Genetic diversity and background linkage disequilibrium in the North American Holstein cattle population

Journal of Dairy Science

Volumn 86, Issue 12, 2003, Pages 4137-4147

  Vallejo, R L ^a   Li, Y L ^a   Rogers, G W ^b   Ashwell, M S ^c  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF TENNESSEE   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

Background linkage disequilibrium; Genetic diversity; Holstein; Linkage disequilibrium

Indexed keywords

BOS TAURUS; MAMMALIA;

FLUORESCENT DYE; MICROSATELLITE DNA;

ANIMAL; ARTICLE; CATTLE; GENE LINKAGE DISEQUILIBRIUM; GENETIC VARIABILITY; GENETICS; GENOTYPE; HETEROZYGOTE; MALE; NORTH AMERICA; POLYMERASE CHAIN REACTION;

ANIMALS; CATTLE; FLUORESCENT DYES; GENOTYPE; HETEROZYGOTE; LINKAGE DISEQUILIBRIUM; MALE; MICROSATELLITE REPEATS; NORTH AMERICA; POLYMERASE CHAIN REACTION; VARIATION (GENETICS);

EID: 1642414288     PISSN: 00220302     EISSN: None     Source Type: Journal    
DOI: 10.3168/jds.S0022-0302(03)74028-4     Document Type: Article

References (31)

1. Ashwell, M. S., and C. P. Van Tassell. 1999. Detection of putative loci affecting milk, health, and type traits in a US Holstein population using 70 microsatellite markers in a genome scan. J. Dairy Sci. 82:2497-2502.
2. Ashwell, M. S., C. E. Rexroad, R. H. Miller, and P. M. VanRaden. 1996. Mapping economic trait loci for somatic cell score in Holstein cattle using microsatellite markers and selective genotyping. Anim. Genet. 27:235-242.
3. Bishop, M. D., S. M. Kappes, J. W. Keele, R. T. Stone, S. L. F. Sunden, G. A. Hawkins, S. Solinas Toldo, R. Fries, M. D. Grosz, J. Yoo, and C. W. Beattie. 1994. A genetic linkage map for cattle. Genetics 136:619-639.
4. Bitti, P. P., B. S. Murgia, A. Ticca, R. Ferrai, L. Musu, M. L. Piras, E. Puledda, S. Campo, S. Durando, C. Montomoli, D. G. Clayton, A. P. Mander, and L. Bernardinelli. 2001. Association between the ancestral haplotype HLA A30B18DR3 and multiple sclerosis in central Sardinia. Genet. Epidemiol. 20:271-283.
5. Blott, S., J. J. Kim, S. Moisio, A. Schmidt-Kuntzel, A. Cornet, P. Berzi, N. Cambisano, C. Ford, D. Johnson, L. Karim, P. Simon, R. Snell, R. Spelman, J. Wong, J. Vilkki, M. Georges, F. Farnir, and W. Coppieters. 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 163:253-266.
6. de la Chapelle, A., and F. A. Wright. 1998. Linkage disequilibrium mapping in isolated populations: the example of Finland revisited. Proc. Natl. Acad. Sci. USA 95:12416-12423.
7. Devlin, B., K. Roeder, C. Otto, S. Tiobech, and W. Byerley. 2001. Genome-wide distribution of linkage disequilibrium in the population of Palau and its implications for gene flow in remote Oceania. Hum. Genet. 108:521-528.
8. Farnir, F., W. Coppieters, J. J. Arranz, P. Berzi, N. Cambisano, B. Grisart, L. Karim, F. Marcq, L. Moreau, M. Mni, C. Nezer, P. Simon, P. Vanmanshoven, D, Wagenaar, and M. Georges. 2000. Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 10:220-227.
9. Fleiss, J. L. 1981. Statistical Methods for Rates and Proportions. 2nd ed. John Wiley & Sons, New York, NY.
10. Freimer, N. B., S. K. Service, and M. Slatkin. 1997. Expanding on population studies. Nat. Genet. 17:371-373.
11. Gaspar, C., I. Lopes-Cendes, S. Hayes, J. Goto, K. Arvidsson, A. Dias, I. Silveira, P. Maciel, P. Coutinho, M. Lima, Y. X. Zhou, B. W. Soong, M. Watanabe, P. Giunti, G. Stevanin, O. Riess, H. Sasaki, M. Hsieh, G. A. Nicholson, E. Brunt, J. J. Higgins, M. Lauritzen, L. Tranebjaerg, V. Volpini, N. Wood, L. Ranum, S. Tsuji, A. Brice, J. Sequeiros, and G. A. Rouleau. 2001. Ancestral origins of the Machado-Joseph disease mutation: A worldwide haplotype study. Am. J. Hum. Genet. 68:523-528.
12. Georges, M., D. Nielsen, M. Mackinnon, A. Mishra, R. Okimoto, A. T. Pasquino, L. S. Sargeant, A. Sorensen, M. R. Steele, X. Zhao, J. E. Womack, and I. Hoeschele. 1995. Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics 139:907-920.
13. Grisart, B., W. Coppieters, F. Farnir, L. Karim, C. Ford, P. Berzi, N. Cambisano, M. Mni, S. Reid, P. Simon, R. Spelman, M. Georges, and R. Snell. 2002. Positional candidate cloning of a QTL in dairy cattle: Identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res. 12:222-231.
14. Huttley, G. A., M. W. Smith, M. Carrington, and S. J. O'Brien. 1999. A scan for linkage disequilibrium across the human genome. Genetics 152:1711-1722.
15. Kappes, S. M., J. W. Keele, R. T. Stone, R. A. McGraw, T. S. Sonstegard, T. P. L. Smith, N. L. Lopez Corrales, and C. W. Beattie. 1997. A second-generation linkage map of the bovine genome. Genome Res. 7:235-249.
16. Kim, K. S., J. S. Yeo, and C. B. Choi. 2002. Genetic diversity of North-East Asian cattle based on microsatellite data. Anim. Genet. 33:201-204.
17. Laan, M., and S. Paabo. 1997. Demographic history and linkage disequilibrium in human populations. Nat. Genet. 17:435-438.
18. Lange, K., M. Boehnke, and D. E. Weeks. 1988. Programs for pedigree analysis: Mendel, Fisher, and dGene. Genet. Epidemiol. 5:471-472.
19. Lewontin, R. C. 1964. The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49:49-67.
20. Long, J. C. 1999. Documentation for program 3locus.pas version 5.0. Laboratory of Neurogenetics, National Institute on Alcoholism and Alcohol Abuse, National Institutes of Health, Bethesda, MD.
21. Maudet, C., G. Luikart, and P. Taberlet. 2002. Genetic diversity and assignment tests among seven French cattle breeds based on microsatellite DNA analysis. J. Anim. Sci. 80:942-950.
22. Mukhopadhyay, N., L. Almasy, M. Schroeder, W. P. Mulvihill, and D. E. Weeks. 1999. Mega2, a data handling program for facilitating genetic linkage and association analysis. Am. J. Hum. Genet. 65(Suppl.):A436. (Abstr.)
23. Peltonen, L. 2000. Positional cloning of disease genes: Advantages of genetic isolates. Hum. Hered. 50:66-75.
24. Pritchard, J. K., and M. Przeworski. 2001. Linkage disequilibrium in humans: Models and data. Am. J. Hum. Genet. 69:1-14.
25. Schneider, S., D. Roessli, and L. Excoffier. 2000. Arlequin: A software for population genetics data analysis, version 2.0. Genetics and Biometry Lab., Department of Anthropology, University of Geneva.
26. Service, S. K., R. A. Ophoff, and N. B. Freimer. 2001. The genome-wide distribution of background linkage disequilibrium in a population isolate. Hum. Mol. Genet. 10:545-551.
27. Sheffield, V. C., E. M. Stone, and R. Carmi. 1998. Use of isolated inbred human populations for identification of disease genes. Trends Genet. 14:391-396.
28. Shinar, Y., B. Ben-Zeev, N. Brand, H. Lahat, V. Gross-Zur, D. MacGregor, T. Bahan, D. L. Kastner, and E. Pras. 2002. A common ancestral haplotype in carrier chromosomes from different ethnic backgrounds in vacuolating megalencephalic leucoencephalopathy with subcortical cysts. J. Med. Genet. 39:54-57.
29. Slatkin, M. 1994. Linkage disequilibrium in growing and stable populations. Genetics 137:331-336.
30. Terwilliger, J. D., S. Zollner, M. Laan, and S. Paabo. 1998. Mapping genes through the use of linkage disequilibrium generated by genetic drift: "drift mapping" in small populations with no demographic expansion. Hum. Hered. 48:138-154.
31. Wright, A. F., A. D. Carothers, and M. Pirastu. 1999. Population choice in mapping genes for complex diseases. Nat. Genet. 61:151-161.