A gradient model for studying genotype- environment interactions

Open Access
Chen, Weihan
Graduate Program:
Master of Science
Document Type:
Master Thesis
Date of Defense:
Committee Members:
  • Rongling Wu, Thesis Advisor
  • QTL genotypes
  • EM algorithm
The genetic architecture of how genes interact with the environemnt to determine complex phenotypes remains eclusive. We know little about the genes that underlie the adaptation and microevolution of biological traits to changing environments, their number, chromosomal locations and genetic interactions as well as the environment-dependent pattern of their effects. Here we address this problem by developing a computational model for mapping specific quantitative trait loci (QTLs) that affect the gradient expression of a complex trait across a range of environments. The distinction of our model is in the incorporation of gradient changes of environmental factors into the analysis of genotypeenvironment interactions, thereby better unraveling the attribute of quantitative traits to vary continuously in response to the environment. The model is formulated within the maximum likelihood context and implemented with a hybrid EM-simplex algorithm to estimate the model parameters. By testing the curve parameters that model environment-dependent trajectories of the trait for individual QTL genotypes, the model allows the quantitative test of a series of fundamental hypotheses about the interplay between gene action/interaction and environmental sensitivity and the prediction of genetic control over the phenotypic plasticity of any complex trait to changing environments.