Drawing up worldwide goat diversity and post-domestication history: update from ADAPTmap project

Abstract

The study of goat adaptation to different environments is a major aim of the international ADAPTmap project, which joins the genotyping and re-sequencing efforts of the International Goat Genome Consortium (IGGC), the African Goat Improvement Network (AGIN), Feed the Future program of United States Agency for International Development and NEXTGEN EU project. Having a worldwide distribution, and thriving across a variety of contrasting habitats, goats offer an attractive opportunity to address the genetics of adaptation. This has to start with extensive analyses of the patterns of diversity, thus, a set of 144 breeds, representing 36 countries from 5 continents, has been genotyped with the Illumina GoatSNP50 BeadChip. Several analytical approaches have been adopted to describe the patterns of molecular variation across Africa, Europe and western Asia. The results obtained so far reveal a strong partitioning among continents. Three major gene pools correspond to goats from Europe, Africa and western Asia, while further sub-structuring reflects the main post-domestication migration routes. The reconstruction of past migration events highlighted several exchanges mainly between African populations, which often involve admixed and cosmopolitan breeds. In addition, extensive gene flow was revealed within specific areas (e.g., southern Europe, Morocco and Mali-Burkina FasoNigeria), while isolation due to geographical causes (e.g. insularity) or human management has brought a decrease in local gene flow. Taken together, these results confirm that after domestication in the Fertile Crescent in the early Neolithic era (approx. 15,000 BP), 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 local level. This has been accompanied by additional migrations and/or importations, the traces of which are still detectable, such as the clear African signatures in the goat populations of the Canary Islands and Southern America