Genetic variability of mtDNA sequences in Chinese native chicken breeds

The variability of mtDNA hypervariable segment I (HVS I) sequences was investigated in a total of 48 birds belonging to 12 Chinese native chicken breeds. Sixteen haplotypes were identified from 35 polymorphic nucleotide sites which accounted for 6.4% of a sequenced 544 bp fragment. Diversity analysis of the haplotypes showed that Tibetan, Langshan and Henan cockfight chicken had only one haplotype, while ancient haplotypes existed in Taihe silky and Chahua chicken. Phylogenetic analysis of the haplotypes suggested that Chinese native chicken breeds shared 5 maternal lineages and some breeds would share the same maternal lineage, regardless of their external features and ecological types. Both divergent and phylogenetic analysis of the haplotypes indicated the close genetic relationships between the Chinese native chicken breeds and G g. gallus and G g. spadiceus from different areas, which implied that G g. gallus and G g. spadiceus were the original ancestors of the Chinese native chicken breeds.