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Project Summary

2000-2005 Funding Period

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.

2005-2010 Funding Period

Polyploidy is recognized an evolutionary innovation in all eukaryotes and especially in plants, including most important agricultural crops. Whole genome duplication may occur via autopolyploidization by multiplying a single genome or allopolyploidization by combining two or more divergent genomes. Auto- and allopolyploidization not only promotes functional divergence of duplicate genes, but also generates heterozygosity and novel interactions leading to genetic and phenotypic variability and heterosis. Results from this consortium group and others have collectively demonstrated that non-additive gene regulation (different from the mid-parent value) in hybrids and allopolyploids mediates a large number of genes, including rDNA loci, transposons, and the genes involved in various biological pathways. In this project, we will test several hypotheses concerning the mechanisms of dosage-dependent and non-additive gene regulation in three complementary plant systems, namely, Arabidopsis, Brassica and Corn (ABC). We will study the genetic bases of inbreeding depression, hybrid vigor, allopolyploid incompatibility, and their underlying mechanisms using reporters and non-additively expressed endogenous genes. The roles of chromatin modification and RNA interference in non-additive gene regulation will be rigorously tested. Gene expression changes in new polyploid populations will be compared to determine genetic loci affecting de novo phenotypic variation and hybrid vigor following polyploidization.

Direct and Broad Impacts: In the post-sequencing era, polyploidy is one of the most challenging fields in plant biology. Results from this research will not only illuminate our understanding of polyploidy, but also enable us to eventually improve the production of agricultural crops. As a convention in this project, plant seeds, DNA sequences, and microarray and gene expression data will be timely deposited in Arabidopsis and maize Resource Centers, GenBank, and microarray data repositories (e.g., GEO), respectively. Our research team will continue to streamline microarray data analysis and management using genome informatics and statistical methodologies. Research and training activities will be updated monthly in the project website. We have trained postdoctoral researchers to become elite plant biologists in primarily teaching colleagues and research universities and will continue our contributions to biological research as well as educating postdoctoral researchers, graduate and undergraduate students. Moreover, the senior personnel in two primarily teaching colleges will implement contemporary polyploidy and genomics modules into traditional genetics and biology curricula. The research and teaching partners will actively participate in exposing underrepresented students to research and teaching career opportunities by organizing summer internships and workshops in research laboratories in collaboration with local high and middle schools.

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