JSM 2005 - Toronto

Abstract #304735

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Legend: = Applied Session, = Theme Session, = Presenter
Activity Number: 482
Type: Contributed
Date/Time: Thursday, August 11, 2005 : 8:30 AM to 10:20 AM
Sponsor: Biometrics Section
Abstract - #304735
Title: Strategies for Fine Mapping of QTL in Complex Pedigrees Using Combined Linkage and Linkage Disequilibrium Method
Author(s): Natascha Vukasinovic*+ and Fengxing Du
Companies: Monsanto and Monsanto
Address: 800 N Lindbergh Blvd, St Louis, MO, 63167, United States
Keywords: QTL ; genetic marker ; haplotype ; linkage analysis ; linkage disequilibrium
Abstract:

Advances in genome sequencing and high-throughput genotyping have stimulated use of single nucleotide polymorphism (SNP) markers in mapping of quantitative trait loci (QTL). Statistical methods for QTL fine mapping have been developed to make use of dense maps of tightly linked markers. A novel LA/LD method that combines linkage analysis and linkage disequilibrium information is becoming common for fine mapping of QTL in complex pedigrees. Probabilities of QTL alleles being identical by descent (IBD) are estimated based on similarity of marker haplotypes. Usually, maps that contain both polymorphic microsatellite and biallelic SNP markers are used in LA/LD analysis. However, when a large number of markers is used to construct haplotypes, inclusion of polymorphic along with biallelic markers results in overestimated QTL effects at positions near more informative markers. When only SNP markers are used, mapping precision is low, especially when a QTL is small. In this work, we explore strategies for efficient haplotype construction in complex pedigrees, regarding use of markers with various information content, optimal marker spacing, and optimal number of loci in a haplotype.

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