The Kumamoto sub-breed of Japanese Brown cattle is famous for its heavy carcass weight, and increasing carcass weight is one of the most important breeding goals for this sub-breed. Genetic approaches may be especially useful for breeding this cattle and improving its traits. In this study, we elucidated the genetic characteristics of the Kumamoto sub-breed by analyzing the genotype and allele frequencies of DNA polymorphisms. Seven DNA polymorphisms were selected from the SREBP1 , SCD, FASN, EDG1, NCAPG, LYST , and F11 genes, which affect economically important traits. For genotyping, 112 offspring of 19 sires were collected. Our genotyping results show an extremely low allele frequency of the S allele of SREBP1, which affects fatty acid composition in intramuscular fat, in the Kumamoto sub-breed. Therefore, this polymorphism might not be useful for enhancing the breeding of this sub-breed. The causative mutation of LYST was not detected in our sampling population, suggesting a lower risk of Chediak-Higashi syndrome in the Kumamoto sub-breed. On the other hand, the Kumamoto sub-breed possessed high frequencies of desirable alleles of the SCD and NCAPG genes, which affect fatty acid composition and carcass weight, respectively, possibly because of artificial selection. Hence, these DNA markers could be used to improve economically important traits of the Kumamoto sub-breed. Our results also indicate that the causative mutation of factor XI deficiency might be common in the population because multiple sires were carriers of this disease. Since this disease may cause fetal losses, elimination of this disease from the Kumamoto sub-breed would be desirable.

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