Genetic variability and associations of Trakehner and other horse populations in Lithuania

To obtain genetic parameters relevant for the management of animal genetic resources, this study provides a comparative characterization of the Trakehner (TRAK) horse population in relation to four other horse populations maintained in Lithuania - Arabian (ARAB), Baltic Warmblood (BW), Lithuanian Warmblood (LW), and Zemaitukai (ZEM). These populations represent diverse histories, selection goals, and breeding practices. Pedigree data ( $n=$ 22 666) and parentage verification genetic data based on blood group markers ( $n=$ 1293) were used to evaluate genetic diversity, population structure, and inter-population relationships. Despite a 25 % population decline in recent years, the TRAK population maintained moderate inbreeding ( $F=$ 0.037) and a balanced genetic structure. The effective population size ( $N_e$ ) was lower than in BW and LW but higher than in the endangered ZEM population. TRAK retained a high number of alleles ( $N_a=$ 3.83), with observed heterozygosity ( $H_o=$ 0.460) slightly lower than that observed in open sport horse populations. Comparison of all individuals and the Lithuanian reference populations revealed stable or increased heterozygosity in currently breeding individuals, particularly within TRAK. Genetic distances and assignment tests confirmed close relationships among TRAK, BW, and LW, reflecting shared ancestry. In contrast, ARAB and ZEM populations remained genetically distinct. PCA and heatmap analyses further supported the separation between closed and open populations in the current breeding context. These findings highlight that population structure, historical gene flow, and management practices jointly shape genetic variability. The results can be used to optimize mating plans by balancing sire and dam contributions, monitor inbreeding and effective population size trends, manage gene flow between related populations (TRAK, BW, LW), and develop targeted conservation strategies for genetically distinct breeds such as ZEM and ARAB.