Abstract
Epistatic interactions among quantitative trait loci (QTL) contribute substantially to the variation in complex traits. The main objectives of this study were to (i) compare three- vs. four-step genome scans to identify three-way epistatic interactions among QTL belonging to a metabolic pathway, (ii) investigate by computer simulations the power and proportion of false positives (PFP) for detecting three-way interactions among QTL in recombinant inbred line (RIL) populations derived from a nested mating design, and (iii) compare these estimates to those obtained for detecting three-way interactions among QTL in RIL populations derived from diallel and different partial diallel mating designs. The single-nucleotide polymorphism haplotype data of B73 and 25 diverse maize inbreds were used to simulate the production of various RIL populations. Compared to the three-step genome scan, the power to detect three-way interactions was higher with the four-step genome scan. Higher power to detect three-way interactions was observed for RILs derived from optimally allocated distance-based designs than from nested designs or diallel designs. The power and PFP to detect three-way interactions using a nested design with 5000 RILs were for both the 4-QTL and the 12-QTL scenario of a magnitude that seems promising for their identification.
Highlights
UNTIL now estimation of the positions of quantitative trait loci (QTL) in plant genetics was accomplished by classical linkage mapping (Lander and Botstein 1989)
The main objectives of this study were to (i) compare three- vs. four-step genome scans to identify three-way epistatic interactions among QTL belonging to a metabolic pathway, (ii) investigate by computer simulations the power and proportion of false positives (PFP) for detecting three-way interactions among QTL in recombinant inbred line (RIL) populations derived from a nested mating design, and (iii) compare these estimates to those obtained for detecting three-way interactions among QTL in RIL populations derived from diallel and different partial diallel mating designs
The objectives of our research were to (i) compare three- vs. four-step genome scans to identify three-way interactions among QTL involved in a metabolic pathway, (ii) investigate by computer simulations the power and proportion of false positives (PFP) for detecting three-way interactions among QTL in RIL populations derived from a nested mating design, and (iii) compare these estimates to those obtained for detecting threeway interactions among QTL using RIL populations derived from diallel and different partial diallel mating designs
Summary
UNTIL now estimation of the positions of quantitative trait loci (QTL) in plant genetics was accomplished by classical linkage mapping (Lander and Botstein 1989). The adaption of association mapping in plant genetics has been proposed by several authors (e.g., Vuylsteke et al 2000; Thornsberry et al 2001). While linkage mapping methods offer a high power to detect QTL in genomewide approaches, association mapping methods have the merit of a high resolution to detect QTL (Remington et al 2001). We examine a genomewide QTL mapping strategy using genome sequence information of recombinant inbred lines (RILs) that were generated. The new mapping strategy will show a high power to detect QTL in genomewide approaches and a high mapping resolution when both linkage and LD information are used. Information about the power for genomewide detection of epistatic interactions among more than two QTL is still lacking
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