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 – merk.9@osu.edu

• David Francis – francis.77@osu.edu

• Alex Stone – stonea@hort.oregonstate.edu