Analysis of Inbreeding, Population Structure, and Genetic Diversity in the Kumamoto Sub-Breed of Japanese Brown Cattle

Introduction: The Kumamoto sub-breed of Japanese Brown cattle is a small population facing increasing inbreeding and declining effective population size driven by the intensive use of a limited number of elite sires. Methods: We analyzed 811 Japanese Brown cows genotyped using a 30K SNP array, retaining 19,745 SNPs after quality control. We calculated and compared ten genomic inbreeding estimators, including SNP-by-SNP and segment-based measures. Population structure was first assessed by rearing region using principal component analysis (PCA) and was then evaluated using ADMIXTURE-based clustering and distance-based hierarchical clustering, from which representative subsets were retained under predefined filtering criteria and further examined using PCA and neighbor-joining (NJ) tree analyses. Finally, we calculated the contribution of each ADMIXTURE group to total gene and allelic diversity, and integrated these two measures into a final conservation index after Z-score standardization. Results: ROH- and HBD-based estimators showed high concordance, whereas allele-frequency-dependent SNP-by-SNP estimators exhibited distinct distributions. Rearing region did not explain the main genetic structure. Instead, four representative ADMIXTURE-based groups, supported by independently identified family groups, captured the major genetic structure associated with paternal backgrounds. ADMIXTURE group 2 made the largest contribution to both gene and allelic diversity, and showed lowest genomic inbreeding. Conclusions: These findings suggest that ROH- and HBD-based estimators may serve as valuable indicators of genomic inbreeding in the Kumamoto sub-breed of Japanese Brown cattle; paternal background has played an important role in shaping the current genomic structure; and ADMIXTURE group 2, mainly associated with the Haru-yama-to/-sakae sire background, may provide a valuable breeding resource for limiting future inbreeding accumulation and maintaining genetic diversity.