Modeling extent and distribution of zygotic disequilibrium: Implications for a multigenerational canine pedigree

Genetics

Volumn 174, Issue 1, 2006, Pages 439-453

  Liu, Tian ^a   Todhunter, Rory J ^b   Lu, Qing ^a   Schoettinger, Lindsay ^a   Li, Hongying ^a   Littell, Ramon C ^a   Burton Wurster, Nancy ^b   Acland, Gregory M ^b   Lust, George ^b   Wu, Rongling ^a  

^a University of Florida ^*  (United States)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME PAIRING; CONTROLLED STUDY; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; MICROSATELLITE MARKER; NONHUMAN; PEDIGREE ANALYSIS; PRIORITY JOURNAL; SIMULATION; ZYGOTE;

ANIMALS; BREEDING; COMPUTER SIMULATION; CROSSES, GENETIC; DOGS; GERM CELLS; HIP DYSPLASIA, CANINE; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; PEDIGREE; QUANTITATIVE TRAIT LOCI; ZYGOTE;

CANIS FAMILIARIS;

EID: 33748891388     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.060137     Document Type: Article

References (35)

1. ARDLIE, K. G., L. KRUGLYAK and M. SEIELSTAD, 2002 Patterns of linkage disequilibrium in the human genome. Nat. Rev. Genet. 3: 299-309.
2. BARTON, N. H., and K. S. GALE, 1993 Genetic analysis of hybrid zones, pp. 13-45 in Hybrid Zones and the Evolutionary Process, edited by R. G. HARRISON. Oxford University Press, Oxford.
3. BENNETT, J. H., and F. E. BINET, 1956 Association between Mendelian factors with mixed selfing and random mating. Heredity 10: 51-55.
4. BLISS, S., R. J. TODHUNTER, R. QUAAS, G. CASELLA, R. L. WU et al., 2002 Quantitative genetics of traits associated with hip dysplasia in a canine pedigree constructed by mating dysplastic Labrador retrievers with unaffected greyhounds. Am. J. Vet. Res. 63: 1029-1035.
5. BREEN, M., S. JOUQUAND, C. RENIER, C. S. MELLERSH, C. HITTE et al., 2001 Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes. Mamm. Genome 11: 1784-1795.
6. CHARLESWORTH, B., 1991 The evolution of sex chromosomes. Science 251: 1030-1033.
7. FARNIR, F., W. COPPIETERS, J. J. ARRANZ, P. BERZI, N. CAMBISANO et al., 2000 Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 10: 220-227.
8. HALDANE, J. B. S., 1949 The association of characters as a result of inbreeding and linkage. Ann. Eugen. 15: 15-23.
9. HALL, D., E. M. WIJSMAN, J. L. ROOS, J. A. GOGOS and M. KARAYIORGOU, 2002 Extended intermarker linkage disequilibrium in the Afrikaners. Genome Res. 12: 956-961.
10. HAMILTON, D. C., and D. E. COLE, 2004 Standardizing a composite measure of linkage disequilibrium. Ann. Hum. Genet. 68: 234-239.
11. HYUN, C., L. J. FILIPPICH, R. A. LEA, G. SHEPHERD, I. P. HUGHES et al., 2003 Prospects for whole genome linkage disequilibrium mapping in domestic dog breeds. Mamm. Genome 14: 640-649.
12. LEWONTIN, R. C., 1964 The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49: 49-67.
13. LEWONTIN, R. C., 1988 On measures of gametic disequilibrium. Genetics 120: 849-852.
14. LINDBLAD-TOH, K., C. M. WADE, T. S. MIKKELSEN, E. K. KARLSSON, D. B. JAFFE et al., 2005 Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438: 803-819.
15. LOU, X.-Y., R. J. TODHUNTER, M. LIN, Q. LU, T. LIU et al., 2003 The extent and distribution of linkage disequilibrium in canine. Mamm. Genome 14: 555-564.
16. LYNCH, M., and B. WALSH, 1998 Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.
17. MCRAE, A. F., J. C. MCEWAN, K. G. DODDS, T. WILSON, A. M. CRAWFORD et al., 2002 Linkage disequilibrium in domestic sheep. Genetics 160: 1113-1122.
18. MELLERSH, C. S., A. A. LANGSTON, G. M. ACLAND, M. A. FLEMING, K. RAY et al., 1997 A linkage map of the canine genome. Genomics 46: 326-336.
19. MELLERSH, C. S., C. HITTE, M. RICHMAN, F. VIGNAUX, C. PRIAT et al., 2000 An integrated linkage-radiation hybrid map of the canine genome. Mamm. Genome 11: 120-130.
20. PARKER, H. G., and E. A. OSTRANDER, 2005 Canine genomics and genetics: running with the pack. PLoS Genet. 1(5): e58.
21. OSTRANDER, E. A., and R. K. WAYNE, 2005 The canine genome. Genome Res. 15: 1706-1716.
22. REMINGTON, D. L., J. M. THORNSBERRY, Y. MATSUOKADAGGER, L. M. WILSON, S. R. WHITT et al., 2001 Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. USA 98: 11479-11484.
23. RICHMAN, M., C. S. MELLERSH, C. ANDRE, F. GAILBERT and E. A. OSTRANDER, 2001 Characterization of a minimal screening set of 172 microsatellite markers for genome-wide screens of the canine genome. J. Biochem. Biophys. Methods 47: 137-149.
24. SUTTER, N. B., and E. A. OSTRANDER, 2004 Dog star rising: the canine genetic system. Nat. Rev. Genet. 5: 900-910.
25. SUTTER, N. B., M. A. EBERLE, H. G. PARKER, B. J. PULLAR, E. F. KIRKNESS et al., 2004 Extensive and breed-specific linkage disequilibrium in Canis familiaris. Genome Res. 14: 2388-2396.
26. TENESA, A., A. F. WRIGHT, S. A. KNOTT, A. D. CAROTHERS, C. HAYWARD et al., 2004 Extent of linkage disequilibrium in a Sardinian subisolate: sampling and methodological considerations. Hum. Mol. Genet. 13: 25-33.
27. TODHUNTER, R. J., G. M. ACLAND, M. OLIVIER, A. J. WILLIAMS, M. VERNIER-SINGER et al., 1999 An outcrossed canine pedigree for linkage analysis of hip dysplasia. J. Hered. 90: 83-92.
28. TODHUNTER, R. J., G. CASELLA, S. P. BLISS, G. LUST, A. J. WILLIAMS et al., 2003a Power of a dysplastic Labrador retriever-greyhound pedigree for linkage analysis of hip dysplasia. Am. J. Vet. Res. 64: 418-424.
29. TODHUNTER, R. J., S. R. BLISS, S. R. QUAAS, G. LUST, G. CASELLA et al., 2003b Genetic structure of susceptibility traits for hip dysplasia and microsatellite informativeness of an outcrossed canine pedigree. J. Hered. 94: 39-48.
30. VARILO, T., T. PAUNIO, A. PARKER, M. PEROLA, J. MEYER et al., 2003 The interval of linkage disequilibrium (LD) detected with microsatellite and SNP markers in chromosomes of Finnish populations with different histories. Hum. Mol. Genet. 12: 51-59.
31. WEIR, B. S., 1996 Genetic Data Analysis II. Sinauer Associates. Sunderland, MA.
32. WEIR, B. S., and C. C. COCKERHAM, 1989 Complete characterization of disequilibrium at two loci, pp. 86-110 in Mathematical Evolutionary Theory, edited by M. W. FELDMAN. Princeton University Press, Princeton, NJ.
33. YANG, R.-C., 2000 Zygotic associations and multilocus statistics in a nonequilibrium diploid population. Genetics 155: 1449-1458.
34. YANG, R.-C., 2002 Analysis of multilocus zygotic associations. Genetics 161: 435-445.
35. ZAYKIN, D. V., 2004 Bounds and normalization of the composite linkage disequilibrium coefficient. Genet. Epidemiol. 27: 252-257.