Abstract：China is one of the richest countries of chicken (Gallus gallus domesticus) genetic resources, with the more and more cultivated varieties appearing constantly, so how to distinguish these breeds is very important. The aim of this study was to explore the utility of mtDNA D-loop as DNA barcoding for identifying the chicken breeds. Four chicken breeds about Anka chicken, Recessive white chicken, Henan Game chicken and Silky were used as materials. By PCR amplification and sequencing technique, completed mtDNA D-loop sequences of 115 chickens were studied, and the genetic polymorphism characteristics and genetic distances between species and within population were analyzed. The results showed that, the D-loop region of four chickens were 1231~1232 bp, and the 1231 bp samples existed a base C deficiency in 859 site. In the 115 samples assay, there were 26 mutation sites and 15 haplotype. Anka chicken had 3 especial haplotypes. Recessive white chicken had 4 especial haplotypes, Henan Game chicken had 3 especial haplotypes, and Silky had 2 especial haplotypes. Haplotype diversity(Hd) and nucleotide diversity(Pi) of 4 chickens were 0.467~0.799 and 0.00 217~0.00 561 respectively. The biggest values of average number of nucleotide differences(K)(6.910), Pi(0.00561) and Hd (0.799) were all from Recessive white chicken, and the smallest value of Hd was from Silky(0.467). Kiumura 2-parameter distance and Net distance of 4 chicken breeds were 0.435%~0.940% and 0.150%~0.712% respectively. Clustering analysis showed that the cluster results of four chickens were consistent to the morphological class. According to the public standard of haplotypes classification, Anka chicken and Recessive white chicken mainly converged into clade E, Henan Game chicken mainly converged into clade B and Silky mainly converged into clade A. The results indicated that the divergence between 4 chicken breeds is much farther, and it was feasible to identify chicken breeds using DNA barcoding of D-loop region. This study can provide theory basis for chicken variety identification, genetic resources protection and the development and utilization.
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