QTL allele state and allele origin probabilities are used in linear model methods to map QTL. When data are from complex pedigrees, MCMC methods are useful to compute these probabilities. Early applications of MCMC methods relied on obtaining candidate samples from simple proposal distributions; these are then accepted or rejected by the Metropolis-Hastings algorithm. We show here that these simple methods can give erroneous results, and discuss using proposal distributions that closely approximate the posterior distribution of the genetic variables. Our results indicate that this is a promising strategy.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 20.11, 2006
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