Mitochondrial DNA diversity and demographic history of Black-boned chickens in China

Xunhe Huang; Zhuoxian Weng; Yujing He; Yongwang Miao; Wei Luo; Xiquan Zhang; Fusheng Zhong; Bingwang Du

doi:10.1080/23802359.2021.1912668

Mitochondrial DNA diversity and demographic history of Black-boned chickens in China

Mitochondrial DNA B Resour. 2021 Apr 23;6(4):1462-1467. doi: 10.1080/23802359.2021.1912668.

Authors

Xunhe Huang¹, Zhuoxian Weng^{1

2}, Yujing He¹, Yongwang Miao³, Wei Luo⁴, Xiquan Zhang⁴, Fusheng Zhong^{1

2}, Bingwang Du¹

Affiliations

¹ Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China.
² College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.
³ Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.
⁴ College of Animal Science, South China Agricultural University, Guangzhou, China.

Abstract

Black-boned chickens (Gallus domesticus, herein abbreviated BBCs) are well known for their unique appearance and medicinal properties and have a long breeding history in China. However, the genetic diversity and demographic history of BBCs remain unclear. In this study, we analyzed 844 mitochondrial DNA D-loop sequences, including 346 de novo sequences and 498 previously published sequences from 20 BBC breeds. We detected a generally high level of genetic diversity among the BBCs, with average haplotype and nucleotide diversities of 0.917 ± 0.0049 and 0.01422, respectively. Nucleotide diversity was highest in populations from Southwest China (0.01549 ± 0.00026), particularly in Yunnan Province (0.01624 ± 0.00025). Significant genetic divergence was detected between most breeds, particularly between Yunnan chickens and those from all other provinces. Haplogroups F and G had the highest levels of genetic diversity and were restricted to Southwest China, particularly Yunnan Province. Based on neutrality tests and mismatch distribution analyses, we did not obtain evidence for rapid population expansions and observed similar demographic histories in BBCs and local non-BBCs. Our results suggest that Chinese BBCs have complex breeding histories and may be selected in situ from local domestic chickens. These results improve our understanding of the genetic heritage and breeding histories of these desirable chickens.

Keywords: Black-boned chicken; Genetic diversity; breeding history; haplogroup; mtDNA d-loop.

Grants and funding

This work was supported by Science & Technology Planning Project of Guangdong Province [2016A030303068], and open project of State Key Laboratory of Genetic Resources and Evolution [GREKF18-03].