Imputing missing genotypes using numerator relationship matrix

Genotyping does not work for all samples for all markers, so genetic data from a lab might have many missing genotypes. Yet, predictions of genetic merit of trees across markers require complete genotyping information or gene content. Excluding individuals with missing genotypes is not desired, since it will reduce the number of individuals in the population considerably, thus reducing the power of association of markers and traits. It is therefore important to use efficient statistical methods to accurately impute missing genotypes. Human geneticists rely on genetic maps and linkage disequilibrium (LD) information from nearby markers to replace missing genotypes. Their algorithms rely on known map positions for the SNPs. Since completely sequenced reference genomes are available for only two forest tree species, methods developed by human geneticists do not work well for most forest trees.


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Author(s): Funda Ogut

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