Whole genome resequencing reveals genetic diversity, population structure, and selection signatures in local duck breeds.

Journal: BMC genomics
Published Date:

Abstract

BACKGROUND: Shandong's local duck breeds are renowned for their outstanding egg-laying performance and are regarded as valuable assets within China's waterfowl germplasm. Understanding the genetic characteristics of these populations, along with monitoring and conserving their genetic diversity, is of paramount importance. In this study, we analyzed the genetic diversity, population structure, and genetic characteristic of 89 ducks, including the Weishan Partridge (WS, n = 30), Matahu (MT, n = 29), and Wendeng Black (WD, n = 30), using genome resequencing data. We also used a random forest model algorithm to identify specific breed-identification SNPs, ensuring accurate differentiation of the three breeds.

Authors

  • Pengwei Ren
    Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Targeted Tracer Research and Development Laboratory, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, China.
  • Yongdong Peng
    College of Agricultural and Biology, Liaocheng University, Liaocheng, 252000, China.
  • Liu Yang
    Department of Ultrasound, Hunan Children's Hospital, Changsha, China.
  • Muhammad Zahoor Khan
    College of Agricultural and Biology, Liaocheng University, Liaocheng, 252000, China.
  • Yadi Jing
    College of Agricultural and Biology, Liaocheng University, Liaocheng, 252000, China.
  • Chao Qi
    College of Engineering, Nanjing Agricultural University, Nanjing, 210031, China.
  • Zhansheng Liu
    Faculty of Architecture, Civil and Transportation Engineering, Beijing University of Technology, Beijing 100124, China.
  • Shuer Zhang
    Shandong Animal Husbandry Station, Jinan, 250010, China.
  • Nenzhu Zheng
    Fujian Key Laboratory of Animal Genetics and Breeding, Institute of Animal Husbandry and Veterinary Medicine of Fujian Academy of Agricultural Sciences, Fuzhou, 350013, China.
  • Meixia Zhang
    Center for Clinical Translational Innovations and Biomedical Big Data Center, West China Hospital and Sichuan University, Chengdu, China.
  • Xiang Liu
    College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China; Anhui Provincial Key Laboratory of Environmental Pollution Control and Resource Reuse, Anhui Jianzhu University, Hefei 230009, China.
  • Zhiming Zhu
    Department of Hypertension and Endocrinology, Daping Hospital, Center for Hypertension and Metabolic Diseases, Army Medical University of PLA, Chongqing Institute of Hypertension, Chongqing, China.
  • Mingxia Zhu
    College of Agricultural and Biology, Liaocheng University, Liaocheng, 252000, China. zhumingxia@lcu.edu.cn.