Prediction of IBD based on population history for fine gene mapping.

Genetics, Selection, Evolution : GSE
Jules Hernández-SánchezJohn A Woolliams

Abstract

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBDL are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher...Continue Reading

Citations

Mar 26, 2009·Bioinformatics·Jules Hernández-SánchezSara Knott
Oct 27, 2007·BMC Bioinformatics·Dario GasbarraElja Arjas
May 18, 2007·Genetics·William G Hill, Jules Hernández-Sánchez
Jan 24, 2009·Journal of Dairy Science·G FreyerB Cassell
Aug 7, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Ming Fang
Aug 8, 2007·Theoretical Population Biology·Dario GasbarraElja Arjas
Jan 25, 2008·Theoretical Population Biology·Danielle Jones, John Wakeley

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