Indvidual Research Project Overviews

Development of an oligonucleotide microarray for the rice genome

Microarray technology permits biologists to concurrently measure the expression levels of thousands of genes in single experiment. Computational tools can be used to extract biologically significant information from gene expression data, assign functions to genes, and identify genetic regulatory networks. Public-sector access to microarrays is critical to ensure that the public's large investment in rice structural genomics is converted to public scientific and economic benefits.

Development of Rice Genome Tiling Microarray

Computer assisted genome annotation suggests that there are about 60,000 genes in the rice genome. However, it is estimated that the combination of all experimental data available (such as those from MPSS, SAGE, EST and full-length cDNA analyses) can only provide expression validation for about 50% of the predicted genes. Thus there is need for experimental verification of all predicted genes to discover rice genes that were missed by current prediction programs.

Construction of a protein interaction database for 275 rice kinases

Reversible protein phosphorylation appears to be the most widely used biochemical mechanism in cellular signaling and has been found to regulate aspects of transcription, translation, and post-translational processes. One measure of this important role is that protein kinases and phosphatases constitute 5 percent of the completed Arabidopsis genome and are estimated to be a similar percentage of the rice (Oryza sativa) genome. Although it is clear that kinases and phosphatases play a key role in many stress responses, functional roles have not been identified for most of the protein kinases and phosphatases in the genome.

Specificity and control of XA21-mediated signal transduction: the role of the juxtamembrane domain, WRKY factors and a PP2C phosphatase

Perception of extracellular signals by cell surface receptors is of central importance to eukaryotic development and immunity. Many of these receptors possess intrinsic protein kinase activity in their cytoplasmic domains (RKs) and regulate transcription of target genes through phosphorylation events.

xoo genomics and Identification of the avrXa21 molecule

Most R genes encode presumed intracellular proteins that are predicted to bind intracellular ligands encoded by bacterial avr genes. In contrast, XA21 appears to bind its ligand, called avrXa21, extracellularly. We have identified three Xanthomonas oryze pv. oryzae (Xoo) genes required for AvrXa21 activity (raxA, raxB and raxC). These genes encode the three components of a bacterial type1 secretion system. Type I secretion systems secrete molecules from the bacterial cytoplasm directly to the bacterial cell surface or the extracellular environment.

Systemic acquired resistance, age-related resistance and programmed cell death

A plant defense response effective against a broad-spectrum of pathogens is termed systemic acquired resistance (SAR). In dicotyledonous plants both local infection by a necrotizing pathogen and exogenous application of salicylic acid (SA) induce SAR. In Arabidopsis, the gene NPR1 (also called NIM1) is a key regulator of SAR. Arabidopsis plants over-expressing NPR1 display enhanced resistance to pathogens. Similarly, we have found that transgenic rice that over-express the NPR1 gene (NPR1-OX) show enhanced resistance to Xoo, suggesting that NPR1 can mediate a defense pathway in rice. We have also identified a gene with significant sequence similarity to NPR1, named NPR1 homolog 1 (NH1).

The molecular basis for broad spectrum resistance to rice blast

Rice blast, caused by Magnaporthe grisea is one of the most destructive diseases of rice costing farmers $5 billion a year. Relatively broad spectrum or durable resistance has been observed in some cultivars. For example, Tetep, an indica rice cultivar exhibits broad-spectrum resistance to rice blast and has been used as resistance donors in breeding programs.

Genomics and proteomics of the rice defense response

Computer assisted genome annotation suggests that there are about 60,000 genes in the rice genome. However, it is estimated that the combination of all experimental data available (such as those from MPSS, SAGE, EST and full-length cDNA analyses) can only provide expression validation for about 50% of the predicted genes. Thus there is need for experimental verification of all predicted genes to discover rice genes that were missed by current prediction programs.

Identification of Cell Wall Synthesis Regulatory Genes Controlling Biomass Characteristics and Yield in Rice (Oryza_sativa)

Cost efficient conversion of lignocellulosic biomass into bioethanol requires an improvement in cell wall characteristics and yield.

Submergence tolerance

A gene that enables rice to survive complete submergence has been identified by a team of researchers at the International Rice Research Institute in the Philippines and at the University of California's Davis and Riverside campuses. The discovery allows for development of new rice varieties that can withstand flooding, thus overcoming one of agriculture's oldest challenges and offering relief to millions of poor rice farmers around the world.