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   Research Summary

Our research is focused on the comparative and functional genomics of disease resistance in plants, particularly Arabidopsis, tomato and lettuce. Our investigations of Arabidopsis involve the large-scale genomic analysis of resistance gene function and evolution in Arabidopsis as well as a comparative genomics analysis of resistance across multiple species. Our studies of disease resistance in tomato focus on structure-function analyses on the resistance gene Pto, Prf and dissection of the Pto-mediated disease resistance signaling pathway. Studies on lettuce and its pathogens includes classical studies of disease resistance, development of detailed genetic maps using molecular markers, studies on transgene expression and characterization of resistance genes at the molecular level. All of these projects are supported by the lab bioinformatics group.

Plants express hundreds, maybe thousands, of disease resistance genes. Many of these are related at the sequence level and therefore by inference at the functional level. Approximately 0.7% of the annotated genes in Arabidopsis encode NBS-LRR proteins. We are conducting a genome-wide analysis to determine whether all function as resistance genes or whether they are involved in other aspects of plant biology (http://niblrrs.ucdavis.edu/). This has involved a bioinformatics analysis and reannotation of the gene family, global expression analysis using a range of approaches, and microarray analysis of known resistance resistance phenotypes in collaboration with others. We are also conducting a comparative analysis of resistance genes within and between genotypes in lettuce, tomato and Arabidopsis as well as other species to determine the mechanisms that control the evolution of resistance gene specificities (http://charge.ucdavis.edu/). These studies range from population genetics to molecular analysis of spontaneous mutations. These experiments revealed that some resistance genes are not evolving as fast had been previously supposed and led us to a new model for the evolution of resistance genes. An ultimate aim of these studies is to be able to direct the evolution of resistance genes ex planta using DNA shuffling, to recognize new ligands.

A major focus of our studies on tomato is on understanding and engineering the early events in resistance of tomato to Pseudomonas syringae pv tomato. We are dissecting the signal transduction pathway involving the Prf, Pto and Fen genes. We have completely sequenced the Pto locus from resistant and susceptible haplotypes. This revealed that a variety of unequal cross-over events had occurred in the evolution of this locus. Ligand-independent, constitutive gain-of-function variants provided powerful tools to investigate the function of Pto and its homologs. Subsequently, we have been investigating the role of Prf (a NBS-LRR protein) in the Pto-mediated resistance pathway. We are using DNA shuffling to dissect the functional domains of Pto for binding pathogen-derived ligands and signaling downstream to induce the resistance response.

The classical genetic studies of lettuce involve screening lettuce germplasm for resistance, determining its genetic basis, and introgression of resistance into genotypes that are resistant to multiple diseases. Most of our efforts have focused on resistance to downy mildew (Bremia lactucae), corky root (Rhizomonas suberifaciens), and lettuce mosaic virus. We are expanding our efforts on resistance to bacterial diseases and Verticillium dahliae. These classical studies provide genotypes for our molecular investigations as well as advanced breeding lines for the commercial breeding industry. We are also continually monitoring variation in B. lactucae to understand the basis of variation in the pathogen and direct the deployment of resistance genes. We have developed a genetic map for B. lactucae and working towards cloning avirulence genes. We also have a moderately extensive set of ESTs from B. lactucae.

We developed a detailed genetic map of lettuce using a variety of molecular markers (http://compositdb.ucdavis.edu/). Numerous resistance genes have been mapped and molecular markers identified for them. Genes for resistance to diverse pathogens are clustered in the genome indicating a common origin and function. The genetics and evolution of resistance is being analyzed in wild and cultivated populations.

We are coordinating The Compositae Genome Project (http://compgenomics.ucdavis.edu) to develop genomics tools for species within the Compositae, particularly lettuce and sunflower, to determine the degree of synteny between lettuce, sunflower and Arabidopsis, and to exploit functional information being generated in model species such as Arabidopsis. This involves a large-scale EST sequencing project, SNP development, and mapping of candidate genes to agriculturally important traits. Candidate genes will be validated by RNAi.

We developed stable and transient transformation systems for lettuce mediated by Agrobacterium tumefaciens. However, while it is relatively easy to introduce DNA into lettuce, transgenes are often not expressed well in stable transgenics. The reasons for this are under investigation. Transient assays work very well in lettuce and are being used to investigate the reactions to numerous bacterial effector proteins.

We utilize a combination of map-based and candidate gene strategies to clone genes for disease resistance. We saturated target regions with molecular markers (RAPDs and AFLPs), generated a BAC library with large genomic inserts, isolated numerous induced mutants of Dm genes, and constructed a detailed genetic and physical map of the largest cluster of resistance genes. We have also isolated resistance gene homologs using degenerate oligonucleotide primers to sequences that are conserved in resistance genes cloned from other species. The cloning of Dm3 was confirmed by transgenic complementation experiments. We are now developing more efficient approaches to clone additional resistance genes. RNAi is being used to demonstrate which resistances are encoded by homologs of Dm3.

The lab bioinformatics group supports all the above projects. This involves the acquisition and curation of genetic, sequence and microarray data, queries of EST data, the analysis of microarray data, and building tools for comparative genomics.

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