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

Quan-Kuan Shen; Min-Sheng Peng; Adeniyi C Adeola; Ling Kui; Shengchang Duan; Yong-Wang Miao; Nada M Eltayeb; Jacqueline K Lichoti; Newton O Otecko; Maria Giuseppina Strillacci; Erica Gorla; Alessandro Bagnato; Olaogun S Charles; Oscar J Sanke; Philip M Dawuda; Agboola O Okeyoyin; John Musina; Peter Njoroge; Bernard Agwanda; Szilvia Kusza; Hojjat Asadollahpour Nanaei; Rana Pedar; Ming-Min Xu; Yuan Du; Lotanna M Nneji; Robert W Murphy; Ming-Shan Wang; Ali Esmailizadeh; Yang Dong; Sheila C Ommeh; Ya-Ping Zhang

doi:10.1093/gbe/evab090

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

Genome Biol Evol. 2021 Jun 8;13(6):evab090. doi: 10.1093/gbe/evab090.

Authors

Quan-Kuan Shen^{1

2

3}, Min-Sheng Peng^{1

2

3}, Adeniyi C Adeola^{1

2

4}, Ling Kui⁵, Shengchang Duan⁶, Yong-Wang Miao⁷, Nada M Eltayeb⁸, Jacqueline K Lichoti⁹, Newton O Otecko^{1

2

3}, Maria Giuseppina Strillacci¹⁰, Erica Gorla¹⁰, Alessandro Bagnato¹⁰, Olaogun S Charles¹¹, Oscar J Sanke¹², Philip M Dawuda¹³, Agboola O Okeyoyin¹⁴, John Musina¹⁵, Peter Njoroge¹⁵, Bernard Agwanda¹⁵, Szilvia Kusza¹⁶, Hojjat Asadollahpour Nanaei¹⁷, Rana Pedar¹⁷, Ming-Min Xu^{1

2

3}, Yuan Du⁶, Lotanna M Nneji^{1

2}, Robert W Murphy¹⁸, Ming-Shan Wang^{19

20}, Ali Esmailizadeh^{1

17}, Yang Dong^{21

22

23}, Sheila C Ommeh^{15

24}, Ya-Ping Zhang^{1

2

3

25

26}

Affiliations

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

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.

Keywords: Africa; breed; domestication; genome; guineafowl; selection.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Domestication*
Galliformes / genetics*
Genetic Variation
Genome*
Male
Phylogeny*
Phylogeography
Selection, Genetic