Farnir F, Coppieters W, Arranz JJ, Berzi P, Cambisano N, Grisart B, Karim L, Marcq F, Moreau L, Mni M, Nezer C, Simon P, Vanmanshoven P, Wagenaar D, Georges M: Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 2000, 10 (2): 220-227. 10.1101/gr.10.2.220.
Article
CAS
PubMed
Google Scholar
Vallejo RL, Li YL, Rogers GW, Ashwell MS: Genetic diversity and background linkage disequilibrium in the North American Holstein cattle population. J Dairy Sci. 2003, 86 (12): 4137-4147.
Article
CAS
PubMed
Google Scholar
Tenesa A, Knott SA, Ward D, Smith D, Williams JL, Visscher PM: Estimation of linkage disequilibrium in a sample of the United Kingdom dairy cattle population using unphased genotypes. J Anim Sci. 2003, 81 (3): 617-623.
CAS
PubMed
Google Scholar
Khatkar MS, Collins A, Cavanagh JA, Hawken RJ, Hobbs M, Zenger KR, Barris W, McClintock AE, Thomson PC, Nicholas FW, Raadsma HW: A first-generation metric linkage disequilibrium map of bovine chromosome 6. Genetics. 2006, 174 (1): 79-85. 10.1534/genetics.106.060418.
Article
PubMed Central
CAS
PubMed
Google Scholar
Varilo T, Paunio T, Parker A, Perola M, Meyer J, Terwilliger JD, Peltonen L: The interval of linkage disequilibrium (LD) detected with microsatellite and SNP markers in chromosomes of Finnish populations with different histories. Hum Mol Genet. 2003, 12 (1): 51-59. 10.1093/hmg/ddg005.
Article
CAS
PubMed
Google Scholar
Odani M, Narita A, Watanabe T, Yokouchi K, Sugimoto Y, Fujita T, Oguni T, Matsumoto M, Sasaki Y: Genome-wide linkage disequilibrium in two Japanese beef cattle breeds. Anim Genet. 2006, 37 (2): 139-144. 10.1111/j.1365-2052.2005.01400.x.
Article
CAS
PubMed
Google Scholar
Vignal A, Milan D, SanCristobal M, Eggen A: A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol. 2002, 34 (3): 275-305. 10.1051/gse:2002009.
Article
PubMed Central
CAS
PubMed
Google Scholar
Thallman RM, Bennett GL, Keele JW, Kappes SM: Efficient computation of genotype probabilities for loci with many alleles: I. Allelic peeling. J Anim Sci. 2001, 79 (1): 26-33.
CAS
PubMed
Google Scholar
Thallman RM, Bennett GL, Keele JW, Kappes SM: Efficient computation of genotype probabilities for loci with many alleles: II. Iterative method for large, complex pedigrees. J Anim Sci. 2001, 79 (1): 34-44.
CAS
PubMed
Google Scholar
McKay SD, Schnabel RD, Murdoch BM, Aerts J, Gill CA, Gao C, Li C, Matukumalli LK, Stothard P, Wang Z, Van Tassell CP, Williams JL, Taylor JF, Moore SS: Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping. Anim Genet. 2007, 38 (2): 120-125. 10.1111/j.1365-2052.2006.01564.x.
Article
PubMed Central
CAS
PubMed
Google Scholar
Baylor College of Medicine- Bovine Genome Project Website: http://www.hgsc.bcm.tmc.edu/projects/bovine/.
Schaeffer SW, Miller EL: Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura. Genetics. 1993, 135 (2): 541-552.
PubMed Central
CAS
PubMed
Google Scholar
Du FX, Clutter AC, Lohuis MM: Characterizing linkage disequilibrium in pig populations. Int J Biol Sci. 2007, 3 (3): 166-178.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SM, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES: Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005, 438 (7069): 803-819. 10.1038/nature04338.
Article
CAS
PubMed
Google Scholar
Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR: Whole-genome patterns of common DNA variation in three human populations. Science. 2005, 307 (5712): 1072-1079. 10.1126/science.1105436.
Article
CAS
PubMed
Google Scholar
Schnabel RD, Kim JJ, Ashwell MS, Sonstegard TS, Van Tassell CP, Connor EE, Taylor JF: Fine-mapping milk production quantitative trait loci on BTA6: analysis of the bovine osteopontin gene. Proc Natl Acad Sci U S A. 2005, 102 (19): 6896-6901. 10.1073/pnas.0502398102.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ardlie KG, Kruglyak L, Seielstad M: Patterns of linkage disequilibrium in the human genome. Nat Rev Genet. 2002, 3 (4): 299-309. 10.1038/nrg777.
Article
CAS
PubMed
Google Scholar
Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, Ghori J, Whittaker P, Collins A, Morris AP, Bentley D, Cardon LR, Deloukas P: The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum Mol Genet. 2004, 13 (6): 577-588. 10.1093/hmg/ddh060.
Article
CAS
PubMed
Google Scholar
Khatkar MS, Zenger KR, Hobbs M, Hawken RJ, Cavanagh JA, Barris W, McClintock AE, McClintock S, Thomson PC, Tier B, Nicholas FW, Raadsma HW: A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle. Genetics. 2007, 176 (2): 763-772. 10.1534/genetics.106.069369.
Article
PubMed Central
CAS
PubMed
Google Scholar
Boyles AL, Scott WK, Martin ER, Schmidt S, Li YJ, Ashley-Koch A, Bass MP, Schmidt M, Pericak-Vance MA, Speer MC, Hauser ER: Linkage disequilibrium inflates type I error rates in multipoint linkage analysis when parental genotypes are missing. Hum Hered. 2005, 59 (4): 220-227. 10.1159/000087122.
Article
PubMed Central
PubMed
Google Scholar
Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES: High-resolution haplotype structure in the human genome. Nat Genet. 2001, 29 (2): 229-232. 10.1038/ng1001-229.
Article
CAS
PubMed
Google Scholar
Zhao H, Nettleton D, Soller M, Dekkers JC: Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL. Genet Res. 2005, 86 (1): 77-87. 10.1017/S001667230500769X.
Article
CAS
PubMed
Google Scholar
Pritchard JK, Przeworski M: Linkage disequilibrium in humans: models and data. Am J Hum Genet. 2001, 69 (1): 1-14. 10.1086/321275.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kruglyak L: Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet. 1999, 22 (2): 139-144. 10.1038/9642.
Article
CAS
PubMed
Google Scholar
Weiss KM, Clark AG: Linkage disequilibrium and the mapping of complex human traits. Trends Genet. 2002, 18 (1): 19-24. 10.1016/S0168-9525(01)02550-1.
Article
CAS
PubMed
Google Scholar
Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, Goddard ME, Visscher PM: Recent human effective population size estimated from linkage disequilibrium. Genome Res. 2007, 17 (4): 520-526. 10.1101/gr.6023607.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sanders JO: History and development of Zebu cattle in the United States. J Anim Sci. 1980, 50: 1188-1200.
Google Scholar
Hu ZL, Reecy JM: Animal QTLdb: beyond a repository : A public platform for QTL comparisons and integration with diverse types of structural genomic information. Mamm Genome. 2007, 18 (1): 1-4. 10.1007/s00335-006-0105-8.
Article
PubMed
Google Scholar
Polineni P, Aragonda P, Xavier SR, Furuta R, Adelson DL: The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci. BMC Bioinformatics. 2006, 7: 283-10.1186/1471-2105-7-283.
Article
PubMed Central
PubMed
Google Scholar
Website, NCBI, Mapview: . [http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9913]
Website, USDA, MARC: . [http://www.marc.usda.gov/genome/genome.html]
Yu A, Zhao C, Fan Y, Jang W, Mungall AJ, Deloukas P, Olsen A, Doggett NA, Ghebranious N, Broman KW, Weber JL: Comparison of human genetic and sequence-based physical maps. Nature. 2001, 409 (6822): 951-953. 10.1038/35057185.
Article
CAS
PubMed
Google Scholar
Website, NCBI, dbSNP: . [http://www.ncbi.nlm.nih.gov/projects/SNP/]
Website, Medicine BC, FTP: . [ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Btaurus/snp]
Oliphant A, Barker DL, Stuelpnagel JR, Chee MS: BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques. 2002, Suppl: 56-8, 60-1..
PubMed
Google Scholar
Website, Illumina: . [http://www.illumina.com]
Abecasis GR, Cookson WO: GOLD--graphical overview of linkage disequilibrium. Bioinformatics. 2000, 16 (2): 182-183. 10.1093/bioinformatics/16.2.182.
Article
CAS
PubMed
Google Scholar