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doi:10.1534/genetics.106.066480
A more recent version of this article appeared on April 1, 2007.
REGULAR RESEARCH PAPERS |
Power and Precision of Alternate Methods for Linkage Disequilibrium Mapping of QTL in Livestock
Honghua Zhao 1, Rohan L. Fernando 1 and Jack C. M. Dekkers 1*
1 Iowa State University
* To whom correspondence should be addressed. E-mail: jdekkers{at}iastate.edu.
Submitted on October 4, 2006
Revised on November 22, 2006
Accepted on 18 January 2007
Linkage disequilibrium (LD) analysis in outbred populations uses historical recombinations to detect and fine map quantitative trait loci (QTL). Our objective was to evaluate the effect of various factors on power and precision of QTL detection and to compare LD mapping methods based on regression and identity by descent (IBD) in populations of limited effective population size (Ne). An 11 cM region with 6 to 38 segregating single nucleotide polymorphisms (SNPs) and a central QTL was simulated. After 100 generations of random mating with Ne of 50, 100 or 200, SNP genotypes and phenotypes were generated on 200, 500 or 1000 individuals with the QTL explaining 2 or 5% of phenotypic variance. To detect and map the QTL, phenotypes were regressed on genotypes or (assumed known) haplotypes, in comparison with the IBD method. Power and precision to detect QTL increased with sample size, marker density and QTL effect. Power decreased with Ne, but precision was little affected by Ne. Single marker regression had similar or greater power and precision than other regression models, and was comparable to the IBD method. Thus, for rapid initial screening of samples of adequate size in populations in which drift is the primary force that has created LD, QTL can be detected and mapped by regression on SNP genotypes without recovering haplotypes.
Key Words: High density SNP genotyping, Identity by descent, Linkage Disequilibrium Mapping, QTL, Regression
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