RosBREED Never Sleeps

Integration & value ofinternational partners

Amy Iezzoni, Michigan State UniversityCameron Peace, Washington State University

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

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

RosBREED and our international partners:

an introduction

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

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

RosBREED

CROPS of the ROSACEAE FAMILY

We’re In It Together

Demonstration Breeding Programs

RosBREED

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!

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

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)

Attracting key international collaborators

RosBREED

• International collaborators were “attracted” by a common problem that needed a solution

Attracting Key Collaborators

The Chasm

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

Bridging the Chasm

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…

International collaborators become international partners

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

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

Full integration and value of international partners

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?

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

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

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

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

  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

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 

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)

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

Location of European institutions that

provided key populations

Populations imported from – France– Spain– Netherlands– UK

Example 2: Strawberry

RosBREED

Example 2: Strawberry

And… Two new U.S. partners joined RosBREED at their own expense, providing additional field plot locations and evaluation data

Breeding Program Locations

Phil Stewart, Driscoll’s Strawberry Associates

Vance Whitaker, University of Florida

Partnering strawberry breeders

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

RosBREED

Example 2: Strawberry

International partnerships grown well beyond initial proposal

RosBREED began bridge building, and others joined

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

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!

Acknowledgements

This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture

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