The genome-wide legacy of Baroque horse breeds

The Baroque horse breeds, originating from Southern Europe, are known for their unique characteristics and roles in High School dressage and ceremonial contexts. These breeds have been shaped by centuries of selective breeding, geographic isolation, and interactions with other equine populations. This study explores the genetic diversity and population structure of Baroque breeds (Lipizzan, Murgese, Lusitano, and Pura Raza Española) alongside eleven relevant equine populations including Baroque-derived, cold-blood and warm/hot-blood breeds. After quality control and subsampling, the final dataset included 440 genotyped individuals. The overall variability was assessed using genetic diversity indices while population structure and genetic relationships were inferred using PCA, ADMIXTURE, Neighbour-net and TreeMix analysis. The results show that the Baroque and Baroque-derived breeds form a cohesive genetic group exhibiting heterogeneous genetic diversity. Within the Baroque breeds, the Pura Raza Española was more closely related to Lusitano while Lipizzan to Murgese. This genetic relatedness conforms with both historical connections and geographic proximity of these breeds. A widespread ancestral component of the Pura Raza Española can be observed in both Baroque and Baroque-derived breeds reflecting its past role in moulding modern breeds. However, the Pura Raza Española showed moderate genetic diversity and positive values of inbreeding suggesting the need for conservation efforts. Our results also highlight a more recent influence in terms of gene exchange of several warm/hot-blood breeds in shaping current Baroque breeds. These findings underscore the uniqueness of Baroque breeds and lays the foundation for clarifying their origin and impact on equine biodiversity.