Genetic Diversity and Population Structure of Locally Adapted Brazilian Horse Breeds Assessed Using Genome-wide Single Nucleotide Polymorphisms

•Northern Brazilian breeds share a genetic basis, hindering their differentiation.•Geographic division of Brazilian equine breeds (Northern, Southern and Midwest).•High genetic variability and endogamy in most Brazilian naturalized breeds.•Iberoamerican horse breeds envolved in origin of Brazilian naturalized breeds.•Genetic base to backup decisions in Germplasm Program sampling and conservation.