Originally published as Genetics Published Articles Ahead of Print on January 16, 2005.

Genetics, Vol. 169, 1711-1725, March 2005, Copyright © 2005
doi:10.1534/genetics.104.035857

Modeling Quantitative Trait Loci and Interpretation of Models

Zhao-Bang Zeng^*,,1, Tao Wang and Wei Zou^*

^* Bioinformatics Research Center and Department of Statistics, North Carolina State University, Raleigh, North Carolina 27695
Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
Division of Biostatistics and Human Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226

¹ Corresponding author: Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC 27695-7566.
E-mail: zeng{at}stat.ncsu.edu

A quantitative genetic model relates the genotypic value of an individual to the alleles at the loci that contribute to the variation in a population in terms of additive, dominance, and epistatic effects. This partition of genetic effects is related to the partition of genetic variance. A number of models have been proposed to describe this relationship: some are based on the orthogonal partition of genetic variance in an equilibrium population. We compare a few representative models and discuss their utility and potential problems for analyzing quantitative trait loci (QTL) in a segregating population. An orthogonal model implies that estimates of the genetic effects are consistent in a full or reduced model in an equilibrium population and are directly related to the partition of the genetic variance in the population. Linkage disequilibrium does not affect the estimation of genetic effects in a full model, but would in a reduced model. Certainly linkage disequilibrium would complicate the detection of QTL and epistasis. Using different models does not influence the detection of QTL and epistasis. However, it does influence the estimation and interpretation of genetic effects.

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