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Joint Apple cgc and Prunus cgc meeting October 6-8, 2009 Wenatchee and Prosser, wa


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Joint Apple CGC and Prunus CGC Meeting

October 6-8, 2009

Wenatchee and Prosser, WA
Apple CGC: Tuesday Oct 6, Wenatchee

Joint CGC: Wednesday Oct 7, Wenatchee

Prunus CGC: Thursday Oct 8, Prosser
MINUTES
October 6

Apple CGC Meeting

WSU Tree Fruit Research & Extension Center (TFREC)

1100 N. Western Ave, Wenatchee, WA 98801


Local tours – 8:30 AM – 12:00 PM, Hosted by Cameron Peace and Kate Evans

Sunrise Research Orchard, WSU Apple breeding program


Apple CGC Business Session

Attendees: Phil Forsline, Herb Aldwinckle, Jim McFerson, Margarita Litha, Phil Baugher, Tom Auvil, Kate Evans, Cheryl Hampson, Susan Brown, Cameron Peace, Gary Kinard, Peter Hirst, Yanmin Zhu, Nahla Bassil, David Rudell, Gayle Volk, Carole Bassett (phone) Gennaro Fazio (phone), Jay Norelli (phone), Angela Baldo (phone)
Opening comments:

Herb Aldwinckle thanked Cameron and Kate for the morning tours.

Phil Baugher (Chair of the US Apple Research Committee) expressed concern that industry isn’t very aware of the CGC, Clean Plant Network, Fazio funding issues, and the SCRI.

Aldwinckle reminded the committee that the role of the CGC is primarily as an opportunity for the germplasm users to provide guidance to the apple curator.

Jim McFerson stated that it’s key that delivery systems for genetics and associated information needs get to the growers sooner rather than later.

Angela Baldo reported that the genome cooperative agreement was completed on the ARS side and that they are now working with IASMA for the agreement working for the CRADA. Genomic analyses will be performed as part of a cooperative research program involving Baldo, Fazio, Bassett, Wisniewski, and Norelli. IASMA will be submitting the paper on the apple genome sequence soon.

McFerson and Peace reported that sequence data will be released through GDR when the sequence manuscript is accepted.

Recommendation: Neil Manly (Willow Drive Nursery) be invited for future participation.


Retirement: Phil Forsline, Apple collection curator, will be retiring Jan. 1. 2010. This meeting is his last CGC meeting. Aldwinckle thanked Forsline for being a catalyst for collection growth. McFerson requested that the committee contact Dr. Swietlik (via Aldwinckle) to discuss the timetable and to expedite the process of filling the curator position.
Reports provided digitally, brief summary below:

Norelli: Provided an update on the M. sieversii GMAL 4593 x Gala mapping project. The team has found that SSR markers are more transferable across species than SNP markers.

Bassett: Stomatal density, size, leaf area, delta 13Carbon uptake, and tree architecture are being compared for M. sieversii core collections from site 6, with plans to include site 9 individuals in the future.

Janisiewicz: CGC Evaluation funding for measuring bitter rot and blue mold in 440 accessions.

Leskey: Fruit was sent for resistance research this year.

Forsline: M. sieversii 6&9 cores were propagated for addition to the main collection.

Fazio: New funding received. Using micropropagation to provide new releases of rootstocks to nurseries. Expect to have 4 releases within the next 6-7 months. Trying to bring in new Chinese materials.

Volk: Identified core collections for M. sieversii and M. orientalis. Published on the diversity of M. sieversii. Have ploidy data for Chinese species. In collaboration with Ian Merwin, working toward comparing wild Malus and domestic cider types. Developing methods for cryopreservation of accessions not amenable to dormant bud cryo techniques.

Licha, APHIS: CGC expressed concern that the backlog is large. Latent virus contamination is the primary deterrent to releasing materials quickly. It was requested that future APHIS reports be more detailed so users can evaluate why their materials are held up. It may be appropriate to do a Risk Assessment and revisit the quarantine process and procedures.

Brown: Two varieties will be released this year.

Luby/Bedford: Frostbite is a new variety that is hardy in northern Minnesota.

Peace: Looking to identify candidates for functional diversity.



Auvil: Expressed desire to see materials move from a research environment to an industry environment quickly.

Van Nocker: Developing a demonstration garden to show domestication and breeding.

Hampson: Lost most of the M. sieversii due to fire blight. Performing antioxidant assays.

Evans: First full year with Washington State. Will be putting SSR data for Brogdale and East Malling collections into a public database.
Ongoing Projects:

Texture NRI (Peace) uses standardized phenotyping methods. Developed crop reference sets for RosBREED SCRI project.

Phenotypic disease descriptors (Aldwinckle): Considering international controls for disease resistance descriptors. Need to check with ECPCGR to confirm European standards.

Main Core Collection of apples: Forsline thinks the 4 copy core collection in Geneva will have to be replanted within the next year. WSU will have two replicates of the main core collection.

Genetic Vulnerability Status: no progress this year

Underrepresented germplasm: Brogdale/European ciders; What should be obtained?

7-8 Chinese species are missing from the collection. A long term goal should be to work toward getting those materials.



Quarantine issues- Evans, Peace, and Aldwinckle will compare lists to identify which materials Licha already has in quarantine.
Oct 7, 2009

Joint meeting between Prunus and Malus CGCs

Additional attendees: Bonnie Koneski, David Bedford, Bill Howell, Ksenija Gasic

National Program Leader Report (Kinard) (see digital for details)

Funds are available for explorations.

PI books are being digitized back to 1898.

GRIN Taxonomy: Much of the GRIN traffic is to GRIN taxonomy.

July 2010, PGOC, 42CGC Chairs, and RTEC meeting next July in Geneva.

Comment: (McFerson) Concern that some collections need more characterization than exploration.



Kinard: Research program PPT

Licha: Plant Protection and Quarantine approaches PPT

Kinard: Pest risk assessment issues

Requested that a letter be written to the pathology committee by the Prunus and Apple CGC chairs with a focus on identifying methods to move materials through quarantine more quickly. Howell will draft a letter.



National Clean Plant Network Bill: Addresses virus issues in fields with a fruit and grape emphasis.
Standardized Phenotyping

Peace Presentation:

Instrumental vs Sensory Analysis

Key: relevance to industry value and consumer perception.

Heritability and precision desired (genetic relevance)

Measures should represent genetic potential

Minimize environmental variation

Replicate as necessary

Avoid redundancy

Use available and familiar instruments/techniques

Keep up with sample flow (or store samples properly)



Volk Presentation:

Descriptor information is available for Apple

Read the descriptors for disease, and Aldwinckle is working on revising descriptors

Nahla Bassil (pear, small fruits), Ksenija Gasic (Prunus), and Gayle Volk (Malus) will summarize existing standards for various Rosaceae crops.


RosBREED Presentation (Peace):

Exploit shared ancestry of Rosaceae species to make functional connections.



www.rosbreed.org
RosEXEC: Serves as a communication and coordination focal point for US Rosaceae genomics, genetics, and breeding community. Facilitate scientific communication with joint research, outreach, and education.
Botany of Desire, Apple portion. Viewed Forsline’s pre-release DVD.
Database Interoperability: GRIN update, Gary Kinard

Database interoperabilities

GRIN Global: Where it’s at and where it’s heading.

GRIN continues to be accessible to all, free and without restriction.

All source code is in the public domain and will be freely distributed.

Written using software development tools that are free.


Microsoft .NET Framework 3.5.

SVN version control system.

Visual Studeio Express 2008.

Written to support free database systems.

MySQL Community database.

Oracle express.

Microsoft SQL Server Express.
3 Tier architecture: Data tier, business tier (web services), presentation tier (web browser, desktop client PDA).

Webmased XML to share structured data between all clients in the business tier.

Adaptable and flexible.

Readily adaptable to changes in operating systems.

Easier to make changes to individual tiers without affecting other tiers.

Desktop client (on local machine)

Curator tool, limited distrubtion, designed for: inserts/updates/deletes

Feature-rich application eases curator tasks

Targeted to operating systems that support the .NET 3.5 framework

Browser/web based client (on web server)

Open to public

Designed for searches and ordering germplasm

Project team:

Global crop diversity trust: Cary Fowler, Luigi Guarino

USDA; Bretting, et al

Bioversity: Michael Mackay, Tito Franco, Fawzy Nawar, Fred Atieno, Brock Waver, Rachelle Little

EMBRAPA

Crop Research institute


Current progress
Curator tool: search engine, support for the 5 languages, data functionality to get data in/out

Full system installer

Accessions/inventory/order list

Data view tab management

Spreadsheet customization

Custom reports

Switching databases

To do curator: security, image loading, cleanup existing


To do public website:

Images, save results, favorites, order completion, order status management, seasonal availability, page through search results from the accession detail page

Pre-framed hot topic searches on the front page

Taxonomy pages

Enhanced search tools

Observation data

Search by list of PI numbers

Persistent search result preferences


Features/functions sought for the public version
Each Monday: new updates to development searcher for testing

1st beta release of curator application release at the end of 2009

1st beta release of public: 1 q 2010

Gold release public 4th 2010


Scope of GRIN-Global is to take the current GRIN and move into a more user friendly environment. Scope is focused and deliverables to international

Breeder toolbox would be nice, but is beyond scope of grant.


GRIN team doesn’t want to show widespread testing until it’s stable. Not showing the curator tool. Kinard did not bring curator tool to show to the CGC.

Who will the beta tester of public release? Testers: wide audience, but not too many. Nahla recommended Gayle as a public tester.

Curatorial tool: smaller group than public.

Registered user on GRIN global? Is there interest in that?

Regulations in web environment: security

Bioversity sent out a survey on forms and features only to CGC chairs. Specifically not to be forwarded to committee members (was subsequently forwarded after the CGC meeting).

What is the format for providing feedback? Will there be a response and feedback?

Interoperability is a big issue.

People want more images (survey responses).

E-mail or post to website on the forum

New database should improve searching features.
Features we would like to see:

More collaborative open process for ongoing future improvements.

Once GRIN-global’s grant is over, who will be involved in future of GRIN?

Gary would like to see more sites involved in the GRIN product.

CG Singer group: met in Beltsville in August as a primary topic.

What will CG system do? They will be testing it.

EU-US database conference in December in UK. All the database people are going to be there. Will GRIN be there? Although they are aware of the meeting, GRIN was not planning to attend. Dorrie will send more information and Gary will revisit their attendance at the conference.

Gayle: how can other groups be working toward GDR-GRIN interoperability? Discussions are OK, but nothing will probably happen until GRIN Global is out on the street.

Dorrie will be contacting MaizeGDB about their webservices activity and interoperability with GRIN.
Tree Fruits GDR:

Tree fruits GDR will include Citrus, Rosaceae, and Cacao. The Tree Fruits GDR has funding for 2 post-docs for 4 years and additional phenotypic data will be added.

The genome databases are structured to organize, store, curate, integrate and disseminated associated genomic, genetic and breeding data, provide centralized access to data for researcher,

provide data mining opportunities via intuitive online tools, provide data sharing and communication opportunities for the community.


Tree Fruits GDR will

  1. Increase the value and cross-utilization of tree fruit data by integration and ontology association

    1. Whole genome sequences and annotation

    2. Comparative analysis

    3. Phenoypte/genotype and breeding data

    4. Ontology association

  2. Increase the accessibility of tree fruit data to basic, translational, and applied researchers by a) enhancing existing genomic and genetic interfaces, b) developing interface and tools for new types of users, c) web-services for computational access

  3. active use of open-source tools and collaboration with other bioinformatic communities,

Plant ontology consortium, SGN, Gramene, FLYbase

  1. Extend community outreach in genomics, marker-assisted breeding and crop management


Discussion of CGC descriptor lists:

Key descriptors for consideration in GRIN/GDR

Malic acid, titratable acidity, S alleles, soluble solids

Prioritize list of descriptors: target evaluation data for this


Which accessions should be characterized?

Most sought accessions?

Most sought physiologists?

Brogdale S alleles: will be put into GDR

Source of the scab resistance gene?

RosBREED will identify breeding value over time


Issues regarding the validity of the data

Crop load

Age of tree

Issues related to the 1 tree

How much replication is required before it becomes useful?

Strategy for characterization:

Most requested

Core/expanded core/designer cores

Some accessions will have more data than others

Must describe sample size and collection method. No replication by year performed for most data.

Need to reprioritize descriptor list for apple.

Traits/replication must be described

Curator needs priority lists from CGC

Maturity must be standardized. Starch assays were performed this year. Previously, color change determined maturity.


Action item: Congruent meetings for Prunus, Pyrus, Malus (Cameron, Herb, and Richard will coordinate)

Adjourn.





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