Abstract
Indigenous breeds, such as the Balkan goat, represent valuable genetic resources due to their adaptation to specific ecological and socio-economic conditions. Goats are vital to rural livestock systems, particularly in regions with limited infrastructure, due to their resilience and low resource demands. This study presents a comprehensive genetic characterization of the Balkan goat in Serbia using microsatellite and mitochondrial DNA markers. Nuclear variation was assessed using 13 polymorphic microsatellite loci, revealing a mean expected heterozygosity of 0.756 and a mean polymorphic information content (PIC) of 0.721, indicating a high level of genetic diversity. The overall inbreeding coefficient (FIS = 0.042 ) was low. Maternal lineage diversity was analyzed by sequencing the mitochondrial DNA control region in 42 individuals, identifying 23 distinct haplotypes predominantly belonging to haplogroup A, with a rare occurrence of haplogroup C. Together, the results demonstrate substantial genetic variation within the population at both nuclear and mitochondrial levels, providing essential insights for conservation and sustainable management of this autochthonous breed.