Jaemin Kim1†, Olivier Hanotte2,3†, Okeyo Ally Mwai4, Tadelle Dessie3, Salim Bashir5, Boubacar Diallo6, Morris Agaba7, Kwondo Kim1,8, Woori Kwak1, Samsun Sung1, Minseok Seo1, Hyeonsoo Jeong9, Taehyung Kwon10, Mengistie Taye10,11, Ki-Duk Song12,18, Dajeong Lim13, Seoae Cho1, Hyun-Jeong Lee8,14, Duhak Yoon15, Sung Jong Oh16, Stephen Kemp4,17, Hak-Kyo Lee12,18*† and Heebal Kim1,10,19*†
1C&K genomics, Seoul National University Research Park, Seoul 151-919, Republic of Korea. 2The University of Nottingham, School of Life Sciences, Nottingham NG7 2RD, UK. 3International Livestock Research institute (ILRI), P. O. Box 5689, Addis Ababa, Ethiopia. 4International Livestock Research Institute (ILRI), Box 30709 -00100, Nairobi, Kenya. 5Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, 13314 Khartoum North, Sudan. 6National Coordinateur RGA, Ministere Elevage. Productions Animales, B.P. 559, Conakry, Guinea. 7Nelson Mandela African Institution of Science and Technology, Nelson Mandela Road. P. O. Box 447, Arusha, Tanzania. 8Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-741, Republic of Korea. 9Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA. 10Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-742, Republic of Korea. 11College of Agriculture and Environmental Sciences, Bahir Dar University, P. O. Box 79, Bahir Dar, Ethiopia. 12The Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju 54896, Republic of Korea. 13Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea. 14Animal Nutritional & Physiology Team, National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea. 15Department of Animal Science, Kyungpook National University, Sangju 742-711, Republic of Korea. 16National Institute of Animal Science, RDA, Jeonju 565-851, Republic of Korea. 17The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK. 18Department of Animal Biotechnology, Chonbuk National University, Jeonju 561-756, Republic of Korea. 19Institute for Biomedical Sciences, Shinshu University, Nagano, Japan.
*Correspondence: Heebal Kim; Hak-Kyo Lee
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.
Keywords : African cattle, Genome, Adaptation, Diversity