Draft Minutes
CottonGen Steering Committee Meeting
Meeting Location: Preservation Hall Studio 7, Marriot New Orleans, 555 Canal Street, New Orleans, LA
70130; meeting held in conjunction with Beltwide Cotton Conferences
Wednesday, January 8, 2014
Members Present: Todd Campbell (chair), USDA-ARS, Florence; Peng Chee, University of Georgia,
Tifton; Jane Dever, Texas A&M AgriLife Research, Lubbock
Members Absent: Ramesh Buyyarapu, Dow AgroSciences ; Paolo Canci, Monsanto; Mike Gore, Cornell;
Andy Paterson, University of Georgia, Athens; Allen Sessions, Bayer CropScience
Ex-officio Members Present: Don Jones, Cotton Incorporated; Richard Percy, USDA-ARS, College Station
CottonGen Staff Present: Dorrie Main, Washington State University, Pullman; Jing Yu, Washington State
University, College Station
Others Present: Rauindu Gui, Monsanto; Basavaraj Huggi, Monsanto India; Johnie Jenkins, USDA-ARS,
Mississippi State; Jack McCarty, USDA-ARS, Mississippi State; Babbu Sharma, Texas Tech University
Dr. Todd Campbell (chair) called the meeting to order at 1:30 PM.
Comments from Todd Campbell on role of steering committee:
Mission statement of the steering committee is to communicate the current and emerging database
needs of the cotton research community and other stakeholders for development, implementation and
dissemination of CottonGen. Through this mission statement, the role of the steering committee is to
act as the interface between the cotton research community and Dorrie Main and staff at Cotton Gen.
Discussion on steering committee membership:
Todd Campbell stated current membership is a mix of public, both USDA and state University, and
private representatives from three companies providing funding to CottonGen, Bayer CropScience, Dow
AgroSciences and Monsanto. Mike Gore has moved from USDA-ARS, Maricopa, to Cornell University.
His work on cotton will be limited, but he remains involved to a degree in high throughput (HTP)
phenotyping (of all crops). Potential amount of data gleaned from HTP phenotyping could be beneficial
in future to CottonGen. Don Jones commented current funding sources for Dr. Gore could continue to
make him an attractive option for membership, especially iPLANT. Steering committee members and
staff members present suggested Josh Udall would be an excellent candidate for steering committee
membership.
Steering committee meeting schedule:
Todd Campbell put forward for discussion holding one annual face-to-face meeting in first quarter of
calendar year, followed by teleconference during 2nd, 3rd, and 4th quarters; continuing to hold steering
committee face-to-face meeting in conjunction with larger meetings, rotating between Beltwide and
PAG. Don Jones commented Beltwide attendees would continue to go to Beltwide, PAG attendees
would continue to go to PAG, and few would attend both or rotate years. Dorrie Main asked the
steering committee to consider not holding the annual face-to-face meeting in conjunction with another
meeting. She prefers a dedicated meeting with more detailed agenda (1/2 to full day). Todd Campbell
suggested asking Cotton Incorporated to host an annual face-to-face meeting of the CottonGen steering
committee and Don Jones indicated it could be possible with advance notification. The structure of one
face-to-face and 3 teleconference meetings was still regarded favorably by the committee members.
Peng Chee recommended a group visit to Pullman (not annually), and Don Jones seconded the idea.
2013 CottonGen activities:
Dorrie Main reported on staff activity for 2013. Two major activities were in response to feedback from
the September 15, 2013 presentation at Overton Hotel in Lubbock, Texas, held in conjunction with the
Cotton Breeder Tour. Responses from Cotton Breeder Tour participants included availability of digital
images and query interfaces. Approximately 12,000 images were uploaded in 2013, and several
improvements were made to query interfaces, especially in the area of publications, markers and QTL.
Jing Yu gave a presentation at 8:15 AM on Wednesday, January 8, 2014 during the Beltwide Cotton
Conference that detailed numbers on all database activities and demonstrated use of the query
interfaces (presentation available on CottonGen website). Jing also repeated specific numbers during
the steering committee and responded to questions from committee members. CottonGen also hosted
ICGI elections during 2013, performed routine updates to the database and accessed abstracts from
three major conferences; Beltwide, ICGI and PAG. Todd Campbell suggested adding Agronomy
meetings, getting permission from ASA and CSSA. Dorrie Main reported that Cotton Incorporated
receives quarterly and annual reports on CottonGen activities, nine to date. One outstanding issue
discussed was inability of Jing Yu to get access to Texas A&M library as a Washington State employee.
Richard Percy will try again to secure access for her.
Germplasm collection standardized descriptor activities:
Richard Percy reported that 23,000 images from 4,500 accessions are available and 12,000 are currently
online. A standardized descriptor set has been developed by his team. Todd Campbell asked if
additional phenotypic data are available or if current date is from GRIN. To date, most phenotypic data
in linked from GRIN, and Richard Percy reported that descriptor data from two years of phenotyping will
be standardized to new descriptor set before being included. Jack McCarty asked if database could
show whether phenotypic data are from old descriptor sets or from the new standardized descriptor
set. He requested information be included so user would know origin of descriptor set used to score
phenotypic data available on an accession. Jing Yu suggested some ways this could be done in the
database.
Discussion on CottonGen funding:
In response to a question on plans for private breeder toolbox, Don Jones said one risk has been
breeders would be reluctant to supply data if funding for the database is not secure. Dorrie Main
reported on status of a proposal that could provide five years of stable funding, giving time to build the
database into a quality product with attractive potential for contracted use of database services,
providing additional income for operational expenses. Don Jones noted the database is currently
funded by Cotton Incorporated, USDA-ARS, Washington State, Dow, Bayer, Monsanto and Southern
Experiment Station Directors at an annual level of $150,000-$175,000. The proposal funding source is
National Experiment Station Directors, and cotton is a regional crop (as database is currently partially
funded by Southern region). Many other crops besides cotton are included in the proposal and it has
been submitted, and favorable reviews received. Funding level requested was ~$5 million and support
decision should be known by July, 2014. Dorrie Main reported on current staff members.
CottonGen plans for 2014:
Dorrie Main distributed a handout outlining CottonGen work plan for 2014. Committee members did
not receive an electronic copy prior to the meeting, so the plan outline is repeated here:
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USDA-ARS germplasm
o Add remaining images after curation (~10,000)
o Add standardized trait descriptors
o Add trait evaluation data
Assign ontologies for cotton
o Trait
o Plant
Add more genome sequence data as available
Develop more breeders tools
o Implement a more advanced trait evaluation search site
o Create a private breeders toolbox
 Compatible with AgroBase
Add SNP data
o Illumina SNP platform
o Suggest standardized SNP naming
o Add other SNP data
Add genotype data
o From Josh Udall’s publication
o From Illumina SNP platform screening?
o Others?
Add QTL data and maps
o New pubs
o Old pubs
Host ICGI conference
Cotton Book – Bioinformatics Chapter
Routine updates Implement GBrowse-Syn ?
o Cotton D Genome/Cacao/Arabidopsis analysis
o Possible publication
Develop a CottonCyc pathways database?
Discussion on 2014 planned activities:
Richard Percy indicated standardized trait descriptors would be available in first quarter of 2014 and
trait evaluation data would be available in first half of 2014.
Dorrie Main asked from guidance from the steering committee on who can work with them on
ontologies for cotton.
The Chinese A genome has been submitted and reviewed, and is in revision. Dorrie understands
Chinese colleagues agree to make data available when publication is accepted. Don Jones reported
second A genome project has not been submitted for publication. Todd Campbell asked how the
community makes sure sequencing data are available as more and more data are generated. Peng Chee
asked about availability of RNAseq data. It was suggested that handling of RNAseq data should be
further discussed during the steering committee meeting held in conjunction with PAG on January 12,
2014. Also deferred to PAG meeting was discussion on standardizing SNP/QTL nomenclature for the
database. Peng Chee volunteered to work with Jing, especially on standardizing QTL names.
Dorrie Main asked how important it was to get QTL data from publications for CottonGen. Guidance
was requested on prioritization because this activity would be very time-consuming. Jing Yu stated that
it would be very helpful if QTL data in publication could be made available to database staff in electronic
table file format. She also suggested working through the ICGI Structural Genomics group to ask authors
to provide published QTL data in this format to CottonGen.
Other business discussions:
Dorrie Main inquired about asking for data when a publication is accepted, indicating data did not have
to be in CottonGen format as her staff could convert it. One issue identified is the complexity of
following up on cotton publications because there is not one major publication for the crop.
Dorrie Main inquired about other images that might be available to the database. Jane Dever indicated
images generated by her group would be submitted only through Richard Percy’s group. Other images
identified during discussion desirable for the database include Mutant Marker Sets and associated
cotton disease and entomology images. Richard Percy will follow up to see of an existing database, such
as an updated Compendium of Cotton Diseases, is available and could be shared with CottonGen.
The meeting was adjourned at 3 PM.