Gene-to-phenotype models and complex trait genetics

M Cooper, DW Podlich, OS Smith - Australian Journal of …, 2005 - CSIRO Publishing
The premise that is explored in this paper is that in some cases, in order to make progress in
the design of molecular breeding strategies for complex traits, we will need a theoretical …

The E(NK) model: Extending the NK model to incorporate gene‐by‐environment interactions and epistasis for diploid genomes

M Cooper, DW Podlich - Complexity, 2002 - Wiley Online Library
The haploid NK model developed by Kauffman can be extended to diploid genomes and to
incorporate gene‐by‐environment interaction effects in combination with epistasis. To …

[HTML][HTML] Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding

FA Van Eeuwijk, D Bustos-Korts, EJ Millet, MP Boer… - Plant science, 2019 - Elsevier
New types of phenotyping tools generate large amounts of data on many aspects of plant
physiology and morphology with high spatial and temporal resolution. These new …

[PDF][PDF] Modelling crop improvement in a G× E× M framework via gene-trait-phenotype relationships

C Messina, G Hammer, Z Dong, D Podlich… - Crop physiology …, 2009 - researchgate.net
Crop performance is determined by the combined effects of the genotype of the crop and the
environmental conditions of the production system. Improving crop performance to satisfy an …

The GP problem: quantifying gene-to-phenotype relationships

M Cooper, SC Chapman, DW Podlich… - In Silico …, 2002 - content.iospress.com
In this paper we refer to the gene-to-phenotype modeling challenge as the GP problem.
Integrating information across levels of organization within a genotype-environment system …

[PDF][PDF] Modelling plant breeding programs

M Cooper, DW Podlich, NM Jensen… - Trends in …, 1999 - researchgate.net
Quantitative genetics provides a theoretical framework that can be used to relate information
on the inheritance and heritability of traits to predictions of selection response for a breeding …

Linking biophysical and genetic models to integrate physiology, molecular biology and plant breeding.

SC Chapman, GL Hammer… - … , genomics and plant …, 2002 - cabidigitallibrary.org
This chapter discusses many of the key aspects of a modelling framework for linking gene
effects to their effects on a trait phenotype. Utilizing a modular, structured modelling …

Complexity, quantitative traits and plant breeding: a role for simulation modelling in the genetic improvement of crops.

M Cooper, DW Podlich, KP Micallef… - … genomics and plant …, 2002 - cabidigitallibrary.org
11 Complexity, Quantitative Traits and Plant Breeding: a Role for Simulation Modelling in the
Genetic Improvement of Crops Page 1 11 Complexity, Quantitative Traits and Plant Breeding: a …

QU-GENE: a simulation platform for quantitative analysis of genetic models.

DW Podlich, M Cooper - Bioinformatics (Oxford, England), 1998 - academic.oup.com
MOTIVATION: Classical quantitative genetics theory makes a number of simplifying
assumptions in order to develop mathematical expressions that describe the mean and …

Predicting the future of plant breeding: complementing empirical evaluation with genetic prediction

M Cooper, CD Messina, D Podlich… - Crop and Pasture …, 2014 - CSIRO Publishing
For the foreseeable future, plant breeding methodology will continue to unfold as a practical
application of the scaling of quantitative biology. These efforts to increase the effective scale …