1. Plant Research Intl, Netherlands
Cornell
Susan Brown
Kenong Xu
Clemson
Ksenija Gasic
Gregory Reighard
Texas A&M
Dave Byrne
Univ. of CA-Davis
Tom Gradziel
Carlos Crisosto 
Univ. of New Hamp.
Tom Davis
MSU
Amy Iezzoni (PD)
Jim Hancock
Dechun Wang
Cholani Weebadde
WSU
Cameron Peace
Dorrie Main
Kate Evans
Karina Gallardo
Raymond Jussaume
Vicki McCracken
Nnadozie Oraguzie
Mykel Taylor
Univ. of Arkansas
John Clark
USDA-ARS
Nahla Bassil
Gennaro Fazio
Chad Finn
Univ. of Minnesota
Jim Luby
Chengyan Yue
Oregon State Univ.
Alexandra Stone
Plant Research Intl, Netherlands
Eric van de Weg
Marco Bink

2. Outline of Presentation
RosBREED
Outline of Presentation
The RosBREED Project
The Need for RosBREED
Objectives and Major Activities
Advances in Enabling MAB

3. The RosBREED Project

4. RosBREED The RosBREED Project
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)
RosBREED

5. RosBREED The RosBREED Project
U.S.-wide and international collaboration
10 Teams
32 members of 3 Advisory Panels (Stakeholder, Extension, Scientific)
Administration
Pedigree-Based Analysis
Industry
Genomics
Breeders’ Toolbox
Socio-Economics
Genotyping
Extension
Breeding
MAB Pipeline
RosBREED

6. The RosBREED Project Centered on breeders & breeding programs
Project Director,
Amy Iezzoni
-breeder (tart cherry)
-geneticist
-genomicist
-leader

7. RosBREED The RosBREED Project Vision
Integration of modern genomics tools with traditional breeding approaches will transform crop improvement in Rosaceae, significantly improving profitability and sustainability of U.S. rosaceous crop industries and contributing to increased consumption and enjoyment of these fruit, nut, and floral products.
RosBREED

8. Socio-economics information
The RosBREED Approach
Socio-economics information
Objectively define
SELECTION TARGETS
IMPROVED CULTIVARS
Optimize
SELECTION STRATEGIES
DNA information
RosBREED

9. The Need for RosBREED

10. The Chasm
good intentions
skeptical dismissal
Genomics
Breeding

11. Bridging the Chasm RosBREED Genomics Breeding Public reference
Genome scan
capability
Public
reference
germplasm
sets
New QTLs
Comprehensive fruit
phenotypic database
PBA training
MAB
Pipeline
Bridging the Chasm
RosBREED
Genomics
Breeding

12. Objectives & Major Activities

13. RosBREED Project Objectives
Enhance new cultivar adoption, enlarge market potential, increase consumption
– socio-economics knowledge of trait values
2) Establish sustainable infrastructure for MAB in Rosaceae
– genome scanning capability, new QTLs (“jewels”)
3) Integrate socio-econ and genomics resources into breeding
– breeding information management system
4) Conduct MAB in demo breeding programs, fruit quality focus
– MAB implementation
5) Enhance sustainability of cultivar development
– MAB tech transfer to breeders & engage other stakeholders
RosBREED

14. Overview of Activities
TRAIT & MARKET SEGMENT BREEDING TARGET ESTABLISHMENT
GENOME RESOURCES INTERFACE
Socio-economics information
GENOME SCANS
Marker priorities
Screening services
MAB PIPELINING
Breeding markers
DNA information
REFERENCE GERMPLASM CHOICE
PBA: crop-wide
STANDARDIZED PHENOTYPING
New QTLs discovered
PBA: breeding program
Crossing scheme
Efficient routine breeding operations
Better fruit!
MAB PIPELINING
Seedling selection scheme
BREEDERS’ TOOLBOX DEVELOPMENT
Trial MASS

15. Advances in Enabling MAB

16. RosBREED What trait is my next breeding target?
We like disease resistant apple trees!
We like firm tart cherries that pit well!
I like tasty strawberries!
Processors
Socio-Economics Team will determine trait values
Breeder survey 2010
Producer survey
Fall 2011-
Winter 2012
Market Intermediary survey Fall 2010-
Winter 2011
Household data analysis 2010;
consumer survey 2012
RosBREED

17. Challenges faced when determining priorities
Technical challenges
Socio-economic challenges
Blue, red and green is what we identify as “technical” challenges the purple yellow pink and orange is more related to socio-economics
Cumulative of mean 1-10 score
Cumulative of mean 1-10 score
RosBREED

18. RosBREED Phenotype Databases
for Valuable Fruit Traits of Reference Germplasm 1 2 3 4 5
Reference Germplasm Sets
Public: 480 individuals
Standardized Phenotyping at multiple locations (
Data collected 2010 & 2011
Available at Genome Database for Rosaceae (
Now playing: Apple
Coming soon: Peach, Cherry, Strawberry
RosBREED

19. Pedigree-Based Analysis Team
FlexQTLTM
for discovering QTLs
Pedimap
for visualizing pedigrees (with IBD, alleles, traits)
Fruit firmness in apple
Flow of a specific linkage block
RosBREED

20. Pedigree-Based Analysis Team
Software training
RosBREED

21. RosBREED Genomics Peach: 9K Apple: 8K Cherry: 6K
Cherry array success
Illumina Infinium® arrays:
Peach: 9K Apple: 8K Cherry: 6K
Peach & Cherry genome scan strategy
“SNP chip”
SNP genotyping
Genotype obtained for screened sweet cherry germplasm
SNP failed
Example use: peach mapping
Apple genome scan strategy
RosBREED

22. RosBREED Genotyping High quality DNA extraction 3 x 1000 samples
PCR for SSRS
(QTL-flanking & CG)
Genotype calling
SSRs
9K, 8K, 6K SNP genome scans
RosBREED

23. MAB Pipeline
RosBREED

24. RosBREED MAB Pipeline “Fast-tracked pipelining” of available jewels
Tables of functional genotypes
Peach fruit texture type
Apple fruit storability
RosBREED

25. MAB Pipeline
“How To” diagrams
RosBREED

26. Breeders’ Toolbox Modules
“Crop Reference & Breeding Pedigree Germplasm Databases”
“Marker-Locus-Trait Association Warehouse” * * * *
“Technology Portfolio”
“Selection Target Identifier” *
“Cross Assist” * * *
“Genome Database Resources”
“Seedling Select”

27. RosBREED Breeders’ Toolbox Cross Assist (prototype)
Step 1. Specify data source
Step 2. Select up to 5 target traits
Step 3. Enter trait weights, heritabilities, and max. co-parentage, or use defaults, or Calculate from data
Step 4. Click Generate Parents List
Cross Assist
(prototype)
Identifies efficient crossing schemes by mobilizing all available data
RosBREED

28. Extension
Our outreach is all about staying connected with our stakeholders and project participants
Various ways:
Website
Quarterly Newsletters
Presentations at professional meetings
Community Breeders Page ! ! ! !
RosBREED

29. Extension: Coming soon…!
Participation in grower meetings near you! ( )
TITLE: Tell us what you want! Quantifying your priorities for new cultivars
Visits to U.S. Rosaceae breeding programs ( )
- to enable MAB, share successful approaches
RosBREED Participatory Workshop (30 July 2012) just a day prior to ASHS 2012 in Miami, Florida ! !
RosBREED

30. Evaluation of Outreach
Surveys and interviews to:
- Gather project feedback
- Monitor changes in Rosaceae breeding programs
RosBREED

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

32. RosBREED MAB posters Apple #145 Peach #144 Cherry #146
Tues 1:15-2:00, Kona Ballroom