Molecular genetic identification of Wuzhishan ant chicken, a newly discovered resource in China

Lihong Gu; Fanghu Wu; Xinli Zheng; Xiaohui Zhang; Yanmin Chen; Lizhi Lu; Xiangxiang Liu; Shuhui Mo; Zhe Chao; Zhongchun He; Yuanyuan Shang; Dong Wei; Sheng Wei; Youyi Chen; Tieshan Xu

doi:10.3389/fvets.2024.1319854

Molecular genetic identification of Wuzhishan ant chicken, a newly discovered resource in China

Front Vet Sci. 2024 Jun 19:11:1319854. doi: 10.3389/fvets.2024.1319854. eCollection 2024.

Authors

Lihong Gu¹, Fanghu Wu², Xinli Zheng¹, Xiaohui Zhang², Yanmin Chen³, Lizhi Lu⁴, Xiangxiang Liu³, Shuhui Mo³, Zhe Chao¹, Zhongchun He¹, Yuanyuan Shang², Dong Wei⁵, Sheng Wei⁵, Youyi Chen³, Tieshan Xu⁶

Affiliations

¹ Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, China.
² College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China.
³ Wuzhishan Animal Science and Veterinary Medicine and Fishery Service Center, Wuzhishan Agricultural and Rural Bureau, Wuzhishan, China.
⁴ Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
⁵ Wuzhishan Ant Chicken Cooperative, Wuzhishan, China.
⁶ Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.

Abstract

Introduction: The Wuzhishan ant (MY) chicken exhibits significant differences from other chicken breeds. However, the molecular genetic relationship between the MY breed and other chicken breeds has not been assessed.

Methods: Whole-genome resequencing was used to compare genetic diversity, nucleotide diversity, the fixation index, the linkage disequilibrium coefficient, and phylogenetic tree relationships between the MY breed and the Wenchang (WC), Danzhou (DZ), Bawangling (BW), and Longsheng Feng (LF) breeds.

Results: A total of 21,586,378 singlenucleotide polymorphisms and 4,253,341 insertions/deletions were screened out among the five breeds. The MY breed had the second highest genomic genetic diversity and nucleotide diversity and the lowest LD coefficient among the five breeds. Moreover, the phylogenetic tree analysis showed that individual birds of each breed clustered together with those of their respective breeds.

Discussion: Our data indicated that the MY breed is distinct from the other breeds and can be considered a new genetic resource.

Keywords: Wuzhishan ant chicken; genetic diversity; genetic resource; genetic structure; whole-genome resequencing.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported in part by the Key R&D projects in Hainan Province (SQ2020XDNY0161), the National Key R&D Program of China (2021YFD1300100), the Project of Wenchang Chickens Research Institute (2,426), the Basal Research Fund for Hainan Academy of Agricultural Sciences (JBKYYMF-2020-09), and the Identification of Genetic Resources of Wuzhishan Ant Chickens (202204001B).