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This study aimed to determine the phylogenetic and bottleneck analyses of Turkish Thoroughbred and Arabian horse populations. In the study, genotyping was performed using a total of 17 microsatellite markers in the samples taken from 959 Thoroughbred and 813 Arabian horses. The average effective allele number in Arabian horses was 3.338 and the average number of alleles was 7.412 in Thorougbred horses. Genetic distance and genetic identity between Thoroughbred and Arabian breeds was 0.411 and 0.663, respectively. Also genetic identity in each Arabian and Thoroughbred horse populations was 1.000. The FCA table showed that the two breeds were completely separated from each other and were compatible. In conclusion; the bottlenecks of Thoroughbred and Arabian horse populations were in a normal L distribution and these horse breeds do not appear to have succumbed to introgression. Therefore, they are not yet at risk of extinction any time soon.

The aim of this study was to determine the genetic structure of Coloured horses in Turkey by analysis of the D-loop sequence of mitochondrial DNA (mtDNA). A total of 28 Coloured horses were examined. DNA was extracted from blood samples using DNA isolation kit; 519 bp long mtDNA D-loop region was amplified by PCR and sequenced by capillary electrophoresis system. Population parameters and phylogenetic trees were drawn by using MEGA4 software package. It was also compared with the DNA sequences of horse populations from different countries. In this study, 42 different polymorphism regions and 10 different haplogroups were detected. Additionaly, Tajima D value was found to be -0.31 and population expansion was determined. It was determined that the base differences among the horses ranged between 0.000 and 0.032. It was detected that the horses formed different clusters from each other and they were intertwined with the populations of different countries. Moreover, it was also observed that some horses formed their own populations at different points from the other countries" horses. As a result, it was observed that the genetic structures of horses which used in population were different from each other and they originated from different mothers. According to the results obtained, it is considered that Coloured horses can be a native horse breed of Turkey.