Application of highly differentiated SNPs between Japanese Black and Holstein to a breed assignment test between Japanese Black and F(1) (Japanese Black x Holstein) and Holstein.

Two taurine breeds, Japanese Black and Holstein, established from geographically distant origins and selected for different uses, beef and dairy, were extensively genotyped using a genome-wide single nucleotide polymorphism (SNP) chip with more than 1000 animals of each breed. The genetic structure was examined by principal component analysis, in which the first principal component clearly separated the two breeds and explained more than 15% of the variance. Highly differentiated SNPs were detected throughout the genome, some of which were clustered within small regions on BTA4 (79.2-79.7 Mb, Btau4.0) and BTA26 (22.2-23.6 Mb). A breed assignment test was developed using 18 highly differentiated SNPs to distinguish Japanese Black from F(1) (Japanese Black × Holstein) and Holstein. The error rate that an F(1) or Holstein animal is misjudged as Japanese Black was expected to be < 0.8%, while the error rate that a Japanese Black animal is misjudged as F(1) or Holstein was expected to be < 0.001%. This test provides a reliable and powerful method to detect breed label falsification in retail beef.