Cotton Functional Genomics Center

Regulatory Role of R2R3-MYB Transcription Factors in Determining Agronomic Properties of Cotton Fibers within a developmental, physiological, environmental and evolutionary context. Most, if not all of the important agronomic fiber traits are related to the composition, structure and modification of the cell wall and the environmental impact on fiber development. Thus, our interest in the functional dissection of cotton fiber R2R3-MYB genes will focus on the regulation of secondary metabolism (phenylpropanoids), cell wall-related pathways, and how these genes respond to specific stimuli (stress and hormones). In-depth data mining of our fiber dbEST revealed as many as 56 novel R2R3-MYB genes are expressed in developing cotton fibers, many of which do not appear to have close Arabidopsis orthologs. Our goal is to determine the functional role of the cotton fiber R2R3-MYB genes using functional genomic and reverse genetic approaches to address the following specific objectives:

1. Determine the differential expression of the cotton fiber genes by analyzing expression profiles in response to developmental signals, hormones, and stress (heat and cold) using oligomer subarrays. The spatial regulation will be complemented with expression of MYB promoter-reporter gene constructs in Arabidopsis.
2. Dissect the combinatorial (positive and negative) regulation of phenylpropanoid metabolism and cell wall biosynthesis derived from expression profiles of downstream targets in response to ectopic expression of cotton fiber R2R3-MYB genes, coupled to metabolic profiles.
3. Determination of the fiber initiation complex using yeast hybrid systems and genetic approaches to test our working model, including study of motifs and signatures.
4. To study fiber evolution and domestication, a branch pathway of phenylpropanoid metabolism will serve as a diagnostic marker. The target genes will be recovered from a modest EST project (~6,000) based on subtractive suppression plasmid libraries constructed from pivotal cotton species. These ESTs will be used to expand cotton fiber oligo arrays for expression profiling to track changes in regulation and expression of this key biochemical pathway over the course of evolution.

This project is fully anticipated to provide novel insight into our understanding of fiber gene function from an agronomic, developmental and evolutionary perspective. The results of this study will undoubtedly enrich other cotton functional genomic studies, our understanding of the regulation of an important biochemical pathway, and of course, promises to significantly impact the Arabidopsis trichome model.