ArticleBMC genetics2014
Mapping epistatic quantitative trait loci.
Article in BMC genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Identification of race 2 anthracnose resistance Quantitative Trait Loci using biparental and association panel of diverse watermelon germplasm accessions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Applying gradient tree boosting to QTL mapping with Shapley additive explanations.Breeding science · 2025Article
- Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis.BioData mining · 2024Article
- Susceptibility ofmBio · 2024Article
- Assessing the opportunity for selection to impact morphological traits in crosses between twoPeerJ · 2024Article
- Searching for gene-gene interactions through variance quantitative trait loci of 29 continuous Taiwan Biobank phenotypes.Frontiers in genetics · 2024Article
- Integration of eQTL and GWAS analysis uncovers a genetic regulation of natural ionomic variation in Arabidopsis.Plant cell reports · 2023Article
- Efficiency of mapping epistatic quantitative trait loci.Heredity · 2023Article
- Genetic, morphometric, and molecular analyses of interspecies differences in head shape and hybrid developmental defects in the wasp genus Nasonia.G3 (Bethesda, Md.) · 2021Article
- RIL-StEp: epistasis analysis of rice recombinant inbred lines reveals candidate interacting genes that control seed hull color and leaf chlorophyll content.G3 (Bethesda, Md.) · 2021Article
- Multiple QTL Mapping in Autopolyploids: A Random-Effect Model Approach with Application in a Hexaploid Sweetpotato Full-Sib Population.Genetics · 2020Article
- Rapid generation of ecologically relevant behavioral novelty in experimental cichlid hybrids.Ecology and evolution · 2020Article
- High Density Mapping of Quantitative Trait Loci Conferring Gluten Strength in Canadian Durum Wheat.Frontiers in plant science · 2020Article
- Collective interaction effects associated with mammalian behavioral traits reveal genetic factors connecting fear and hemostasis.BMC psychiatry · 2018Article
- Epistasis: Searching for Interacting Genetic Variants Using Crosses.G3 (Bethesda, Md.) · 2017Article
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4 authors.
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Abstract
backgroundHow to map quantitative trait loci (QTL) with epistasis efficiently and reliably has been a persistent problem for QTL mapping analysis. There are a number of difficulties for studying epistatic QTL. Linkage can impose a significant challenge for finding epistatic QTL reliably. If multiple QTL are in linkage and have interactions, searching for QTL can become a very delicate issue. A commonly used strategy that performs a two-dimensional genome scan to search for a pair of QTL with epistasis can suffer from low statistical power and also may lead to false identification due to complex linkage disequilibrium and interaction patterns.
resultsTo tackle the problem of complex interaction of multiple QTL with linkage, we developed a three-stage search strategy. In the first stage, main effect QTL are searched and mapped. In the second stage, epistatic QTL that interact significantly with other identified QTL are searched. In the third stage, new epistatic QTL are searched in pairs. This strategy is based on the consideration that most genetic variance is due to the main effects of QTL. Thus by first mapping those main-effect QTL, the statistical power for the second and third stages of analysis for mapping epistatic QTL can be maximized. The search for main effect QTL is robust and does not bias the search for epistatic QTL due to a genetic property associated with the orthogonal genetic model that the additive and additive by additive variances are independent despite of linkage. The model search criterion is empirically and dynamically evaluated by using a score-statistic based resampling procedure. We demonstrate through simulations that the method has good power and low false positive in the identification of QTL and epistasis.
conclusionThis method provides an effective and powerful solution to map multiple QTL with complex epistatic pattern. The method has been implemented in the user-friendly computer software Windows QTL Cartographer. This will greatly facilitate the application of the method for QTL mapping data analysis.
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