Genetics, Vol. 160, 1243-1261, March 2002, Copyright © 2002

Modeling Epistasis of Quantitative Trait Loci Using Cockerham's Model

Chen-Hung Kaoa and Zhao-Bang Zengb
a Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan, Republic of China
b Bioinformatics Research Center, Departments of Statistics and Genetics, North Carolina State University, Raleigh, North Carolina 27695-7566

Corresponding author: Chen-Hung Kao, Academia Sinica, Taipei 11529, Taiwan, Republic of China., chkao{at}stat.sinica.edu.tw (E-mail)

Communicating editor: M. A. F. NOOR

We use the orthogonal contrast scales proposed by Cockerham to construct a genetic model, called Cockerham's model, for studying epistasis between genes. The properties of Cockerham's model in modeling and mapping epistatic genes under linkage equilibrium and disequilibrium are investigated and discussed. Because of its orthogonal property, Cockerham's model has several advantages in partitioning genetic variance into components, interpreting and estimating gene effects, and application to quantitative trait loci (QTL) mapping when compared to other models, and thus it can facilitate the study of epistasis between genes and be readily used in QTL mapping. The issues of QTL mapping with epistasis are also addressed. Real and simulated examples are used to illustrate Cockerham's model, compare different models, and map for epistatic QTL. Finally, we extend Cockerham's model to multiple loci and discuss its applications to QTL mapping.




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