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Genetics. Oct 2003; 165(2): 867–883.
PMCID: PMC1462771

Bayesian model choice and search strategies for mapping interacting quantitative trait Loci.


Most complex traits of animals, plants, and humans are influenced by multiple genetic and environmental factors. Interactions among multiple genes play fundamental roles in the genetic control and evolution of complex traits. Statistical modeling of interaction effects in quantitative trait loci (QTL) analysis must accommodate a very large number of potential genetic effects, which presents a major challenge to determining the genetic model with respect to the number of QTL, their positions, and their genetic effects. In this study, we use the methodology of Bayesian model and variable selection to develop strategies for identifying multiple QTL with complex epistatic patterns in experimental designs with two segregating genotypes. Specifically, we develop a reversible jump Markov chain Monte Carlo algorithm to determine the number of QTL and to select main and epistatic effects. With the proposed method, we can jointly infer the genetic model of a complex trait and the associated genetic parameters, including the number, positions, and main and epistatic effects of the identified QTL. Our method can map a large number of QTL with any combination of main and epistatic effects. Utility and flexibility of the method are demonstrated using both simulated data and a real data set. Sensitivity of posterior inference to prior specifications of the number and genetic effects of QTL is investigated.

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Selected References

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  • Krause BR, Schork NJ, Kieft KA, Smith MP, Maciejko JJ. High correlation but lack of agreement between direct high-performance gel chromatography analysis and conventional indirect methods for determining lipoprotein cholesterol. Clin Chem. 1996 Dec;42(12):1996–2001. [PubMed]
  • Culverhouse Robert, Suarez Brian K, Lin Jennifer, Reich Theodore. A perspective on epistasis: limits of models displaying no main effect. Am J Hum Genet. 2002 Feb;70(2):461–471. [PMC free article] [PubMed]
  • Daw EW, Heath SC, Wijsman EM. Multipoint oligogenic analysis of age-at-onset data with applications to Alzheimer disease pedigrees. Am J Hum Genet. 1999 Mar;64(3):839–851. [PMC free article] [PubMed]
  • Dong Chuanhui, Wang Shuang, Li Wei-Dong, Li Ding, Zhao Hongyu, Price R Arlen. Interacting genetic loci on chromosomes 20 and 10 influence extreme human obesity. Am J Hum Genet. 2003 Jan;72(1):115–124. [PMC free article] [PubMed]
  • Fernández JR, Tarantino LM, Hofer SM, Vogler GP, McClearn GE. Epistatic quantitative trait loci for alcohol preference in mice. Behav Genet. 2000 Nov;30(6):431–437. [PubMed]
  • Fijneman RJ, de Vries SS, Jansen RC, Demant P. Complex interactions of new quantitative trait loci, Sluc1, Sluc2, Sluc3, and Sluc4, that influence the susceptibility to lung cancer in the mouse. Nat Genet. 1996 Dec;14(4):465–467. [PubMed]
  • Frankel WN, Schork NJ. Who's afraid of epistasis? Nat Genet. 1996 Dec;14(4):371–373. [PubMed]
  • Gauderman WJ, Thomas DC. The role of interacting determinants in the localization of genes. Adv Genet. 2001;42:393–412. [PubMed]
  • Haley CS, Knott SA. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity (Edinb) 1992 Oct;69(4):315–324. [PubMed]
  • Heath SC. Markov chain Monte Carlo segregation and linkage analysis for oligogenic models. Am J Hum Genet. 1997 Sep;61(3):748–760. [PMC free article] [PubMed]
  • Hoeschele I, Uimari P, Grignola FE, Zhang Q, Gage KM. Advances in statistical methods to map quantitative trait loci in outbred populations. Genetics. 1997 Nov;147(3):1445–1457. [PMC free article] [PubMed]
  • Hoti Fabian J, Sillanpä Mikko J, Holmström Lasse. A note on estimating the posterior density of a quantitative trait locus from a Markov chain Monte Carlo sample. Genet Epidemiol. 2002 Apr;22(4):369–376. [PubMed]
  • Hurme P, Sillanpä MJ, Arjas E, Repo T, Savolainen O. Genetic basis of climatic adaptation in scots pine by bayesian quantitative trait locus analysis. Genetics. 2000 Nov;156(3):1309–1322. [PMC free article] [PubMed]
  • Ball RD. Bayesian methods for quantitative trait loci mapping based on model selection: approximate analysis using the Bayesian information criterion. Genetics. 2001 Nov;159(3):1351–1364. [PMC free article] [PubMed]
  • Jannink JL, Jansen R. Mapping epistatic quantitative trait loci with one-dimensional genome searches. Genetics. 2001 Jan;157(1):445–454. [PMC free article] [PubMed]
  • Bink M, Uimari P, Sillanpä J, Janss G, Jansen C. Multiple QTL mapping in related plant populations via a pedigree-analysis approach. Theor Appl Genet. 2002 Apr;104(5):751–762. [PubMed]
  • Jansen RC, Stam P. High resolution of quantitative traits into multiple loci via interval mapping. Genetics. 1994 Apr;136(4):1447–1455. [PMC free article] [PubMed]
  • Boer Martin P, Ter Braak Cajo J F, Jansen Ritsert C. A penalized likelihood method for mapping epistatic quantitative trait Loci with one-dimensional genome searches. Genetics. 2002 Oct;162(2):951–960. [PMC free article] [PubMed]
  • Kao Chen-Hung, Zeng Zhao-Bang. Modeling epistasis of quantitative trait loci using Cockerham's model. Genetics. 2002 Mar;160(3):1243–1261. [PMC free article] [PubMed]
  • Kao CH, Zeng ZB, Teasdale RD. Multiple interval mapping for quantitative trait loci. Genetics. 1999 Jul;152(3):1203–1216. [PMC free article] [PubMed]
  • Carlborg O, Andersson L, Kinghorn B. The use of a genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci. Genetics. 2000 Aug;155(4):2003–2010. [PMC free article] [PubMed]
  • Lander ES, Botstein D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989 Jan;121(1):185–199. [PMC free article] [PubMed]
  • Cheverud JM, Routman EJ. Epistasis and its contribution to genetic variance components. Genetics. 1995 Mar;139(3):1455–1461. [PMC free article] [PubMed]
  • Lark KG, Chase K, Adler F, Mansur LM, Orf JH. Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another. Proc Natl Acad Sci U S A. 1995 May 9;92(10):4656–4660. [PMC free article] [PubMed]
  • Thomas DC, Richardson S, Gauderman J, Pitkäniemi J. A Bayesian approach to multipoint mapping in nuclear families. Genet Epidemiol. 1997;14(6):903–908. [PubMed]
  • Lee JK, Thomas DC. Performance of Markov chain-Monte Carlo approaches for mapping genes in oligogenic models with an unknown number of loci. Am J Hum Genet. 2000 Nov;67(5):1232–1250. [PMC free article] [PubMed]
  • Uimari P, Hoeschele I. Mapping-linked quantitative trait loci using Bayesian analysis and Markov chain Monte Carlo algorithms. Genetics. 1997 Jun;146(2):735–743. [PMC free article] [PubMed]
  • Uimari P, Sillanpä MJ. Bayesian oligogenic analysis of quantitative and qualitative traits in general pedigrees. Genet Epidemiol. 2001 Nov;21(3):224–242. [PubMed]
  • Uimari P, Thaller G, Hoeschele I. The use of multiple markers in a Bayesian method for mapping quantitative trait loci. Genetics. 1996 Aug;143(4):1831–1842. [PMC free article] [PubMed]
  • Wade MJ. Epistasis, complex traits, and mapping genes. Genetica. 2001;112-113:59–69. [PubMed]
  • Satagopan JM, Yandell BS, Newton MA, Osborn TC. A bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. Genetics. 1996 Oct;144(2):805–816. [PMC free article] [PubMed]
  • Xu S, Yi N. Mixed model analysis of quantitative trait loci. Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14542–14547. [PMC free article] [PubMed]
  • Sen S, Churchill GA. A statistical framework for quantitative trait mapping. Genetics. 2001 Sep;159(1):371–387. [PMC free article] [PubMed]
  • Yi N, Xu S. Bayesian mapping of quantitative trait loci for complex binary traits. Genetics. 2000 Jul;155(3):1391–1403. [PMC free article] [PubMed]
  • Sillanpä MJ, Arjas E. Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics. 1998 Mar;148(3):1373–1388. [PMC free article] [PubMed]
  • Yi N, Xu S. Bayesian mapping of quantitative trait loci under complicated mating designs. Genetics. 2001 Apr;157(4):1759–1771. [PMC free article] [PubMed]
  • Sillanpä MJ, Arjas E. Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. Genetics. 1999 Apr;151(4):1605–1619. [PMC free article] [PubMed]
  • Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang Q, Saghai Maroof MA. Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9226–9231. [PMC free article] [PubMed]
  • Sillanpä Mikko J, Corander Jukka. Model choice in gene mapping: what and why. Trends Genet. 2002 Jun;18(6):301–307. [PubMed]
  • Yuan B, Neuman R, Duan SH, Weber JL, Kwok PY, Saccone NL, Wu JS, Liu KY, Schonfeld G. Linkage of a gene for familial hypobetalipoproteinemia to chromosome 3p21.1-22. Am J Hum Genet. 2000 May;66(5):1699–1704. [PMC free article] [PubMed]
  • Zeng ZB. Precision mapping of quantitative trait loci. Genetics. 1994 Apr;136(4):1457–1468. [PMC free article] [PubMed]
  • Zeng ZB, Kao CH, Basten CJ. Estimating the genetic architecture of quantitative traits. Genet Res. 1999 Dec;74(3):279–289. [PubMed]
  • Sugiyama F, Churchill GA, Higgins DC, Johns C, Makaritsis KP, Gavras H, Paigen B. Concordance of murine quantitative trait loci for salt-induced hypertension with rat and human loci. Genomics. 2001 Jan 1;71(1):70–77. [PubMed]

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