High quality gaits play an important role in many breeding programs, but the genes of gait were limited at the moment. Here, we present an analysis of genomic selection signatures in 53 individuals from two breeds, using genotype data from the Affymetrix Equine 670K SNP genotyping array. The 11 selection regions of Yili horse were identified using an FST statistic and XP-EHH calculated in 200-kb windows across the genome. In total, 50 genes could be found in the 11 regions, and two candidate genes related to locomotory behavior (CLN6, FZD4). The genome of Yili horse and Russian horse were shaped by natural and artificial selection. Our results suggest that gait trait of Yili horse may related to two genes. This is the first time when whole genome array data is utilized to study genomic regions affecting gait in Yili horse breed.

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