QTL fine mapping with Bayes C(π): A simulation study

Genetics Selection Evolution

Volumn 45, Issue 1, 2013, Pages

  Van Den Berg, Irene ^a,b   Fritz, Sébastien ^c   Boichard, Didier ^a  

^a UMR1313 GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE   (France)

^b AARHUS UNIVERSITY   (Denmark)

^c UNCEIA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CATTLE; CHROMOSOME; GENETIC MARKER; GENOMICS; HERITABILITY; MAPPING; MUTATION; NUMERICAL MODEL;

BOS;

ALGORITHM; ALLELE; ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; CATTLE; CHROMOSOME MAP; COMPUTER SIMULATION; GENOTYPE; MUTATION; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; ALLELES; ANIMALS; BAYES THEOREM; CATTLE; CHROMOSOME MAPPING; COMPUTER SIMULATION; GENOTYPE; MODELS, GENETIC; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84879064699     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/1297-9686-45-19     Document Type: Article

References (31)

1. Quantitative trait loci mapping in dairy cattle: review and meta-analysis. Khatkar MS, Thomson PC, Tammen I, Raadsma HW, Genet Sel Evol 2004 36 163 190 10.1186/1297-9686-36-2-163 15040897 (Pubitemid 38272284)
2. Review of quantitative trait loci identified in the chicken. Abasht B, Dekkers JCM, Lamont SJ, Poultry Sci 2006 85 2079 2096 (Pubitemid 46063978)
3. Advances in QTL mapping in pigs. Rothschild MF, Hu ZL, Jiang Z, Int J Biol Sci 2007 3 192 197 17384738 (Pubitemid 46280055)
4. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Goddard ME, Hayes BJ, Nat Rev Genet 2009 10 381 391 10.1038/nrg2575 19448663
5. Detection of genes influencing economic traits in three French dairy cattle breeds. Boichard D, Grohs C, Bourgeois F, Cerqueira F, Faugeras R, Neau A, Rupp R, Amigues Y, Boscher MY, Levéziel H, Genet Sel Evol 2003 35 77 101 10.1186/1297-9686-35-1-77 12605852 (Pubitemid 36530731)
6. Mutations in the bovine ABCG2 and the ovine MSTN gene added to the few quantitative trait nucleotides identified in farm animals: a mini-review. Braunschweig MH, J Appl Genet 2010 51 289 297 10.1007/BF03208858 20720303
7. High resolution of quantitative traits into multiple loci via interval mapping. Jansen RC, Stam P, Genetics 1994 136 1447 1455 8013917 (Pubitemid 24097871)
8. Advances in Bayesian multiple quantitative trait loci mapping in experimental crosses. Yi N, Shriner D, Heredity 2008 100 240 252 10.1038/sj.hdy.6801074 17987056 (Pubitemid 351282128)
9. Prediction of total genetic value using genome-wide dense marker maps. Meuwissen THE, Hayes BJ, Goddard ME, Genetics 2001 157 1819 1829 11290733 (Pubitemid 32298846)
10. Comparison of association mapping methods in a complex pedigreed population. Sahana G, Guldbrandtsen B, Janss L, Lund MS, Genet Epidemiol 2010 34 455 462 10.1002/gepi.20499 20568276
11. Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage and type in Holstein cattle as contrasting model traits. Hayes BJ, Pryce J, Chamberlain AJ, Bowman PJ, Goddard ME, PLoS Genet 2010 6 1001139 10.1371/journal.pgen.1001139 20927186
12. Additive genetic variability and the Bayesian alphabet. Gianola D, Delos Campos G, Hill WG, Manfredi E, Fernando R, Genetics 2009 183 347 363 10.1534/genetics.109.103952 19620397
13. Extension of the Bayesian alphabet for genomic selection. Habier D, Fernando RL, Kizilkaya K, Garrick DJ, BMC Bioinformatics 2011 12 186 10.1186/1471-2105-12-186 21605355
14. Genomic breeding value prediction and QTL mapping of QTLMAS 2010 data using Bayesian methods. Sun X, Habier D, Fernando RL, Garrick DJ, Dekkers JCM, BMC Proc 2011 5 13 22373437
15. Bayesian genome-wide association analysis of growth and yearling ultrasound measures of carcass traits in Brangus heifers. Peters SO, Kizilkaya K, Garrick DJ, Fernando RL, Reecy JM, Weaber RL, Silver GA, Thomas MG, J Anim Sci 2012 90 3398 3409 23038745
16. Heritability and Bayesian genome-wide association study of first service conception and pregnancy in Brangus heifers. Peters SO, Kizilkaya K, Garrick DJ, Fernando RL, Reecy JM, Weaber RL, Silver GA, Thomas MG, J Anim Sci 2013 91 605 612 10.2527/jas.2012-5580 23148252
17. Genome-wide association study of insect bite hypersensitivity in two horse populations in the Netherlands. Schurink A, Wolc A, Ducro BJ, Frankena K, Garrick DJ, Dekkers JCM, van Arendonk JAM, Genet Sel Evol 2012 44 31 10.1186/1297-9686-44-31 23110538
18. Whole-genome association analyses for lifetime reproductive traits in the pig. Onteru SK, Fan B, Nikkilä MT, Garrick DJ, Stalder KJ, Rothschild MF, J Anim Sci 2011 89 988 995 10.2527/jas.2010-3236 21183715
19. Genome-wide association study identifies loci for body composition and structural soundness traits in pigs. Fan B, Onteru SK, Du ZQ, Garrick DJ, Stalder KJ, Rothschild MF, PLoS One 2011 6 14726 10.1371/journal.pone.0014726 21383979
20. Accuracy of breeding values when using and ignoring the polygenic effect in genomic breeding value estimation with a marker density of one SNP per cM. Calus MPL, Veerkamp RF, J Anim Breed Genet 2007 124 362 368 10.1111/j.1439-0388. 2007.00691.x 18076473 (Pubitemid 350231128)
21. The impact of genetic architecture on genome-wide evaluation methods. Daetwyler HD, Pong-Wong R, Villanueva, Woolliams JA, Genetics 2010 185 1021 1031 10.1534/genetics.110.116855 20407128
22. Different models of genetic variation and their effect on genomic evaluation. Clark SA, Hickey JM, van der Werf JHJ, Genet Sel Evol 2011 43 18 10.1186/1297-9686-43-18 21575265
23. From QTL to QTN identification in livestock-winning by points rather than knock-out: a review. Ron M, Weller JI, Anim Genet 2007 38 429 439 10.1111/j.1365-2052.2007.01640.x 17697134 (Pubitemid 47480951)
24. Efficient mapping of Mendelian traits in dogs through genome-wide association. Karlsson EK, Baranowska I, Wade CM, Salmon, Hillbertz NH, Zody MC, Anderson N, Biagi TM, Patterson N, Pielberg GR, Kulbokas EJ 3rd, Comstock KE, Keller ET, Mesirov JP, Von Euler H, Kämpe O, Hedhammar A, Lander ES, Andersson G, Andersson L, Lindblad-Toh K, Nat Genet 2007 39 1321 1328 10.1038/ng.2007.10 17906626 (Pubitemid 350034994)
25. Legarra A, Ricard A, Filangi O, GS3 User Manual 2012 [ http://snp.toulouse.inra.fr/∼alegarra/manualgs3-last.pdf ]
26. A hidden markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping. Druet T, Georges M, Genetics 2010 184 789 798 10.1534/genetics.109. 108431 20008575
27. Kaufman L, Rousseeuw PJ, Finding Groups in Data: An Introduction to Cluster Analysis Hoboken: John Wiley & Sons 2005
28. Hennig C, fpc: Flexible procedures for clustering R package version 2.0-3 2010 http://cran.rproject.org/web/packages/fpc/
29. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. Rousseeuw PJ, J Comput Appl Math 1987 20 53 65
30. Calculating cow and daughter yield deviations and partitioning of genetic evaluations under a random regression model. Mrode RA, Swanson GJT, Livest Prod Sci 2004 86 253 260 10.1016/j.livprodsci.2003.09.001 (Pubitemid 38215267)
31. Increased accuracy of artificial selection by using the realized relationship matrix. Hayes BJ, Visscher PM, Goddard ME, Genet Res 2009 91 47 60 10.1017/S0016672308009981