OBJ. 1TRAIT AND MARKET SEGMENT
BREEDING TARGET ESTABLISHMENT
Year 2 Deliverables, Challenges,Year 3 Goals
RosBREED
• Objectively identify important breeding trait targets
• Prioritize the most valuable target traits for marker-assisted breeding development
Help accelerate and increase efficiency of cultivar development and adoption by identifying valuable
breeding trait targets
Socio-Economics Team Goal
RosBREEDTrait Values
Breeder survey 2010
Producer survey Fall 2011/
Winter 2012
Market Intermediary
survey Spring 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
What
• Grower Clicker Survey developed and given across U.S. (14)
To Whom
• U.S. Rosaceae industry
Year 2
Impact
• Trait values will be known and will be used to prioritize traits for development of DNA diagnostics
RosBREED
Motivate the crop producers to participate in the mail-in grower survey
• Work with breeding and extension teams to deliver integrated information to industry by emphasizing utility of the integrated knowledge gained
• Clicker surveys used to familiarize growers with forthcoming mail in grower survey and encourage their participation
Challenges, Plan for tackling
What
• Surveys of trait priorities for breeders, market intermediaries and growers analyzed and interpreted
To whom
• MAB Team and Rosaceae community
Year 3
• Knowledge of trait priorities and economic values for traits by breeders, market intermediaries and growers used to objectively define selection targets
Intended Impact
What
• Survey of trait priorities for consumers of apples, peaches, cherries, and strawberries developed and disseminated
To whom
• U.S. Rosaceae industries, U.S. Rosaceae genomics, genetics, and breeding community
Year 3
Intended Impact
• Knowledge of trait priorities and economic values for traits by consumers used to objectively define selection targets
RosBREED
Summary
• The search for Jewels in the Genome will be prioritized for identified high impact traits
• How are we doing? Cross-check of available Jewels in the Genome with industry trait values (talk later today)
OBJ. 2GENOME SCANS AND
COMPARATIVE GENOMICS
Year 2 Deliverables, Challenges, Year 3 Goals
• Genome-wide genotyping platforms for apple, peach, cherry and strawberry – development & utilization
• Comparative genomics to accelerate identification and validation of Jewels in the Genome
Year 2 Goals
What
• Infinium SNP arrays designed and commercially available (8K apple, 9K peach, and 6K cherry)
To whom
• International Rosaceae scientific community
Year 2 Deliverables
Impact
• Research community has access to reasonably priced high-throughput genome scan technology
RosBREED
What
• Prior knowledge of Jewels was used to “populate” SNP arrays
Year 2 Deliverables
•Validated SNPs•RosCOS •Candidate genes
What
• Genome-wide genetic data obtained for plant material (peach and cherry completed, apple ~90% completed)
• Informativeness of genetic data assessed for the three crops
Year 2 Deliverables
5954425 476
Total 6855 polymorphic SNPs
EU US
Evaluation of Peach 9K Chip
What
• Strawberry High-Throughput Platform Strategy
- Re-sequencing bin population and identifying segregating SNPs
Year 2 Deliverables
- Synthetic octoploid pilot study (using peach)
AABB
1:31:52:61:7
What
• Peach reference genome used to choose cherry SNPs
Year 2 Comparative Approaches
• RosCOS loci included for each crop
Computer Demo: Peach Gbrowse
& Toolbox
• Genome-scan strategy for strawberry (octoploid) difficult
• Robust flexible database infrastructure that suits diverse needs of genomics, genetics, and breeding communities
Challenges, Plan for tackling
2011
What
• Dissemination and comparison of genotyping results
• High-throughput genome scans of strawberry
• Cross-species markers available on GDR
To whom• Rosaceae scientific community
Planned Year 3 Deliverables
Intended Impact
• Genome-scan capability for octoploid strawberry and new Jewels in the Genome...
RosBREED
What
• Dissemination and comparison of results
• Scientific discussion tomorrow, Jan 13th
• Two talks at PAG (Chagne et al. & Gasic et al.in Fruits/Nuts Workshop)
• Three manuscripts:
- Apple – accepted
- Peach – very advanced stage of preparation
- Cherry – advanced stage of preparation
Planned Year 3 Deliverables
RosBREED
OBJ. 3PEDIGREE-BASED BREEDING INFORMATION MANAGEMENT
SYSTEM Year 2 Deliverables, Challenges,
Year 3 Goals
RosBREED
Develop, deliver, and implement software that leverages genomics and phenotypic trait information
to maximize breeding efficiency
Goal
Who
Software teams (Pedigree-Based Analysis and Toolbox) and breeding teams that provide and collect the data
used for analysis
What
To whom
Year 2 Deliverables – PBA software team
Impact
• New software capable of doing the full range of necessary statistical analysis to include identification and validation of marker-locus-trait associations
• Demonstration breeders and trainees
Information Required
Pedigree+
Genotypic+
Phenotypic
PBA Analyses
Discovery Jewels markers for traits
+Role in the bracelet impact & coherence
Impact
Jewels available
for breeding
What
To whom
Y2 Deliverables – PBA: new software
Impact
• Improved user friendliness − Ease data handling (align with GenomeStudio output) − Ease interpretation output
• Reduction of computation time for massive data sets• New functionalities: Pipeline for filtering most robust markers
• Demonstration breeders & trainees, scientists
• Eased discovery of Jewels• Eased qualification of their beauty & use
− Characteristics of individual jewels − Contribution to the colier as a whole: coherence
What
To whom
Y2 Deliverables – PBA implementation
Impact
• Familiarity with software & way of thinking− Training through a 2½ day workshop; − Individual consulting with MSU-based post-doc− Bi-weekly conference calls on marker issues
• Demonstration breeders and trainees, scientists
• Basic understanding on concepts project wide• PhD students have started PBA analyses on RB data
• PBA Software development – Dealing with massive data sets of new marker type Explore expertise of a wide range of colleagues
• PBA implementation – Transfer of experience in PBA analyses workshops, conference calls, one-on-one support
• PBA Use in breeding– Integrate results in the various Breeders Tools Regular conference calls among teams
Challenges, Plans for Tackling, & Solving
RosBREED
What
To whom
Planned Year 3 Deliverables
Intended Impact
• New software modules and functionalities• Trainings, consultations
• Demonstration breeders & trainees, scientists
• PBA software adjusted to massive data sets• PBA experienced trainees & breeders• Scrutinized marker & pedigree data sets• Discovery and polishing of new jewels
RosBREED and Affiliated Breeding Programs produce TRILLIONS of DATA POINTS!
How do we facilitate the application of all this?
The Toolbox: a user-friendly database and tools that leverage genomics information for maximum utility within the Marker-Assisted Breeding (MAB) Pipeline, including
functions to aid breeding decision-making
What is the Toolbox?
What To
Year 2 Deliverables
Impact
Breeding Programs able to enter PBA
information and own breeding data
Demo Breeders
and Trainees
Templates for breeding
databases compatible with PBA software:
Developed
Breeding Databases – parentage information, phenotypic data, performance at multiple locations,
genetic data
RosBREED
What To
Year 2 DeliverablesImpact
Understand capability; ability to plan crosses with Cross Assist and
other MAB applications
Demo Breeders
and Trainees
Database and Capabilities:
Delivered during RBIII and through
program visits
Computer Demo:Toolbox
Which parents have the jewels?
Which combinations to create?
Which seedlings have the jewels?
• Diversity of Breeder’s own program needs and desires
- Assess the capacities of Toolbox team to fulfill as many priorities as possible
• Complexity, Enormity – Break into workable chunks and communicate through web and file sharing.
• Gaining breeder’s understanding – Present at RosBREED III Annual Project Meeting, Web Tutorials, Live Demonstrations
Challenges and plans for tackling
RosBREED
DELIVERABLES
• TOOLBOX V 1.0
• TOOLBOX V 1.0 demonstrated at RBIII
• TOOLBOX V 1.5
• TOOLBOX V 1.5 demonstrated at ASHS meeting
Planned Year 3 Deliverables
INTENDED IMPACT
• Plan crosses using Cross Assist based on PBA data and work through the MAB pipeline from discovered QTL to marker development, genotyping, validation, and utility assessment in own breeding program.
• Understanding of TOOLBOX through demos and tutorials
Breeders & Breeding Trainees
• assist in the finding and polishing of the Jewel in the Genome
• adopt Marker-Assisted Breeding for these Jewels
Goal
What
• Pedigree-linked U.S. reference germplasm sets
• Standardized phenotyping protocols
Year 2
• Updated germplasm sets and protocols, videos added
Year 2 Deliverables
RosBREED
What
• Phenotypic data for apple, peach, cherry and strawberry germplasm sets collected and combined with prior data
By whom
• Demonstration breeders and associates
Year 2 Deliverables
Impact
• Ability to discover and validate M-L-T associations in relevant germplasm
RosBREED
• Transforming massive amounts of data to format usable for PBA
• Divide tasks and provide assistance from PBA and genotyping teams
Challenges and plans for tackling
RosBREED
What
• Phenotypic data for apple, peach, cherry and strawberry germplasm sets collected and combined with prior data and archived
• Data analysis using softwareBy whom
• Demonstration breeders, associates, and PBA and Toolbox Teams
Planned Year 3 Deliverables
Intended Impact
• New Jewels in the Genome….
RosBREED
Computer Demonstrations
Gennaro FazioToolbox
Eric van de Weg PBA Software
Umesh Rosyara PBA Software
Dorrie Main GBrowse
Cholani WeebaddeVideos