Estimation of the extent of linkage disequilibrium in seven regions of the porcine genome

Animal Biotechnology

Volumn 16, Issue 1, 2005, Pages 41-54

  Jungerius, Bart J ^a,c   Jingjing, Gu ^a   Crooijmans, Richard P M A ^a   Van Der Poel, Jan J ^a   Groenen, Martien A M ^a   Van Oost, Bernard A ^b   Te Pas, Marinus F W ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b UTRECHT UNIVERSITY   (Netherlands)

^c UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

Author keywords

Linkage disequilibrium; Pig; Single nucleotide polymorphism

Indexed keywords

CHROMOSOMES; CLONING; COMPUTER SIMULATION; DNA; MUTAGENESIS; PARAMETER ESTIMATION;

LINKAGE DISEQUILIBRIUM (LD); MUTATIONS; PIG; SINGLE NUCLEOTIDE POLYMORPHISM;

GENES;

PIERIS BRASSICAE; SUIDAE; SUS SCROFA;

DNA;

ANIMAL; ANIMAL DISEASE; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHEMISTRY; CROSS BREEDING; DNA SEQUENCE; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOME; GENOTYPE; HAPLOTYPE; MALE; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; SWINE;

ANIMALS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CROSSES, GENETIC; DNA; FEMALE; GENOME; GENOTYPE; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; MALE; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SWINE;

EID: 18844429813     PISSN: 10495398     EISSN: None     Source Type: Journal    
DOI: 10.1081/ABIO-200053402     Document Type: Article

References (24)

1. Clark AG, Weiss KM, Nickerson DA, Taylor SL, Buchanan A, Stengard J, Salomaa V, Vartiainen E, Perola M, Boerwinkle E, Sing CF. Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am J Hum Genet 1998; 63(2):595-612.
2. Rieder MJ, Taylor SL, Clark AG, Nickerson DA. Sequence variation in the human angiotensin converting enzyme. Nat Genet. 1999; 22(1):59-62.
3. Moffatt MF, Traherne JA, Abecasis GR, Cookson Wo. Single nucleotide polymorphism and linkage disequilibrium within the TCR alpha/delta locus. Hum Mol Genet 2000; 12;9(7):1011-9.
4. Templeton AR, Clark AG, Weiss KM, Nickerson DA, Boerwinkle E, Sing CF. Recombinational and mutational hotspots within the human lipoprotein lipase gene. Am J Hum Genet 2000; 66(1):69-83.
5. Dunning AM, Durocher F, Healey CS, Teare MD, McBride SE, Carlomagno F, Xu CF, Dawson E, Rhodes S, Ueda S, Lai E, Luben RN, Van Rensburg EJ, Mannermaa A, Kataja V, Rennart G, Dunham I, Purvis I, Easton D, Ponder BA. The extent of linkage disequilibrium in four populations with distinct demographic histories. Am J Hum Genet 2000; 67(6): 1544-54.
6. Bonfield JK, Staden R. Experiment files and their application during large-scale sequencing projects. DNA Seq 1996; 6(2): 109-17.
7. Bonfield JK, Smith K, Staden R. A new DNA sequence assembly program. Nucleic Acids Res 1995; 23(24):4992-9.
8. Goddard KA, Hopkins PJ, Hall JM, Witte JS. Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms in five populations. Am J Hum Genet 2000; 66(1):216-34.
9. Kidd JR, Pakstis AJ, Zhao H, Lu RB, Okonofua FE, Odunsi A, Grigorenko E, Tamir BB, Friedlaender J, Schulz LO, Parnas J, Kidd KK. Haplotypes and linkage disequilibrium at the phenylalanine hydroxylase locus, PAH, in a global representation of populations. Am J Hum Genet 2000; 66(6): 1882-99.
10. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES. Linkage disequilibrium in the human genome. Nature 2001; 411 (6834): 199-204.
11. Janss LL, Van Arendonk JA, Brascamp EW. Segregation analyses for presence of major genes affecting growth, backfat, and litter size in Dutch Meishan crossbreds. J Anim Sci 1997; 75(11):2864-76.
12. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8(3): 186-94.
13. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8(3):175-85.
14. Aerts JA, Jungerius BJ, Groenen MA. POSA: perl objects for DNA sequencing data analysis. BMC Genomics 2004; 5(1):60.
15. Sobel E, Lange K. Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics. Am J Hum Genet 1996; 58(6): 1323-37.
16. Nei M, Li WH. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA. 1979; 76(10):5269-73.
17. Fahrenkrug SC, Freking BA, Smith TP, Rohrer GA, Keele JW. Single nucleotide polymorphism (SNP) discovery in porcine expressed genes. Anim Genet 2002; 33(3):186-95.
18. Jungerius BJ, Rattink AP, Crooijmans RP, van der Poel JJ, van Oost BA, te Pas MF, Groenen MA. Development of a single nucleotide polymorphism map of porcine chromosome 2. Anim Genet 2003; 34(6):429-37.
19. Kruglyak L. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 1999; 22(2): 139-44.
20. Ardlie KG, Kruglyak L, Seielstad M. Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 2002; 3(4):299-309.
21. Devlin B, Risch N. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics. 1995; 29(2):311-22.
22. Pritchard JK, Przeworski M. Linkage disequilibrium in humans: models and data. Am J Hum Genet. 2001; 69(1):1-14.
23. Weiss KM, Clark AG. Linkage disequilibrium and the mapping of complex human traits. Trends Genet. 2002; 18(1):19-24.
24. Nsengimana J, Baret P, Haley CS, Visscher PM. Linkage disequilibrium in the domesticated pig. Genetics. 2004; 166(3): 1395-404.