A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate region approximately 50 kb downstream of the Endothelin 3 (EDN3) gene. EDN3 and other endothelin family members are associated with blood pressure regulation in humans and other species, but similar association studies in horses are lacking. We hypothesized that the sweep region includes a regulatory element acting on EDN3 transcription, ultimately affecting blood pressure regulation and athletic

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... ance in horses. Selective sweep fine-mapping identified a 5.5 kb haplotype of 14 SNPs shared within Coldblooded trotters (CBT) and Standardbreds (SB). Most SNPs overlapped potential transcription factor binding sites, and haplotype analysis showed significant association with all tested performance traits in CBTs and earnings in SBs. From those, two haplotypes were defined: an elite performing haplotype (EPH) and a sub-elite performing haplotype (SPH). While the majority of SNPs in the haplotype were part of the standing variation already found in pre-domestication horses, there has been an increase in the frequencies of the alternative alleles during the whole history of horse domestication. Horses homozygous for EPH had significantly higher plasma levels of EDN3, lower levels of EDN1, and lower exercise-related blood pressure compared to SPH homozygous horses. Additionally, a global proteomic analysis of plasma from EPH or SPH homozygous horses revealed higher levels of proteins involved in pathways related to immune response and complement activation in the SPH horses. This is the first study to demonstratean association between the EDN3 gene, blood pressure regulation, and athletic performance in horses. The results advance our understanding of the molecular genetics of athletic performance, exercise-related blood pressure regulation, and biological processes activated by intense exercise.