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The objective of this study was to evaluate the inter-breed genetic diversity of Lithuanian Trakehner horses. The current population in Lithuania numbers 1 039 Trakehner horses. The study included the immunogenetic data analysis of 316 blood samples. Pedigree was traced back to 7–11 generations. The horses were assigned to genealogical clusters originating from East Prussian Trakehner Stud, Thoroughbred and Arab sires. The first two clusters were subdivided into nine-horse groups according to the most important ancestors. The evaluation of genetic diversity was based on six blood groups and five protein polymorphism systems. The differences between genealogical groups were confirmed by principal component analysis and applied cluster analysis. According to the allelic frequency, the Trakehner population changed very slightly through a 30-year period, and only one rare (0.013) allele Tf RR  (frequent in other Trakehner populations), has been newly found. The analysis of genetic polymorphism systems based on a very low rate of alleles Q abc  (0.093) and D dkl  (0.046), which are typical of other populations, indicated the exclusivity of the Trakehner population in Lithuania. The average expected heterozygosity by blood protein polymorphism and blood groups were 0.409 and 0.441, respectively. The genetic clustering diverged by observed heterozygosity of blood groups and by pedigree data in Pilger through Egoist, Bay Ronald through Dark Ronald and Dampfross through Hyperion subgroups. The determined distinctiveness of subdivided Trakehner horse groups suggests reconsidering the breeding strategies and conservation programme of Trakehner horses. Breeding and selection of subdivided sire lines could be among the appropriate solutions for the maintenance and extension of the genealogical structure.    

Evaluation of genetic diversity of subdivided genealogical groups in Lithuanian Trakehner horse population using immunogenetic tools