The transition from quantitative trait loci to diagnostic test in cattle and other livestock

Australian Journal of Experimental Agriculture

Volumn 45, Issue 7-8, 2005, Pages 831-836

  Barendse, W ^a  

^a CSIRO   (Australia)

Author keywords

DNA; Genomics; Pigs; QTL; Sheep

Indexed keywords

CATTLE; GENETIC ANALYSIS; LIVESTOCK;

BOS TAURUS; OVIS ARIES; SUS SCROFA;

EID: 33644762635     PISSN: 08161089     EISSN: None     Source Type: Journal    
DOI: 10.1071/EA05067     Document Type: Conference Paper

References (52)

1. Andersson L, Haley CS, Ellegren H, Knott SA, Johansson M, et al. (1994) Genetic mapping of quantitative trait loci for growth and fatness in pigs. Science 263, 1771-1774.
2. Barendse W (2002) Development and commercialisation of a genetic marker for marbling of beef in cattle: a case study. In 'Intellectual property rights in animal breeding and genetics'. (Eds MF Rothschild, S Newman) pp. 197-212. (CABI Publishing: Oxford)
3. Barendse W (2003) DNA markers for marbling. Patent publication WO2004070055.
4. Barendse W, Bunch RJ, Harrison BE (2005) The leptin C73T missense mutation is not associated with marbling and fatness traits in a large gene mapping experiment in Australian cattle. Animal Genetics 36, 86-88. doi:10.1111/j.1365-2052.2004.01224.x
5. Beh KJ, Hulme DJ, Callaghan MJ, Leish Z, Lenane I, Windon RG, Maddox JF (2002) A genome scan for quantitative trait loci affecting resistance to Trichostrongylus colubriformis in sheep. Animal Genetics 33, 97-106. doi:10.1046/j.1365-2052.2002. 00829.x
6. Breese EL, Mather K (1957) The organisation of polygenic activity within a chromosome in Drosophila I. Hair characters. Heredity 11, 373-395.
7. Buchanan FC, Fitzsimmons CJ, van Kessel AG, Thue TD, Winkelman-Sim DC, Schmutz SM (2002) Association of a missense mutation in the bovine leptin gene with carcass fat content and leptin mRNA levels. Genetics, Selection, Evolution. 34, 105-116. doi:10.1051/gse:2001006
8. Carlson CS, Eberle MA, Rieder MJ, Smith JD, Kruglak L, Nickerson DA (2003) Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nature Genetics 33, 518-521. doi:10.1038/ng1128
9. Collins FS (1995) Positional cloning moves from perditional to traditional. Nature Genetics 9, 347-350. doi:10.1038/ng0495-347
10. Collins HE, Li H, Inda SE, Anderson J, Laiho K, Tuomilehto J, Seldin M (2000) A simple and accurate method for determination of micro satellite total allele content differences between DNA pools. Human Genetics 106, 218-226. doi:10.1007/s004390051031
11. Darvasi A (1997) The effect of selective genotyping on QTL mapping accuracy. Mammalian Genome 8, 67-68. doi:10.1007/s0033599 00353
12. Davis GP, Hetzel DJS, Corbel NJ, Scacheri S, Lowden S, Renaud J, Mayne C, Stevenson R, Moore SS, Byrne K (1998) The mapping of quantitative trait loci for birth weight in a tropical beef herd. In 'Proceedings of the 6th world congress of genetics applied to livestock production. Vol. 26'. pp. 441-444. (WCGALP: Armidale, NSW)
13. Dominik S (2005) Quantitative trait loci for internal nematode resistance in sheep: a review. Genetics, Selection, Evolution. 37, S83-S96. doi:10.1051/gse:2004027Suppl. 1
14. Edwards JH (1997) Recessive disease and allelic association. In 'Genetic mapping of disease genes'. (Eds I-H Pawlowitzki, JH Edwards, EA Thompson) pp. 31-57. (Academic Press: San Diego)
15. Farnir F, Coppieters W, Arranz J-J, Berzi P, Cambisano N, et al. (2000) Extensive genome-wide linkage disequilibrium in cattle. Genome Research 10, 220-227. doi:10.1101/gr.10.2.220
16. Franklin IR, Mayo O (1996) The place of QTL in the basis of quantitative genetics. II. Mapping QTL from a wide cross. In 'Proceedings of the 6th world congress of genetics applied to livestock production. Vol. 26'. pp. 273-276. (WCGALP: Armidale, NSW)
17. Georges M, Nielsen D, Mackinnon M, Mishra A, Okimoto R, et al. (1995) Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics 139, 907-920.
18. Grobet L, Martin LJR, Poncelet D, Pirottin D, Browers B, et al. (1997) A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nature Genetics 17, 71-74. doi:10.1038/ng0997-71
19. Hardenbol P, Baner J, Jain M, Nilsson M, Namsaraev EA, et al. (2003) Multiplex genotyping with sequence-tagged molecular inversion probes. Nature Biotechnology 21, 673-678. doi:10.1038/nbt821
20. Hanotte O, Ronin Y, Agaba M, Nilsson P, Gelhaus A, et al. (2003) Mapping of quantitative trait loci controlling trypanotolerance in a cross of tolerant West African N'Dama and susceptible East African Boran cattle. Proceedings of the National Academy of Sciences of the United States of America 100, 7443-7448. doi:10.1073/pnas.1232392100
21. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921. doi:10.1038/35057062
22. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431, 931-945. doi:10.1038/nature03001
23. Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genetics 22, 139-144. doi:10.1038/9642
24. Kuhn Ch, Leveziel H, Renand G, Goldammer T, Schwerin M, Williams J (2005) Genetic markers for beef quality. In 'Indicators of milk and beef quality'. EAAP publication No. 112. (Eds JF Hocquette, S Gigli) pp. 23-32. (Wageningen Academic Publishers: Wageningen, The Netherlands)
25. Lander ES, Kruglyak L (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nature Genetics 11, 241-247. doi:10.1038/ng1195-241
26. Lisitsyn NA, Segre JA, Kusumi K, Lisitsyn NM, Nadeau JH, Frankel WN, Wigler MH, Lander ES (1994) Direct isolation of polymorphic markers linked to a trait by genetically directed representational difference analysis. Nature Genetics 6, 57-63. doi:10.1038/ng0194-57
27. Luo LJ, Li Z-K, Mei HW, Shu QY, Tabien R, Zhong DB, Ying CS, Stansel JW, Khush GS, Paterson AH (2001) Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. II. Grain yield components. Genetics 158, 1755-1771.
28. McRae AF, McEwan JC, Dodds KG, Wilson T, Crawford AM, Slate J (2002) Linkage disequilibrium in domestic sheep. Genetics 160, 1113-1122.
29. Mira MT, Alcais A, Thuc NV, Moraes MO, Di Flumeri C, et al. (2004) Susceptibility to leprosy is associated with PARK2 and PACRG. Nature 427, 636-640. doi:10.1038/nature02326
30. Mohlke KL, Erdos MR, Scott LJ, Fingerlin TE, Jackson AU, Silander K, Hollstein P, Boehnke M, Collins FS (2002) High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools. Proceedings of the National Academy of Sciences of the United States of America 99, 16928-16933. doi:10.1073/pnas.262661399
31. Morton NE, Lio P (1997) Oligogenic linkage and map integration. In 'Genetic mapping of disease genes'. (Eds I-H Pawlowitski, JH Edwards, EA Thompson) pp. 17-21. (Academic Press: San Diego)
32. Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562. doi:10.1038/nature01262
33. Nagamine Y, Haley CS, Sewalem A, Visscher PM (2003) Quantitative trait loci variation for growth and obesity between and within line of pigs (Sus scrofa). Genetics 164, 629-635.
34. Nsengimana J, Baret P, Haley CS, Visscher PM (2004) Linkage disequilibrium in the domesticated pig. Genetics 166, 1395-1404. doi: 10.1534/genetics.166.3.1395
35. Otsu K, Khanna VK, Archibald AL, Maclennan DH (1991) Cosegregation of porcine malignant hyperthermia and a probable causal mutation in the skeletal-muscle ryanodine receptor gene in backcross families. Genomics 11, 744-750. doi:10.1016/0888-7543(91)90083-Q
36. Ott J (1985) 'Analysis of human genetic linkage.' (The Johns Hopkins University Press: Baltimore)
37. Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Lincoln SE, Lander ES, Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato - comparison across species generations and environments. Genetics 127, 181-197.
38. Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete RFLP linkage map. Nature 335, 721-726. doi:10.1038/335721a0
39. Perneger TV (1998) What's wrong with Bonferroni adjustments. British Medical Journal 316, 1236-1238.
40. Purvis IW, Franklin IR (2005) Major genes and QTL influencing wool production and quality: a review. Genetics, Selection, Evolution 37(Suppl. 1), S97-107. doi:10.1051/gse:2004028
41. Riordan JR, Rommens JM, Kerem BS, Alon N, Rozmahel R, et al. (1989) Identification of the cystic-fibrosis gene-cloning and characterization of complementary-DNA. Science 245, 1066-1072.
42. Rothschild MF, Plastow GS (2002) Development of a genetic marker for litter size in the pig: a case study. In 'Intellectual property rights in animal breeding and genetics'. (Eds MF Rothschild, S Newman) pp. 179-196. (CABI Publishing: Oxford)
43. Shrimpton AE, Robertson A (1988) The isolation of polygenic factors controlling bristle score in Drosophila melanogaster. I. Allocation of third chromosome sternopleural bristle effects to chromosome sections. Genetics 118, 437-443.
44. Soller M, Brody T, Genizi A (1976) On the power of experimental designs for the detection of linkage between marker loci and quantitative loci in crosses between inbred lines. Theoretical and Applied Genetics 47, 35-39. doi:10.1007/BF00277402
45. Stone RT, Keele JW, Shackelford SD, Kappes SM, Koohmaraie M (1999) A primary screen of the bovine genome for quantitative trait loci affecting carcass and growth traits Journal of Animal Science 77, 1379-1384.
46. Tenesa A, Knott SA, Ward D, Smith D, Williams JL, Visscher PM (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.
47. Thompson EA (1997) Conditional gene identity in affected individuals. In 'Genetic mapping of disease genes'. (Eds I-H Pawlowitski, JH Edwards, EA Thompson) pp. 137-146. (Academic Press: San Diego)
48. Toda T, Momose Y, Murata M, Tamiya G, Yamamoto M, Hattori N, Inoko H (2003) Toward identification of susceptibility genes for sporadic Parkinson's disease. Journal of Neurology 250, iii40-iii43. doi:10.1007/s00415-003-1307-6
49. Vos P, Hogers R, Bleeker M, Reijans M, Lee T, et al. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 21, 4407-4414.
50. Wang DL, Zhu J, Li ZK, Paterson AH (1999) Mapping QTLs with epistatic effects and QTLxenvironment interactions by mixed linear model approaches. Theoretical and Applied Genetics 99, 1255-1264. doi:10.1007/s001220051331
51. Weller JI (2001) 'Quantitative trait loci analysis in animals.' (CABI Publishing: New York)
52. Wilson T, Wu X-Y, Juengel JL, Ross IK, Lumsden JM, et al. (2001) Highly prolific Booroola sheep have a mutation in the intracellular kinase domain of Bone Morphogenetic Protein IB Receptor (ALK-6) that is expressed in both oocytes and granulosa cells. Biology of Reproduction 64, 1225-1235.