Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL

Genetical Research

Volumn 86, Issue 1, 2005, Pages 77-87

  Zhao, H ^a   Nettleton, D ^b   Soller, M ^c   Dekkers, J C M ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b Department of Statistics Center for Statistics and Applications in Forensic Evidence Iowa State University 2438 Osborn Dr Ames   (United States)

^c HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; BIOINFORMATICS; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC POLYMORPHISM; HETEROZYGOSITY; MARKER ASSISTED SELECTION; MARKER GENE; POPULATION GENETICS; QUANTITATIVE TRAIT LOCUS; SIMULATION;

ALLELES; ANIMALS; CHROMOSOME MAPPING; COMPUTER SIMULATION; CROSSES, GENETIC; GENETIC MARKERS; GENETICS, POPULATION; HAPLOTYPES; HETEROZYGOTE; LIKELIHOOD FUNCTIONS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, GENETIC; QUANTITATIVE TRAIT LOCI; REGRESSION ANALYSIS;

EID: 26444599671     PISSN: 00166723     EISSN: None     Source Type: Journal    
DOI: 10.1017/S001667230500769X     Document Type: Article

References (33)

1. Ardlie, K. G., Kruglyak, L. & Seielstad, M. (2002). Patterns of linkage disequilibrium in the human genome. Nature Reviews: Genetics 3 299-309.
2. Bulmer, M. G. (1971). The effect of selection on genetic variability. The American Naturalist 105, 201-211.
3. Cleveland, W. S. (1979). Robust locally weighted regression and smoothing scatterplots. Journal of the American Statistical Association 74, 829-836.
4. Dekkers, J. C. M. & Hospital, F. (2002). The use of molecular genetics in the improvement of agricultural populations. Nature Reviews: Genetics 3, 22-32.
5. Devlin, B. & Risch, N. (1995). A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29, 311-322.
6. Falconer, D. S. & Mackay, T. F. C. (1996). Introduction to Quantitative Genetics, 4th edn. Harlow, UK: Addison-Wesley Longman.
7. Farnir, F., Coppieters, W., Arranz, J.-J., Berzi, P., Cambisano, N., Grisart, B., Karim, L., Marcq, F., Moreau, L., Mni, M., Nezer, C., Simon, P., Vanmanshoven, P., Wagenaar, D. & Georges, M. (2000). Extensive genome-wide linkage disequilibrium in cattle. Genome Research 10, 220-227.
8. Flint-Garcia, S. A., Thornsberry, J. M. & Buckler IV, E. S. (2003). Structure of linkage disequilibrium in plants. Annual Review of Plant Biology 54, 357-374.
9. Haldane, J. B. S. (1919). The combination of linkage values and the calculation of distances between the loci of linked factors. Journal of Genetics 8, 299-309.
10. 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, 635-643.
11. Hedrick, P. W. (1987). Gametic disequilibrium measures: Proceed with caution. Genetics 117, 331-341.
12. Hedrick, P. W. & Thomson, G. (1986). A two-locus neutrality test: applications to humans, E. coli and Lodgepole pine. Genetics 112, 135-156.
13. Heifetz, E. M., Fulton, J. E., O'Sullivan, N., Zhao, H., Dekkers, J. C. M. & Soller, M. (2005). Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations. Genetics (accepted).
14. Hill, W. G. (1975). Linkage disequilibrium among multiple neutral alleles produced by mutation in finite population. Theoretical Population Biology 8, 117-126.
15. Hill, W. G. & Robertson, A. (1968). Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38, 226-231.
16. Kalantari, B., Lari, I., Rizzi, A. & Simeone, B. (1993). Sharp bounds for the maximum of the chi-square index in a class of contingency tables with given marginals. Computational Statistics & Data Analysis 16, 19-34.
17. Karlin, S. & Piazza, A. (1981). Statistical methods for assessing linkage disequilibrium at the HLA-A, B, C loci. Annals of Human Genetics 45, 79-94.
18. Kim, Y. & Nielsen, R. (2004). Linkage disequilibrium as a signature of selective sweeps. Genetics 167, 1513-1524.
19. Lande, R. & Thompson, R. (1990). Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124, 743-756.
20. Lewontin, R. C. (1964). The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49, 49-67.
21. Maruyama, T. (1982). Stochastic integrals and their application to population genetics. In Molecular Evolution, Protein Polymorphism and the Neutral Theory, pp. 151-166. Tokyo: Japan Scientific Societies Press.
22. McRae, A. F., McEwan, J. C., Dodds, K. G., Wilson, T., Crawford, A. M. & Slate, J. (2002). Linkage disequilibrium in domestic sheep. Genetics 160, 1113-1122.
23. Morton, N. E., Zhang, W., Taillon-Miller, P., Ennis, S., Kwok, P.-Y. & Collins, A. (2001). The optimal measure of allelic association. Proceedings of the National Academy of Sciences of the USA 98, 5217-5221.
24. Nordborg, M. & Tavar, S. (2002). Linkage disequilibrium: What history has to tell us. Trends in Genetics 18, 83-90.
25. Nsengimana, J., Baret, P., Haley, C. S. & Visscher, P. M. (2004). Linkage disequilibrium in the domesticated pig. Genetics 166 1395-1404.
26. Pritchard, J. K. & Przeworski, M. (2001). Linkage disequilibrium in humans: Models and data. American Journal of Human Genetics 69 1-14.
27. Sabatti, C. & Risch, N. (2002). Homozygosity and linkage disequilibrium. Genetics 160, 1707-1719.
28. Sved, J. A. (1971). Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theoretical Population Biology 2, 125-141.
29. Taillon-Miller, P., Bauer-Sardiña, I., Saccone, N. L., Putzel, J., Laitinen, T., Cao, A., Kere, J., Pilia, G., Rice, J. P. & Kwok, P.-Y. (2000). Juxtaposed regions of extensive and minimal linkage disequilibrium in human Xq25 and Xq28. Nature Genetics 25, 324-328.
30. Tenesa, A., Knott, S. A., Ward, D., Smith, D., Williams, J. L. & Visscher, P. M. (2003). Estimation of linkage disequilibrium in a sample of the United Kingdom dairy cattle population using unphased genotypes. Journal of Animal Science 81, 617-623.
31. Terwilliger, J. D. & Weiss, K. M. (1998). Linkage disequilibrium mapping of complex disease: Fantasy or reality? Current Opinion in Biotechnology 9, 578-594.
32. Winston, W. L. (1991). Operations Research: Applications and Algorithms, 2nd edn. Boston: PWS-Kent.
33. Yamazaki, T. (1977). The effects of overdominance on linkage in a multilocus system. Genetics 86, 227-236.