Bioinformatics, Vol 14, 632-653, Copyright © 1998 by Oxford University Press
DW Podlich and M Cooper
MOTIVATION: Classical quantitative genetics theory makes a number of
simplifying assumptions in order to develop mathematical expressions that
describe the mean and variation (genetic and phenotypic) within and among
populations, and to predict how these are expected to change under the
influence of external forces. These assumptions are often necessary to
render the development of many aspects of the theory mathematically
tractable. The availability of high-speed computers today provides
opportunity for the use of computer simulation methodology to investigate
the implications of relaxing many of the assumptions that are commonly
made. RESULTS: QU-GENE (QUantitative- GENEtics) was developed as a flexible
computer simulation platform for the quantitative analysis of genetic
models. Three features of the QU- GENE software that contribute to its
flexibility are (i) the core E(N:K) genetic model, where E is the number of
types of environment, N is the number of genes, K indicates the level of
epistasis and the parentheses indicate that different N:K genetic models
can be nested within types of environments, (ii) the use of a two-stage
architecture that separates the definition of the genetic model and
genotype- environment system from the detail of the individual simulation
experiments and (iii) the use of a series of interactive graphical windows
that monitor the progress of the simulation experiments. The E(N:K)
framework enables the generation of families of genetic models that
incorporate the effects of genotype-by-environment (G x E) interactions and
epistasis. By the design of appropriate application modules, many different
simulation experiments can be conducted for any genotype-environment
system. The structure of the QU-GENE simulation software is explained and
demonstrated by way of two examples. The first concentrates on some aspects
of the influence of G x E interactions on response to selection in plant
breeding, and the second considers the influence of multiple-peak epistasis
on the evolution of a four-gene epistatic network. AVAILABILITY: QU-GENE is
available over the Internet at http://pig.ag.uq.edu.au/qu-gene/ CONTACT:
m.cooper@mailbox.uq.edu. au
ARTICLES
QU-GENE: a simulation platform for quantitative analysis of genetic models
School of Land and Food, The University of Queensland, Brisbane, Queensland 4072, Australia.
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