriptome) data from ten tissues to the rabbit genome and incorporated these information into the gene note project.

Time to come directions

The genomic resources collected during this research provide a expert basis for farther study, including research into the early stages of species formation. Contrary to what y'all might look, we did not find show to support the idea that domestication is driven by the inactivation of a small-scale number of genes. Instead, the pocket-sized changes (variations) that we observed in many genes were already present in the wild populations and have simply had their frequency altered in domestic populations. This means that rabbits may as well be a good model for studying what happens when domestic and wild populations breed.

Bronwen Aken is the Primary Assay Coordinator for the Ensembl project at EMBl-EBI. Ensembl is a genomic estimation system, providing genome notation, querying tools and access methods for chordates and key model organisms.

References

  • Carneiro, M et al (2014). Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Scientific discipline. DOI: 10.1126/scientific discipline.1253714
  • The ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature. DOI:10.1038/nature11247
  • Carneiro, Yard et al (2014). The Genomic Architecture of Population Difference betwixt Subspecies of the European Rabbit. PlOS Genetics. DOI: 10.1371/journal.pgen.1003519

Caption and credit for homepage image: Experimental design and population data. Credit: Carneiro et al., Science/AAAS DOI: ten.1126/science.1253714

Related Links:

  • Ensembl website
  • ENCODE website
  • EMBL-European Bioinformatics Institute website