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