Transposable Elements in Rice: A Whole Genome Approach

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A large fraction of the DNA sequence output from plant genome projects will be derived from transposable elements (TEs). It is estimated that 30% of the small genome of rice (Oryza sativa cv. Nipponbare, 438 Mb), which is the focus of the next major plant genome project, is derived from TEs. Unlike a TE, the function of a gene can be deduced, in part, through the phenoytpe of a knockout mutant, the localization of protein or mRNA and the analysis of microarrays. Such functional genomics approaches are of little value in understanding the contribution of TEs to genome evolution and function. What distinguishes TEs from the genic complement of an organism, among other things, is an ability to transpose and amplify. TEs shake up an otherwise conservative genome and, in this way, both threaten and enhance genomic potential. This project uses a functional genomics approach to discern the contribution of the TEs of rice that includes three components: (1) the identification and characterization of all TE families, (2) the quantification of TE-mediated diversity in closely related Oryza sativa cultivars, subspecies and related species and (3) an assessment of the contribution of TE- diversity to the creation of phenotypic variation. To this an interdisciplinary, whole genome approach will be used with five specific objectives.(i) To computationally identify rice TEs and phylogenetically characterize TE families. A major focus will be the testing of a novel automated repeat element identification algorithm.(ii) To assess the activity of select TE families by using a rapid transposon display screen to assay a panel of wide-species crosses and a variety of stress environments.(iii) To determine the chromosomal distribution of 1000 TE insertion sites that are polymorphic in two different mapping populations and to develop a subset of these into anchor markers.(iv) To use the mapping populations and the anchor markers as the basis for correlating TE-based genetic variation with phenotypic variation for selected plant traits.(v) To integrate all data from this project into the RiceGenes database thus adding value to the infomation in the form of annotation linking TEs to QTLs, mutant phenoytpes, genetic markers and germplasm diversity. Transposable elements probably account for the huge difference in size among the agronomically important members of the grass clade including rice, sorghum, maize and wheat. This consortium will serve as a model for how TEs should be studied in these more complex genomes.