On fine mapping of quantitative trait loci using linkage disequilibrium in inbred plant populations

M.C.A.M. Bink, T.H.E. Meuwissen

    Research output: Contribution to conferenceAbstract

    Abstract

    Linkage disequilibrium mapping has been successful in mapping genetic disorders. The method attempts to find a chromosomal region that is identical by descent (IBD) among the diseased individuals. The IBD region is detected by closely linked marker loci that carry identical alleles at this region in the diseased individuals. The size of the IBD region decreases with the number of meioses since the disease mutation occurred and may be small, which leads to the detection of a small region that contains the disease gene. Meuwissen & Goddard (2000) developed a multimarker linkage disequilibrium mapping method for the fine mapping of quantitative trait loci (QTL) using a dense marker map for outbred (livestock) populations. The method compares the expected covariances between haplotype effects given a postulated QTL position to the covariances that are found in the data. The expected covariances between the haplotype effects are proportional to the probability that the QTL position is identical by descent (IBD) given the marker haplotype information, which is calculated using a genedropping method. Assuming multivariate normality, estimates can be obtained via restricted Maximum Likelihood. In this paper we describe the modification of the statistical methodology to study inbred plant populations. We study the accuracy of estimation the QTL position and the robustness of the developed methodology to assumptions made on the studied plant population, for example the effective population size, density of marker loci, the distribution of the effect of the QTL, and the inbreeding process. Literature: T.H.E. Meuwissen & M.E. Goddard (2000) Fine mapping of quantitative trait loci using linkage disequilibrium with closely linked marker loci. Genetics 155:421-430.
    Original languageEnglish
    Publication statusPublished - 2004

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