CHRONOBOS: Extant and ancient genomic diversity (SNPs) associated with domestication : Application to cattle and small ruminants

Background The genetic diversity of domestic species determines the potential of future selections of breeds able to adapt to new challenges, e.g., to resist to yet unknown diseases. Thus, it is important to evaluate the diversity of extant species to better protect it in the future and to maintain it at a high level. If the genetic diversity of mitochondrial DNA for the majority of extant domestic mammals is relatively well known, our knowledge of the nuclear genome diversity is relatively poor. Moreover, the evolution of this diversity since the beginning of the domestication process is unknown up to now. Objectives Our project was focused on three domestic species: cattle, sheep and goats. The first aim was to have a better knowledge of the present-day diversity of these 3 species : at the mitochondrial level, by completing previous phylogeographic studies; at the nuclear level, by identifying diagnostic small nuclear polymorphisms (SNPs) on markers presumably selected during the domestication process to satisfy phenotypical criteria or needs of resistance. A dozen of nuclear genes candidates were identified for a large scale sequencing approach in the three species. The second aim was to evaluate the ancient diversity of domestic species at a large time and space scale, i.e., from the beginning of domestication in the Near East 11,000 years ago to the diffusion of the domesticates in Europe during Neolithic times via the Danubian and Mediterranean routes. The analysis of DNA extracts from fossils has a higher yield when genetic loci with a high copy number are analysed, as it is the case for mitochondrial DNA. So, the first ancient DNA analyses performed focused on mtDNA. That allowed us to identify fossil samples in which DNA was preserved enough to analyse the nuclear diversity at the level of newly determined markers (SNPs). Results The mitochondrial DNA diversity of present-day sheep and goats has been completed by analyzing samples from peculiar area, never studied up to now. The results obtained in this project for goats permitted to detect a new haplogroup never observed before (Naderi et al. PlosOne 2007, PNAS 2008). Different nuclear markers have also been sequenced with the help of the Econogene consortium and SNPs identified for the further paleogenetic studies. For the paleogenetic approach, bones of the Neolithic period have been sampled by the archeozoologists from many archeological sites along the both Routes, Mediterranean and Danubian. Mitochondrial studies, from which one was directly at the origin of a part of this project, were already published for ancient goats (Fernandez et al. PNAS 2006) and cattle (Edwards et al. Proc. Roc. Soc. B 2007). Trying to amplify nuclear DNA from fossils is a challenge since ancient DNA is degraded and only small amount of DNA available, if any. Methodological studies have been thus developed for this project concerning the preservation of DNA in bones (Pruvost et al. 2007; Bollongino et al. 2008). Conclusion and perspectives The overall goal of the project was an attempt to improve our knowledge about the genetic diversity of domestic species and its possible management in the coming years to preserve the genetic potential for the selection of new breeds (Taberlet et al. 2008). By proposing to assess this diversity through time (and as early as the beginning of the domestication process), this project presented an innovative and very interdisciplinary approach based on four complementary research groups specialised in population genetics of extant populations, palaeogenetics or archaeozoology.