The Genome Landscape of Indigenous African Cattle
Open accessAbstract
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.
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In African cattle, genomic selection signatures have been identified in genes involved in antigen response, keratin formation, light coat color, and sebum secretion.
“In African cattle, genomic selection signatures have been identified in genes involved in antigen response (BoLA, SLC25A48), keratin formation (KRT33A, KRT222, KRT24, KRT25, KRT26, KRT27, TGM1, TGM3), light coat color (MLPH), and sebum secretion (MC5R) [81,82,99,103].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [82]
In Results and discussion (page not provided), the paper identifies a selection signal at BoLA, an immunity-related gene, and candidate regions involving coat-color genes in Ankole cattle. It does not identify the cited keratin-formation genes, SLC25A48, MLPH, or MC5R as selection signatures, so it supports only part of the attributed gene list. (LLM, conf=0.88)
Experimental — accuracy not yet measuredMC1R mutations generate the red coat color phenotype in Ankole and Evolèner cattle populations.
“MC1R mutations generate the red coat color phenotype in Ankole and Evolèner cattle populations [82,139].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [82]
In Results and discussion (page unavailable), the paper identifies MC1R as a coat-color candidate locus in predominantly red Ankole cattle and says previous reports link MC1R mutations to red coat color. It does not establish a causal MC1R mutation in Ankole or address Evolèner cattle. (LLM, conf=0.88)
Experimental — accuracy not yet measuredIn the N'Dama breed, HCRTR1 and anemia-related genes were found to be under strong selection.
“In the N’Dama breed, known for its trypanotolerance, the HCRTR1 gene (encoding hypocretin receptor 1) and anemia-related genes (SLC40A1, STOM, SBDS, EPB42, RPS26) were found to be under strong selection [82].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [82]
Compared with commercial taurine cattle, the superoxide dismutase gene SOD1 and prolactin releasing hormone gene PRLH were under selection in African indicine cattle populations.
“Compared with commercial taurine cattle, the superoxide dismutase gene SOD1 and prolactin releasing hormone gene PRLH were under selection in African indicine cattle populations [82].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [82]
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References 105 · Cited by 271
- Authors
- Kim, J., Hanotte, O., Mwai, O. A., Dessie, T., Bashir, S., Diallo, B., Agaba, M., Kim, K., Kwak, W., Sung, S., Seo, M., Jeong, H., Kwon, T., Taye, M., Song, K.-D., Lim, D., Cho, S., Lee, H.-J., Yoon, D., Oh, S. J., Kemp, S., Lee, H.-K., & Kim, H.
- Affiliations
- Seoul National University (KR)
- University of Nottingham (GB)
- International Livestock Research Institute (KE)
- Nelson Mandela African Institution of Science and Technology (TZ)
- University of Illinois Urbana-Champaign (US)
- Jeonbuk National University (KR)
- National Institute of Animal Science (KR)
- Kyungpook National University (KR)
- Roslin Institute (GB)
- Shinshu University (JP)
- Corresponding author
- Lee, Hak-Kyo
- Kim, Heebal
- ORCID
- Venue
- Genome biology
- Published
- 2017-02-20
- Volume
- 18
- Issue
- 1
- Pages
- 34-34
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC5319050
- OpenAlex
- W2589273673
- Cited by
- 271
- References
- 105
- Citations by year
- 2026: 18 · 2025: 23 · 2024: 37 · 2023: 25 · 2022: 29 · 2021: 42 · 2020: 29 · 2019: 32 · 2018: 25 · 2017: 11
- FWCI
- 17.61
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) (submittedVersion, other-oa)
- Nottingham ePrints (University of Nottingham) (submittedVersion, cc-by)
- Repository@Nottingham (University of Nottingham) (submittedVersion, cc-by)
- Funders
- Rural Development Administration (PJ01104401)
- National Institute of Animal Science
- Consortium of International Agricultural Research Centers
- Biotechnology and Biological Sciences Research Council (BBS/E/D/30002275)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Livestock Farming and Management
- Keywords
- genetic diversity, selection signatures, Bos indicus, Sanga cattle, N'Dama cattle, Ankole cattle, trypanotolerance, heat tolerance, tick resistance, anemia, feeding behavior, coat color, horn development, livestock adaptation
- MeSH terms
- Adaptation, Biological, Animals, Cattle, Environment, Genetics, Population, Geography, Humans, Population Dynamics, Stress, Physiological, Genetic Variation, Genome, Evolution, Molecular, Polymorphism, Single Nucleotide, Genomics, Gene-Environment Interaction
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