Chèvre | EPFL Graph Search

vignette|Chèvre domestique d'Angora, photographie (avant 1910) d'Eugène Trutat conservée au Muséum de Toulouse. vignette|Gandhi à Marseille en 1931 avec deux chèvres qui lui fournissaient sa ration quotidienne de lait. La chèvre domestique (Capra hircus Linnaeus, 1758 ou Capra aegagrus hircus) est une espèce de mammifères herbivore ruminant, appartenant à la famille des bovidés, sous-famille des caprins. La plupart du temps, les chèvres sont domestiquées, mais on les trouve aussi à l'état sauvage dans quelques contrées du Caucase, d'Iran, d'Afghanistan ou d'Irak. Leur domestication est ancienne (au moins ). On les élève pour leur lait, leur cuir, leur poil et leur viande. Étymologie et évolution de l'appellation Les termes « chèvre », Capra et « caprin » dérivent du latin capra (chèvre) et caprinus (adj. relatif à la chèvre, caprin). L'épithète spécifique dérive du latin hircus, nom désignant le bouc. Le mot « bouc » proviendrait du gaulois bucco auquel pourrait aussi ê

Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes

Stéphane Joost, Estelle Rochat, Elia Vajana

Background: Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats. Results: A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows. Conclusions: After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.

BMC2018

The characterization of goat genetic diversity: Towards a genomic approach

Stéphane Joost, Pierre Taberlet

The investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers for each of the main livestock species, FAO has promoted the meta-analysis of local datasets, to achieve a global view of molecular genetic diversity. Analysis within the EU Globaldiv project of two large goat microsatellite datasets produced by the Econogene Consortium and the IAEA CRP–Asia Consortium, respectively, has generated a picture of goat diversity across continents. This indicates a gradient of decreasing diversity from the domestication centre towards Europe and Asia, a clear phylogeographic structure at the continental and regional levels, and in Asia a limited genetic differentiation among local breeds. The development of SNP panels that assay thousands of markers and the whole genome sequencing of livestock permit an affordable use of genomic technologies in all livestock species, goats included. Preliminary data from the Italian Goat Consortium indicate that the SNP panel developed for this species is highly informative. The existing panel can be improved by integrating additional SNPs identified from the whole genome sequence alignment of goats adapted to extreme climates. Part of this effort is being achieved by international projects (e.g. EU FP7 NextGen and 3SR projects), but a fair representation of the global diversity in goats requires a large panel of samples (i.e. as in the recently launched 1000 cattle genomes initiative). Genomic technologies offer new strategies to investigate complex traits difficult to measure. For example, the comparison of patterns of diversity among the genomes in selected groups of animals (e.g. adapted to different environments) and the integration of genome-wide diversity with new GIScience-based methods are able to identify molecular markers associated with genomic regions of putative importance in adaptation and thus pave the way for the identification of causative genes. Goat breeds adapted to different production systems in extreme and harsh environments will play an important role in this process. The new sequencing technologies also permit the analysis of the entire mitochondrial genome at maximum resolution. The complete mtDNA sequence is now the common standard format for the investigation of human maternal lineages. A preliminary analysis of the complete goat mtDNA genome supports a single Neolithic origin of domestic goats rather than multiple domestication events in different geographic areas.

Elsevier2014

Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data

Stéphane Joost, Kevin Leempoel, Sylvie Stucki, Pierre Taberlet

Since the time of their domestication, goats (Capra hircus) have evolved in a large variety of locally adapted populations in response to different human and environmental pressures. In the present era, many indigenous populations are threatened with extinction due to their substitution by cosmopolitan breeds, while they might represent highly valuable genomic resources. It is thus crucial to characterize the neutral and adaptive genetic diversity of indigenous populations. A fine characterization of whole genome variation in farm animals is now possible by using new sequencing technologies. We sequenced the complete genome at 12X coverage of 44 goats geographically representative of the three phenotypically distinct indigenous populations in Morocco. The study of mitochondrial genomes showed a high diversity exclusively restricted to the haplogroup A. The 44 nuclear genomes showed a very high diversity (24 million variants) associated with low linkage disequilibrium. The overall genetic diversity was weakly structured according to geography and phenotypes. When looking for signals of positive selection in each population we identified many candidate genes, several of which gave insights into the metabolic pathways or biological processes involved in the adaptation to local conditions (e.g. panting in warm/desert conditions). This study highlights the interest of WGS data to characterize livestock genomic diversity. It illustrates the valuable genetic richness present in indigenous populations that have to be sustainably managed and may represent valuable genetic resources for the long-term preservation of the species.