msu amy iezzoni (pd) jim hancock dechun wang cholani weebadde wsu cameron peace dorrie main kate...
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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
Outline of Presentation
RosBREED
The RosBREED Project
The Need for RosBREED
Objectives and Major Activities
Advances in Enabling MAB
The RosBREED
Project
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
RosBREED
• U.S.-wide and international collaboration
• 10 Teams
• 32 members of 3 Advisory Panels (STAKEHOLDER, EXTENSION, SCIENTIFIC)
The RosBREED Project
SOCIO-ECONOMICS
INDUSTRY
BREEDING
PEDIGREE-BASED ANALYSIS
ADMINISTRATION
BREEDERS’ TOOLBOX
GENOMICS
GENOTYPING
MAB PIPELINEEXTENSION
• Centered on breeders & breeding programsThe RosBREED Project
Project Director,Amy Iezzoni
-breeder (tart cherry)-geneticist-genomicist-leader
RosBREED
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.
The RosBREED Project
Vision
SELECTION TARGETS
SELECTION STRATEGIES
Objectively define
Optimize
DNA information
Socio-economics information
RosBREED
The RosBREED Approach
The Need for RosBREED
The Chasm
Bridging the Chasm
Genome scan
capability
Public
reference
germ
plasm
sets
New QTLs
Comprehensive fru
it
phenotyp
ic database
PBA training
MAB
Pipelin
e
Objectives & Major
Activities
RosBREED
1) 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
Project Objectives
TRAIT & MARKET SEGMENT BREEDING TARGET ESTABLISHMENT
GENOME SCANS
GENOME RESOURCES INTERFACE
New QTLs discovered
PBA: crop-wide
PBA: breeding program
Breeding markersScr
eenin
g
serv
ices
Mar
ker
prior
ities
Cross
ing
sche
me
Trial
MASSBREEDERS’
TOOLBOX DEVELOPMENT
Socio-economics
information
DNA information
Efficient routine breeding operations
Better fruit!
MA
B P
IPE
LIN
ING
MA
B P
IPE
LIN
ING
Overview of Activities
Seedli
ng
selec
tion
sche
me
REFERENCE GERMPLASM CHOICE
STANDARDIZED PHENOTYPING
Advances in Enabling
MAB
RosBREEDSocio-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
What trait is my next breeding
target?
We like disease resistant apple
trees!
I like tasty strawberries!
We like firm tart cherries that pit well!
Processors
0 5 10 15 20 0 5 10 15 20 25
Challenges faced when determining priorities
RosBREED
Cumulative of mean 1-10 score Cumulative of mean 1-10 score
Technical challenges Socio-economic challenges
RosBREED
Phenotype Databasesfor Valuable Fruit Traits of Reference Germplasm
• Reference Germplasm SetsPublic: 480 individuals
• Standardized Phenotyping at multiple locations (www.rosbreed.org)
• Data collected 2010 & 2011
• Available at Genome Database for Rosaceae (www.rosaceae.org/resources/fruit-evaluation)
Now playing: Apple
Coming soon: Peach, Cherry, Strawberry
1
2
3
4
5
RosBREED
Pedimap
for visualizing pedigrees (with IBD, alleles, traits)
FlexQTLTM
for discovering QTLsRallsJan Delicious Winesap RomBeauty Jonathan M_PRI668-100 GoldenDel F2_26829-2-2
Fuji Crandall PRI14-126
PRI668-100
X-2771
X-3143
X-3318
Fruit firmness in apple
Pedigree-Based Analysis Team
Flow of a specific linkage block
RosBREED
Pedigree-Based Analysis Team
Software training
RosBREED
Genomics
Genotype obtained for screened sweet cherry germplasm
SNP failed
Illumina Infinium® arrays:
Peach: 9K Apple: 8K Cherry: 6K
“SNP chip”
SNP genotyping
Cherry array success
Example use:
peach mapping
Peach & Cherry
genome scan strategy
Apple genome scan
strategy
RosBREED
GenotypingHigh quality DNA extraction 3 x 1000 samples
PCR for SSRS(QTL-flanking & CG)
Genotype calling- SSRs
- 9K, 8K, 6K SNP genome scans
RosBREED
MAB Pipeline
RosBREED
MAB Pipeline“Fast-tracked
pipelining” of available
jewels
Tables of functional genotypes
Peach fruit texture type
Apple fruit storability
RosBREED
MAB Pipeline
“How To” diagrams
Breeders’ Toolbox Modules
* * **
* **
“Technology Portfolio”
“Selection Target Identifier”
“Genome Database Resources”
“Crop Reference & Breeding Pedigree Germplasm Databases”
“Cross Assist”
“Seedling Select”
“Marker-Locus-Trait Association Warehouse” *
RosBREED
Breeders’ Toolbox
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
(prototype)
Identifies efficient crossing schemes by mobilizing all available data
Cross Assist
Our outreach is all about staying connected with our stakeholders and project participants
Various ways:
Website www.rosbreed.org
Quarterly Newsletters
Presentations at professional meetings
Community Breeders Page
RosBREED
Extension
!!
!!
RosBREED
Extension: Coming soon…Participation in grower meetings near you! (2011-2012)
TITLE: Tell us what you want! Quantifying your priorities for new cultivars
Visits to U.S. Rosaceae breeding programs (2011-2012)- to enable MAB, share successful approaches
RosBREED Participatory Workshop (30 July 2012) - just a day prior to ASHS 2012 in Miami, Florida
!
!
!
RosBREED
Evaluation of Outreach
Surveys and interviews to:- Gather project feedback- Monitor changes in Rosaceae breeding programs
Acknowledgements
This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture
3 posters
Peach #144Apple #145
Cherry #146
RosBREED MAB postersTues 1:15-2:00, Kona Ballroom