Biodiv Sci ›› 2019, Vol. 27 ›› Issue (6): 667-676.  DOI: 10.17520/biods.2019013

• Original Papers: Animal Diversity • Previous Articles     Next Articles

Genetic diversity and population structure of black-bone chickens in China revealed by mitochondrial COI gene sequences

Weng Zhuoxian1,2,3,Huang Jiaqiong2,Zhang Shihao2,Yu Kaichun2,Zhong Fusheng1,2,3,Huang Xunhe2,3,*(),Zhang Bin1,*()   

  1. 1 College of Animal Science & Technology, Hunan Agricultural University, Changsha 410128
    2 School of Life Science, Jiaying University, Meizhou, Guangdong 514015
    3 Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, Guangdong 514015
  • Received:2019-01-17 Accepted:2019-05-20 Online:2019-06-20 Published:2019-06-14
  • Contact: Huang Xunhe,Zhang Bin


Comprehensively evaluating the genetic diversity of Chinese black-bone chickens will facilitate conservation and utilization initiatives for this invaluable genetic resource. Mitochondrial cytochrome c oxidase subunit I (COI) gene sequences were obtained from 12 black-bone chicken breeds in China. These sequences were then used to analyze the genetic variation and population structure. A total of 22 mutation sites were detected from 255 individuals representing 3.17% of all sites. The nucleotide diversity and haplotype diversity ranged from 0.00142 to 0.00339 and from 0.380 to 0.757, respectively. Lueyang black chicken has the highest level of genetic diversity and Dehua the lowest. Seven amino acid variations were detected from 11 individuals from six breeds. A total of 24 haplotypes were defined, where haplotype H1 and H3 are shared by 12 black-bone chicken breeds with a frequency of 115 and 64, respectively. Yanjin had the greatest number of haplotypes, while Guangxi has the fewest. Neutrality tests and mismatch distribution analysis revealed that these populations have not experienced significant population expansion. Most of the genetic variations observed were intra-population variation (81.06%) as indicated in AMOVA analysis. Pairwise fixation indexes Fst values among 12 populations range from -0.035 to 0.594, and genetic distance ranges from 0.002 to 0.004. The genetic differentiation indexes between Xuefeng and other populations was the greatest. Black-bone chickens cannot be separated from domestic chickens and red junglefowls within the neighbor-joining tree. The median-joining network of black-bone chickens is classified into three main clusters with the characteristic of specific breeds, while haplotype H8, H9, H11 and H12 existing in Wuliangshan, Yanjin, Xuefeng are not directly related to the three main clusters. The median-joining network of black-bone chickens and additional domestic chickens and red junglefowls does not change the main structure of the tree. The results presented here indicate that the genetic diversity of Chinese black-bone chickens is low but significant genetic differentiation is evident. The Chinese black-bone chickens may be selected in situ from domestic chickens. Overall, the results suggest that more attention should be paid to germplasm resource protection of these fascinating breeds.

Key words: black-bone chicken, mitochondrial COI, genetic variation, genetic divergence