Functional Genomics of Plant Polyploids

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Polyploidy has played a prominent role in plant evolution. More than 70% of flowering plants have had at least one polyploid event in their lineage, either by doubling of a single genome (autopolyploidy) or, more commonly, by combining two or more distinct but related genomes (allopolyploidy). Many important crop plants, such as alfalfa, canola, cotton, potato and wheat, are obvious polyploids, and others, such as maize, soybean, and cabbage, retain the vestiges of ancient polyploid events. Although the importance of polyploidy has been widely recognized, the reasons for its success are not fully understood. Genome redundancy may provide some selective advantage, both through interactions of the combined genomes causing novel patterns of gene expression and through genome changes causing functional divergence of duplicated genes. Thus, polyploidy does not merely result in additivity for all traits from the progenitors, but often produces novel phenotypes that are not present in the parents or exceed the range of the parents. This phenomenon is analogous to heterosis, in which hybrid genotypes often have phenotypes that exceed those of their inbred parents.Rapid progress in genomic research of model plants and important crops has prompted the assembly of this consortium to study functional genomics of plant polyploids. The consortium is aimed at uncovering molecular mechanisms responsible for the evolutionary success of plant polyploids and agricultural utilization of plant hybrids. The theme of the proposed research is to investigate changes in gene expression and genome structure in resynthesized and natural autopolyploids and/or allopolyploids of Arabidopsis, Brassica and maize. Gene expression changes will be assayed using mRNA display and EST microarrays. New microarrays of the genes identified in heterochromatic regions will be developed and used for gene expression assays in Arabidopsis and Brassica. Changes in methylation state, transposon activity, chromatin status, and chromosomal arrangements will be determined using a combination of molecular, biochemical, and cytological techniques. The diploids, autopolyploids, and allopolyploids of each plant system will be compared to determine the effects of polyploidy on gene expression and genome structure. Inbred and hybrid maize at different ploidy levels will be compared to determine the relative effects of ploidy and heterozygosity on gene expression. Early and advanced generation polyploids of Brassica will be compared to test for stabilization of changes in the generations after polyploid formation and whether these changes are concerted and mimic natural polyploids. These studies will provide a comprehensive survey of the gene expression and genome changes accompanying polyploid formation and evolution. Most importantly, they should reveal some of the major mechanisms giving rise to these changes, and illuminate our overall understanding of why polyploids have been so successful in nature and agriculture.Participants:Thomas C. Osborn, PI, University of WisconsinJames A. Birchler, Co-PI, University of MissouriZ. Jeffery Chen, Co-PI, Texas A & M UniversityLuca Comai, Co-PI, University of WashingtonRobert A. Martienssen, Co-PI, Cold Spring Harbor LaboratoryRebecca Doerge, Co-PI, Purdue University