CoChat
Sign Up
Cited by 69Genetic and phenotypic traits in livestockGenetic diversity and population structureLivestock Farming and Management

Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya

Open access
Mbole-Kariuki, M N, Sonstegard, T, Orth, A, Thumbi, S M, Bronsvoort, B M de C, Kiara, H, Toye, P, Conradie, I +5 more·2014·Heredity
DOI 10.1038/hdy.2014.31PMC PMC4181064
Open this paper in CoChat — free accountOpen PDF

Abstract

The Kenyan East African zebu cattle are valuable and widely used genetic resources. Previous studies using microsatellite loci revealed the complex history of these populations with the presence of taurine and zebu genetic backgrounds. Here, we estimate at genome-wide level the genetic composition and population structure of the East African Shorthorn Zebu (EASZ) of western Kenya. A total of 548 EASZ from 20 sub-locations were genotyped using the Illumina BovineSNP50 v. 1 beadchip. STRUCTURE analysis reveals admixture with Asian zebu, African and European taurine cattle. The EASZ were separated into three categories: substantial (⩾12.5%), moderate (1.56%<X<12.5%) and non-introgressed (⩽1.56%) according to the European taurine genetic proportion. The non-European taurine introgressed animals (n=425) show an unfluctuating zebu and taurine ancestry of 0.84±0.009 s.d. and 0.16±0.009 s.d., respectively, with significant differences in African taurine (AT) and Asian zebu backgrounds across chromosomes (P<0.0001). In contrast, no such differences are observed for the European taurine ancestry (P=0.1357). Excluding European introgressed animals, low and nonsignificant genetic differentiation and isolation by distance are observed among sub-locations (Fst=0.0033, P=0.09; r=0.155, P=0.07). Following a short population expansion, a major reduction in effective population size (Ne) is observed from approximately 240 years ago to present time. Our results support ancient zebu × AT admixture in the EASZ population, subsequently shaped by selection and/or genetic drift, followed by a more recent exotic European cattle introgression.

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/hdy.2014.31

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.

A few free checks a day · papers already verified open instantly · results are public

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

No citation lists for this paper

No citation lists for this paper yet — checked again daily.

References 72 · Cited by 69

Research works printed but not linked: 51

  1. Barendse W Harrison BE Bunch RJ Thomas MB Turner LB 2009 Genome wide signatures of positive selection: the comparison of independent samples and the identification of regions associated to traits BMC Genomics 10 178 19393047 PMC2681478
  2. Berthouly C Do Ngoc D Thévenon S Bouchel D Van TN Danes C 2009 How does farmer connectivity influence livestock genetic structure? A case-study in a Vietnamese goat population Mol Ecol 18 3980 3991 19735449
  3. Blench RM MacDonald KC 2000 The Origins and Development of African Livestock: Archeology, Genetics, Linguistics and EthnographyBlench RM, MacDonald KC, (eds). Routledge: New York 566
  4. Blench R 1993 Ethnographic and linguistic evidence for the prehistory of African ruminant, livestock, horses and poniesIn: Shaw T, Sinclair P, Andah B, Okpoko A, (eds). The Archeology of Africa, Routledge: London 71 103
  5. Bonsma JC 1973 Crossbreeding for adaptabilityIn: Koger M, Cunha TJ, Warnick AC, (eds). Crossbreeding Beef Cattle, Series 2 University of Florida Press: Gainesville, FL, USA
  6. Bradley DG MacHugh DE Cunningham P Loftus RF 1996 Mitochondrial diversity and origin of African and European cattle Proc Natl Acad Sci USA 93 5131 5135 8643540 PMC39419
  7. Carvalho FA Lammoglia MA Simoes MJ Randel RD 1995 Breed affects thermoregulation and epithelial morphology in imported and native cattle subjected to heat stress J Anim Sci 73 3570 3573 8655430
  8. Corbin LJ Liu AYH Bishop SC Woolliams JA 2012 Estimation of historical effective population size using linkage disequilibria with marker data J Anim Breed Genet 129 257 270 22775258
  9. de Roos APW Hayes BJ Spelman R Goddard ME 2008 Linkage disequilibrium and persistence of phase in Holstein Friesian, Jersey and Angus cattle Genetics 179 1503 1512 18622038 PMC2475750
  10. Dumasy JF Daniaux C Donnay I Baret PV 2012 Genetic diversity and networks of exchange: a combined approach to assess intra-breed diversity Genet Sel Evol 44 17 22620856 PMC3406966
  11. Evanno G Regnaut S Goudet J 2005 Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study Mol Ecol 14 2611 2620 15969739
  12. Falush D Stephens M Pritchard JK 2003 Inference of population structure: extensions to linked loci and correlated allele frequencies Genetics 164 1567 1587 12930761 PMC1462648
  13. Flury C Tapio M Sonstegard T Drögemüller C Leeb T Simianer H Hanotte O Rieder S 2010 Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium J Anim Breed Genet 127 339 347 20831557
  14. Gaughan JB Mader TL Holt SM Josey MJ Rowan KJ 1999 Heat tolerance of Boran and Tuli crossbred steers J Anim Sci 77 2398 2405 10492446
  15. Gautier M Flori L Riebler A Jaffrezic F Laloe D Gut I 2009 A whole genome Bayesian scan for adaptive genetic divergence in West African cattle BMC Genomics 10 550 19930592 PMC2784811
  16. Gautier M Laloe D Moazami-Goudarzi K 2010 Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds PLoS ONE 5 e13038 20927341 PMC2948016
  17. Gautier M Naves M 2011 Footprints of selection in the ancestral admixture of a New World Creole cattle breed Mol Ecol 20 3128 3143 21689193
  18. Hammond AC Olson TA Chase CC Jr Bowers EJ Randel RD Murphy CN 1996 Heat tolerance in two tropically adapted Bos taurus breeds, Senepol and Romosinuano, compared with Brahman, Angus, and Hereford cattle in Florida J Anim Sci 74 295 303 8690664
  19. Hanotte O Bradley DG Ochieng JW Verjee Y Hill EW Rege JEO 2002 African pastoralism: genetic imprints of origins and migrations Science 296 336 339 11951043
  20. Hanotte O Ronin Y Agaba M Nilsson P Gelhaus A Horstmann R 2003 Mapping of quantitative trait loci controlling trypanotolerance in a cross of tolerant West African N'Dama and susceptible East African Boran cattle Proc Natl Acad Sci USA 97 7443 7448 12805560 PMC164605
  21. Hansen PJ 2004 Physiological and cellular adaptations of zebu cattle to thermal stress Anim Reprod Sci 83 349 360 15271465
  22. Hayes BJ Visscher PM McPartlan HC Goddard ME 2003 Novel multilocus measure of linkage disequilibrium to estimate past effective population size Genome Res 13 635 643 12654718 PMC430161
  23. Hill WG Robertson A 1968 Linkage disequilibrium in finite populations Theor Appl Genet 38 226 231 24442307
  24. Jakobsson M Rosenberg NA 2007 CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure Bioinformatics 23 1801 1806 17485429
  25. Jombart T 2008 Adegenet: a R package for the multivariate analysis of genetic markers Bioinformatics 24 1403 1405 18397895
  26. Kidd KK Cavalli-Sforza LL 1974 The role of genetic drift in the differentiation of Icelandic and Norwegian cattle Evolution 28 381 395 28564858
  27. Latif AA Punyua DK Nokoe S Capstick PB 1991 Tick infestations on Zebu cattle in western Kenya: individual host variation J Med Entomol 28 114 121 2033602
  28. Latif AA Punyua DK Nokoe S Capstick PB 1991 Tick infestations on Zebu cattle in western Kenya: quantitative assessments of host resistance J Med Entomol 28 122 126 2033603
  29. Lawrence JA Musisi FL Mfitilodze MW Tjorneho JK Whiteland AP Kafuwa PT 1996 Integrated tick and tick-borne disease control trials in crossbred dairy cattle in Malawi Trop Anim Health Prod 28 280 288 8983132
  30. MacHugh DE Shriver MD Loftus RT Cunningham P Bradley DG 1997 Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus) Genetics 146 1071 1086 9215909 PMC1208036
  31. Mattioli RC Bah M Faye J Kora S Cassama M 1993 A comparison of field tick infestation on N'dama, Zebu and N'dama x Zebu crossed cattle Vet Parasitol 47 139 148 8493760
  32. Matukumalli LK Lawley CT Schnabel RD Taylor JF Allan MF Heaton MP 2009 Development and characterization of a high density SNP genotyping assay for cattle PLoS ONE 4 e5350 19390634 PMC2669730
  33. McTavish EJ Decker JE Schnabel RD Taylor JF Hillis DM 2013 New world cattle show ancestry from multiple independent domestication events Proc Natl Acad Sci USA 110 E1398 E1406 23530234 PMC3625352
  34. Melka MG Schenkel FS 2012 Analysis of genetic diversity of Brown Swiss, Jersey and Holstein populations using genome-wide single nucleotide polymorphism markers BMC Res Notes 5 161 22439716 PMC3428661
  35. Murray GGR Woolhouse MEJ Tapio M Mbole-Kariuki MN Sonstegard TS Thumbi SA 2013 Data from: genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression. Dryad Digital Repository 10.5061/dryad.bc598 PMC3828575 24209611 · DOI
  36. Murray GGR Woolhouse MEJ Tapio M Mbole-Kariuki MN Sonstegard TS Thumbi SA 2013 Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression BMC Evol Biol 13 246. http://dx.doi.org/10.1186/1471-2148-13-246. 24209611 PMC3828575 · DOI
  37. Pant SD Schenkel FS Verschoor CP You QM Kelton DF Moore SS 2010 A principal component regression based genome wide analysis approach reveals the presence of a novel QTL on BTA7 for MAP resistance in Holstein cattle Genomics 95 176 182 20060464
  38. Paynes WJA Hodges J 1997 Tropical Cattle: Origins, Breeds and Breeding policies Blackwell Science: Oxford
  39. Pritchard KJ Stephens M Donnelly P 2000 Inference of population structure using multilocus genotype data Genetics 155 945 959 10835412 PMC1461096
  40. Rousset F 1997 Genetic differentiation and estimation of gene flow for Fstatistics under isolation by distance Genetics 145 1219 1228 9093870 PMC1207888
  41. Settles M Zanella R McKay SD Schnabel RD Taylor JF Whitlock R 2009 A whole genome association analysis identifies loci associated with Mycobacterium avium subsp. paratuberculosis infection status in US Holstein cattle Anim Genet 40 655 662 19422364
  42. Tapio M Ozerov M Tapio I Toro MA Marzanov N Ćinkulov M 2010 Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia BMC Genet 11 76 20698974 PMC2931448
  43. The Bovine HapMap Consortium 2009 Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds Science 324 528 532 19390050 PMC2735092
  44. Turner JW 1980 Genetic and biological aspects of Zebu adaptability J Anim Sci 50 1201 1205 7400061
  45. Van Tassell CP Smith TP Matukumalli LK Taylor JF Schnabel RD Lawley CT 2008 SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries Nat Methods 5 247 252 18297082
  46. Verschuren D Laird KR Cumming BF 2000 Rainfall and drought in equatorial east Africa during the past 1,100 years Nature 403 410 414 10667789
  47. Vordermeier M Ameni G Berg S Bishop R Robertson BD Aseffa A 2012 The influences of cattle breed on susceptibility to bovine tuberculosis in Ethiopia Comp Immunol Microbiol Infect Dis 35 227 232 22304898 PMC3339321
  48. Wambura PN Gwakisa PS Silayo RS Rugaimukamu EA 1998 Breed-associated resistance to tick infestation in Bos indicus and their crosses with Bos taurus Vet Parasitol 77 63 70 9652384
  49. Weir BS Hill WG 1980 Effect of mating structure on variation in linkage disequilibrium Genetics 95 477 488 7203003 PMC1214241
  50. Wiggans GR Sonstegard TS VanRaden PM Matukumalli LK Schnabel RD Taylor JF 2008 Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada J Dairy Sci 92 3431 3436 19528621
  51. Wiggans GR VanRaden PM Bacheller LR Tooker ME Hutchison JL Cooper TA 2010 Selection and management of DNA markers for use in genomic evaluation J Dairy Sci 93 2287 2292 20412945

Authors
Mbole-Kariuki, M. N., Sonstegard, T., Orth, A., Thumbi, S. M., Bronsvoort, B. M. D. C., Kiara, H., Toye, P., Conradie, I., Jennings, A., Coetzer, K., Woolhouse, M. E. J., Hanotte, O., & Tapio, M.
Affiliations
  • University of Nottingham (GB)
  • Agricultural Research Service (US)
  • International Livestock Research Institute (KE)
  • Centre for Immunity, Infection and Evolution (GB)
  • University of Pretoria (ZA)
  • Roslin Institute (GB)
  • Agrifood Research Finland (FI)
Corresponding author
  • Mbole-Kariuki, M N
  • Hanotte, O
ORCID
Venue
Heredity
Publisher
Springer Science and Business Media LLC
Published
2014-04-16
Volume
113
Issue
4
Pages
297-305
ISSN
  • 0018-067X (ISSN-L)
  • 1365-2540
DOI
10.1038/hdy.2014.31
PMC
PMC4181064
OpenAlex
W2154804764
Cited by
69
References
72
Citations by year
2026: 3 · 2025: 8 · 2024: 5 · 2023: 3 · 2022: 3 · 2021: 5 · 2020: 7 · 2019: 5 · 2018: 5 · 2017: 9 · 2016: 3 · 2015: 7 · 2014: 4 · 2013: 1
FWCI
5.04
Type
journal article
Language
en
Open access
Licence
Locations
  • Heredity (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Jukuri (Natural Resources Institute Finland (Luke)) (submittedVersion)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
  • CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) (submittedVersion, cc-by)
  • UpSpace Institutional Repository (University of Pretoria) (submittedVersion, other-oa)
Funders
  • U.S. Department of Agriculture
  • Wellcome Trust (07995, 31000, 095831)
  • Agricultural Research Service (1265-31000-104-00D)
  • Biotechnology and Biological Sciences Research Council (BBS/E/D/20211554, BBS/E/D/05191133, BBS/E/D/20211550)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Livestock Farming and Management
Keywords
population structure, effective population size, population growth, isolation by distance, genetic differentiation, cattle genetic resources, Western Kenya
MeSH terms
Animals, Cattle, Genotype, Kenya, Male, Genome, Microsatellite Repeats, Evolution, Molecular

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