Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie
S Ansari-MahyariM S Lund

Abstract

In fine mapping of a large-scale experimental population where collection of phenotypes are very expensive, difficult to record or time-demanding, selective phenotyping could be used to phenotype the most informative individuals. Linkage analyses based sampling criteria (LAC) and linkage disequilibrium-based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However, in order to estimate un...Continue Reading

References

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Citations

Oct 12, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·B Emma HuangColin Cavanagh
Jul 7, 2011·Genetics, Selection, Evolution : GSE·Mario P L Calus, Roel F Veerkamp

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