Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy.
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.
Stich
Benjamin
B
Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany.
Yu
Jianming
J
Melchinger
Albrecht E
AE
Piepho
Hans-Peter
HP
Utz
H Friedrich
HF
Maurer
Hans P
HP
Buckler
Edward S
ES
D002874:Chromosome Mapping; D003198:Computer Simulation; D004843:Epistasis, Genetic; D018745:Genome, Plant / Q000235:genetics; D005838:Genotype; D007178:Inbreeding; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D003313:Zea mays / Q000235:genetics*