Originally published as Genetics Published Articles Ahead of Print on February 4, 2007.

Genetics, Vol. 175, 1975-1986, April 2007, Copyright © 2007
doi:10.1534/genetics.106.066480

Power and Precision of Alternate Methods for Linkage Disequilibrium Mapping of Quantitative Trait Loci

H. H. Zhao, R. L. Fernando and J. C. M. Dekkers1

Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, Iowa 50011

1 Corresponding author: Department of Animal Science, 239D Kildee Hall, Iowa State University, Ames, IA 50011-3150.
E-mail: jdekkers{at}iastate.edu

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 on the basis of regression and identity by descent (IBD) in populations of limited effective population size (Ne). An 11-cM region with 6–38 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 affected little 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.




This article has been cited by other articles:


Home page
 BioinformaticsHome page
J. Hernandez-Sanchez, J.-A. Grunchec, and S. Knott
A web application to perform linkage disequilibrium and linkage analyses on a computational grid
Bioinformatics, June 1, 2009; 25(11): 1377 - 1383.
[Abstract] [Full Text] [PDF]

Home page
 J DAIRY SCIHome page
D. Kolbehdari, Z. Wang, J. R. Grant, B. Murdoch, A. Prasad, Z. Xiu, E. Marques, P. Stothard, and S. S. Moore
A Whole-Genome Scan to Map Quantitative Trait Loci for Conformation and Functional Traits in Canadian Holstein Bulls
J Dairy Sci, July 1, 2008; 91(7): 2844 - 2856.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. P. W. de Roos, B. J. Hayes, R. J. Spelman, and M. E. Goddard
Linkage Disequilibrium and Persistence of Phase in Holstein-Friesian, Jersey and Angus Cattle
Genetics, July 1, 2008; 179(3): 1503 - 1512.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
T. Druet, S. Fritz, M. Boussaha, S. Ben-Jemaa, F. Guillaume, D. Derbala, D. Zelenika, D. Lechner, C. Charon, D. Boichard, et al.
Fine Mapping of Quantitative Trait Loci Affecting Female Fertility in Dairy Cattle on BTA03 Using a Dense Single-Nucleotide Polymorphism Map
Genetics, April 1, 2008; 178(4): 2227 - 2235.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
S. Isobe, A. Nakaya, and S. Tabata
Genotype Matrix Mapping: Searching for Quantitative Trait Loci Interactions in Genetic Variation in Complex Traits
DNA Res, November 13, 2007; (2007) dsm020v1.
[Abstract] [Full Text] [PDF]