Minutes of the Rosexec meeting at Plant & Animal Genome XVII sunday, January 11, 2009



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Minutes of the RosEXEC Meeting at Plant & Animal Genome XVII

Sunday, January 11, 2009
Members present: Cameron Peace (incoming Chair), Nahla Bassil (incoming Vice Chair), Gennaro Fazio (outgoing Chair), Tom Davis, Amit Dhingra, Kevin Folta, Stan Hokanson, Jim Luby, Gayle Volk.

Guests present: Angela Baldo, Susan Brown, Jill Bushakra, Jean-Marc Celton, David Chagne, Mark Davey, Thomas Debener, Beatrice Denoyes-Rothan, Sergio Diez de Medina, Tomoya Esumi, Kate Evans, Sue Gardiner, Andrew Gleave, Renate Horn, Lizex Husselmann, Amy Iezzoni, Dorrie Main, Jim McFerson, Lee Meisel, Eben Ogundiwin, Jim Olmstead, Nnadozie Oraguzie, Ariel Orellana, Jasper Rees, Silvio Salvi, Vladimir Shulaev, Herman Silva, Janet Slovin, Khashief Soeker, Bryon Sosinski, JD Swanson, Ryutaro Tao, Daleen van Dyk, Riccardo Velasco, Richard Veilleux, Kenong Xu, Tom Gradziel, Francois Laurens
General

  • Appointment of minute-taker

Without a new Secretary yet established for 2009, Amit Dhingra volunteered to take minutes.

  • Objectives of RosEXEC

The RosEXEC Mission was read out.

  • Appreciation for leadership of Gennaro in 2008

Gennaro Fazio, RosEXEC Chair for 2008, passed the mantle to Cameron Peace for 2009. A small gift of rosaceous products was presented to Gennaro (and later passed around for all to enjoy).
Coordination

  • U.S. Rosaceae White Paper – now on Wikia

Angela Baldo mentioned that www.rosaceaewhitepaper.com hosts the 2006 version in wikia format. Angela will hold a demo workshop for the wikia to show how to edit the document etc. She will assist during the initial stages of white paper improvement and finally the document will be hosted on GDR once time and resources permit. Editorial control of the White Paper will be with the RosEXEC chair. A need to formalize the referring of the document was felt by the community.

Vladimir Shulaev thanked all who contributed to the opinion paper paper, published in Plant Physiology in 2008. It was suggested that the article be hosted on wikia so it can be updated regularly.

The Genetics and Genomics of Rosaceae book has been in production for 2 months. Proofs expected soon. The community felt that it is expected to be a landmark publication for the Rosaceae community.



  • GDR funding update

Dorrie Main informed that GDR was running on fumes. WSU has provided support. The new proposal to NSF due Jan 21 has several strengths. Additional grant to SCRI for a tree fruit database is also being prepared for resubmission. Matching monies are available for SCRI purposes. Future direction of GDR is to integrate genome and annotation for Fragaria, apple, peach, database to be converted to Chado that is much simpler for the user, expansion of outreach workshops, feedback, grower workshops, high school teacher courses incorporated. Committed to upload the apple genome sequence and maintain it securely till the publication that is expected to be submitted by spring.

A motion passed (8 December 2008 teleconference) in support of GDR was described. The RosEXEC had recommended that all Rosaceae grants going into NRI, SCRI, NSF, etc, must budget support funds for GDR. This would be in the order of $5-15K component to allow maintenance of GDR. A mechanism to invoice the PI is available in GDR. Dorrie mentioned that she is developing a matrix to cover the costs of data upload and maintenance. Further, she is working on ensure sustainability by trying to get perennial funding for GDR. As genome sequences become available there will be a need to expand the utility of GDR. Suggestion made to have a downloadable letter of support or costs from GDR. Letter to be ready for the community soon (Dorrie said by 1/12/09, possibly by weblink) for the PIs to download. Membership fee idea was also discussed.



  • Funded NRI projects

Newly funded NRI projects were mentioned and are listed below. Some excellent community resources and approaches will be developed. Dorrie requested for a summary of the projects that will be hosted on GDR.

  1. SNP AND QTL DISCOVERY OF PEACH FRUIT QUALITY GENES

PI- Carlos Crisosto UC-Davis

  1. THE DEVELOPMENT OF COS MARKERS FOR COMPARATIVE MAPPING IN THE ROSACEAE AND THEIR APPLICATION FOR UNDERSTANDING VARIATION IN FRUIT SIZE

PI- Amy Iezzoni MSU

  1. A MULTI-DIMENSIONAL APPROACH TO COMPARATIVE GENOMICS IN FRAGARIA.

PI: Tom Davis-U of NH

  1. GENOMIC RESOURCES FOR THE FINE HARDWOOD BLACK CHERRY, PRUNUS SEROTINA

PI: J. E. Carlson- Penn State U.

  1. MAPPING STRAWBERRY KNOCKOUTS DEVELOPED THROUGH TRANSPOSON TAGGING

PI: R. E. Veilleux- Virginia Polytech

  1. FUNCTIONAL GENE MARKERS FOR ROSACEAE TREE FRUIT TEXTURE

PI: Cameron Peace-WSU

  1. CANDIDATES GENES FOR FRUIT SOFTENING IN PRUNUS

PI: Cameron Peace-WSU

  1. AN APPLE GENOME SEQUENCING INITIATIVE

PI: Amit Dhingra-WSU

  • SCRI and AFRI funding opportunities in early 2009

SCRI grants were discussed – next round of SCRI expected to be due in April 2009. AFRI (new name for program previously known as NRI) will not be for Rosaceae this year, and we have been told that Rosaceae CAP proposals would not be appropriate for AFRI now that SCRI is available.

CAP-level community proposals were discussed. RosBREED CAP will be resubmitted to SCRI in 2009 with initial focus on Malus, Pyrus and Prunus. Trait focus on disease and fruit quality, marker assisted introgression wild resources encouraged in germplasm phenotyping with disease resistance. Plan is for Rosoideae to be brought in later once required basic genomics resources are developed. Sociology and extension are necessary components that must be fully integrated, not a tack-on.



  • Rosaceae CGC involvement in RosGGB

A “disconnect” (that is being generous) exists between Rosaceae genomics, genetics, and breeding community efforts and Rosaceae CGCs (Crop Germplasm Committees). Greater communication should exist between RosEXEC and the Rosaceae CGCs (Prunus, pear, apple and small fruits) and not just by having members in common. Utilization of germplasm resources in RosGGB programs should be encouraged more, especially in CAP level projects (RosTRAIT proposal in 2008 led by Gayle Volk did this very well). Jim McFerson suggested sending a letter to NPGS requesting/suggesting formal linkage between RosEXEC and the CGCs. Who would be the person we need to connect with? At ARS more official linkage required and the minutes of CGCs should also be linked to GDR.

  • Upcoming RosGGB meetings

    • Markers in Horticulture Symposium (Nahla)

Nahla Bassil mentioned the ISHA Molecular Markers in Horticulture Symposium, 29 July to 1 August in Corvallis, OR. Registration deadline April 20th. May 1st author notifications. All welcome to join and visit and present

    • CGCs

2009 CGC meetings will be announced on the GDR.

    • Others

In 2009

ASHS in St Louis in July.

Rose meeting japan Hanover about Roses genome in 2009

Beyond 2009:


  • Aug 2010 IHC genomics of hort crops section: Rosaceae-friendly berry-friendly nutraceuticals in Lisbon.

  • RGC5 South Africa, March 15-19, 2010.

  • Biotechfruit mtg 2012 in New Zealand.

Terminology

Standardization of terms (QTL nomenclature, QTL vs major locus, MAS, MAB, etc) required – Ontology Committee? Locus pages – community annotated pages as done for Sol could be adapted.


  • Standardized Phenotyping

Phenotyping, with cross-program transferability of data, is crucially important. Gayle Volk is assembling methodology on standardized protocols for various traits. Will continue to do even without funding. RosTRAIT and any new info will be provided to GDR. Community annotation possible - wikia format?
Non-Research updates

  • Industry update

Jim McFerson reported on a good year for apple, pear, but tough for cherry. Interest in healthy eating has increased, with positive impact on rosaceous crops. Industry is focused on product movement, prices, costs – the impact of GGB is not highly appreciated. Honeycrisp is a rare example of a gret product that has arisen through breeding. SCRI in 2008: automation and technology projects in Ros crops awarded $17 mil ($35 mil with matching).

  • RosGGB Outreach update

Jim Olmstead mentioned that SolCAP has established eXtension.org, based at OSU. John McQueen of SolCAP present here, described eXtension: it is a content management package, done in drupal, to identify and interact with narrow audiences. Developing a CoP (community of practice) on Plant breeding and genetics. To be part of this, we have to provide the content. They provide the tool for facilitating ongoing community efforts.

IASMA is developing an international community on fruits. New Zealand is developing a postgrad degree in plant breeding – open to international students. Jim Luby teaches a successful grad course in breeding and genetics.
Research Fields, Technologies, and Techniques updates

  • Structural Genomics

    • Whole genome sequences

Updates were provided on whole genome sequencing projects

Apple (Riccardo Velasco)

Peach (Bryon Sosinski) – peach appears to be smaller than previously understood – closer to 200 Mb. Sequence is doubled haploid Lovell. In a couple of months the sequence will be put on GDR even if “dirty”. EST sequencing of ‘Contender’ also being sequenced for SNP identification. Peach (Eben Ogundiwin) – peach cultivar ‘Dr. Davis’ and ¾ peach ¼ almond breeding line (‘F8,1-42’) are also being sequenced for additional SNP data.

Strawberry (Vladimir Shulaev) – 18X already.

Others: (Amit Dhingra) sweet cherry initiated, pear (‘Commice’ doubled haploid) – BLAST pear to apple. Almond at UC Davis.

The idea of a joint publication on genome comparison of apple, peach, and strawberry was discussed (following the publications of the individual projects) – consensus was that this would be great for promoting Rosaceae GGB and highlighting (in a big way) functional connections between Rosaceae species.



  • Functional Genomics

Janet Slovin mentioned that Fragaria vesca (‘Yellow Wonder’) is being used as a functional genomics tool. Inbred lines available.

  • Comparative Genomics

    • Taxonomic revisions

Taxonomic revisions in 2008 – publication by Potter. The previous 4 subfamilies was adjusted to 3, with two of crop importance (Spiraeoideae = previous Maloideae, Amygdaloideae, and Spiraeoideae; Rosoideae = Rosoideae).

    • Efforts?

David Chagne mentioned efforts in the Comparative Mapping and Transferrable Markers Initiative that was established after RGC4 – Dan Sargent is Coordinator. Details of participants are on website on GDR.

Jasper Rees described cutting edge technologies – Illumina (Solexa), 454. ABI SOLiD is apparently not so good. Sanger Center has 28 Illumina Solexas, two 454s, and one SOLiD. De novo sequencing works, but need long reads (kits are almost available). Paired ends behave like long reads, precision, high-throughput, multiplex (64 max).

    • Annotation

Dorrie Main said that a standardized annotation pipeline should be implemented. One of the five gene predictors available to the GDR is FGENESH. GO (gene ontology) terms utilized existing medicago… terms. Appears to be best predictor for Rosaceae data. We need a standard annotation pipeline for Rosaceae – standard terminology and approach. Rosaceae community training is planned for ab initio predictions – Bryon Sosinski to organize ‘annotation jamborees”. This will be the basis for a SCRI proposal. Bryon Sosinski will chair a RosEXEC Ontology Committee, Angela Baldo will help organize. IASMA will work with Bryon to help train FGENESH. Tom Davis proposed idea to purchase FGENESH for the Rosaceae community - $5K could be readily covered by 10 labs each providing $500.

    • Transcriptional profiling

Nothing mentioned.

    • Gene silencing

Nothing mentioned.

    • Transferrable markers

SNPs based on COS markers across Rosaceae are being developed in the new NRI project of Amy Iezzoni.

  • Genetics

    • Reference maps

Genetic maps are available for all crops with varying levels of saturation. Reference genetic maps with community consensus available for Prunus, apple, strawberry (diploid). These are important genomics resources.

    • Major and QTLs located

RosBREED proposal preparations in 2008 produced a review table of known marker-trait associations (available online – summary table: http://www.hrt.msu.edu/faculty/Iezzoni/Links/Summary Table of MT Associations.pdf; full table: http://www.hrt.msu.edu/faculty/Iezzoni/Links/TABLE of M-T associations for website_Sept2008.pdf). This could be continually updated if hosted on the GDR, in wikia format.

    • QTL detection approaches – standard QTL analysis, PBA, assoc. mapping

Std QTL analyses – JoinMap and MapQTL commonly used in Rosaceae. Mapmaker also used – 3.0 version is freeware. New program multipoint QTL from Israel not good for pseudo testcrosses.

  • MAB Pipeline

RosBREED proposal preparations in 2008 described in detail the “Marker-Assisted Breeding Pipeline”. Shines a spotlight on an area we don’t have protocols, infrastructure, or expertise in. Cameron Peace gave a talk in the Fruit & Nut Crops Workshop yesterday on this approach and need for community coordination. RosBREED proposal in 2009 will include this again.

  • Genetic Transformation

Nothing mentioned.

  • Breeding

Two new breeders at WSU (sweet cherry – Nnadozie Oraguzie, apple – Kate Evans replacing retired Bruce Barritt). New strawberry breeder hired at NC State. Kevin Folta is looking for a strawberry breeder at UF.

  • Germplasm

Phil Forsline (Geneva apple collection curator) is retiring Dec 31.

  • GDR features

Dorrie Main mentioned new GDR features (see homepage for more details), including Unigene version 4.0 now available.

  • Other bioinformatics resources

Gayle Volk mentioned that GRIN is being updated for public interface (two more years).
Minutes taken by Amit Dhingra, edited by Cameron Peace and Nahla Bassil

AGENDA

RosEXEC Meeting at Plant & Animal Genome XVII

Towne Room

Towne & Country Hotel, San Diego, CA
Sunday, Jan 11th, 2009

8:00 – 10:00 am
General

  • Appointment of minute-taker

  • Objectives of RosEXEC

  • Appreciation for leadership of Gennaro in 2008


Coordination

  • U.S. Rosaceae White Paper – now on Wikia (Angela)

  • Opinion Paper – published in 2008 (Vladimir)

  • GDR funding update (Dorrie)

  • Funded NRI projects

  • SCRI and AFRI funding opportunities in early 2009

  • Rosaceae CGC involvement in RosGGB

  • Upcoming RosGGB meetings

    • Markers in Horticulture Symposium (Nahla)

    • CGCs

    • Others

  • Terminology

  • Standardized Phenotyping (Gayle)


Non-Research updates

  • Industry update (Jim McF)

  • RosGGB Outreach update (Jim O)

  • RosGGB Education update


Research Fields, Technologies, and Techniques updates

  • Structural Genomics

    • Whole genome sequences

      • Apple (Riccardo, Amit)

      • Peach (Bryon)

      • Strawberry (Vladimir)

      • Others?

    • Physical maps

  • Functional Genomics (Kevin)

  • Comparative Genomics (David)

    • Taxonomic revisions

    • Efforts?

  • Enabling Technologies in Genomics

    • Sequencing (Jasper)

    • Annotation (Dorrie)

    • Transcriptional profiling (Chris)

    • Gene silencing (Jay)

    • Transferrable markers (Amy)

  • Genetics

    • Reference maps

    • Major and QTLs located – RosBREED  Wikia?

    • QTL detection approaches – standard QTL analysis, PBA, assoc. mapping

  • MAB Pipeline (Cameron)

  • Genetic Transformation

  • Breeding (Jim L)

  • Germplasm (Gayle)

  • GDR features (Dorrie)

  • Other bioinformatics resources


Membership

  • Roster 2008 (Cameron)

  • Officer responsibilities (Gennaro)

  • Subcommittees (Jay)

  • Election process, elections for 2009 (Nahla)

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