Association studies in QTL regions linked to bovine trypanotolerance in a West African crossbred population

Animal Genetics

Volumn 43, Issue 2, 2012, Pages 123-132

  Dayo, G K ^a,b   Gautier, M ^c   Berthier, D ^d   Poivey, J P ^d,e   Sidibe, I ^b   Bengaly, Z ^b   Eggen, A ^f,g   Boichard, D ^f   Thevenon, S ^d  

^a Institut de recherche pour le développement   (France)

^b CIRDES   (Burkina Faso)

^c CENTRE DE BIOLOGIE ET DE GESTION DES POPULATIONS   (France)

^d CIRAD   (France)

^e CEMAGREF   (France)

^f UMR1313 GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE   (France)

^g Optegra Eye Sciences UK Ltd   (United Kingdom)

Author keywords

association study; cattle; heritability; kinship; microsatellite; trypanotolerance

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; BURKINA FASO; CATTLE; GENETIC ASSOCIATION; GENETICS; IMMUNOLOGY; NAGANA; QUANTITATIVE TRAIT LOCUS;

ANIMALS; BURKINA FASO; CATTLE; GENETIC ASSOCIATION STUDIES; MICROSATELLITE REPEATS; QUANTITATIVE TRAIT LOCI; TRYPANOSOMIASIS, BOVINE;

ANIMALIA; BOS; BOS INDICUS; BOVINAE; GLOSSINA (GENUS);

EID: 84858337596     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2011.02227.x     Document Type: Article

References (52)

1. Akaike H., (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control 19, 716-23.
2. Bradbury P.J., Zhang Z., Kroon D.E., Casstevens T.M., Ramdoss Y., &, Buckler E.S., (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633-5. (Pubitemid 350048371)
3. Coltman D.W., (2005) Testing marker-based estimates of heritability in the wild. Molecular Ecology 14, 2593-9. (Pubitemid 40886053)
4. Csilléry K., Johnson T., Beraldi D., Clutton-Brock T., Coltman D., Hansson B., Spong G., &, Pemberton J.M., (2006) Performance of marker-based relatedness estimators in natural populations of outbred vertebrates. Genetics 173, 2091-101. (Pubitemid 44285687)
5. Dayo G.K., Thevenon S., Berthier D., Moazami-Goudarzi K., Denis C., Cuny G., Eggen A., &, Gautier M., (2009) Detection of selection signatures within candidate regions underlying trypanotolerance in outbred cattle populations. Molecular Ecology 18, 1801-13.
6. Dayo G.K., Bengaly Z., Messad S., Bucheton B., Sidibe I., Cene B., Cuny G., &, Thevenon S., (2010) Prevalence and incidence of bovine trypanosomosis in an agro-pastoral area of southwestern Burkina Faso. Research in Veterinary Science 88, 470-7.
7. Desquesnes M., &, Davila A.M., (2002) Applications of PCR-based tools for detection and identification of animal trypanosomes: a review and perspectives. Veterinary Parasitology 109, 213-31. (Pubitemid 35356254)
8. Desquesnes M., Michel J.F., De La Rocque S., Solano P., Millogo L., Bengaly Z., &, Sidibe S., (1999) Enquête parasitologique et sérologique (Elisa-indirect) sur les trypanosomes des bovins dans la zone de Sidéragoudou, Burkina Faso. Revue d'Elevage et de Médecine Vétérinaire des Pays tropicaux 52, 223-32.
9. Desquesnes M., Bengaly Z., Millogo L., Meme Y., &, Sakande H., (2001) The analysis of the cross-reactions occurring in antibody-ELISA for the detection of trypanosomes can improve identification of the parasite species involved. Annals of Tropical Medicine and Parasitology 95, 141-55. (Pubitemid 32304212)
10. Frentiu F.D., Clegg S.M., Chittock J., Burke T., Blows M.W., &, Owens I.P., (2008) Pedigree-free animal models: the relatedness matrix reloaded. Proceedings of the Royal Society of London. Serie B, Biological sciences 275, 639-47. (Pubitemid 351198035)
11. Gautier M., Flori L., Riebler A., Jaffrezic F., Laloë D., Gut I., Moazami-Goudarzi K., &, Foulley J.L., (2009) A whole genome scan for adaptive divergence in West African cattle. BMC Genomics 10, 550.
12. Hanotte O., Ronin Y., Agaba M., Nilsson P., Gelhaus A., Horstmann R., et al. (2003) Mapping of quantitative trait loci controlling trypanotolerance in a cross of tolerant West African N'Dama and susceptible East African Boran cattle. Proceedings of the National Academy of Sciences of the United States of America 100, 7443-8. (Pubitemid 36759988)
13. Hanotte O., Dessie T., &, Kemp S., (2010) Ecology. Time to tap Africa's livestock genomes. Science 328, 1640-1.
14. Hardy O.J., &, Vekemans X., (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2, 618-20. (Pubitemid 35436766)
15. Hedrick P.W., (1987) Gametic disequilibrium measures: proceed with caution. Genetics 117, 331-41.
16. Hendrickx G., De La Rocque S., &, Mattioli R.C., (2004) Long-term tse-tse and Trypanosomiasis Management Options in West Africa, pp. 75. FAO, Rome.
17. Hill W.G., &, Robertson A., (1968) The effects of inbreeding at loci with heterozygote advantage. Genetics 60, 615-28.
18. d'Ieteren G., (2001) Trypanosomosis Management, Trypanotolerant Livestock and Integrated Disease Control: Trypanotolerance and its Exploitation for Genetic Improvement. Situation report, pp. 44. ILRI, Nairobi, Kenya.
19. Ihara N., Takasuga A., Mizoshita K., Takeda H., Sugimoto M., Mizoguchi Y., et al. (2004) A comprehensive genetic map of the cattle genome based on 3802 microsatellites. Genome Research 14, 1987-98. (Pubitemid 39386513)
20. Itard J., Cuisance D., &, Tacher G., (2003) Trypanosomoses: Historique-Répartition géographique. In: Principales maladies infectieuses et parasitaires du bétail. Europe et régions chaudes (Ed. by, P.C. Lefèvre, J. Blancou, &, R. Chermette,), pp. 1607-15. Editions médicales internationales. Lavoisier, Paris, France.
21. Laird N.M., &, Ware J.H., (1982) Random-effects models for longitudinal data. Biometrics 38, 963-74.
22. Lewontin R., (1964) The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49, 49-67.
23. Liu Y., Qin X., Song X.Z., Jiang H., Shen Y., Durbin K.J., et al. (2009) Bos taurus genome assembly. BMC Genomics 10, 180.
24. Lynch M., &, Ritland K., (1999) Estimation of pairwise relatedness with molecular markers. Genetics 152, 1753-66. (Pubitemid 29370352)
25. Masiga D.K., Smyth A.J., Hayes P., Bromidge T.J., &, Gibson W.C., (1992) Sensitive detection of trypanosomes in tsetse flies by DNA amplification. International Journal for Parasitology 22, 909-18.
26. Mattioli R.C., Faye J.A., &, Buscher P., (1999) Susceptibility of N'Dama cattle to experimental challenge and cross-species superchallenges with bloodstream forms of Trypanosoma congolense and T. vivax. Veterinary Parasitology 86, 83-94. (Pubitemid 29397527)
27. Murray M., Murray P.K., &, McIntyre W.I.M., (1977) An improved parasitological technique for the diagnosis of African trypanosomiasis. Transactions of the Royal Society of Tropical Medicine and Hygiene 71, 325-6. (Pubitemid 8164446)
28. Murray M., Trail J.C., Davis C.E., &, Black S.J., (1984) Genetic resistance to African Trypanosomiasis. The Journal of Infectious Diseases 149, 311-9. (Pubitemid 14138232)
29. Ogawa J., Funaba M., &, Tsujimoto M., (2008) A dual role of activin A in regulation immunoglobulin production of B cells. Journal of Leukocyte Biology 83, 1451-8. (Pubitemid 351960326)
30. Paling R.W., Moloo S.K., Scott J.R., McOdimba F.A., Logan-Henfrey L.L., Murray M., &, Williamson D.J., (1991) Susceptibility of N'Dama and Boran cattle to tsetse-transmitted primary and rechallenge infections with a homologous serodeme of Trypanosoma congolense. Parasite Immunology 13, 413-25.
31. Paris J., Murray M., &, McOdimba F., (1982) A comparative evaluation of the parasitological techniques currently available for the diagnosis of African trypanosomiasis in cattle. Acta Tropica 39, 307-16. (Pubitemid 13178184)
32. Pritchard J.K., Stephens M., &, Donnelly P., (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-59. (Pubitemid 30397141)
33. Queller D.C., &, Goodnight K.F., (1989) Estimating relatedness using genetic markers. Evolution 43, 258-75.
34. R Development Core Team (2007) R: A Language and Environment for Statistical Computing. R foundation for Statistical Computing, Vienne, Austria.
35. Ritland K., (1996) Marker-based method for inferences about quantitative inheritance in natural populations. Evolution 50, 1062-73.
36. Ritland K., (2000) Marker-inferred relatedness as a tool for detecting heritability in nature. Molecular Ecology 9, 1195-204.
37. Robson N.C., Phillips D.J., McAlpine T., Shin A., Svobodova S., Toy T., et al. (2008) Activin-A: a novel dendritic cell-derived cytokine that potently attenuates CD40 ligand-specific cytokine and chemokine production. Blood 111, 2733-43.
38. Robson N.C., Wei H., McAlpine T., Kirkpatrick N., Cebon J., &, Maraskovsky E., (2009) Activin-A attenuates several human natural killer cell functions. Blood 113, 3218-25.
39. Rowlands G.J., Mulatu W., Nagda S.M., &, d'Ieteren G.D., (1995) Variations in packed red cell volume and trypanosome prevalence and relationships with reproductive traits in east African Zebu cows exposed to drug-resistant trypanosomes. Acta Tropica 59, 105-16.
40. Shikano T., (2008) Estimation of quantitative genetic parameters using marker-inferred relatedness in Japanese flounder: a case study of upward bias. Journal of Heredity 99, 94-104. (Pubitemid 351430979)
41. Solano P., Michel J.F., Lefrancois T., de La Rocque S., Sidibe I., Zoungrana A., &, Cuisance D., (1999) Polymerase chain reaction as a diagnosis tool for detecting trypanosomes in naturally infected cattle in Burkina Faso. Veterinary Parasitology 86, 95-103. (Pubitemid 29397528)
42. Storey J.D., &, Tibshirani R., (2003) Statistical significance for genomewide studies. Proceedings of the National Academy of Sciences of the United States of America 100, 9440-5. (Pubitemid 37033947)
43. Swallow B.M., (1999) Impact of Trypanosomiasis on African Agriculture. PAAT Information paper, pp. 46. FAO (Food and Agricultural Organization of the United Nations), Rome, Italy.
44. Thevenon S., Dayo G.K., Sylla S., Sidibe I., Berthier D., Legros H., Boichard D., Eggen A., &, Gautier M., (2007) The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies. Animal Genetics 38, 277-86. (Pubitemid 46848880)
45. Thomas S.C., Pemberton J.M., &, Hill W.G., (2000) Estimating variance components in natural populations using inferred relationships. Heredity 84, 427-36. (Pubitemid 30400029)
46. Trail J.C., d'Ieteren G.D., Feron A., Kakiese O., Mulungo M., &, Pelo M., (1991a) Effect of trypanosome infection, control of parasitaemia and control of anaemia development on productivity of N'Dama cattle. Acta Tropica 48, 37-45. (Pubitemid 20323230)
47. Trail J.C., d'Ieteren G.D., Maille J.C., &, Yangari G., (1991b) Genetic aspects of control of anaemia development in trypanotolerant N'Dama cattle. Acta Tropica 48, 285-91.
48. Trail J.C., d'Ieteren G.D., Murray M., Ordner G., Yangari G., Collardelle C., Sauveroche B., Maille J.C., &, Viviani P., (1993) Measurement of trypanotolerance criteria and their effect on reproductive performance of N'Dama cattle. Veterinary Parasitology 45, 241-55. (Pubitemid 23038617)
49. Van de Casteele T., Galbusera P., &, Matthysen E., (2001) A comparison of microsatellite-based pairwise relatedness estimators. Molecular Ecology 10, 1539-49. (Pubitemid 32526126)
50. 2 cross of N'Dama and Boran cattle. Livestock Production Science 84, 219-30. (Pubitemid 38012560)
51. Wang J., (2002) An estimator for pairwise relatedness using molecular markers. Genetics 160, 1203-15. (Pubitemid 34263480)
52. Yu J., Pressoir G., Briggs W.H., Vroh Bi I., Yamasaki M., Doebley J.F., et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38, 203-8. (Pubitemid 43177234)