Characteristics of PCR fragments amplified using five microsatellite markers for identifying the Nagoya breed

The Nagoya breed is a native chicken of Aichi Prefecture, Japan, a dual-purpose breed for eggs and meat. A method for distinguishing the Nagoya breed from Aichi Prefecture from other chickens using five microsatellite markers (ABR0015, ABR0257, ABR0417, ABR0495 and ADL0262) has already been utilized in order to check the authenticity of Nagoya breed-labeled chicken on the market. The present study was conducted to investigate nucleotide sequences and sizes of PCR fragments containing the five microsatellite regions for the Nagoya breed and to confirm that the genomic identification could continue to be applied in the future. The DNA sequencing of fragments containing the five markers showed that ABR0015, ABR0417 and ABR0495 had a single haplotype, ABR0257 had three haplotypes, and ADL0262 had two haplotypes, although all the markers exhibited one fixed fragment size each upon sequencing of the fragments and fragment analysis. The results of the fragment analysis of each marker using DNA samples of 28 Nagoya breed males (G0 generation) reared in 2000-2001 and 20 of their offspring males (G8) reared in 2008-2009 showed one fixed fragment size in both populations. Therefore, we confirmed that the five microsatellite markers are useful tools for accurately distinguishing the Nagoya breed from other chickens.