rosbreed never sleeps integration & value of international partners amy iezzoni, michigan state...
TRANSCRIPT
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RosBREED Never Sleeps
Integration & value ofinternational partners
Amy Iezzoni, Michigan State UniversityCameron Peace, Washington State University
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Found a nice QTL for
crispness!
Cool!
Cool!
Alright, I’m figuring out
the functional alleles…
Great! Try these new predictive primers
Primers work great! Info
ready for our breeders
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Outline of Presentation
RosBREED
RosBREED and our international partners: an Introduction
Attracting key international collaborators
International collaborators become international partners
Full integration and value of international partners
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RosBREED and our international partners:
an introduction
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RosBREED
• PI: Amy Iezzoni, MICHIGAN STATE UNIVERSITY
• 4 years, SEP 2009 – AUG 2013
• Funded by SCRI (USDA-NIFA’s Specialty Crop Research Initiative)
• $14.4 M ($7.2 M SCRI, $7.2 M in-kind Partners)
The RosBREED Project
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We will create a dynamic, sustained program in research, infrastructure establishment, training, and outreach for developing and applying marker-assisted breeding based on improved knowledge of industry value and consumer preferences to accelerate and increase the efficiency of rosaceous cultivar release and successful cultivar adoption.
RosBREED
The RosBREED Project
Mission
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RosBREED
CROPS of the ROSACEAE FAMILY
We’re In It Together
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Demonstration Breeding Programs
RosBREED
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RosBREED
Challenge 1QTLs found in experimental populations
are rarely used for MAB – validation with breeding germplasm done rarely and ad hoc!
Challenge 2 >63 Mil genetic data points will be generated
in RosBREED from genome scans of apple, peach, and cherry!
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International Collaboration Solution
World class Dutch stats & software team at Plant Research International/Wageningen University
is a critical RosBREED subcontract
RosBREED
Netherlands MSU local expertise
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Plant Research International, NetherlandsEast Malling Research, UKCRA-FRU, Rome, ItalyIASMA, Trento, ItalyINRA (Bordeaux, Avignon, Angers), France
Andres Bello University, Chile Plant & Food Research, New Zealand
ARC, South Africa
RosBREED participant
location
International Collaborators
+ 2 Scientific Advisory Panel members (Spain, New Zealand)
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Attracting key international collaborators
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RosBREED
• International collaborators were “attracted” by a common problem that needed a solution
Attracting Key Collaborators
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The Chasm
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RosBREED
• “The Chasm” was not unique to the U.S.
• Many leading groups on the Genomics side of the chasm were not in the U.S. – to be successful we had to involve these key groups
• Discussions of how to bridge the chasm were ongoing (including international forums) for many years prior to our SCRI proposal
The PROBLEM = The CHASM
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Bridging the Chasm
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RosBREED
• RosBREED would provide solutions to a shared problem
• Solving would be more efficient, faster, and cost effective if we all worked together
• They supported the approach
• They were comfortable with the leadership team – due to prior relationships
Bridging the Chasm
Collaborators joined because…
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International collaborators become international partners
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RosBREED
• Collaborators and Partners work together towards common mutually agreed-upon goals
• Partners, in partnerships, have legally binding agreements that define tasks and expectations
Collaborators vs. Partners
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RosBREED
• The fund-matching requirement of SCRI projects created opportunities in innovation and partnership
• We required partners to make financial commitments and document expenditures for USDA audit
• This is very time consuming. Therefore partners need to be very supportive and committed to the project
The Funding Match
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Full integration and value of international partners
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RosBREED
Example 1: The SNP Summit
Goal: Develop genome-scanning capability at medium-resolution (1 fully informative marker per 5 cM) for peach, apple, and cherry
• What genotyping technology to use?• Which specific markers to include?• How can we do this most cost effectively?
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RosBREED
Example 1: The SNP Summit
Step 1Bring everyone together in person to develop strategies, obtain buy-in, and assemble international teams to do the work
Include representation from Illumina, the company that would commercialize the SNP arrays
The SNP Summit
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RosBREED
Example 1: The SNP Summit
SNP Summit13-14 November 2010, held with 5th International Rosaceae Genomics Conference in South Africa. RosBREED paid for our matching partners to attend
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RosBREED
Example 1: The SNP Summit
Step 2No formal presentations – only brainstorming for 2 days
But, did have mandated outcomes, and everyone felt the pressure
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SNP Summit was a great success;
- strategies agreed upon- crop teams given one month (!) to choose all SNPs- Illumina recognized us as an Ag Consortium
and committed to commercialization of SNP arrays
Example 1: The SNP Summit
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SPECIAL EARLY ACCESS PRICING
For 9000 SNPs Tier A Tier B Tier C Tier D
Number of Samples (Total orders received for all Consortium members)
<2016 2016+ 4032+ 6000+
Price per Sample (USD) $100 $75 $65 $60
Met our 1-month goalSNP arrays available to world for purchase from Illumina from Dec 2010 – at much lower cost than if RosBREED had gone it alone
Example 1: The SNP Summit
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RosBREED
Example 1: The SNP Summit
And… Entire international Rosaceae genomics, genetics, & breeding community can continue to collaborate and share information – because identical genetic markers used
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RosBREED
Example 2: Strawberry
56 chromosomes with much genetic redundancy
Regarded as too scary to tackle by many scientists!
Goal: Develop genome-scanning capability at medium-resolution (1 fully informative marker per 5 cM) for cultivated strawberry (octoploid)
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RosBREED
Example 2: Strawberry
• Undaunted, commitment made at SNP Summit
• Word got out RosBREED not shying away from this challenge people joined
• Four international groups donated key segregating populations for inclusion in replicated RosBREED reference germplasm set
Increased chance of success – all major strawberry genetics teams working together, sharing germplasm and markers
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Location of European institutions that
provided key populations
Populations imported from – France– Spain– Netherlands– UK
Example 2: Strawberry
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RosBREED
Example 2: Strawberry
And… Two new U.S. partners joined RosBREED at their own expense, providing additional field plot locations and evaluation data
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Breeding Program Locations
Phil Stewart, Driscoll’s Strawberry Associates
Vance Whitaker, University of Florida
Partnering strawberry breeders
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Dr. Nahla Bassil, USDA-ARS
Drs. Cindy Lawley, Mark Hansen & Jill
Orwick, Illumina Inc.
Drs Dorrie Main & Cameron Peace Wash State Univ.
Dr. Eric van de Weg, Plant Research Int.
Dr. Béatrice Denoyes-Rothan,
INRA
Drs. Iraida Amaya & José F. Sánchez Sevilla, IFAPA-Centro de
Churriana
Dr. Jasper Rees, ARC
Dr. Dan Sargent, Istituto Agrario San Michele all’Adige
Drs. Tom Davis & Hailong
Zhang, Univ. New Hampshire
For genetic challenges, strategy developed through weekly conference calls
Example 2: Strawberry
Dr. Stephen Ficklin, Clemson Univ. Genomics
Institute
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RosBREED
Example 2: Strawberry
International partnerships grown well beyond initial proposal
RosBREED began bridge building, and others joined
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RosBREED
Summary
RosBREED tackles major scientific challenges that others share, and fills knowledge gaps
Keys to attracting & benefiting from inclusion of international partners:
- great ideas
- communication
- trust
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RosBREED
Summary
Working together vastly increases accomplishments
- greater conceptual breakthroughs by sharing ideas
- further reach by standing on each other’s shoulders with shared datasets
And of course someone, somewhere, is always working
RosBREED never sleeps!
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Acknowledgements
This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture
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MSUAmy Iezzoni (PD)
Jim HancockDechun Wang
Cholani Weebadde
WSUCameron Peace
Dorrie MainKate Evans
Karina Gallardo Raymond Jussaume
Vicki McCracken Nnadozie Oraguzie
Mykel Taylor
CornellSusan BrownKenong Xu
Clemson Ksenija Gasic
Gregory Reighard
Texas A&MDave Byrne
Univ. of CA-DavisTom Gradziel
Carlos Crisosto
Univ. of New Hamp.Tom Davis
Univ. of MinnesotaJim Luby
Chengyan Yue
Oregon State Univ.Alexandra Stone
Plant Research Intl, Netherlands
Eric van de WegMarco Bink
USDA-ARSNahla Bassil
Gennaro FazioChad Finn
Univ. of ArkansasJohn Clark