Marker Assisted Best Linear Unbiased Prediction (MABLUP) with large livestock pedigrees depends critically on efficient algorithms to invert the gametic covariance matrix for the marked QTL. These algorithms are based on tracing the QTL alleles of an individual to its grandmother and grandfather. When marker information is complete, there are simple rules to compute the probabilities (PDQ's) of these events. When marker information is incomplete, even if the PDQ's are computed exactly, the efficient algorithms would be approximate. In this study we examined the effect of estimating the PDQ's by MCMC on response to MABLUP. The results of this study show that by estimating the PDQ's by MCMC the loss on response could be reduced to about 20%. Further, the loss in response due to missing markers was smaller in the case with four markers compared to when only two bi-allelic markers were used.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 22.57, 2006
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