|
Organizers |
Calculation of the power of tests for QTL detection
by
Peter Alspach
The Horticulture and Food Research Institute of New Zealand Ltd
Coauthors: H. Nihal De Silva, Sue Gardiner, Erik Rikkerink
Quantitative Trait Loci are positions on the genome of genetic factors responsible for characters that show continuous variation in their phenotype. Search for QTL is often a difficult task, and statistical methods are used for both the detection and location. A whole genome scan of specific QTL starts with a dense linkage map of polymorphic molecular markers. The mating design usually involves crossing of two parents differing in both the trait value and marker variants. A sample from the progeny population is then genotyped for the markers and phenotyped for the trait of interest. The simplest analysis that follows defines the null hypothesis of no linkage between each marker and a putative QTL in terms of recombination fraction between the two loci, i.e. H0: rMQ=0.5 against H1: rMQ < 0.5. Then, the power of detecting a QTL is, 1-Type II error. In outbreeding horticultural plant species such as apple and kiwifruit the power calculations are more complex. There are a number of factors that affect the power of QTL detection, but from a design point of view the marker density and the sample size are the most important. The issue is, therefore, one of relative costs of producing larger families vs more markers. We have developed a spreadsheet calculator that takes these as parameters to compute the power of QTL detection for both inbreds and outbreds. This will be illustrated with respect to designing of experiments for QTL detection in apple. We will discuss the implications of the GxE interaction, and the need for establishing multi-site phenotyping trials.
Date received: August 20, 2001
Copyright © 2001 by the author(s). The author(s) of this document and the organizers of the conference have granted their consent to include this abstract in Atlas Conferences Inc. Document # cahg-17.