Mapping quantitative trait loci with epistatic effects.

Epistatic variance can be an important source of variation for complex traits. However, detecting epistatic effects is difficult primarily due to insufficient sample sizes and lack of robust statistical methods. In this paper, we develop a Bayesian method to map multiple quantitative trait loci (QTLs) with epistatic effects. The method can map QTLs in complicated mating designs derived from the cross of two inbred lines. In addition to mapping QTLs for quantitative traits, the proposed method can even map genes underlying binary traits such as disease susceptibility using the threshold model. The parameters of interest are various QTL effects, including additive, dominance and epistatic effects of QTLs, the locations of identified QTLs and even the number of QTLs. When the number of QTLs is treated as an unknown parameter, the dimension of the model becomes a variable. This requires the reversible jump Markov chain Monte Carlo algorithm. The utility of the proposed method is demonstrated through analysis of simulation data.

[1]  W. K. Hastings,et al.  Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .

[2]  M. Sillanpää,et al.  Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. , 1998, Genetics.

[3]  S. Heath.  Markov chain Monte Carlo segregation and linkage analysis for oligogenic models. , 1997, American journal of human genetics.

[4]  Z. Zeng.  Precision mapping of quantitative trait loci. , 1994, Genetics.

[5]  David A. Stephens,et al.  BAYESIAN ANALYSIS OF QUANTITATIVE TRAIT LOCUS DATA USING REVERSIBLE JUMP MARKOV CHAIN MONTE CARLO , 1998 .

[6]  S. Chib,et al.  Bayesian analysis of binary and polychotomous response data , 1993 .

[7]  N. Yi,et al.  Mixed model analysis of quantitative trait loci. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[8]  R. Jansen,et al.  University of Groningen High Resolution of Quantitative Traits Into Multiple Loci via Interval Mapping , 2022 .

[9]  R. Doerge,et al.  Empirical threshold values for quantitative trait mapping. , 1994, Genetics.

[10]  P M Visscher,et al.  Confidence intervals in QTL mapping by bootstrapping. , 1996, Genetics.

[11]  M. Sillanpää,et al.  Bayesian mapping of multiple quantitative trait loci from incomplete outbred offspring data. , 1999, Genetics.

[12]  Z B Zeng,et al.  Estimating the genetic architecture of quantitative traits. , 1999, Genetical research.

[13]  N. Yi,et al.  Bayesian mapping of quantitative trait loci under complicated mating designs. , 2001, Genetics.

[14]  E. Lander,et al.  Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. , 1989, Genetics.

[15]  A. Paterson,et al.  Mapping QTLs with epistatic effects and QTL×environment interactions by mixed linear model approaches , 1999, Theoretical and Applied Genetics.

[16]  R Jansen,et al.  Mapping epistatic quantitative trait loci with one-dimensional genome searches. , 2001, Genetics.

[17]  Cai-guo Xu,et al.  Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[18]  N. Yi,et al.  Bayesian mapping of quantitative trait loci under the identity-by-descent-based variance component model. , 2000, Genetics.

[19]  Z. Zeng,et al.  Multiple interval mapping for quantitative trait loci. , 1999, Genetics.

[20]  M A Newton,et al.  A bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. , 1996, Genetics.

[21]  C. Haley,et al.  A simple regression method for mapping quantitative trait loci in line crosses using flanking markers , 1992, Heredity.

[22]  P. Green.  Reversible jump Markov chain Monte Carlo computation and Bayesian model determination , 1995 .

[23]  K. Chase,et al.  Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[24]  N. Yi,et al.  Bayesian mapping of quantitative trait loci for complex binary traits. , 2000, Genetics.

[25]  B. Kinghorn,et al.  The use of a genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci. , 2000, Genetics.

[26]  Donald Geman,et al.  Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images , 1984, IEEE Transactions on Pattern Analysis and Machine Intelligence.