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Originally published as Genetics Published Articles Ahead of Print on November 3, 2008.
Genetics, Vol. 181, 247-257, January 2009, Copyright © 2009
doi:10.1534/genetics.108.093047
Unraveling Epistasis With Triple Testcross Progenies of Near-Isogenic Lines
Jochen C. Reif*,
,1,
Barbara Kusterer*,1,
Hans-Peter Piepho
,
Rhonda C. Meyer
,
Thomas Altmann,
Chris C. Schön** and
Albrecht E. Melchinger*,2
* Institute of Plant Breeding, Seed Science, and Population Genetics, State Plant Breeding Institute and Institute of Crop Production and Grassland Research, Bioinformatics Unit, University of Hohenheim, 70599 Stuttgart, Germany, Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany and ** Institute of Plant Breeding, Technical University of Munich, 85350 Freising, Germany
2 Corresponding author: Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany.
E-mail: melchinger{at}uni-hohenheim.de
Libraries of near-isogenic lines (NILs) are a powerful plant genetic resource to map quantitative trait loci (QTL). Nevertheless, QTL mapping with NILs is mostly restricted to genetic main effects. Here we propose a two-step procedure to map additive-by-additive digenic epistasis with NILs. In the first step, a generation means analysis of parents, their F1 hybrid, and one-segment NILs and their triple testcross (TTC) progenies is used to identify in a one-dimensional scan loci exhibiting QTL-by-background interactions. In a second step, one-segment NILs with significant additive-by-additive background interactions are used to produce particular two-segment NILs to test for digenic epistatic interactions between these segments. We evaluated our approach by analyzing a random subset of a genomewide Arabidopsis thaliana NIL library for growth-related traits. The results of our experimental study illustrated the potential of the presented two-step procedure to map additive-by-additive digenic epistasis with NILs. Furthermore, our findings suggested that additive main effects as well as additive-by-additive digenic epistasis strongly influence the genetic architecture underlying growth-related traits of A. thaliana.