This project is awarded under the Minority Postdoctoral Research Fellowships and Supporting Activities Program for 2006. The recent genome sequencing of two flowering plants, thale cress and rice, has revealed evidence of duplicated genome structures and that genome duplication may be common. Because this evidence is ancient and recurrent in two distantly related plants, it suggests that all flowering plants have undergone genome duplication (GD). The effect of GD or chromosome doubling, the duplication of all genes in a nucleus, produces immediate sometimes lethal effects such as rapid gene loss, gene silencing, gene expression changes, chromosome rearrangements, and transposon activation. GD in plants, also known as polyploidy, may contribute to genetic novelty, diversity, and survival advantage, e.g. the ability to colonize wider ranges of habitats and climates compared to diploid progenitors. Classical models predict that gene duplicates are rapidly lost or either, retain the same function or acquire a new one, and that they mutate faster when a second copy is present. However, recent surveys contradict this model: gene loss is gradual and selective, certain gene classes appear to be duplication resistant (are repeatedly restored to singleton status), and singletons acquire more severe mutations than duplicates. Surveys of gene loss and retention following GD may identify genes and pathways that are maladaptive in duplicate or that contribute to polyploid lineage survival. The genome sequencing of several important crop plants now underway, along with gene expression profiles from Arabidopsis (thale cress) and Oryza (rice) can now be used to uncover relationships between three properties of ancient duplicated segments: (1) molecular evolutionary analysis of DNA and proteins, (2) patterns of gene loss and retention, and (3) patterns of gene expression. These studies will increase our understanding about gene, chromosome, and genome evolution. Additionally, this work will increase our knowledge about plant biology, and the evolution, preservation, and further improvement of domesticated crops, many of which are polyploids.
My career goal is to be a professor of genome biology and a principal investigator of research at a minority serving institution of higher education. As an NSF Fellow, I want additional research experience in: the critical evaluation and design of experiments; the critical evaluation of scientific papers, research methods, and data outcomes; and the design of genome-scale research. My training plan, at the University of Georgia under the mentorship of Dr. Andrew H. Paterson, consists of: 1) the design and execution of whole genome surveys using computational phylogenomic approaches, 2) dating candidate genome duplication events in various taxa, 3) using whole genome surveys to ask focused questions about genome biology, 4) tracking evolutionary fates of duplicate genes following GD, 5) calculating mutation rates of DNA and proteins, and 6) identifying conserved and rapidly evolving genome structures. A further training opportunity exists in the development of computational protocols and software tools for identifying genome segment duplications. I intend to gain more expertise in computer programming in order to evaluate and devise software tools that exploit machine learning algorithms and dynamic programming algorithms for the alignment of genomic DNA sequences. These tools will help to clarify the extent of segment duplications in plant genomes and help interpret their role in the evolutionary history of flowering plants.
