Genomic insights into diversity, population structure and selection signatures in Sicilian horse breeds

Sicilian horse breeds represent a valuable genetic resource shaped by environmental and selective processes. This study investigated the genetic diversity and population structure of three Sicilian horse breeds: Purosangue Orientale (68–ORI), Sanfratellano (70–SAN) and Cavallo Siciliano (96–SIC) genotyped using the Illumina Equine80K BeadChip. Furthermore, the potential selection signatures were investigated in ORI and SAN using complementary within- and between-population approaches based on Runs of Homozygosity (ROH), the integrated Haplotype Score (iHS) and the standardised log-ratio of extended haplotype homozygosity (Rsb) statistics. The analyses provided an updated overview of the genomic architecture of Sicilian horses, distinguishing established breeds (ORI and SAN) from the recently recognised SIC breed. The candidate selection sweeps identified in ORI, revealed genomic regions previously reported in the literature related to athletic performance, temperament, and environmental resilience, whereas those detected in SAN overlapped genomic regions previously implicated in environmental adaptability, immune response, and fertility. The SIC breed exhibited greater heterogeneity than the other two Sicilian horse breeds, supporting its ongoing process of genetic standardisation. Overall, the results contribute to the conservation and sustainable management of Sicilian horses’ genetic resources, providing genomic information useful for future breeding, conservation, and selection strategies.