Landscape Genomics of Local Adaptation in Sheep and Goats

Since their domestication 10 kyears ago followed by a worldwide spread, sheep and goats have accumulated highly valuable adaptive traits allowing them to be raised within highly diversified environments. Besides the current rapid development and wide spread of just a few productive cosmopolitan breeds marked by limited genetic diversity, indigenous populations may keep adaptive traits that would constitute crucial genomic resources in the context of environmental changes. We sequenced the genomes of 160 indigenous sheep and 161 goats representative of the Moroccan-wide diversity in ecology, climate and geographic origin. We detected 39 million variants in sheep and 32 million in goats showing a very weak geographic structure over the country in both species. We used population-based and correlative approaches to identify several sets of loci and genes that likely have a role in local adaptation globally to altitude, slope, sunshine, rainfall, temperature and their variation. The main adaptive pathways were associated with respiration and circulation for the adaptation to altitude. The major genes identified showed different patterns of variation of genetic differentiation along environmental gradients. Candidate genes for adaptation to the same environmental variable were generally different between the two species, suggesting different adaptive mechanisms in sheep and goats. However, similar or functionally linked genes responding to the same environmental variable were also found.