Minutes
RosEXEC Meeting at Plant & Animal Genome XXII
Stratford Room, Town & Country Hotel, San Diego, CA
8:00 – 10:00 am Sunday, 12 Jan 2014
Skype: Contact JD Swanson for details (jd.swanson@salve.edu)
Welcome
 JD Swanson, 2014 Chair (jd.swanson@salve.edu)
 Gayle Volk, 2014 Vice-Chair (Gayle.Volk@ars.usda.gov)
 Self-introductions and sign-up sheet
 Minutes (Alexandra Barbella)
 Adoption of previous minutes, 23 August 2013, 6 January, 2014
Attendees: Sue Gardiner, Tyson Koepke, Greg Reighard, Scott Schaeffer, Elisabeth Dirlewagner*, Maria
A. Moya-Leon, Ariel Orellana, J-D Swanson, Claudio Meneses, Cecilia Deng, Chen Niu, Albert Herrera,
Awpero Noufost*, Nahla Bassil, Angela Baldo, Albert Abbot, Jasper Rees, Bearria Denoyes*, Lise
Mahoney, Ksenija Gasic, Jeremey Pillet, Kevin Folta, Jim McFerson, Michael Wisniewski, Alexandra
Barbella, Chunxian Chen, Pieter J Wolters*, Dorrie Main, Sook Jung*, Renate Horn
Membership (current membership table attached) (JD Swanson)
 Election announcement and swearing-in ceremony
o New members: Gina Fernandez, Ksenjia Gasic, Briana Gross, Duke Lane, and Gregory
Reighard
o New International liaisons: Fabrizio Costa and Michael Considine
o 2014 Secretary: Cameron Peace
 Appreciation for leadership in 2012
o Chris Dardick, Chair
o Jay Norelli, immediate past Chair
o departing Committee members
 US: Kate Evans, Mercy Olmstead, Janet Slovin, Vance Whitaker, and Jay Norelli
 Intl: Emily Buck and Lee Meisel
 Election process review
o Nominations: quality of election depends on recruiting good nominees
 if you are interested in serving, contact Gayle Volk with list of people familiar
with your work and he will help to solicit a nomination
o Secretary: starting in 2013 an affirmation of willingness was required
o targeted groups for the Committee: new members
 former RosEXEC members can be nominated 1 yr after end of previous term
o Gayle Volk, 2013 Chair of Governance and Membership Sub-Committee
Report from the Rosaceae Gene Naming Standardization subcommittee (Sook Jung)
Subcommittee members: Sook Jung (chair), Robert Schaffer, Lee Meisel, Doug Bielenberg, Carole
Bassett, Michela Troggio, Janet Slovin, Dorrie Main, Chris Dardick).
 Committee Goal: To come up with Rosaceae gene naming principle and mechanism for
enforcement
o Meet three times last year, need to meet again to finalize discussions
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Discussion topics:
 How to put Species prefix on gene names (in past was 2 letter prefix) concluded
that 3 letter prefix should capture enough info;
 Gene symbols (e.g. MAD) (problem: homeologs, splice variants, alleles)
(previously: add number e.g. MAD 1, MAD2); proposed adding letter for
subgenome MADh1, splice variant version #, alleles get letter
o Plan on using GDR and writing a manuscript to summarize conclusions of their meetings
 Suggested use of GDR – submit gene names prior to publication; already has
NCBI gene symbols; could use a gene family or gene symbol page
 Suggested that committee reach out to other communities (Solanaceae) for
advice
QTL nomenclature (Cameron Peace)
o Perhaps provide a link to trait ontology and function?
o Same issues as gene naming and considering the same solutions
New SNP naming Committee (Dorree)?
o Maintain reference genome and updates designated by version numbers
Rosaceae Species Webpages for GDR (JD Swanson)
 Volunteers are requested to come forward to write informational pages on their crops of
interest. The idea is to deposit this data into GDR.
 One example page will be up shortly (Apple)
 Contact Gayle Volk if interested.
o Apple example needs to be up for template; and template information is being
distributed to curators and CGC chairs
Sustainable funding for GDR (Sook or Dorrie)
 Current application for a NSRP grant that will provide significant funding for GDR:
o Finish with in 5 years so that all that left is curating costs, Dorrie has funding for
the rest of this year
 Dorrie is in the process of contacting project participants, it is VITAL that you help her
out by signing up –
o Shows community use to the funders – need to be official representative of
their institution so that a research group instead of an individual is counted;
need participant coverage of as many crops as possible;
o Continuous enrollment, but need by 1/15/2014 to put on proposal
 If you have not been contacted and are interested please contact Sook or Dorrie; Dorrie
will follow-up with emails to the group
Revision of U.S. Rosaceae Whitepaper (JD Swanson)
http://rosaceaewhitepaper.wikia.com/wiki/US_Rosaceae_Whitepaper
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Brief review of current Whitepaper
o Living document: needs Updates
RosEXEC Expansion
o In 2012 and 2013 RosEXEC held some of its annual meetings at ASHS and RGC6 in
attempt to expand involvement to Rosaceae community members who do not regularly
attend PAG.
o Was this successful? Should RosEXEC continue these activities? Open discussion.
 Conclusion: General agreement for continuing this
Evolution of the committee moving forward
 Should we make changes?
 Is the current structure still working?
 Do we need to reevaluate roles?
 Conclusions: need still there – great broad format for communication
o Dorrie proposed that RosEXEC become official committee for GDR; precedent in Cotton;
@ quarterly meetings prepare document for committee review to ensure that GDR is
meeting community needs
o Industry involvement historically low, increase?, Typically was only people who attend
PAG and only attend when compelling topics are on the agenda (maybe that’s ok) and
maintain transparency with them and allow them chances to communicate instead of
attending general meetings; typically involved in funding arena
 Solutions: teleconference calls timing dependent on crop and time of year  try
inviting to existing quarterly teleconference calls
o Invite germplasm representatives? CGC to summarize their reports at RosEXEC meetings
Role of industry
o Can we involve industry members more effectively?
 Get into leadership roles?
 Involve more in discussions of grand ideas
 Is it worthwhile to have a few teleconferences per year just with industry folks
directed only on industry problems?
Coordination and updates
 GDR Update (Dorrie Main, Sook Jung)
 Moved to Tripal platform; added genetic and QTL data;
 Instituting a quarterly newsletter to summarize updates; new publication search
site (mirror NCBI), conference abstracts, monthly updates
 Twitter and LinkedIn account;
 Sequence retrieval tool;
 Want RNA-Seq data as well as other new data (mostly post-publication; genomes
are exceptions); if you submit to TGG you must get an accession number from
GDR;
 Non-research Update (Jim McFerson and other industry experts present)
o Industry update
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US Farm Bill Renewal/Specialty Crop Farm Bill Alliance
Outlook regarding federal Specialty Crop grant program
 SCRI
 SCBGP
 Regional Centers
Extension: Info and tech transfer
GMO regulatory & market update (Arctic Apples & HoneySweet Plums; others?)
 Artic Apple in Federal Comment stage; strong backlash against GMO product;
please publicly support science and reach out an explain science to people
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Competitive Federal Grant Project Reports
o Newly funded projects within the Rosaceae
 (Michael W.) continued funding for disease resistance – BARD fund (US and Israel
US fund Israel matches) US contribution trying to utilize NEFA to maintain the USIsrael interaction; has a post-doc program and an exchange program and
conference grants thesis are typically underutilized
o RosBREED (Amy, Cameron, Nahla)
o RosBREED 2 update
 Expanded to all Rosaceae crops, and has current functions of RosBREED; involve
DNA info, pre- and post- breeding, capture wild diversity information in a usable
format, etc.
 Same long term and medium term goals – also possibly expand into
international communities such as EU and possibly Asia and Australia
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Other workshop reports or announcements
o Other funded AFRI/NSF projects
o Projects submitted: USDA, NSF, etc.
Leverage of large scale opportunities
o RosBREED
o CGC’s
International Project Collaborations
o FruitBreedomics Some funding for infrastructure (eg. Bioinformatics)
o EUBerry
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Research Fields and Technology updates
 Whole genome sequences and physical maps
o Updates on status of Rosaceae genomes from community.
 CGC: some data from some genomes via consortia
 Rose genome underway
 Raspberry genome almost to publication; in addition a draft of a linkage map of
Raspberry underway
 Enabling Technologies in Genomics
o Sequencing
o Annotation
o Transcriptional profiling
o Markers and genotyping
 Genetics
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o Reference maps
o Major and QTLs located
Phenotyping/Phenomics
o Standardized phenotyping
o High throughput phenotyping/Phenomics
o Suggested connection of genomic, phenomic, and metabolomics data on GDR or house
in one repository
Germplasm/genetic resources
o RosBREED populations as germplasm resource
o USDA-ARS germplasm
o Other resources
Geneva colletion – GBS data and want to submit to GDR - GRIN data connected to GDR
data
Peach segregating population – fruit quality, metabolomics and sequencing -
Meeting reports and announcements for upcoming meetings
 Crop Germplasm Committees (CGC)
 Upcoming Meetings
o ASHS 2014. July 28th – 31st, Orlando FL.
o RGC7. June 24-26, 2014, Seattle, WA
o NAPB (National Association of Plant Breeders) hosted by WSU June 2015
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Jim Hancock retiring, Amy Iezzoni is looking for a blueberry and strawberry breeder to replace
him
Adjourn: 10:00 am
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