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

Authors: COLLI, LICIA - Università Cattolica Del Sacro Cuore; MILANESI, MARCO - Università Cattolica Del Sacro Cuore; TALENTI, ANDREA - Università Cattolica Del Sacro Cuore; BERTOLINI, FRANCESCA - Iowa State University; CHEN, MINHUI - Aarhus University; CRISA, ALESSANDRA - Collaborator; DALY, KEVIN - Trinity College; DEL CORVO, MARCELLO - Università Cattolica Del Sacro Cuore; GULDBRANDTSEN, BRENT - Aarhus University; LENSTRA, JOHANNES - Utrecht University; Rosen, Benjamin - Ben; VAJANA, ELIA - Università Cattolica Del Sacro Cuore; CATILLO, GENNARO - Collaborator; JOOST, STEPAHNE - Ecole Polytechnique Federale De Lausanne (EPFL); NICOLAZZI, EZEQUIEL - Parco Tecnologico Padano; ROCHAT, ESTELLE - Ecole Polytechnique Federale De Lausanne (EPFL); ROTHSCHILD, MAX - Iowa State University; SERVIN, BERTRAND - Institut National De La Recherche Agronomique (INRA); SONSTEGARD, TAD - Recombinetics, Inc; STERI, ROBERTO - Collaborator; Van Tassell, Curtis - Curt; AJMONE-MARSAN, PAOLO - Università Cattolica Del Sacro Cuore; CREPALDI, PAOLA - University Of Milano; 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.