Livestock landscape genomics to detect adaptive loci in 43 European and Near Eastern goat breeds

The domestic goat is one of the five most important livestock species worldwide and plays an important role in the livelihood of a large proportion of small and marginal farmers and landless shepherds. To serve as a rational basis for the conservation of goat germplasm, the molecular characterization of local goat breeds has to consist of information on genetic diversity, on the genetic structure of the populations, but also on their potential to adapt to the local environment. We analyzed 101 AFLP markers in 43 goat breeds distributed across Europe and Middle East to assess population genetic diversity and population structure. In parallel, a livestock landscape genomics approach (Hanotte et al. 2010) was implemented in order to detect signatures of natural selection. The results obtained show a weak overall genetic differentiation compared with other domestic species like cattle, horse and sheep. The breeds sampled close to the domestication centre cluster together and form an Eastern gene pool, while breeds originating from Swiss, Italian and Austrian mountains belong to a common Alpine gene pool. As for the adaptive potential, landscape genomics identified 4 loci possibly under natural selection – also detected by standard FST-outlier methods – and significantly associated with environmental variables.