Measuring the extent of linkage disequilibrium in commercial pig populations

Animal Genetics

Volumn 37, Issue 3, 2006, Pages 225-231

  Harmegnies, N ^a   Farnir, F ^a   Davin, F ^a   Buys, N ^b   Georges, M ^a   Coppieters, W ^a  

^a UNIVERSITY OF LIÈGE   (Belgium)

^b Gentec NV   (Belgium)

Author keywords

Effective population size; Linkage disequilibrium; Pigs

Indexed keywords

MICROSATELLITE DNA;

ALLELE; ANIMAL; ARTICLE; CHROMOSOME; CHROMOSOME MAP; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOTYPE; POPULATION DENSITY; SWINE;

ALLELES; ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES, MAMMALIAN; GENOTYPE; LINKAGE DISEQUILIBRIUM; MICROSATELLITE REPEATS; POPULATION DENSITY; SWINE;

ANIMALIA; SUS SCROFA; SUS SCROFA DOMESTICA;

EID: 33744492858     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2006.01438.x     Document Type: Article

References (27)

1. Altschuler D., Brooks L.D., Chakravarti A., Collins F.S., Daly M.J. Donnelly P., International HapMap Consortium. 2005 A haplotype map of the human genome. Nature 437, 1299 320.
2. Amarger V., Nguyen M., Van Laere A.S., Nezer C., Georges M. Andersson L. 2002 Comparative sequence analysis of the INS-IGF2-H19 gene cluster in pigs. Mammalian Genome 13, 388 98.
3. Blott S., Kim J.-J., Moisio S. et al. 2003 Molecular dissection of a QTL: a phenylalanine to tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics 163, 253 66.
4. Charlier C., Farnir F., Berzi P., Vanmanshoven P., Brouwers B. Georges M. 1996 IBD mapping of recessive traits in livestock, application to map the bovine syndactyly locus to chromosome 15. Genome Research 6, 580 9.
5. Crow J.F. Kimura M. 1970 An introduction to population genetics theory. Harper and Row, New York.
6. Farnir F., Coppieters W., Arranz J.-J. et al. 2000 Extensive genome-wide linkage disequilibrium in cattle. Genome Research 10, 220 7.
7. Grisart B., Coppieters W., Farnir F. et al. 2002 Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT gene with major effect on milk yield and composition. Genome Research 12, 222 31.
8. Grisart B., Farnir F., Karim L. et al. 2004 Genetic and functional confirmation of the causality of the DGAT1 K232A quantitative trait nucleotide in affecting milk yield and composition. Proceedings of the National Academy of Sciences, USA 24, 2398 403.
9. Hayes B.J., Visscher P.M., McPartlan H.C. Goddard M.E. 2003 Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research 13, 635 43.
10. Hill W.G. 1981 Estimation of effective population size from data on linkage disequilibrium. Genetical Research 38, 209 16.
11. Hudson R.R. 2003 Linkage disequilibrium and recombination. In : Handbook of Statistical Genetics, 2nd edn Ed. by D.J. Balding, M. Bishop C. Cannings pp. 662 80. John Wiley & Sons, Ltd.
12. Jungerius B.J., Gu J., Crooijmans R.P.M.A., der Poel J.J., Groenen M.A.M., van Oost B.A. te Pas M.F.W. 2005 Estimation of the extent of linkage disequilibrium in seven regions of the porcine genome. Animal Biotechnology 16, 41 54.
13. Kruglyak L. 1999 Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genetics 22, 139 44.
14. McRae A.F., McEwan J.C., Dodds K.G., Wilson T., Crawford A.M. Slate J. 2002 Linkage disequilibrium in domestic sheep. Genetics 160, 1113 22.
15. Meuwissen T.H., Karlsen A., Lien S., Olsaker I. Goddard M.E. 2002 Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping. Genetics 161, 373 9.
16. Milan D., Jeon J.T., Looft C. et al. 2000 A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle. Science 288, 1248 51.
17. Nezer C., Collette C., Moreau L., Brouwers B., Kim J.J., Giuffra E., Buys N., Andersson L. Georges M. 2003 Haplotype sharing refines the location of an imprinted QTL with major effect on muscle mass to a 90 Kb chromosome segment containing the porcine IGF2 gene. Genetics 165, 277 85.
18. Nsengimana J., Baret P., Haley C.S. Visscher P.M. 2004 Linkage disequilibrium in the domesticated pig. Genetics 166, 1395 404.
19. Olsen H.G., Lien S., Gautier M., Nilsen H., Roseth A., Berg P.R., Sundsaasen K.K., Svendsen M. Meuwissen T.H. 2005 Mapping of a milk production quantitative trait locus to a 420-kb region on bovine chromosome 6. Genetics 169, 275 83.
20. Pritchard J.K. Przeworski M. 2001 Linkage disequilibrium in humans: models and data. American Journal of Human Genetics 69, 1 14.
21. Reich D.E., Cargill M., Bolk S. et al. 2001 Linkage disequilibrium in the human genome. Nature 411, 199 204.
22. Riquet J., Coppieters W., Cambisano N. et al. 1999 Identity-by-descent fine-mapping of QTL in outbred populations: application to milk production in dairy cattle. Proceedings of the National Academy of Sciences, USA 96, 9252 7.
23. Rohrer G.A., Alexander L.J., Hu Z., Smith T.P., Keele J.W. Beattie C.W. 1996 A comprehensive map of the porcine genome. Genome Research 6, 371 91.
24. Sutter N.B., Eberle M.A., Parker H.G., Pullar B.J., Kirkness E.F., Kruglyak L. Ostrander E.A. 2004 Extensive and breed-specific linkage disequilibrium in Canis familiaris. Genome Research 14, 2388 96.
25. Van Laere A.-S., Nguyen M., Braunschweig M. et al. 2003 A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425, 832 6.
26. Weir B.S. 1996 Genetic data analysis. Sinauer, Sunderland, MA.
27. Weiss K.W. Clark A.G. 2002 Linkage disequilibrium and the mapping of complex human traits. Trends in Genetics 18, 19 24.