Epistasis: Obstacle or advantage for mapping complex traits?

PLoS ONE

Volumn 5, Issue 8, 2010, Pages

  Verhoeven, Koen J F ^a   Casella, George ^b   McIntyre, Lauren M ^c  

^a NETHERLANDS INSTITUTE OF ECOLOGY NIOO KNAW   (Netherlands)

^b UNIVERSITY OF FLORIDA   (United States)

^c Department of Statistics University of Florida ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER SIMULATION; CONTROLLED STUDY; EXPERIMENTAL MODEL; GENE FREQUENCY; GENE LOCUS; GENE MAPPING; GENETIC ANALYSIS; GENETIC EPISTASIS; GENETIC IDENTIFICATION; GENETIC TRAIT; MATHEMATICAL MODEL; PREDICTION; PROCESS MODEL; QUANTITATIVE TRAIT LOCUS; ANIMAL; BIOLOGICAL MODEL; HUMAN; STATISTICAL MODEL;

ANIMALS; EPISTASIS, GENETIC; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; QUANTITATIVE TRAIT LOCI;

EID: 77957878334     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012264     Document Type: Article

References (65)

1. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: the NCBI database of genetic variation. Nucl Acids Res 29: 308-311.
2. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51: 910-918.
3. Kim S, Plagnol V, Hu TT, Toomajian C, Clark RM, et al. (2007) Recombination and linkage disequilibrium in Arabidopsis thaliana. Nat Genet 39: 1151-1155.
4. Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, et al. (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 5: 247-252.
5. Duran C, Appleby N, Clark T, Wood D, Imelfort M, et al. (2009) AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucl Acids Res 37: 951-953.
6. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273: 1516-1517.
7. Doerge RW (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3: 43-52.
8. Wang WYS, Barratt BJ, Clayton DG, Todd JA (2005) Genome-wide association studies: Theoretical and practical concerns. Nat Rev Genet 6: 109-118.
9. Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 22: 185-199.
10. Haley CS, Knott SA (1992) A Simple Regression Method for Mapping Quantitative Trait Loci in Line Crosses Using Flanking Markers. Heredity 69: 315-324.
11. Martinez O, Curnow RN (1992) Estimating the Locations and the Sizes of the Effects of Quantitative Trait Loci Using Flanking Markers. Theor Appl Genet 85: 480-488.
12. Jansen RC (1993) Interval Mapping of Multiple Quantitative Trait Loci. Genetics 135: 205-211.
13. Jansen RC, Stam P (1994) High-Resolution of Quantitative Traits into Multiple Loci Via Interval Mapping. Genetics 136: 1447-1455.
14. Xu SH, Atchley WR (1995) A Random Model Approach to Interval Mapping of Quantitative Trait Loci. Genetics 141: 1189-1197.
15. Zeng ZB (1994) Precision Mapping of Quantitative Trait Loci. Genetics 136: 1457-1468.
16. Jannink JL, Bink M, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. TRENDS Plant Sci 6: 337-342.
17. Ewens WJ, Spielman RS (2001) Locating genes by linkage and association. Theor Pop Biol 60: 135-139.
18. Zheng MX, McPeek MS (2007) Multipoint linkage-disequilibrium mapping with haplotype-block structure. Am J Human Genet 60: 112-125.
19. Strahs A, Cox N, McPeek MS (2000) Multipoint fine-scale linkage disequilibrium mapping by the Decay of Haplotype Sharing using marker genotypes rather than haplotype data. Am J Human Genet 67: 1748 Suppl 2.
20. Ober C, Abney M, McPeek MS (2001) The genetic dissection of complex traits in a founder population. Am J Human Genet 69: 1068-1079.
21. Park M, Lee JW, Kim C (2007) Correspondence analysis approach for finding allele associations in population genetic study. Comp Stat Data Anal 51: 3145-3155.
22. Schulze TG, McMahon FT (2002) Genetic association mapping at the crossroads: Which test and why? Overview and practical guidelines. Am J Med Genet 114: 1-11.
23. Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Human Genet 65: 220-228.
24. Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208.
25. Saxena R, Voight BF, Lyssenko V, Burtt NP, de Bakker PIW, et al. (2007) Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316: 1331-1336.
26. Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456: 720-723.
27. Thomas G, Jacobs KB, Yeager M, Kraft P, Wacholder S, et al. (2008) Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet 40: 310-315.
28. Thorleifsson G, Walters GB, Gudbjartsson DF, Steinthorsdottir V, Sulem P, et al. (2009) Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. Nat Genet 41: 18-24.
29. Elena SF, Lenski RE (1997) Test of synergistic interactions among deleterious mutations in bacteria. Nature 390: 395-398.
30. Templeton AR (2000) Epistasis and complex traits. In: Wade MJ, Brodie BI, Wolf F, eds. Epistasis and the evolutionary process. Oxford University Press. pp 41-57.
31. Remold SK, Lenski RE (2004) Pervasive joint influence of epistasis and plasticity on mutational effects in Escherichia coli. Nat Genet 36: 423-426.
32. Brem RB, Storey JD, Whittle J, Kruglyak L (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature 436: 701-703.
33. Carlborg O, Haley CS (2004) Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5: 618-625.
34. Carlborg O, Jacobsson L, Ahgren P, Siegel P, Andersson L (2006) Epistasis and the release of genetic variation during long-term selection. Nat Genet 38: 418-420.
35. Ehrenreich IM, Stafford PA, Purugganan MD (2007) The genetic architecture of shoot branching in Arabidopsis thaliana: A comparative assessment of candidate gene associations vs quantitative trait locus mapping. Genetics 176: 1223-1236.
36. Shao HF, Burrage LC, Sinasac DS, Hill AE, Ernest SR, et al. (2008) Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis. Proc Natl Acad Sci U S A 105: 19910-19914.
37. Hartl DL, Jones EJ (2004) Genetics: Analysis Of Genes And Genomes. Sudbury: Jones & Bartlett.
38. Wade MJ (2001) Epistasis complex traits and mapping genes. Genetica 112-113: 59-69.
39. Evans DM, Marchini J, Morris AP, Cardon LR (2006) Two-stage two-locus models in genome-wide association. PLoS Genet 2: 1424-1432.
40. Phillips PC (1998) The language of gene interaction. Genetics 149: 1167-1171.
41. Phillips PC (2008) Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9: 855-867.
42. Holland JB, Moser HS, Odonoughue LS, Lee M (1997) QTLs and epistasis associated with vernalization responses in oat. Crop Sci 37: 1306-1316.
43. Peripato AC, de Brito RA, Vaughn TT, Pletscher LS, Matioli SR, et al. (2002) Quantitative trait loci for maternal performance for offspring survival in mice. Genetics 162: 1341-1353.
44. Carlborg O, Kerje S, Schutz K, Jacobsson L, Jensen P, et al. (2003) A global search reveals epistatic interaction between QTL for early growth in the chicken. Genome Res 13: 413-421.
45. Carlborg O, Brockmann GA, Haley CS (2005) Simultaneous mapping of epistatic QTL in DU6i x DBA/2 mice. Mamm Genome 16: 481-494.
46. Coffman CJ, Doerge RW, Simonsen KL, Nichols KM, Duarte C, et al. (2005) Model selection in binary trait locus mapping. Genetics 170: 1281-1297.
47. Marchini J, Donnelly P, Cardon LR (2005) Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 37: 413-417.
48. Moore JH, Gilbert JC, Tsai CT, Chiang FT, Holden T, et al. (2006) A flexible computational framework for detecting characterizing and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility. J Theor Biol 241: 252-261.
49. Xiao J, Li J, Yuan L, Tanksley SD (1996) Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross. Theor Appl Genet 92: 230-244.
50. Li ZK, Pinson SRM, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L). Genetics 145: 453-465.
51. Routman EJ, Cheverud JM (1997) Gene effects on a quantitative trait: Twolocus epistatic effects measured at microsatellite markers and at estimated QTL. Evolution 51: 1654-1662.
52. Gurganus MC, Nuzhdin SV, Leips JW, Mackay TFC (1999) High-resolution mapping of quantitative trait loci for sternopleural bristle number in Drosophila melanogaster. Genetics 152: 1585-1604.
53. Jannink JL, Jansen RC (2001) Mapping epistatic quantitative trait loci with onedimensional genome searches. Genetics 157: 445-454.
54. Eaves LJ (1994) Effects of genetic architecture on the power of human linkage studies to resolve the contribution of quantitative trait loci. Heredity 72: 175-192.
55. Broman KW, Speed TR (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses. J Theor Stat Soc Series B-Stat Method 64: 641-656.
56. Burnham KP, Anderson DR (2002) Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach. Second edition. New York: Springer Science+Business Media.
57. Neter J, Kutner MH, Nachtsheim CJ, Wasserman L (1996) Applied Linear Statistical Models. Boston: McGraw Hill.
58. Lehmann EL (1986) Testing Statistical Hypotheses. Second edition. New York: John Wiley.
59. Hudson RR (1990) Gene genealogies and the coalescent process. In: Futuyma DAJ, ed. Oxford Surveys in Evolutionary Biology. New York: Oxford University Press. pp 1-44.
60. Kaplan NL, Hudson RR (1985) The use of sample genealogies for studying a selectively neutral m-loci model with recombination. Theor Pop Biol 28: 382-396.
61. Simonsen KL, Churchill GA (1997) A Markov chain model of coalescence with recombination. Theor Pop Biol 52: 43-59.
62. Verhoeven KJF, Simonsen KL (2005) Genomic haplotype blocks may not accurately reflect spatial variation in historic recombination intensity. Mol Biol Evol 22: 735-740.
63. Kruglyak L (1999) Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 22: 139-144.
64. Cohen J (1990) Statistical Power Analysis for the Behavioral Sciences. Second edition. Hillsdale: Lawrence Erlbaum.
65. Nordborg M, Tavare S (2002) Linkage disequilibrium: What history has to tell us. TRENDS Genet 18: 83-90.