Genomic Analyses Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa-Reference-Cited by-同舟云学术

Genomic Analyses Unveil Helmeted Guinea Fowl (Numida meleagris) Domestication in West Africa

Published:2021-05-01 Issue:6 Volume:13 Page:
ISSN:1759-6653
Container-title:Genome Biology and Evolution
language:en
Short-container-title:

Author:

Shen Quan-Kuan¹²³,Peng Min-Sheng¹²³,Adeola Adeniyi C¹²⁴,Kui Ling⁵,Duan Shengchang⁶,Miao Yong-Wang⁷,Eltayeb Nada M⁸,Lichoti Jacqueline K⁹,Otecko Newton O¹²³,Strillacci Maria Giuseppina¹⁰^ORCID,Gorla Erica¹⁰,Bagnato Alessandro¹⁰,Charles Olaogun S¹¹,Sanke Oscar J¹²,Dawuda Philip M¹³,Okeyoyin Agboola O¹⁴,Musina John¹⁵,Njoroge Peter¹⁵,Agwanda Bernard¹⁵,Kusza Szilvia¹⁶,Nanaei Hojjat Asadollahpour¹⁷,Pedar Rana¹⁷,Xu Ming-Min¹²³,Du Yuan⁶,Nneji Lotanna M¹²,Murphy Robert W¹⁸,Wang Ming-Shan¹⁹²⁰,Esmailizadeh Ali¹¹⁷^ORCID,Dong Yang²¹²²²³,Ommeh Sheila C¹⁵²⁴,Zhang Ya-Ping¹²³²⁵²⁶

Affiliation:

1. State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China

2. Sino-Africa Joint Research Center, Chinese Academy of Sciences, Nairobi, Kenya

3. Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China

4. Centre for Biotechnology Research, Bayero University, Kano, Nigeria

5. Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA

6. Nowbio Biotechnology Company, Kunming, China

7. Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China

8. Department of Animal breeding and Reproduction Technology, College of Animal Production, University of Bahri, Khartoum, Sudan

9. State Department of Livestock, Ministry of Agriculture Livestock Fisheries and Irrigation, Nairobi, Kenya

10. Department of Veterinary Medicine, Università degli Studi di Milano, Italy

11. Department of Veterinary Medicine, University of Ibadan, Nigeria

12. Taraba State Ministry of Agriculture and Natural Resources, Jalingo, Nigeria

13. Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture, Makurdi, Nigeria

14. National Park Service Headquarter, Federal Capital Territory, Abuja, Nigeria

15. Department of Zoology, National Museums of Kenya, Nairobi, Kenya

16. Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, Hungary

17. Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Iran

18. Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada

19. Howard Hughes Medical Institute, University of California Santa Cruz, California, USA

20. Department of Ecology and Evolutionary Biology, University of California Santa Cruz, California, USA

21. College of Biological Big Data, Yunnan Agriculture University, Kunming, China

22. State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China

23. Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China

24. Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya

25. State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, Yunnan University, Kunming, China

26. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China

Abstract

Abstract Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long- and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300–5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

Publisher

Oxford University Press (OUP)

Subject

Genetics,Ecology, Evolution, Behavior and Systematics

Link

http://academic.oup.com/gbe/advance-article-pdf/doi/10.1093/gbe/evab090/37753636/evab090.pdf

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