Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data.

A novel fine structure mapping method for quantitative traits is presented. It is based on Bayesian modeling and inference, treating the number of quantitative trait loci (QTLs) as an unobserved random variable and using ideas similar to composite interval mapping to account for the effects of QTLs in other chromosomes. The method is introduced for inbred lines and it can be applied also in situations involving frequent missing genotypes. We propose that two new probabilistic measures be used to summarize the results from the statistical analysis: (1) the (posterior) QTL intensity, for estimating the number of QTLs in a chromosome and for localizing them into some particular chromosomal regions, and (2) the locationwise (posterior) distributions of the phenotypic effects of the QTLs. Both these measures will be viewed as functions of the putative QTL locus, over the marker range in the linkage group. The method is tested and compared with standard interval and composite interval mapping techniques by using simulated backcross progeny data. It is implemented as a software package. Its initial version is freely available for research purposes under the name Multimapper at URL http://www.rni.helsinki.fi/mjs.

[1]  M. Sillanpää,et al.  Genetic basis of adaptation: flowering time in Arabidopsis thaliana , 1997, Theoretical and Applied Genetics.

[2]  I. Hoeschele,et al.  Mapping-linked quantitative trait loci using Bayesian analysis and Markov chain Monte Carlo algorithms. , 1997, Genetics.

[3]  P. Green,et al.  Corrigendum: On Bayesian analysis of mixtures with an unknown number of components , 1997 .

[4]  P. Green,et al.  On Bayesian Analysis of Mixtures with an Unknown Number of Components (with discussion) , 1997 .

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

[6]  Chris Haley,et al.  MAPPING QTLS FOR BINARY TRAITS IN BACKCROSS AND F2 POPULATIONS , 1996 .

[7]  G Thaller,et al.  The use of multiple markers in a Bayesian method for mapping quantitative trait loci. , 1996, Genetics.

[8]  W. Atchley,et al.  Mapping quantitative trait loci for complex binary diseases using line crosses. , 1996, Genetics.

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

[10]  R. Jansen.  A general Monte Carlo method for mapping multiple quantitative trait loci. , 1996, Genetics.

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

[12]  C. Hackett,et al.  Genetic mapping of quantitative trait loci for traits with ordinal distributions. , 1995, Biometrics.

[13]  S. Chib,et al.  Understanding the Metropolis-Hastings Algorithm , 1995 .

[14]  L Kruglyak,et al.  A nonparametric approach for mapping quantitative trait loci. , 1995, Genetics.

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

[16]  E. Thompson.  Monte Carlo Likelihood in Genetic Mapping , 1994 .

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

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

[19]  C. Haley,et al.  Mapping quantitative trait loci in crosses between outbred lines using least squares. , 1994, Genetics.

[20]  Z B Zeng,et al.  Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[21]  R. Jansen,et al.  Interval mapping of multiple quantitative trait loci. , 1993, Genetics.

[22]  R. Neuman.  Analysis of human genetic linkage, revised edition , 1993 .

[23]  A F Smith,et al.  Bayesian inference in multipoint gene mapping , 1993, Annals of human genetics.

[24]  E A Thompson,et al.  A Monte Carlo method for combined segregation and linkage analysis. , 1992, American journal of human genetics.

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

[26]  G. Casella,et al.  Explaining the Gibbs Sampler , 1992 .

[27]  D. Thomas,et al.  A Gibbs sampling approach to linkage analysis. , 1992, Human heredity.

[28]  J. J. Tai.  Application of Bayesian Decision Procedure to the Inference of Genetic Linkage , 1989 .

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

[30]  Adrian F. M. Smith,et al.  Bayesian computation via the gibbs sampler and related markov chain monte carlo methods (with discus , 1993 .

[31]  J. Ott.  Analysis of Human Genetic Linkage , 1985 .

[32]  D. Rubin,et al.  Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .

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

[34]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.