Analysis of Inbreeding, Population Structure, and Genetic Diversity in the Kumamoto Sub-Breed of Japanese Brown Cattle
Simple Summary The Kumamoto sub-breed of Japanese Brown cattle is a local beef cattle population in Japan. It is facing increasing inbreeding and a declining effective population size because of the intensive use of a limited number of elite sires. This study used genetic marker information from 811 cows to evaluate inbreeding, describe the genetic structure of the population, and identify genetic subpopulations that may help to preserve genetic diversity. We found that segment-based measures gave consistent information about inbreeding. The main genetic differences among animals were not explained by where they were raised, but were closely related to their paternal background. Among the identified subpopulations, we found that the subpopulation mainly associated with the Haru-yama-to/-sakae sire background contributed most to overall genetic diversity and showed the lowest level of genomic inbreeding. These results suggest that individuals from this subpopulation may be useful for breeding designing aimed at controlling inbreeding and maintaining genetic diversity in the Kumamoto sub-breed.