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Genome Biol. 2017 Feb 20;18(1):34. doi: 10.1186/s13059-017-1153-y.

The genome landscape of indigenous African cattle.

Kim J1, Hanotte O2,3, Mwai OA4, Dessie T3, Bashir S5, Diallo B6, Agaba M7, Kim K1,8, Kwak W1, Sung S1, Seo M1, Jeong H9, Kwon T10, Taye M10,11, Song KD12,13, Lim D14, Cho S1, Lee HJ8,15, Yoon D16, Oh SJ17, Kemp S4,18, Lee HK19,20, Kim H21,22,23.

Author information

1
C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea.
2
The University of Nottingham, School of Life Sciences, Nottingham, NG7 2RD, UK.
3
International Livestock Research institute (ILRI), P. O. Box 5689, Addis Ababa, Ethiopia.
4
International Livestock Research Institute (ILRI), Box 30709 -00100, Nairobi, Kenya.
5
Department of Parasitology, Faculty of Veterinary Medicine, University of Khartoum, 13314, Khartoum North, Sudan.
6
National Coordinateur RGA, Ministère Elevage - Productions Animales, B.P. 559, Conakry, Guinea.
7
Nelson Mandela African Institution of Science and Technology, Nelson Mandela Road. P. O. Box 447, Arusha, Tanzania.
8
Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-741, Republic of Korea.
9
Department of Animal Sciences, University of Illinois, Urbana, IL, 61801, USA.
10
Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea.
11
College of Agriculture and Environmental Sciences, Bahir Dar University, P. O. Box 79, Bahir Dar, Ethiopia.
12
The Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju, 54896, Republic of Korea.
13
Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
14
Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju, 565-851, Republic of Korea.
15
Animal Nutritional & Physiology Team, National Institute of Animal Science, RDA, Jeonju, 565-851, Republic of Korea.
16
Department of Animal Science, Kyungpook National University, Sangju, 742-711, Republic of Korea.
17
National Institute of Animal Science, RDA, Jeonju, 565-851, Republic of Korea.
18
The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
19
The Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju, 54896, Republic of Korea. breedlee@empal.com.
20
Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea. breedlee@empal.com.
21
C&K genomics, Seoul National University Research Park, Seoul, 151-919, Republic of Korea. heebal@snu.ac.kr.
22
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.
23
Institute for Biomedical Sciences, Shinshu University, Nagano, Japan. heebal@snu.ac.kr.

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

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:

Adaptation; African cattle; Diversity; Genome

PMID:
28219390
PMCID:
PMC5319050
DOI:
10.1186/s13059-017-1153-y
[Indexed for MEDLINE]
Free PMC Article

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