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

Author(s):Show less -

Colli, Licia ^{[1, 2]} ; Milanesi, Marco ^{[1, 3]} ; Talenti, Andrea ^[4] ; Bertolini, Francesca ^{[5, 6]} ; Chen, Minhui ^{[7, 8]} ; Crisa, Alessandra ^[9] ; Daly, Kevin Gerard ^[10] ; Del Corvo, Marcello ^[1] ; Guldbrandtsen, Bernt ^[7] ; Lenstra, Johannes A. ^[11] ; Rosen, Benjamin D. ^[12] ; Vajana, Elia ^{[13, 1]} ; Catillo, Gennaro ^[9] ; Joost, Stephane ^[13] ; Nicolazzi, Ezequiel Luis ^[14] ; Rochat, Estelle ^[13] ; Rothschild, Max F. ^[5] ; Servin, Bertrand ^[15] ; Sonstegard, Tad S. ^[16] ; Steri, Roberto ^[9] ; Van Tassell, Curtis P. ^[12] ; Ajmone-Marsan, Paolo ^{[1, 2]} ; Crepaldi, Paola ^[4] ; Stella, Alessandra ^{[14, 17]} ; Consortium, AdaptMap

Affiliation:Show less -

^[1] Univ Cattolica S Cuore, DIANA Dipartimento Sci Anim Nutr & Alimenti, Piacenza - Italy

^[2] Univ Cattolica S Cuore, BioDNA Ctr Ric Biodiversita & DNA Ant, Piacenza - Italy

^[3] Sao Paulo State Univ UNESP, Sch Vet Med, Dept Support Prod & Anim Hlth, Aracatuba - Brazil

^[4] Univ Milan, Dipartimento Med Vet, Milan - Italy

^[5] Iowa State Univ, Dept Anim Sci, Ames, IA - USA

^[6] Tech Univ Denmark, DTU, Natl Inst Aquat Resources, Lyngby - Denmark

^[7] Aarhus Univ, Ctr Quantitat Genet & Genom, Dept Mol Biol & Genet, Aarhus - Denmark

^[8] Univ Southern Calif, Keck Sch Med, Dept Prevent Med, Ctr Genet Epidemiol, Los Angeles, CA - USA

^[9] Consiglio Ric Agr & Anal Econ Agr CREA, Res Ctr Anim Prod & Aquaculture, Rome - Italy

^[10] Trinity Coll Dublin, Smurfit Inst Genet, Populat Genet Lab, Dublin - Ireland

^[11] Univ Utrecht, Fac Vet Med, Utrecht - Netherlands

^[12] ARS, Anim Genom & Improvement Lab, USDA, Beltsville, MD - USA

^[13] Ecole Polytech Fed Lausanne, Lab Geog Informat Syst LASIG, Sch Architecture Civil & Environm Engn ENAC, Lausanne - Switzerland

^[14] Fdn Parco Tecnol Padano, Lodi - Italy

^[15] Univ Toulouse, INRA, GenPhySE, INPT, ENVT, F-31326 Castanet Tolosan - France

^[16] Recombinetics Inc, St Paul, MN - USA

^[17] CNR, Ist Biol & Biotecnol Agr, Milan - Italy

• Document type: Journal article
• Source: GENETICS SELECTION EVOLUTION; v. 50, NOV 19 2018.
• Web of Science Citations: 12

Abstract

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. (AU)

• FAPESP's process: 16/05787-7 - Combining high-density SNP genotypes and next generation sequence data to map disadvantageous genetic variants in Nellore cattle
• Grantee: Marco Milanesi
• Support Opportunities: Scholarships in Brazil - Post-Doctoral