Biodiv Sci ›› 2017, Vol. 25 ›› Issue (5): 540-548.  DOI: 10.17520/biods.2017012

• Original Papers: Animal Diversity • Previous Articles     Next Articles

Genetic diversity of local chicken breeds in East China based on mitochondrial DNA D-loop region

Xiaoxu Jia, Xiujun Tang, Yanfeng Fan, Junxian Lu, Shenghai Huang, Qinglian Ge, Yushi Gao*(), Wei Han   

  1. Jiangsu Institute of Poultry Science, Yangzhou, Jiangsu 225125
  • Received:2017-01-08 Accepted:2017-04-10 Online:2017-05-20 Published:2017-06-06
  • Contact: Gao Yushi


The objective of this study was to determine the origin and evolution of chickens in Eastern China by assessing the genetic diversities and structures of 11 local chicken breeds. The complete D-loop region of mitochondrial DNA (mtDNA) of 319 chickens from 11 local breeds were sequenced and analyzed together with published data for the red junglefowl. These sequences were then used in a neighbor-joining method to construct the phylogenetic tree of these breeds and the red junglefowl. The D-loop regions of the local breeds were characterized by 1,231 and 1,232 bp; the 1,231 bp haplotype had 196 sequences, while the 1,232 bp haplotype had 123 sequences, with a base C deficiency from the 859 bp site in the 1,231 bp haplotype. A total of 37 mutation sites were detected in the 319 individuals. The average haplotype diversity, nucleotide diversity, and nucleotide difference were 0.901 ± 0.009, 0.005 73 ± 0.000001 and 6.833, respectively. A total of 35 haplotypes were identified which belonged to four previously published clades, i.e. Clades A, B, C, and E, which contained 11, 10, 9, and 5 haplotypes, respectively. Median-joining network profiles of the haplotype indicated the 11 local breeds were divided into four maternal clades containing 100, 118, 47, and 54 sequences. The cluster of five subspecies of the red junglefowl and 11 local breeds were divided into four distinct groups. Gallus gallus jabouillei was grouped alone. Haplotype C and four subspecies of junglefowl were clustered in one group. Haplotype E and two subspecies of junglefowl were clustered in another group. Haplotypes A, B, and Gallus gallus spadiceus were clustered in another group. Chickens from eastern China revealed abundant genetic diversity in the mtDNA D-loop region, except for the Langshan and Silky breeds. No breed-specific matrilineal clade was observed. We conclude that chicken breeds from eastern China likely share four common maternal lineages, and that some chicken populations may have been mixed with exotic lineage chickens.

Key words: phylogeny, red junglefowl, D-loop region, local breed