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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #352827

Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

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

Author
item Colli, Licia - Università Cattolica Del Sacro Cuore
item Milanesi, Marco - Università Cattolica Del Sacro Cuore
item Talenti, Andrea - Università Cattolica Del Sacro Cuore
item Bertolini, Francesca - Iowa State University
item Chen, Minhui - Aarhus University
item Crisa, Alessandra - Collaborator
item Daly, Kevin - Trinity College
item Del Corvo, Marcello - Università Cattolica Del Sacro Cuore
item Guldbrandtsen, Brent - Aarhus University
item Lenstra, Johannes - Utrecht University
item Rosen, Benjamin
item Vajana, Elia - Università Cattolica Del Sacro Cuore
item Catillo, Gennaro - Collaborator
item Joost, Stepahne - Ecole Polytechnique Federale De Lausanne (EPFL)
item Nicolazzi, Ezequiel - Parco Tecnologico Padano
item Rochat, Estelle - Ecole Polytechnique Federale De Lausanne (EPFL)
item Rothschild, Max - Iowa State University
item Servin, Bertrand - Institut National De La Recherche Agronomique (INRA)
item Sonstegard, Tad - Recombinetics, Inc
item Steri, Roberto - Collaborator
item Van Tassell, Curtis - Curt
item Ajmone-marsan, Paolo - Università Cattolica Del Sacro Cuore
item Crepaldi, Paola - University Of Milano
item Stella, Alessandra - Parco Tecnologico Padano

Submitted to: Genetic Selection Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/15/2018
Publication Date: 11/19/2018
Citation: Colli, L., Milanesi, M., Talenti, A., Bertolini, F., Chen, M., Crisa, A., Daly, K., Del Corvo, M., Guldbrandtsen, B., Lenstra, J.A., Rosen, B.D., Vajana, E., Catillo, G., Joost, S., Nicolazzi, E., Rochat, E., Rothschild, M.F., Servin, B., Sonstegard, T.S., Steri, R., Van Tassell, C.P., Ajmone-Marsan, P., Crepaldi, P., Stella, A. 2018. Genome-wide SNP profiling of worldwide goat populations reveals a strong partitioning of diversity and highlights post-domestication migration routes. Genetic Selection Evolution. 50:58. https://doi.org/10.1186/s12711-018-0422-x.
DOI: https://doi.org/10.1186/s12711-018-0422-x

Interpretive Summary: The post-domestication evolutionary history of goats was reconstructed by looking at the genetic variation in 144 goat populations across Africa, Europe and western Asia. We found three major gene pools corresponding to goats from Europe, Africa and western Asia. Further sub-structuring identifies regional gene pools, whose distribution reflects the main post-domestication migration routes with some regions experiencing extensive gene flow while others remained isolated. After domestication in the Fertile Crescent, domestic goats spread to Europe, Africa and Asia through divergent migration routes, which determined the major genomic background of the populations. Our evidence outlines a remarkable diversity occurring at the global scale, locally partitioned and often affected by introgression from cosmopolitan breeds. This raises concerns for the long-time preservation of goat diversity, but also provides a useful framework for directing improvement and breeding plans.

Technical Abstract: Background: The goat populations characterized by ADAPTmap project cover large part of the worldwide spreading area of the species. Thus they offer an attractive opportunity to assess the distribution of goat diversity at a global scale and to reconstruct post-domestication evolutionary history. We analysed genome-wide 50K SNP data for 144 populations to describe the patterns of molecular variation across Africa, Europe and western Asia, and to highlight the drivers that led to the present day diffusion of the species after its domestication. Results: We highlighted the occurrence of a remarkable variability among the studied goat populations, together with a strong partitioning of molecular diversity between continents. Three major gene pools correspond to goats from Europe, Africa and western Asia. Further sub-structuring discloses regional gene pools, whose distribution reflects the main post-domestication migration routes. Several exchanges, mainly between African populations and which often involve admixed and cosmopolitan breeds, were also identified. Extensive gene flow takes place within specific areas (e.g., southern Europe, Morocco and Mali-Burkina Faso-Nigeria), while elsewhere isolation due to geographical causes (e.g. insularity) or human management has brought a decrease in local gene flow. Conclusions: After domestication in the Fertile Crescent in the early Neolithic era (ca. 10000 BCE), domestic goats spread to Europe, Africa and Asia through divergent migration routes, which determined the major genomic background of the continental populations. During the following centuries, due to geographical and reproductive isolation, further sub-structuring of diversity occurred at the regional level. This has been accompanied by additional migrations and/or importations, the traces of which are still detectable today. Overall, our evidence outlines a remarkable diversity occurring at the global scale, locally partitioned and often affected by introgression from cosmopolitan breeds. This raises concerns for the long-time preservation of goat diversity, but also provides a useful framework for directing improvement and breeding plans.