title: The genome landscape of indigenous African cattle.
abstract: The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African farming systems.
  
  
  
  We analyze patterns of African cattle genetic variation by sequencing 48 genomes from five indigenous populations and comparing them to the genomes of 53 commercial taurine breeds. We find the highest genetic diversity among African zebu and sanga cattle. Our search for genomic regions under selection reveals signatures of selection for environmental adaptive traits. In particular, we identify signatures of selection including genes and/or pathways controlling anemia and feeding behavior in the trypanotolerant N'Dama, coat color and horn development in Ankole, and heat tolerance and tick resistance across African cattle especially in zebu breeds.
  
  
  
  Our findings unravel at the genome-wide level, the unique adaptive diversity of African cattle while emphasizing the opportunities for sustainable improvement of livestock productivity on the continent.
authors.affiliation: C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
authors.forename: Jaemin
authors.initials: J
authors.lastname: Kim
authors.affiliation: The University of Nottingham, School of Life Sciences, Nottingham, NG7 2RD, UK.|International Livestock Research institute (ILRI), P. O. Box 5689, Addis Ababa, Ethiopia.
authors.forename: Olivier
authors.initials: O
authors.lastname: Hanotte
authors.affiliation: International Livestock Research Institute (ILRI), Box 30709 -00100, Nairobi, Kenya.
authors.forename: Okeyo Ally
authors.initials: OA
authors.lastname: Mwai
authors.affiliation: International Livestock Research institute (ILRI), P. O. Box 5689, Addis Ababa, Ethiopia.
authors.forename: Tadelle
authors.initials: T
authors.lastname: Dessie
authors.affiliation: Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, 13314, Khartoum North, Sudan.
authors.forename: Salim
authors.initials: S
authors.lastname: Bashir
authors.affiliation: National Coordinateur RGA, Ministère Elevage - Productions Animales, B.P. 559, Conakry, Guinea.
authors.forename: Boubacar
authors.initials: B
authors.lastname: Diallo
authors.affiliation: Nelson Mandela African Institution of Science and Technology, Nelson Mandela Road. P. O. Box 447, Arusha, Tanzania.
authors.forename: Morris
authors.initials: M
authors.lastname: Agaba
authors.affiliation: C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.|Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-741, Republic of Korea.
authors.forename: Kwondo
authors.initials: K
authors.lastname: Kim
authors.affiliation: C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
authors.forename: Woori
authors.initials: W
authors.lastname: Kwak
authors.affiliation: C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
authors.forename: Samsun
authors.initials: S
authors.lastname: Sung
authors.affiliation: C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
authors.forename: Minseok
authors.initials: M
authors.lastname: Seo
authors.affiliation: Department of Animal Sciences, University of Illinois, Urbana, IL, 61801, USA.
authors.forename: Hyeonsoo
authors.initials: H
authors.lastname: Jeong
authors.affiliation: Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea.
authors.forename: Taehyung
authors.initials: T
authors.lastname: Kwon
authors.affiliation: Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea.|College of Agriculture and Environmental Sciences, Bahir Dar University, P. O. Box 79, Bahir Dar, Ethiopia.
authors.forename: Mengistie
authors.initials: M
authors.lastname: Taye
authors.affiliation: The Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju, 54896, Republic of Korea.|Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
authors.forename: Ki-Duk
authors.initials: KD
authors.lastname: Song
authors.affiliation: Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju, 565-851, Republic of Korea.
authors.forename: Dajeong
authors.initials: D
authors.lastname: Lim
authors.affiliation: C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-741, Republic of Korea.|Animal Nutritional & Physiology Team, National Institute of Animal Science, RDA, Jeonju, 565-851, Republic of Korea.
authors.forename: Hyun-Jeong
authors.initials: HJ
authors.lastname: Lee
authors.affiliation: Department of Animal Science, Kyungpook National University, Sangju, 742-711, Republic of Korea.
authors.forename: Duhak
authors.initials: D
authors.lastname: Yoon
authors.affiliation: National Institute of Animal Science, RDA, Jeonju, 565-851, Republic of Korea.
authors.forename: Sung Jong
authors.initials: SJ
authors.lastname: Oh
authors.affiliation: International Livestock Research Institute (ILRI), Box 30709 -00100, Nairobi, Kenya.|The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
authors.forename: Stephen
authors.initials: S
authors.lastname: Kemp
authors.affiliation: The Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju, 54896, Republic of Korea. breedlee@empal.com.|Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea. breedlee@empal.com.
authors.forename: Hak-Kyo
authors.initials: HK
authors.lastname: Lee
authors.affiliation: C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea. heebal@snu.ac.kr.|Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea. heebal@snu.ac.kr.|Institute for Biomedical Sciences, Shinshu University, Nagano, Japan. heebal@snu.ac.kr.
authors.forename: Heebal
authors.identifier: 0000-0003-3064-1303
authors.initials: H
authors.lastname: Kim
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D002417:Cattle; D004777:Environment; D019143:Evolution, Molecular; D059647:Gene-Environment Interaction; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D023281:Genomics / Q000379:methods; D005843:Geography; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011157:Population Dynamics; D013312:Stress, Physiological
keywords: Adaptation; African cattle; Diversity; Genome