ABSTRACT Intense selection of breeding animals based on an accurate prediction of breeding values has led to a remarkable genetic progress in economically important traits in livestock breeds. In many breeds for livestock products, however, reduction of genetic diversity due to the heavy use of a few prominent breeding animals is an increasing problem. In this article, we reviewed the methodologies to monitor the genetic diversity within livestock breeds, and presented the applications to a major beef breed in Japan, the Japanese Black cattle. The results of analysis showed that although this breed has a substantial number of live animals, the genetic diversity has reduced to a critical level after the initiation of evaluation system with the best linear unbiased prediction (BLUP) of breeding values. The main cause of the reduction was the heavy use of a few sires with prominent estimated breeding values of meat quality. However, it was also revealed that several subpopulations in the breed have still maintained their unique genetic compositions. A strategy to maintain the genetic diversity using the existing genetic materials was proposed in the light of population genetic theories.
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