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NE1033: Biological Improvement of Chestnut through Technologies that Address Management of the Species, its Pathogens and Pests

Annual/Termination Reports (SAES-422): [01/26/2010] [12/16/2010] [01/05/2012]

Date of Annual Report: 01/26/2010

Report Information:
  • Annual Meeting Dates: 09/25/09 to 09/26/09
  • Period the Report Covers: 10/2008 to 09/2009

    • Participants:
    Brief Summary of Minutes of Annual Meeting:
    The meeting was called to order by Chairman Hillman at 9:00 am on September 25, 2009 at the Manchester Inn, Ocean Grove, NJ. As Senior Associate Director for the New Jersey Agriculture Experiment Station and Director of Cooperative Research, Hillman is now the Administrative Advisor for NE-1033.

    2010 Business Meeting
    Sandra Anagnostakis was elected Chair for 2011. Paul Sisco, chair-elect, stated that the 2010 meeting will be held September 16-19, 2010 at Cataloochee Ranch in Maggie Valley, NC. It's about 45 minutes west of Asheville in a gorgeous location at 5,000 feet adjoining the Great Smoky Mountains National Park. The website is: http://www.cataloocheeranch.com/

    Note: Detailed accomplishment report is in the attached Minutes.


    URL: Copy of minutes

    Accomplishments:
    Completion of proposed milestones:
    2005:

    2006:

    2007:

    2008:

    Completion of milestones not proposed:

    2009

    In progress.

    2010

    Impact Statements:
    Last Modified: 26-Jan-2010

    Date of Annual Report: 12/16/2010

    Report Information:
  • Annual Meeting Dates: 09/17/10 to 09/18/10
  • Period the Report Covers: 10/2009 to 09/2010

    • Participants:
    Brief Summary of Minutes of Annual Meeting:

    URL: Copy of minutes
    Accomplishments:
    2009 Outcomes

    " Determine specific genetic fingerprints of tested cultivars through the use of microsatellite markers and find loci useful for parentage analysis (Fulbright) " Refine the genetic linkage and genome sequence maps for map-based cloning of fungal vic and pathogenicity genes " Tom Kubisiak used the C. parasitica Genome sequence generated by the JGI Community Sequencing Program to identify 689 simple sequence repeats (SSRs) and designed 141 primer pairs. One hundred and thirty Four of the 141 primer pairs amplified discrete products, with 96 of the 134 showing polymorphism for the JA17 and X17.8 parents of the mapping cross. Allele data were generated for 96 progeny from the mapping cross for 32 polymorphic SSRs and a total of 30 of these markers were placed within the context of the published C. parasitica linkage map (Kubisiak and Milgroom, 2006, FG&B 43:453-463). The new linkage data were used by the JGI finishing group to connect a number of scaffolds in Version 1 of the genome assembly to generate Version 2 that was released July 10, 2009. Ï Complete assembly and community manual annotation of the C. parasitica genome sequence Nine-hundred and ninety-five of 11,251 transcripts have been manually curated by the C. parasitica annotation team to date. Version 2 of the genome assembly has been released by the JGI consisting of 26 scaffolds. Five of the new scaffolds contain two teleomers and are of a length consistent with a complete chromosome. Six additional scaffolds contain one teleomer and are in excess of 1 MB in length. The assembly release Version 2 of whole genome shotgun reads was constructed with the Arachne assembler and improved with finishing reads. This release contains 26 main genome scaffolds totaling 43.9j Mb. Five scaffolds are considered complete teleomere on one end. The remaining 15 scaffolds are smaller and do not contain teleomers. Roughly half of the genome is contained in four scaffolds all at least 5.1 Mbp in length. Annotation of Version 2 assembly was produced by the JGI Annotation Pipeline using a variety of homology-based and ab initio predictors. The Version 1 Gene Catalog and its manual curations also were mapped to the Version 2 assembly and were included in the filtering procedure that determined the initial Version 2 Gene Catalog. After filtering for EST support, completeness and homology support, a total of 11, 609 genes were structurally and functionally annotated. Ï Use the C. parasitica genome sequence to develop new microarray chip and proteomics platforms for analysis of global gene expression in the blight fungus when challenged by viral pathogens " Orchard established in WV with advanced, back-cross chestnut trees from VA for assessment of host resistance with hypovirulence in the Cryphonectria parasitica populationreplanted in 2009.

    2010 Outcomes Ï Complete characterization of C. parasitica antiviral RNA silencing pathways. Two Dicer genes were identified in the C. parasitica genome, cloned and disrupted. Dicer DCL2 was shown to be required for antiviral RNA silencing while Dicer DCL1 was not required (Segers et al., PNAS 2007, 104:12902-12906). Four Argonaute genes were identified in the C. parasitica genome, cloned and disrupted. Only Argonaute AGL2 was required for antiviral RNA silencing (Sun et al., PNAS, IN PRESS). Three RNA dependent RNA polymerases and an orthologue of the QIP exonuclease involved in transgene silencing in Neurospora crassa have been identified in the C. parasitica genome and are currently being cloned and disrupted. The C. parasitica gene oah, encoding the enzyme Oxaloacetate acetylhyrdolase (OAH), a member of the PEP mutase (PEPM)/isocitrate lysase (ICL) superfamily, that catalyzes the hydrolysis of oxaloacetate to oxalic acid and acetate, was cloned, characterized and disrupted. Knockout of the oah gene reduced the ability to form cankers on chestnut trees, which suggest that the enzyme plays a key role in virulence.

    Completion of milestones not proposed: " A proposal to sequence the C. parasitica genome was approved by the Department of Energy Community Sequencing Program in June of 2006. The assembled 8.5 X C. parasitica genome sequence was released to the public on September 30, 2008. This is a tremendous resource for future studies on the chestnut blight fungus and its interaction with the chestnut tree. " Demonstration that hypovirus p29 suppresses RNA silencing in C. parasitica and in heterologous plant system. This is the first report of a mycovirus-encoded suppressor of RNA silencing. Segers, G.C., van Wezel, R., Zhang, X., Hong, Y. and Nuss, D.L. Hypovirus Papain-like protease p29 suppresses RNA silencing in the natural fungal host and in a heterologous plant system. Eukaryotic Cell 5:896-904, 2006. " Demonstrated that RNA silencing serves as an antiviral defense mechanism in C. parasitica (first example for any fungus) against hypoviruses and mycoreoviruses. Segers, G.C., Zhang, X., Deng, F., Sun, Q. and Nuss, D.L. Evidence that RNA silencing functions as an antiviral defense mechanism in fungi. PNAS USA 104:12902-12906, 2007. " First report of the cloning and sequence analysis of mycovirus-derived small RNAs (vsRNAs) generated by RNA silencing. The vsRNAs were shown to be produced, in a dicer dcl-2-dependent manner, from both positive and negative hypovirus RNA strands at a ratio of 3:2 and to be non-randomly distributed along the viral genome. C. parastiica was shown to respond to mycovirus infection with a 10-15 fold increase in dcl-2 transcript acuumulation while the expression of dcl-1 was modestly increased. The expression of dcl-2 was further increased (~35 fold) following infection by a CHV1-EP713 mutant that lacks the p29 suppressor of RNA silencing. A similar response in dicer gene expression following virus infection of plants or animals has not yet been reported. In this regard, it is anticipated that the evolutionary position of fungi relative to animals and plants will provide insights into additional novel mechanisms for the induction and suppression of RNA silencing pathways yet to be revealed in the other organisms. Zhang, X., Segers, G.C., Sun, Q., Deng, F. and Nuss, D.L. Characterization of hypovirus-derived small RNAs generated in the chestnut blight fungus by an inducible DCL-2-dependnet pathway. Journal of Virology 82:2613-2619, 2008. " Virus RNA recombination is an important component of virus evolution that contributes to the emergence of new viruses and the generation of internally deleted mutant RNAs, termed defective interfering (DI) RNAs, that are derived from, and dependent on, the parental viral genomic RNA. We provided the first experimental evidence that a host RNA silencing pathway is required for DI RNA production and virus vector RNA instability for a single-strand, positive sense RNA virus. Zhang, X. and Nuss, D.L. A host dicer is required for defective viral RNA production and recombinant virus vector instability for a positive sense RNA virus. Proc. Natl. Acad. Sci. USA. Early Edition, October 13, 2008.

    Impact Statements:
    Last Modified: 16-Dec-2010

    Date of Annual Report: 01/05/2012

    Report Information:
  • (STILL IN DRAFT VERSION)
  • Annual Meeting Dates: 10/28/11 to 10/30/11
  • Period the Report Covers: 10/2010 to 09/2011

    • Participants:
    Brief Summary of Minutes of Annual Meeting:
    The meeting was called to order by Chairman Anagnostakis at 9:30 am on October 28, 2011 at the Incarnation Center, Ivoryton, CT.

    Please see attached file for the full version of the minutes (62 pages).


    URL: Copy of minutes

    Accomplishments:
    2005: 2006: 2007: 2008:

    2009:

    2010:

    2011:

    Completion of milestones not proposed.

    2010

    Impact Statements:
    Last Modified: 05-Jan-2012
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