To assist in selection schemes we carried out the first genetic characterization of the Spanish Trotter horse (Trotador Español). We used 16 microsatellite markers to genotype 40 unrelated Spanish trotters, 25 native Balearic horses (11 Menorquina and 14 Mallorquina horses) and 32 Andalusian horses. The observed heterozygosity for the Spanish Trotters was 0.647 ± 0.037 and the expected heterozygosity was 0.696 ± 0.026 while the average number of alleles per locus was 6.0 ± 0.341, these values being similar to the data published for other horse breeds. We also tried to establish the importance of the Mallorquina and Menorquina breeds in the present Spanish Trotter population. Only 9% of the total genetic variability could be attributed to differences between breeds (mean F ST = 0.09 ± 0.010). Recent migration rates were confirmed the low recent genetic relationship between the Balearic breeds and Spanish Trotters, indicating that the genetic background of the present Spanish Trotter population is not based on the native Balearic horse population.
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