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United States Department of Agriculture

Agricultural Research Service

Title: Overview of QTL detection in plants and tests for synergistic epistatic interactions

Authors
item Jannink, Jean-Luc
item Moreau, Laurence - INRA, FRANCE
item Charcosset, Alain - INRA, FRANCE
item Charmet, Gilles - INRA, FRANCE

Submitted to: Genetica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 17, 2008
Publication Date: September 1, 2008
Citation: Jannink, J., Moreau, L., Charcosset, A., Charmet, G. 2008. Overview of QTL detection in plants and tests for synergistic epistatic interactions. Genetica. 136:225-236.

Interpretive Summary: Review of literature on the value of different mating designs for QTL detection should encourage the best designs to be adopted. We perform this review from the perspective of several criteria important to the application of QTL results to plant breeding. The usefulness of QTL detection can also be increased by developing methods that can analyze data accounting for specific kinds of genetic interaction that may occur. We develop two methods that specifically detect and account for synergistic epistasis. Synergistic epistasis occurs when the performance of a genotype with two deleterious alleles is less than predicted on the basis of genotypes with only one such allele. This form of epistasis has important implications from evolutionary (maintenance of sexual reproduction and concealment of cryptic genetic variation) and practical perspectives (response to pyramided favorable alleles). The first method is based on analyzing interactions between single locus effects and predicted individual genotypic values and the second is based on analyzing pairwise locus interactions. Using the first method we detect synergistic epistasis in a barley and a wheat dataset but not in maize dataset. We fail to detect synergistic epistasis with the second method. We discuss our results in the light of theoretical questions concerning the mechanisms of synergistic epistasis.

Technical Abstract: Improvements in the usefulness of QTL analysis arise from better statistical methods applied to the problem, ability to analyze more complex mating designs, and the fitting of less simplified genetic models. Here we review the advantages of different plant mating designs in QTL analysis and conclude that diallel designs have several favorable properties. We then turn to the detection of systematic genome-wide synergistic epistasis. This form of epistasis has important implications from evolutionary (maintenance of sexual reproduction and concealment of cryptic genetic variation) and practical perspectives (response to pyramided favorable alleles). We develop two methods for detecting systematic synergistic epistasis, one based on analyzing interactions between locus effects and predicted individual genotypic values and one based on analyzing pairwise locus interactions. Using the first method we detect synergistic epistasis in a barley and a wheat dataset but not in maize dataset. We fail to detect synergistic epistasis with the second method. We discuss our results in the light of theoretical questions concerning the mechanisms of synergistic epistasis.

Last Modified: 7/22/2014
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