Polymerase chain reaction detection of single nucleotide polymorphisms in the chicken mitochondrial D-loop region

The D‐loop region in mitochondrial DNA (mtDNA) was sequenced and compared among six chickens. Eleven single nucleotide polymorphisms (SNP) were observed. For six of the SNP sites, polymerase chain reaction (PCR) primers that had each base (A, C, G and T) as the penultimate base at the 3′ end (N2 base) and bases specific to both alleles at the 3′ end were produced to type the polymorphisms. Twenty‐one out of 96 primers succeeded in distinguishing the SNP by the presence or absence of PCR product. This method provides an easy way to discriminate SNP in chicken mtDNA.