Open Access Methodology article

Multiallelic epistatic model for an out-bred cross and mapping algorithm of interactive quantitative trait loci

Chunfa Tong12, Bo Zhang1, Zhong Wang23, Meng Xu1, Xiaoming Pang3, Jingna Si3, Minren Huang1 and Rongling Wu23*

Author Affiliations

1 The Key Laboratory of Forest Genetics and Gene Engineering, Nanjing Forestry University, Nanjing, Jiangsu 210037, China

2 Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA

3 Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Beijing Forestry University, Beijing 100083, China

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BMC Plant Biology 2011, 11:148  doi:10.1186/1471-2229-11-148

Published: 31 October 2011



Genetic mapping has proven to be powerful for studying the genetic architecture of complex traits by characterizing a network of the underlying interacting quantitative trait loci (QTLs). Current statistical models for genetic mapping were mostly founded on the biallelic epistasis of QTLs, incapable of analyzing multiallelic QTLs and their interactions that are widespread in an outcrossing population.


Here we have formulated a general framework to model and define the epistasis between multiallelic QTLs. Based on this framework, we have derived a statistical algorithm for the estimation and test of multiallelic epistasis between different QTLs in a full-sib family of outcrossing species. We used this algorithm to genomewide scan for the distribution of mul-tiallelic epistasis for a rooting ability trait in an outbred cross derived from two heterozygous poplar trees. The results from simulation studies indicate that the positions and effects of multiallelic QTLs can well be estimated with a modest sample and heritability.


The model and algorithm developed provide a useful tool for better characterizing the genetic control of complex traits in a heterozygous family derived from outcrossing species, such as forest trees, and thus fill a gap that occurs in genetic mapping of this group of important but underrepresented species.