The use of linkage disequilibrium to map quantitative trait loci

Australian Journal of Experimental Agriculture

Volumn 45, Issue 7-8, 2005, Pages 837-845

  Goddard, M E ^a,b   Meuwissen, T H E ^c  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

^c NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC ANALYSIS; LIVESTOCK FARMING; SELECTIVE BREEDING;

ANIMALIA;

EID: 33645049607     PISSN: 08161089     EISSN: None     Source Type: Journal    
DOI: 10.1071/EA05066     Document Type: Conference Paper

References (42)

1. Andersson L, Georges M (2004) Domestic animal genomics: deciphering the genetics of complex traits. Nature Genetics Reviews 5, 202-212. doi:10.1038/nrg1294
2. Chapman NH, Thompson EA (2003) A model for the length of the tracts of identity by descent in finite random mating populations. Theoretical Population Biology 64, 141-150. doi:10.1016/S0040-5809(03)00071-6
3. Cockerham CC (1954) An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 39, 859-882.
4. Crow JF, Kimura M (1970) 'An introduction to population genetics theory.' (Harper and Row: New York)
5. Devlin B, Roeder K, Wasserman L (2001) Genomic control, a new approach to genetic-based association studies. Theoretical Population Biology 60, 155-160. doi:10.1006/tpbi.2001.1542
6. Farnir F, Coppieters W, Arranz JJ, Berzi P, Cambisano N, et al. (2000) Extensive genome wide linkage disequilibrium in cattle. Genome Research 10, 220-227. doi:10.1101/gr.10.2.220
7. Fernando RL, Grossman M (1989) Marker assisted selection using best linear unbiased prediction. Genetics, Selection, Evolution 21, 467-477.
8. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, et al. (2002) The structure of haplotype blocks in the human genome. Science 296, 2225-2229. doi:10.1126/science.1069424
9. Goddard ME (1991) Mapping genes for quantitative traits using linkage disequilibrium. Genetics, Selection, Evolution 23, 1315-1345. suppl. 1
10. Green ED, Chakravarti A (2001) The human genome sequence expedition: views from the base camp. Genome Research 11, 645-651. doi:10.1101/gr.188701
11. Grignola FE, Hoeschele I, Zhang Q, Thaller G (1996) Mapping linked quantitative trait loci in outcross populations via residual maximum likelihood. 2. A simulation study. Genetics, Selection, Evolution 28, 491-504.
12. Harding RM, McVean G (2004) A structured ancestral population for the evolution of modern humans. Current Opinion in Genetics & Development 14, 667-674. doi:10.1016/j.gde.2004.08.010
13. Hayes BJ, Visscher PE, McPartlan H, Goddard ME (2003) A novel multi-locus measure of linkage disequilibrium and it use to estimate past effective population size. Genome Research 13, 635-643. doi:10.1101/gr.387103
14. Hernández-Sánchez J, Visscher P, Plastow G, Haley C (2003) Candidate gene analysis for quantitative traits using the transmission disequilibrium test: the example of the melanocortin 4-receptor in pigs. Genetics 164, 637-644.
15. Hill WG (1975) Linkage disequilibrium among multiple neutral alleles produced by mutation in finite population. Theoretical Population Biolology 8, 117-126. doi:10.1016/0040-5809(75)90028-3
16. Hill WG, Weir BS (1994) Maximum likelihood estimation of gene location with linkage disequilibrium. American Journal of Human Genetics 54, 705-714.
17. Hudson RR (2001) Two-locus sampling distributions and their application. Genetics 159, 1805-1817.
18. Jeffreys AJ, Kauppi L, Neuman R (2001) Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nature Genetics 29, 217-222. doi:10.1038/ng1001-217
19. Knott SA, Haley CS (1992) Maximum-likelihood mapping of quantitative trait loci using full-sib families. Genetics 132, 1211-1222.
20. Leutenegger A-L, Prum B, Genin E, Verny C, Lemainque A, Clerget-Darpoux F, Thompson EA (2003) Estimation of inbreeding coefficient through the use of genomic data. American Journal of Human Genetics 73, 5516-5523.
21. McVean GAT (2002) A genealogical interpretation of linkage disequilibrium. Genetics 162, 987-991.
22. McVean G, Awadalla P, Fearnhead P (2002) A coalescent based method for detecting and estimating recombination from gene sequences. Genetics 160, 1231-1241.
23. Meuwissen THE, Goddard ME (2001) Prediction of identity by descent probabilities from marker-haplotypes. Genetics, Selection, Evolution 33, 605-634. doi:10.1051/gse:2001134
24. Meuwissen THE, Karlsen A, Lien S, Olsaker I, Goddard ME (2002) Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping. Genetics 161, 373-379.
25. Ohta T, Kimura M (1971) Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics 68, 571-580.
26. Perez-Enciso M (2003) Fine mapping of complex trait genes combining pedigree and linkage disequilibrium: a bayesian unified framework. Genetics 163, 1497-1510.
27. Ptak SE, Voelpel K, Przeworski M (2004) Insights into recombination from patterns of linkage disequilibrium in humans. Genetics 167, 387-397. doi:10.1534/genetics.167.1.387
28. Rafalski A, Morgante M (2004) Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends in Genetics 20, 103-111. doi:10.1016/j.tig.2003.12.002
29. Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, Higgins JM, Richter DJ, Lander ES, Altshuler D (2002) Human genome sequence variation and the influence of gene history, mutation and recombination. Nature Genetics 32, 135-142. doi:10.1038/ng947
30. Risch N, Merikangus K (1996) The future of genetic studies of complex human diseases. Science 272, 1516-1517.
31. Roberts-Thomson M, Paterson KA, Dodds KG, Lee M, Crawford AM, McEwan JC (2005) Fine scale linkage disequilibrium in sheep populations. In 'Proceedings of the plant and animal genomes XIII conference'. p. 540. Available online at: http://www.intl-pag.org/pag/13/abstracts/PAG13_P540.html (verified 12 July 2005).
32. Saez AG, Tatarenkov A, Barrio E, Beterra NH, Ayala FJ (2003) Patterns of DNA sequence polymorphism at Sod vicinities in Drosophila melanogaster: unravelling the footprint of a recent selective sweep. Proceedings of the National Academy of Sciences of the United States of America 100, 1793. doi:10.1073/pnas.242746799
33. Seldin MF, Morii T, Collins-schramm HE, Chima B, Kittles R, Criswell LA, Li H (2004) Putative ancestral origins of chromosome segments in individual african americans: implications for admixture mapping. Genome Research 14, 1076-1084. doi:10.1101/gr.2165904
34. Slatkin M, Bertorelle G (2001) The use of intraallelic variability for testing neutrality and estimating population growth. Genetics 158, 865-874.
35. Spielman RS, McGinnis RE, Ewens WJ (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). American Journal of Human Genetics 52, 506-516.
36. Stam P (1980) The distribution of the fraction of the genome identical by descent in finite random mating populations. Genetical Research 35, 131-155.
37. Sved JA (1971) Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theoretical Population Biology 2, 125-141. doi:10.1016/0040-5809(71)90011-6
38. Thompson JR, Everett RW, Hammerschmidt NL (2000a) Effects of inbreeding on production and survival in Holsteins. Journal of Dairy Science 83, 1856-1864.
39. Thompson JR, Everett RW, Wolfe CW (2000b) Effects of inbreeding on production and survival in Jerseys. Journal of Dairy Science 83, 2131-2138.
40. Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, et al. (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425, 832-836. doi:10.1038/nature02064
41. Visscher PM, Goddard ME (2004) Prediction of the confidence interval of QTL location. Behavior Genetics 34, 477-482. doi:10.1023/B:BEGE.0000023652. 93162.e8
42. Wall JD, Pritchard JK (2003) Assessing the performance of the haplotype block model of linkage disequilibrium. American Journal of Human Genetics 73, 502-515. doi:10.1086/378099