Genome-Wide Scan for Selection Signatures in Six Cattle Breeds in South Africa
Open accessAbstract
BACKGROUND: The detection of selection signatures in breeds of livestock species can contribute to the identification of regions of the genome that are, or have been, functionally important and, as a consequence, have been targeted by selection. METHODS: This study used two approaches to detect signatures of selection within and between six cattle breeds in South Africa, including Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), Bonsmara (n = 44), Angus (n = 31) and Holstein (n = 29). The first approach was based on the detection of genomic regions in which haplotypes have been driven towards complete fixation within breeds. The second approach identified regions of the genome that had very different allele frequencies between populations (F ST). RESULTS AND DISCUSSION: Forty-seven candidate genomic regions were identified as harbouring putative signatures of selection using both methods. Twelve of these candidate selected regions were shared among the breeds and ten were validated by previous studies. Thirty-three of these regions were successfully annotated and candidate genes were identified. Among these genes the keratin genes (KRT222, KRT24, KRT25, KRT26, and KRT27) and one heat shock protein gene (HSPB9) on chromosome 19 between 42,896,570 and 42,897,840 bp were detected for the Nguni breed. These genes were previously associated with adaptation to tropical environments in Zebu cattle. In addition, a number of candidate genes associated with the nervous system (WNT5B, FMOD, PRELP, and ATP2B), immune response (CYM, CDC6, and CDK10), production (MTPN, IGFBP4, TGFB1, and AJAP1) and reproductive performance (ADIPOR2, OVOS2, and RBBP8) were also detected as being under selection. CONCLUSIONS: The results presented here provide a foundation for detecting mutations that underlie genetic variation of traits that have economic importance for cattle breeds in South Africa.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
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 [103]
The Results and Discussion (page unavailable) identify selection signatures involving SLC25A48 in antigen recognition and KRT222 and KRT24–27 in keratin formation. The copy does not identify the other named genes—BoLA, KRT33A, TGM1, TGM3, MLPH, or MC5R—as selected; its coat-colour finding concerns MC1R, not MLPH, and it does not report sebum secretion. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089 · see citing works
ESTIMATING F -STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE
Weir, B. S., & Cockerham, C. C. (1984) · Evolution · doi:10.1111/j.1558-5646.1984.tb05657.x · Cited by 18,909 · see citing works
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
Tajima, F. (1989) · Genetics · doi:10.1093/genetics/123.3.585 · Cited by 13,991 · see citing works
Estimating F-Statistics for the Analysis of Population Structure
Weir, B. S., & Cockerham, C. C. (1984) · Evolution · doi:10.2307/2408641 · Cited by 11,023 · see citing works
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400 · see citing works
Genome-wide detection and characterization of positive selection in human populations
The International HapMap Consortium, Sabeti, P. C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E. H., McCarroll, S. A., et al. (2007) · Nature · doi:10.1038/nature06250 · Cited by 2,131 · see citing works
Detecting recent positive selection in the human genome from haplotype structure
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., et al. (2002) · Nature · doi:10.1038/nature01140 · Cited by 2,106 · see citing works
Mi, H., Muruganujan, A., & Thomas, P. D. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1118 · Cited by 1,693 · see citing works
Molecular Signatures of Natural Selection
Nielsen, R. (2005) · Annual Review of Genetics · doi:10.1146/annurev.genet.39.073003.112420 · Cited by 1,644 · see citing works
Nielsen, R., & Yang, Z. (1998) · Genetics · doi:10.1093/genetics/148.3.929 · Cited by 1,622 · see citing works
Whole-genome resequencing reveals loci under selection during chicken domestication
Rubin, C.-J., Zody, M. C., Eriksson, J., Meadows, J. R. S., Sherwood, E., Webster, M. T., Jiang, L., Ingman, M., Sharpe, T., Ka, S., et al. (2010) · Nature · doi:10.1038/nature08832 · Cited by 1,138 · see citing works
Interrogating a high-density SNP map for signatures of natural selection.Preprint
Akey, J., Zhang, G., Zhang, K., Jin, L., & Shriver, M. (2002) · Genome Research · doi:10.1101/gr.631202 · Cited by 932 · see citing works
Kijas, J., Lenstra, J. A., Hayes, B. J., Boitard, S., Neto, L. R. P., Cristobal, M. S., Servin, B., McCulloch, R. J., Whan, V., Gietzen, K. J., et al. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001258 · Cited by 915 · see citing works
Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds
The Bovine HapMap Consortium, Gibbs, R. A., Taylor, J. F., Van Tassell, C. P., Barendse, W., Eversole, K. A., Gill, C. A., Green, R. D., Hamernik, D. L., Kappes, S. M., et al. (2009) · Science · doi:10.1126/science.1167936 · Cited by 868 · see citing works
Self-citationDetecting Natural Selection in Genomic Data
Vitti, J. J., Grossman, S. R., & Sabeti, P. C. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133526 · Cited by 694 · see citing works
Domestic-animal genomics: deciphering the genetics of complex traits
Andersson, L., & Georges, M. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1294 · Cited by 622 · see citing works
MacHugh, D. E., Shriver, M. D., Loftus, R. T., Cunningham, P., & Bradley, D. G. (1997) · Genetics · doi:10.1093/genetics/146.3.1071 · Cited by 547 · see citing works
A new approach for using genome scans to detect recent positive selection in the human genome
Tang, K., Thornton, K. R., & Stoneking, M. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050171 · Cited by 489 · see citing works
Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges
Helyar, S., Hemmer‐Hansen, J., Bekkevold, D., Taylor, M., Ogden, R., Limborg, M. T., Cariani, A., Maes, G. E., Diopere, E., CARVALHO, G. R., et al. (2011) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2010.02943.x · Cited by 477 · see citing works
A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds
Kijas, J., Townley, D., Dalrymple, B. P., Heaton, M. P., Maddox, J. F., McGrath, A., Wilson, P. J., Ingersoll, R., McCulloch, R. J., McWilliam, S. M., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004668 · Cited by 366 · see citing works
Curnow, R. N., & Wright, S. (1979) · Biometrics · doi:10.2307/2529965 · Cited by 353 · see citing works
Interpretation of Variation Across Marker Loci as Evidence of Selection
Vitalis, R., Dawson, K. J., & Boursot, P. (2001) · Genetics · doi:10.1093/genetics/158.4.1811 · Cited by 274 · see citing works
Moradi, M. H., Nejati‐Javaremi, A., Moradi-Shahrbabak, M., Dodds, K. G., & McEwan, J. C. (2012) · BMC Genetics · doi:10.1186/1471-2156-13-10 · Cited by 274 · see citing works
The Genome Response to Artificial Selection: A Case Study in Dairy Cattle
Flori, L., Fritz, S., Jaffrézic, F., Boussaha, M., Gut, I. G., Heath, S. C., Foulley, J., & Gautier, M. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006595 · Cited by 222 · see citing works
A whole genome Bayesian scan for adaptive genetic divergence in West African cattle
Gautier, M., Flori, L., Riebler, A., Jaffrézic, F., Laloë, D., Gut, I. G., Moazami‐Goudarzi, K., & Foulley, J. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-550 · Cited by 196 · see citing works
Qanbari, S., Gianola, D., Hayes, B. J., Schenkel, F. S., Miller, S. P., Moore, S. S., Thaller, G. E., & Simianer, H. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-318 · Cited by 166 · see citing works
Herráez, D. L., Bauchet, M., Tang, K., Theunert, C., Pugach, I., Li, J., Nandineni, M. R., Gross, A., Scholz, M. R., & Stoneking, M. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007888 · Cited by 161 · see citing works
Relationship between pre-slaughter stress responsiveness and beef quality in three cattle breeds
Muchenje, V., Dzama, K., Chimonyo, M., et al. (2008) · Meat Science · doi:10.1016/j.meatsci.2008.11.004 · Cited by 156 · see citing works
Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production
Stella, A., Ajmone‐Marsan, P., Lazzari, B., & Boettcher, P. J. (2010) · Genetics · doi:10.1534/genetics.110.116111 · Cited by 144 · see citing works
Mattioli, R. C., Pandey, V., Murray, M., & Fitzpatrick, J. L. (2000) · Acta Tropica · doi:10.1016/s0001-706x(00)00063-2 · Cited by 135 · see citing works
Selection for complex traits leaves little or no classic signatures of selection
Kemper, K. E., Saxton, S. J., Bolormaa, S., Hayes, B. J., & Goddard, M. E. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-246 · Cited by 134 · see citing works
NLRC5 Cooperates with the RFX Transcription Factor Complex To Induce MHC Class I Gene Expression
Meissner, T. B., Liu, Y.-J., Lee, K., Li, A., Biswas, A., van Eggermond, M. C. J. A., van den Elsen, P. J., & Kobayashi, K. S. (2012) · The Journal of Immunology · doi:10.4049/jimmunol.1103160 · Cited by 131 · see citing works
An assessment of population structure in eight breeds of cattle using a whole genome SNP panel
McKay, S., Schnabel, R. D., Murdoch, B. M., Matukumalli, L. K., Aerts, J. A., Coppieters, W. R., Crews, D. H., Dias‐Neto, E., Gill, C. A., Gao, C., et al. (2008) · BMC Genetics · doi:10.1186/1471-2156-9-37 · Cited by 129 · see citing works
Self-citationDetection of selective sweeps in cattle using genome-wide SNP data
Ramey, H. R., Decker, J. E., McKay, S., Rolf, M. M., Schnabel, R. D., & Taylor, J. F. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-382 · Cited by 126 · see citing works
Self-citationHayes, B. J., Chamberlain, A. J., MacEachern, S., Savin, K. W., McPartlan, H. C., MacLeod, I. M., Sethuraman, L., & Goddard, M. E. (2008) · Animal Genetics · doi:10.1111/j.1365-2052.2008.01815.x · Cited by 125 · see citing works
Makina, S. O., Muchadeyi, F. C., van Marle-Köster, E., MacNeil, M. D., & Maiwashe, A. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00333 · Cited by 122 · see citing works
Self-citationWu, D.-D., Irwin, D. M., & Zhang, Y.-P. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-241 · Cited by 121 · see citing works
Muchenje, V., Dzama, K., Chimonyo, M., et al. (2008) · animal · doi:10.1017/s1751731107001036 · Cited by 119 · see citing works
The evolution of tropical adaptation: comparing taurine and zebu cattle
Chan, E. K. F., Nagaraj, S. H., & Reverter, A. (2010) · Animal Genetics · doi:10.1111/j.1365-2052.2010.02053.x · Cited by 94 · see citing works
Detecting the form of selection from DNA sequence data
Otto, S. P. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02141-7 · Cited by 79 · see citing works
Marufu, M. C., Qokweni, L., Chimonyo, M., & Dzama, K. (2011) · Ticks and Tick-borne Diseases · doi:10.1016/j.ttbdis.2011.07.001 · Cited by 77 · see citing works
Zhang, L., Zhang, L., Shi, Y., et al. (2011) · Molecular Immunology · doi:10.1016/j.molimm.2011.03.001 · Cited by 65 · see citing works
Biology of epidermal and hair pigmentation in cattle: a mini‐review
Seo, K.-S., Mohanty, T. R., Choi, T., & Hwang, I. (2007) · Veterinary Dermatology · doi:10.1111/j.1365-3164.2007.00634.x · Cited by 64 · see citing works
Development and Characterization of a High Density SNP Genotyping Assay for Cattle
Matukumalli, L. K., Lawley, C. T., Schnabel, R. D., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005350 · Cited by 59 · see citing works
Wang, Y. H., Reverter, A., KEMP, D. H., McWilliam, S. M., Ingham, A. B., Davis, C., Moore, R. J., & Lehnert, S. A. (2007) · Australian Journal of Experimental Agriculture · doi:10.1071/ea07012 · Cited by 58 · see citing works
Beef breeding in South Africa.
Scholtz, M. M. (2010) · Cited by 47 · see citing works
Genome‐wide detection of signatures of selection in K orean H anwoo cattle
Neto, L. R. P., Lee, S. H., Sonstegard, T. S., Tassell, C. P. V., Lee, H. K., Gibson, J. P., & Gondro, C. (2014) · Animal Genetics · doi:10.1111/age.12119 · Cited by 35 · see citing works
Relationships between production and product traits in subpopulations of Bonsmara and Nguni cattle
Strydom, P. E., Naudé, R. T., Smith, M. F., et al. (2001) · South African Journal of Animal Science · doi:10.4314/sajas.v31i3.3801 · Cited by 27 · see citing works
Chen, S.-Y., Huang, Y., Zhu, Q. C., Fontanesi, L., Yao, Y., & Liu, Y. (2009) · BioMed Research International · doi:10.1155/2009/861046 · Cited by 26 · see citing works
Statistical Problems in Livestock Population Genomics
Simianer, H. (2014) · 10th World Congress on Genetics Applied to Livestock Production · Cited by 13 · see citing works
A Perspective on the Impact of Reproductive Technologies on Food Production in Africa
van Marle-Köster, E., & Webb, E. C. (2013) · Advances in experimental medicine and biology · doi:10.1007/978-1-4614-8887-3_10 · Cited by 11 · see citing works
Groenen, M. A. M., Amaral, A. J., Megens, H., et al. (2010) · Socio-Environmental Systems Modeling · Cited by 5 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The Mosaic Genome of Indigenous African Cattle as a Unique Genetic Resource for African Pastoralism
Kim, K., Kwon, T., Dessie, T., Yoo, D., Mwai, O. A., Jang, J., Sung, S., Lee, S., Salim, B., Jung, J., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0694-2 · Cited by 140 · see citing works
Saravanan, K. A., Panigrahi, M., Kumar, H., Parida, S., Bhushan, B., Gaur, G. K., Dutt, T., Mishra, B. P., & Singh, R. K. (2021) · Genomics · doi:10.1016/j.ygeno.2021.02.009 · Cited by 98 · see citing works
Demography and Rapid Local Adaptation Shape Creole Cattle Genome Diversity in the Tropics
Pitt, D., Bruford, M. W., Barbato, M., Orozco‐terWengel, P., Martínez, R., & Sevane, N. (2019) · Evolutionary Applications · doi:10.1111/eva.12641 · Cited by 79 · see citing works
Taye, M., Lee, W., Caetano-Anolles, K., Dessie, T., Cho, S., Jong Oh, S., Lee, H.-K., & Kim, H. (2018) · Cogent Food & Agriculture · doi:10.1080/23311932.2018.1552552 · Cited by 26 · see citing works
The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution
Liu, Y., Dao, W., Gao, R., Fan, X., Yang, R., & Miao, Y. (2026) · Animals · doi:10.3390/ani16050776 · Cited by 1 · see citing works
- Authors
- Makina, S. O., Muchadeyi, F. C., van Marle-Köster, E., Taylor, J. F., Makgahlela, M. L., & Maiwashe, A.
- Affiliations
- Animal Production Institute (ZA)
- Agricultural Research Council of South Africa (ZA)
- University of Missouri (US)
- University of the Free State (ZA)
- Corresponding author
- Makina, Sithembile O.
- Venue
- Genetics Selection Evolution
- Published
- 2015-11-26
- Volume
- 47
- Issue
- 1
- Pages
- 92-92
- ISSN
- 0999-193X (ISSN-L)
- 1297-9686
- PMC
- PMC4662009
- OpenAlex
- W2177200217
- Cited by
- 125
- References
- 52
- Citations by year
- 2026: 5 · 2025: 7 · 2024: 9 · 2023: 12 · 2022: 13 · 2021: 24 · 2020: 19 · 2019: 13 · 2018: 13 · 2017: 6 · 2016: 3
- FWCI
- 5.04
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Genetics Selection Evolution (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- UpSpace Institutional Repository (University of Pretoria) (submittedVersion, cc-by)
- 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 › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- selection signatures, cattle breeds, Afrikaners, Nguni, Bonsmara, Angus cattle, Holstein, FST, keratin genes, tropical adaptation, candidate genes, immune response genes
- MeSH terms
- Alleles, Animals, Breeding, Cattle, Gene Frequency, Genetic Markers, Haplotypes, Selection, Genetic, South Africa, Genome, Computational Biology, Polymorphism, Single Nucleotide, Genomics, Chromosomes, Mammalian, Quantitative Trait Loci, Genome-Wide Association Study, Genetic Association Studies
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
