Genomics-Informed Monitoring and Management of Genetic Diversity in a Small and Endangered Livestock Population: A Case Study of the Slovak Askanian Merino Sheep

The Slovak Askanian Merino is a small, endangered sheep population maintained on two farms in Slovakia. This study assessed its genomic diversity, population structure and the value of genomics-informed management. After quality control, 491 individuals and 45,695 SNPs were retained for within-population analyses, while 927 individuals and 18,143 SNPs were used for comparisons with other Merino and Merino-derived breeds. Observed and expected heterozygosity were 0.411 and 0.412, respectively, while genomic inbreeding based on homozygous-by-descent segments and runs of homozygosity was 0.025 and 0.019. Segments longer than 16 Mb contributed most to inbreeding, indicating recent inbreeding. Effective population size estimates ranged from 46 to 112. Population structure analyses separated Slovak Askanian Merino from other Merino-derived breeds and revealed farm-related subdivision. Forward simulations showed that optimized mating allocation slowed inbreeding accumulation over ten generations. By generation 10, optimized scenarios reached genomic inbreeding values of 0.042–0.044 based on homozygous-by-descent segments longer than 4 Mb, compared with 0.069–0.072 under random mating. Restricting each used ram to 15–50 ewes provided the best compromise between reducing inbreeding and practical feasibility. These findings show that genomic monitoring combined with optimized mating can support the long-term conservation and sustainable management of small endangered livestock populations.