2010 Annual Report
1a.Objectives (from AD-416)
Effective genetic strategies are needed to address major crop loss due to pathogen disease and provide alternatives to current chemically based crop protection strategies that impose human health and environmental risks. The long-term objective of this project is to gain an improved understanding of the structure, function and evolution of key components of the plant innate immune system for strategic deployment of key components of this highly regulated system to reduce the threat of crop loss by pathogens. Our specific objectives are to use evolutionary models and molecular-genetic strategies to identify durable pathogen resistance genes, to use genomics and genetics to identify and understand functional and regulatory components of the plant innate immune system, and to use comparative structural and functional genomics to understand the mechanism of induction and function of cellular and systemic events that constitute effective induced defense responses and plant innate immunity. Identification of functional and regulatory components of the innate immune system, and understanding the process of induction of defense responses will provide the conceptual base for deploying strategies for broad-spectrum resistance.
1b.Approach (from AD-416)
1. Use an evolutionary model developed by this project, in combination with positional cloning, to isolate the PVX resistance gene, Nb.
Develop DNA markers for fine genetic mapping of the virus disease resistance locus Nb.
Develop PCR methods to isolate candidate disease resistance locus Nb. Perform complementation tests for functional confirmation of Nb isolation. Test performance of Nb in potato cultivars.
2. Identify and analyze transposable elements in the Solanaceae and assess their impact on gene expression in plant innate immunity.
Perform comparative analysis of Solanaceae genomic sequences to identify repetitive transposable element-derived sequences inserted within R-gene hotspots and other genes and intergenic regions for further exploration of their role in structural diversity and genome evolution.
Explore transcription of MITE-derive candidate regulatory sequences by mining Solanaceae EST databases for the presence of MITE sequences.
Explore functional role of candidate MITE sequences in biotic stress by: identifying MITE-derived small RNAs, studying their biogenesis and comparing expression of MITE small RNAs and their candidate targets in biotically challenged and unchallenged wild-type and RNAi plant lines.
3. Understand induced defense responses associated with plant innate immunity by studying host and pathogen effector interaction with cell proteins. REPLACES: 5335-21000-006-00D (04/07).
We are focusing on application of an evolutionary model and molecular-genetic strategies to identify, isolate, verify and functionally test cloned candidate cDNAs corresponding to the PVX resistance gene Nb. We are also investigating the role of abundant gene-associated transposable elements (GATEs) in regulating genes with transposon insertions in promoters, 5' and 3' UTRs, and introns in Solanaceae (tomato, potato and tobacco).
Role of Solanaceae repetitive elements. Understanding of the regulatory components for coordinate regulation of the innate immune system, and the process of induction of defense responses in plants is needed to provide the conceptual foundation of strategies for broad-spectrum resistance. ARS scientists in Albany, CA identified abundant transposable elements (TE), genetic pieces in the Solanaceae that can move to different places in the genome and many of which reside within or near genes. ARS scientists used genetic biotechnology to elucidate the means by which these TEs regulate gene expression. These studies will make a significant contribution to understanding gene regulation in biotically challenged plants, an important issue for designing improved crops for American and world agriculture.
Evolutionary model-based strategy for identification of new R-genes. Understanding the generation of new pathogen recognition factors in plants is a current challenge for developing effective strategies for isolation of new resistance traits for crop protection. ARS scientists in Albany, CA hypothesize that “slow evolving” disease resistance genes are conserved among different Solanaceae species and that sequences of isolated active R-genes with characteristic structural properties can be used to isolate new resistance genes from related Solanaceae species. ARS scientists in Albany isolated, mapped and functionally tested cloned candidate genes corresponding to a related resistance gene, Nb. One kind of Nb cDNA conferred a resistance response on tobacco leaves when co-inoculated with a gene encoding the virus movement protein. The work suggests that a functional Nb gene has been obtained. The work established a new strategy based on a comparative genomics-based evolutionary model for isolation of disease resistance genes to protect plants.
Kuang, H., Padmanabhan, C., Li, F., Kamei, A., Bhaskar, P.B., Ouyang, S., Jiang, J., Buell, C., Baker, B.J. 2008. Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs. Genome Research. 19:42-56.
Zhang, L., Brown, C.R., Culley, D., Baker, B.J., Kunibe, E., Denny, H., Smith, C., Ward, N., Beavert, T., Coburn, J., Pavek, J.J., Dauenhauer, N., Dauenhauer, R. 2010. Inferred origin of several Native American potatoes from the Pacific Northwest using SSR markers. Euphytica. 174:15-29.