Putting Research into Practice: The Plant Breeding and Genomics Community of Practice
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Transcript of Putting Research into Practice: The Plant Breeding and Genomics Community of Practice
Putting Research Into Practice: The Plant Breeding and Genomics
Community of Practice on eXtension
Heather Merk (presenter), John McQueen (presenter), Ed Zaborski, Michael Coe, David Douches, Alex Stone, Allen Van Deynze, Deana Namuth-Covert, Roger
Leigh, Walter De Jong, and David Francis
Plant Breeding & Genomics CoP
• Outreach and education initiative of the Solanaceae Coordinated Agricultural Project (SolCAP)– NIFA funded project under the Plant Breeding, Genetics, and
Genomics Program
• Community of interest: public and private plant breeders and their staff (including researchers and educators)
• Includes leaders from eOrganic CoP
• Target audience - professional plant breeders and allied professionals
• Launched January, 2011
Initial Community Survey• Prior to CoP formation
• Conducted by external evaluator
• IRB approved online survey
• Sent to SolCAP target audience– 108 tomato breeders and allied professionals responded– 66 potato breeders and allied professionals responded
• Baseline survey– Assess what audience is thinking about molecular markers
• Do they use?• Intention to use?• How confident are they in using them?
– Allows for future assessment of reported changes in behavior
Additional Training & Tools Recommended
• Self-reported comments• Training– Format: In-person workshops, online– Focus: new technologies, applied learning
• Tools– Databases that include marker information,
marker-trait associations, mapping information, sequence information
– i.e. tools to allow application of basic research
Goal of PBG CoP
Put genomics research and tools into practice through plant breeding by:• Presenting unbiased, science-based, and
peer-reviewed content• Sharing the most current, relevant, and
accurate information available on techniques, procedures, and software
• Show the community how• Fostering collaboration among members of
the plant breeding and genomics community
Collaboration
• Currently collaborating with 3 other CAP projects
• Gives potential to reach wider professional audience, engage multiple communities of interest
www.eXtension.org/plant_breeding_genomics
Trait Reviews
• Demonstrate the use of genomics research for crop improvement
• Value added information for practicing breeders (summary tables, markers)
• Focused on traits relevant to breeding
Software & Data Analysis Tutorials
• Software capabilities
• Downloading & installing software
• Formatting data
• Importing data• Performing
appropriate analyses
• Evaluating hypotheses
GGT2 (Graphical Genotyping)
Tomato Analyzer
Case Studies
• Integrate theory, public resources, sample data, data analyses
• Examples include:• Developing
populations• Accessing
germplasm• Analyzing sample
genotypic and phenotypic data
IBC Population Development
NPGS Tutorial
VideosDNA Extraction and Marker-
Assisted Selection Video
• Developed for general science audience
• Demonstrate making crosses in tomato, DNA extraction & marker-assisted selection
• ~ 12 000 views
Workshops Delivered as Webinars• In 2010, delivered
workshops at 2 research conferences in front of live audience, also streamed as webinars
• Recorded webinars– published to eXtension
• For webinars from 1 workshop – divided into small segments also hosted on YouTube
• In 2011, will stream, record, and publish webinars from 2 research conferences
YouTube Channelhttp://www.youtube.com/user/plantbreedgenomics
• Hosts webinar videos
• Videos also embedded at eXtension
• ~ 7,400 views since December 2010
Webinar Content• Describe relevant
techniques, software, and publicly available resources
• Provide supplementary data, codes and scripts for analysis (allows practice)
• Current topics include:• Genome browsers• Genome sequencing• Sequence resources• High-throughput
genotyping• Genotype analysis
software• Bioinformatics
Bioinformatics 101 Webinar
Content Views(as of June 20, 2011)
• Launched January 15, 2011– ~ 10,300 visits– ~ 38,000 page views– 65% content viewed >1 time/week, includes all
articles but 1
• Popular search terms– Highly technical– Relevant to plant breeding and genomics– Related to theory, experiment design, data
analysis, software
PBG Works – http://pbgworks.org
• Workspace for group collaboration
• Publication vehicle to eXtension
• Password protected
• 200 members
• 55 organizations
PBG Works – http://pbgworks.org
• Workspace for group collaboration• Wiki• Forum• Images• Member list
PBG Works – http://pbgworks.org
• Publication vehicle to eXtension
Workflow Tool
• Organization tool• Facilitates
multiple author contributions• Tracks content
progress
Review Process
• Ensure content quality, accuracy, suitability
• Three-tier process– By experts within the community
(blind review)– By reviewers for indexed publications– By copy editor based on a style
guide developed by the CoP
Peer-Reviewed Publication• Authors encouraged to submit content to
journals such as Journal of Natural Resources and Life Sciences Education (JNRLSE) and Journal of Visualized Experiments (JOVE)
“How To” Webinar Series• Coming summer 2011• Hope to engage a wider audience• Webinars will be recorded, hosted on
YouTube, published to eXtension• Topics– “How to” perform an analysis, use software, etc.
• Evaluation– External evaluator– IRB-approved feedback surveys will be used to
gather data from participants after each webinar
• Active coaching & preparation of speakers – to meet learning objectives
AcknowledgementsSolCAP Executive Committee• Dave Douches, Michigan State• C. Robin Buell, Michigan State• Walter de Jong, Cornell• David Francis, Ohio State• Lukas Mueller, Cornell• Alex Stone, Oregon State• Allen Van Deynze, UC Davis
PBG Content Committee• Barbara Alonso, UC Berkeley• Karen Hertsgaard, North Dakota• Peggy Lemaux, UC Berkeley• Deborah Lewis, Ohio State• Barbara Liedl, West Virginia State• John McQueen, Oregon State• Deana Namuth-Covert, University
of Nebraska-Lincoln• Audrey Sebolt, Michigan State• Kelly Zarka, Michigan StateOthers• Michael Coe, Cedar Lake Research Group• Roger Leigh, Oregon State• Ed Zaborski, University of Illinois• All content contributors & reviewers
Get Involved!
• http://pbgworks.org
• Heather Merk – [email protected]
• David Francis – [email protected]
• Alex Stone – [email protected]