Progress 09/15/08 to 08/31/13
Outputs
OUTPUTS: For additional information, please contact Grant Cramer at 775-784-4204 or cramer@unr.edu PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
For additional information, please contact Grant Cramer at 775-784-4204 or cramer@unr.edu
Publications
- No publications reported this period
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: Our Grape Research Coordination Network (GRCN) held the 3rd annual conference and grape genome annotation jamboree June 2-5, 2011 in Lake Tahoe, CA. GRCN-PI Grant Cramer, University of Nevada Reno, opened the meeting welcomed all, outlined the goals of GRCN and reviewed identified the 6 graduate student or postdoc stipend awards for research and training exchange between USA labs or international labs coming to the USA and a foreign lab, or attending the GRCN meeting. This meeting emphasized the tools and datasets that were available to assist in updating and developing a comprehensive annotation of the 12X Vitis vinifera (PN40024) genome and V0 annotation that was released in 2010. PARTICIPANTS: Anne-Francoise Adam-Blondon Paul Haynes Dennis Gray Mario Pezzotti Josh Stein Nicola Vitulo Serge Delrot Grant Cramer Anne Fennell Lance Cadle-Davidson John Cushman Ryan Ghan Danny Hopper Supakan Rattanakon Steve Van Sluyter Gouthu Satyanarayanan Jub Mahanil Ramesh Katam Min Wang Sean Myles Paola Barba Erin Galarneau TARGET AUDIENCES: Grapevine research community PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Five major outcomes resulted from this meeting: I. Student Training and laboratory research exchange a)Graduate Student/Postdoc Stipend awardees poster presentation. Individuals receiving stipend in (October 2010) presented posters at the conference on ongoing research activities and one poster was selected for a prize based on presentation, research rationale and approach and presentation. b)Seven students were awarded stipends to attend the 3rd GRCN meeting and received training in grape genome annotation and the opportunity to network with the international grape genomics community. II. Speakers presented cutting edge methodologies, annotation tools and data sets available to assist in updating the predominately machine trained structural genome annotation. Structural annotation and functional annotation were reviewed and software tools were presented. III. Speakers presented advancement in areas identified as international grape genomics research priorities in previous GRCN and International Grape Genome Project (IGGP) meetings. IV. Annotation Jamboree, one full day was spent training meeting participants in structural and functional annotation of the grape genome V1 gene prediction. Participants were trained using two systems Apollo Annotation System and CRIBI Query Annotation System. Methods included step by step presentation of an example, group annotation of single genes and finally trained annotators annotated the SnRK kinase gene family. A draft of key annotation processes (covering annotation system steps, structural annotation, naming convention and functional annotation and annotation scoring) was developed as annotation proceeded. V. A meeting report will be drafted for publication in Standards in Genomic Sciences. A first draft of Annotation Best Practices was presented and discussed. Additional improvements for the CRIBI website were presented and discussed. A group was identified to continue working on Best Practices for presentation to broader community for comment and publication. It was decided that additional annotation workshops would be developed to increase the number of people annotating and it was agreed that another annotation training session be included in the Grape RCN in 2013.
Publications
- No publications reported this period
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: During the last year the following outputs were generated: 1. A web page for the GRCN was created on the IGGP web site at www.vitaceae.org/ index.php/Grape_Research_Coordination_Network and has been updated regularly. 2. A second round of stipend applications was accepted and reviewed by the Steering Committee.We had 11 stipend applications from graduate students and postdoctoral research associates. Six of these were from the USA, five from foreign countries. 3. The 2nd Annual Grape Research Conference was held in Geneva, NY, USA from the evening of July 29th, 2010 until mid-day July 31st, 2010. The meeting summary, schedule of events, and list of speakers can be found at: www.vitaceae.org/index.php/Meetings/GrapeResearchCoordinationNetworkC onference2/. 4. One joint proposal (USDA-SCRI) was developed and submitted entitled: "Accelerating grape cultivar improvement via phenotyping centers and next generation markers". 5. Communications were established with a Chinese researcher in grapevine, Dr. Lijun Wang of the Institute of Botany, Chinese Academy of Sciences. He was invited to give a talk at our University of Nevada in the Spring of 2010. This was followed up by Dr. Cramer with a visit to China to present a talk at the 1st Annual Fruit Tree Genomics Conference in Wuhan, China in October. He also visited the Institute of Botany, Chinese Academy of Sciences in Beijing. 6. Protocols have been generated and placed on the IGGP web site. PARTICIPANTS: 10 stipend awards to graduate students and postdocs were given this year. 6 of them were from the USA. All awardees went to another institution to get some sort of training that involved functional genomics of grapes. There were 74 participants in our 2nd Annual Meeting with representation from 34 institutions from 14 countries. Considerable collaborations were established and these have expanded from the previous year to many more countries. TARGET AUDIENCES: The target audiences are grape researchers from around the world who are interested in research on grape functional genomics. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
At the 2nd Annual GRCN meeting held in Geneva, NY, several priorities of the grape functional genomics community were established. The are: 1) Genome Sequencing: capture genome variation from selected species (including wild species) and varieties of viticultural importance by sequencing additional genomes. Use these sequences to determine the pan and dispensable genome of Vitis, for association mapping with phenotypic traits. There is a need to exploit the large natural populations of Vitis. 2) Bioinformatics: more complete genome annotation is needed through manual curation efforts by experts who can focus on specific gene families and metabolic pathways. There is also a need for development and dissemination of standardized protocols for various procedures and a need for a RNA seq database. 3) Phenotyping: standardized international methods need to be established. Centralized databases and high-throughput phenotyping centers are needed. Core genotypes need to be established around the world. 4) Trangenics/functional analyses: Need transgenic and mutant populations for identification of gene function. 5) Funding: need to provide more success stories of breeding and research. Need to coordinate research to reduce redundancy and use funds efficiently.
Publications
- No publications reported this period
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: 1. A web page for the GRCN was created on the IGGP web site at www.vitaceae.org/ index.php/Grape_Research_Coordination_Network. This web page describes the GRCN in detail, with a listing of contacts, objectives and places to get information on the annual meeting and applications for stipends. 2. A stipend application was developed and reviewed by the Steering Committee. It was posted on our web site and advertised by sending emails to different colleagues around the world and well as broadcast through the Cornell international grape research community listserver (grape-research-community-l@cornell.edu) that has over 500 grape participants. We had 13 stipend applications from graduate students and postdoctoral research associates. Eight of these were from the USA, five from foreign countries. The steering community reviewed these applications and we had a discussion via email on who was qualified. Eight awards were given, seven from the USA. There was sufficient money to give full awards to all qualified applicants. The amount varied with the application but averaged around $7,000. 3. The 1st Annual Grape Research Conference was held at Granlibakken at Lake Tahoe, CA, USA from the evening of May 15th, 2009 until mid-day May 17th, 2009. The meeting summary, schedule of events, pdf talks, and list of participants can be found at: www.vitaceae.org/index.php/Meetings/GrapeResearchCoordinationNetworkC onference1/. The meeting was a huge success. On our exit survey, many people who attended the meeting liked the informal style of the meeting because it allowed for very good interactions between the participants. At the end of the talks, we had a round table discussion to determine the top functional genomics priorities needed by the grape research community. PARTICIPANTS: John Cushman (UNR), Lance-Cadle Davidson (USDA), Anne Fennell (SDSU). TARGET AUDIENCES: The information about the RCN is listed on the web page and provided as announcements at meetings to the scientific community. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The top six priorities developed by the community are: 1. Capture genome variation from selected species (including wild species) and varieties of viticultural importance by sequencing additional genomes. Eight are in progress and 10 more are planned for the near future by European groups. 2. More complete genome annotation is needed through manual curation efforts by experts who can focus on specific gene families and metabolic pathways. 3. Development and dissemination of a more efficient transformation system for Vitis. 4. Development and dissemination of standardized protocols for various procedures. 5. Development of a metabolite database for Vitis. 6. Development of mutant collections from chemically (EMS) or physically (radiation) mutagenized population or from surveys of natural diversity within existing germplasm collections. The next GRCN meeting was decided to be held in Geneva, NY at the end of July, 2010 in conjunction with the 10th International Grapevine Breeding and Genetics Conference.
Publications
- No publications reported this period
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: This project has just begun. The steering committee agreed on a stipend application form for graduate students and postdocs. The applications were put on the web and the deadline for receipt of applications has passed. Applications are currently under review to decide on the awards. The annual conference has been organized and will take place from May 15 to the 17th, 2009 at Grannlibakken at Lake Tahoe. The conference is advertised on the International Grape Genome Program (IGGP) web site (vitaceae.org). The invited speakers have been chosen and a schedule is posted. PARTICIPANTS: The steering committee that has participated in the decisions for stipends are: Grant Cramer, John Cushman, Anne Fennell, Julie Dickerson, Violeta Colova, Lance Cadle-Davidson, Deborah Golino, Doug Adams, Wenping Qiu, and David Tricoli. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
None to date.
Publications
- No publications reported this period
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