Allele-specific polymerase chain reaction typing and sequencing of mitochondrial D-loop region in broiler chickens in Japan

Abstract

This study aimed to comprehend a feature of single nucleotide polymorphism (SNP) in mitochondrial DNA (mtDNA) mainly of general broiler chickens in Japan. We typed two SNP sites (199C/T and 792A/G) of the D-loop region in mtDNA by allele-specific PCR (AS-PCR) in 359 broiler (182 chunky and 177 cobb) and 506 layer (233 White Leghorn, 140 Barred Plymouth Rock and 133 Rhode Island Red) chickens. The SNP of 199C or 792A by AS-PCR was observed in the chunky and cobb chickens, and not in the layers. The haplotype 199T/792G was observed in a part of cobb and all layers. By the result of AS-PCR haplotyping and the broiler brands, the D-loop region was sequenced in 44 broiler chickens (20 chunky and 24 cobb) and compared with the layers' sequence data. Among the broiler and layer chickens, 21 SNP sites (including one insertion) and 11 sequence haplotypes were observed. Haplotype variation or correspondence was observed in and between the broiler brands. This study provides important information to establish a chicken meat traceability system by SNP haplotyping of mtDNA in Japan.

Keywords: SNP haplotype; broiler; meat discrimination; mtDNA.