Landscape Genetics Reveals Geographic Structuring of Locally Adapted Goat Populations from Brazil, Spain, and Ecuador

Background: Locally adapted goat populations represent important reservoirs of genetic diversity and play a crucial role in the sustainability of livestock production systems, particularly in marginal environments. However, many of these populations are currently threatened by genetic erosion caused by crossbreeding with highly specialized commercial breeds. Although previous studies have described the genetic diversity of several goat populations from South America and the Iberian Peninsula, the influence of geographic factors on the genetic structure of these populations remains insufficiently understood. In this study, we investigated the influence of geographic distance and spatial factors on the genetic diversity, population structure, and relationships among locally adapted goat populations from Brazil, Spain, and Ecuador. Methods: A total of 561 goats representing 15 populations were genotyped using a panel of 23 microsatellite markers. The dataset included six locally adapted Brazilian breeds, three Spanish breeds, one Ecuadorian population (Chusca Lojana), four exotic breeds, and one undefined genotype group. Genetic diversity parameters, population structure, genetic relationships, and spatial genetic patterns were evaluated through a combination of population genetic and spatial analyses. Results: The locally adapted populations showed considerable levels of genetic diversity, with the Spanish (Ho = 0.629; He = 0.685) and Ecuadorian (Ho = 0.628; He = 0.704) populations displaying higher diversity than the Brazilian populations (Ho = 0.583; He = 0.628). Significant genetic differentiation was observed among geographic groups. A strong and significant correlation between genetic and geographic distances was detected when all local populations were considered (r = 0.77; R2 = 0.59; p < 0.001), as well as when only Brazilian populations were analyzed (r = 0.65; R2 = 0.43; p = 0.0075). Spatial analyses further identified potential genetic barriers that may restrict gene flow among certain populations. Conclusions: These findings suggest that geographic isolation plays an important role in shaping the genetic structure of locally adapted goat populations, while historical connections among Iberian and South American populations may also contribute to the observed genetic relationships. The integration of genetic and spatial information provides valuable insights for understanding the evolutionary dynamics of these populations and supports the development of more effective strategies for the conservation and sustainable management of goat genetic resources.