Date of Award


Level of Access

Campus-Only Dissertation

Degree Name

Doctor of Philosophy (PhD)


Biological Sciences


Benildo G. de los Reyes

Second Committee Member

Stellos Tavantzis

Third Committee Member

Mary E. Rumpho


Plants are exposed perennially to adverse environmental conditions, of which low temperature is among those with the heaviest impact to crop productivity. Past successes of plant breeding had ensured an abundance of food supply despite constant resurgence of various abiotic and biotic factors that compromise the productivity potential. As the global climatic conditions continue to change, our ability to secure abundant food supply by conventional plant breeding will continue to be in jeopardy. There is a great need to continuously explore modern strategies to improve breeding efficiency for traits that are difficult to manipulate via traditional means such as tolerance to adverse climatic conditions. The goal of this study was to contribute to the understanding of integrated cellular and molecular processes that result in cold-adaptive mechanisms by functional and comparative genomics. The study specifically focused on the analysis of plant genetic models, in particular rice (Oryza sativa, subspecies japonica,) and thale cress (Arabidopsis thaliana) in order to understand the intricacies of the aforementioned mechanisms. The specific aims were to establish the functional role of the OsTGA10 regulated transcriptional network in the context of chilling response mechanism in chilling-sensitive species (rice) and to understand the evolutionary conservation of such network in other plants representing a spectrum of variation for low temperature sensitivity. A genome-wide microarray analysis of the transcriptome of a transgenic rice overexpressing OsTGA10 under the control of a constitutive CAMV35S promoter revealed that OsTGA10 acts as a major switch of the early rapid response transcriptome. This was based on signal-independent activation of potential target genes and the enrichment of OsTGA10 target cis-elements among the members of the associated regulatory clusters. However, supraoptimal expression of OsTGA10 led to the activation of a large number of non-target genes that are not involved in chilling response leading to severe growth and developmental abnormalities. Through the analysis of T-DNA insertional mutants, two homologs of OsTGA10 (AtTGA10 and AtbZlP1) were determined to function in a non-identical fashion in the temperate plant Arabidopsis acting both as activator and repressor of the chilling response transcriptome. Results of a pilot study using a phylogenetic footprinting approach to examine the regulatory information content of selected members (including orthologs and paralogs) of a transcriptional network revealed that the composition and organization of the stress response regulatory network are not conserved during speciation, despite the fact that flowering plants had maintained largely similar sets of genes during evolution. Unique spatio-temporal regulatory signatures in each species are indicative of the major contribution of regulatory information shuffling to the evolution of stress tolerance mechanisms in flowering plants.