AdaptMap project : Exploring worldwide goat diversity and adaptation

International audience; The AdaptMap project investigates worldwide goat diversity with a focus on domestication, adaptation associated with local environmental conditions, and adaptation in response to selection for production systems. The ultimate goal of the project is to enable sustainable goat breeding by leveraging the use of genomic information. During the first phase of AdaptMap, several analyses were performed to characterize population genetics and history, to identify selection signatures and signals of environmental adaptation through landscape genomics, and to devise a panel of SNPs for parentage assessment. Overall, our results showed a close association between the distribution of diversity and geography, with a clear partitioning of the populations into groups according to the continental origin. The 3 major gene pools corresponded to goats from Europe, Africa and western Asia, a pattern consistent with the recognized paths of human migration out of the Fertile Crescent. Within these major pools, further patterns of variation mirrored geographical sub-structuring, human history and animal husbandry practices. Comparing the European and African gene pools, European breeds tended to be more discreet, in line with the practice of creating breeds through active human-controlled genetic isolation, while greater gene flow was observed in Africa. Among the observed “hotspots” of runs of homozygosity, some were unique across continental groups. The results of selection signature analysis were generally consistent with previous evidence from independent studies. Signals of adaptation to the environment were also identified, showing the strongest association with differences in mean annual temperature. Finally, a highly informative marker panel for parentage assessment was developed to assist breeding in goat populations worldwide. Taken together, our evidence outlines a remarkable diversity occurring at the global scale, locally partitioned and often affected by introgression from cosmopolitan breeds. This provides a useful framework to direct improvement and conservation actions, and to select breeding targets. After excluding under-performing samples and markers, 970 targeted markers with 50X sequence coverage or greater and an overall average call rate of 98% were included in the data set. Furthermore, novel genetic mutations identified in these important targeted regions were characterized. Data from this panel can be used to identify known causative mutations, improve pedigree accuracy and assist in genetic selection for the sheep industry at a cost of US$15. The application of this cost-effective sheep genomics marker panel can be used to promote improved production, animal health and profitability of the US sheep industry.