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OBJ. 1 TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT PowerPoint PPT Presentation


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OBJ. 1 TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT Year 2 Deliverables, Challenges, Year 3 Goals. Socio-Economics Team Goal. Help accelerate and increase efficiency of cultivar development and adoption by identifying valuable breeding trait targets.

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OBJ. 1 TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT

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Obj 1 trait and market segment breeding target establishment

OBJ. 1

TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT

Year 2 Deliverables, Challenges,Year 3 Goals


Obj 1 trait and market segment breeding target establishment

Socio-Economics Team Goal

  • Help accelerate and increase efficiency of cultivar development and adoption by identifying valuable breeding trait targets

  • Objectively identify important breeding trait targets

  • Prioritize the most valuable target traits for marker-assisted breeding development

RosBREED


Obj 1 trait and market segment breeding target establishment

We like firm tart cherries that pit well!

What trait is my next breeding target?

We like disease resistant apple trees!

I like tasty strawberries!

Processors

Producer survey

Fall 2011/

Winter 2012

Market Intermediary survey Spring 2011

Household data analysis 2010;

consumer survey 2012

Breeder survey 2010

Trait Values

RosBREED


Obj 1 trait and market segment breeding target establishment

Year 2

  • What

  • Grower Clicker Survey developed and given across U.S. (14)

  • To Whom

  • U.S. Rosaceae industry

  • Impact

  • Trait values will be known and will be used to prioritize traits for development of DNA diagnostics

RosBREED


Obj 1 trait and market segment breeding target establishment

Challenges, Plan for tackling

  • 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


Obj 1 trait and market segment breeding target establishment

Year 3

  • What

  • Surveys of trait priorities for breeders, market intermediaries and growers analyzed and interpreted

  • To whom

  • MAB Team and Rosaceae community

Intended Impact

  • Knowledge of trait priorities and economic values for traits by breeders, market intermediaries and growers used to objectively define selection targets


Obj 1 trait and market segment breeding target establishment

Year 3

  • 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

  • Intended Impact

  • Knowledge of trait priorities and economic values for traits by consumers used to objectively define selection targets


Obj 1 trait and market segment breeding target establishment

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)

RosBREED


Obj 1 trait and market segment breeding target establishment

OBJ. 2

GENOME SCANS AND COMPARATIVE GENOMICS

Year 2 Deliverables, Challenges, Year 3 Goals


Obj 1 trait and market segment breeding target establishment

Year 2 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


Obj 1 trait and market segment breeding target establishment

Year 2 Deliverables

  • What

  • Infinium SNP arrays designed and commercially available (8K apple, 9K peach, and 6K cherry)

  • To whom

  • International Rosaceae scientific community

  • Impact

  • Research community has access to reasonably priced high-throughput genome scan technology

RosBREED


Obj 1 trait and market segment breeding target establishment

Year 2 Deliverables

  • What

  • Prior knowledge of Jewels was used to “populate” SNP arrays

  • Validated SNPs

  • RosCOS

  • Candidate genes


Obj 1 trait and market segment breeding target establishment

Year 2 Deliverables

  • 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

EU

US

5954

425

476

Total 6855 polymorphic SNPs

Evaluation of Peach 9K Chip


Obj 1 trait and market segment breeding target establishment

Year 2 Deliverables

  • What

  • Strawberry High-Throughput Platform Strategy

    • Re-sequencing bin population and identifying segregating SNPs

  • Synthetic octoploid pilot study (using peach)

BB

AA

2:6

1:7

1:5

1:3


Obj 1 trait and market segment breeding target establishment

Year 2 Comparative Approaches

  • What

  • Peach reference genome used to choose cherry SNPs

  • RosCOS loci included for each crop

Computer Demo: Peach Gbrowse

& Toolbox


Obj 1 trait and market segment breeding target establishment

Challenges, Plan for tackling

  • Genome-scan strategy for strawberry (octoploid) difficult

  • Robust flexible database infrastructure that suits diverse needs of genomics, genetics, and breeding communities

2011


Obj 1 trait and market segment breeding target establishment

Planned Year 3 Deliverables

  • What

  • Dissemination and comparison of genotyping results

  • High-throughput genome scans of strawberry

  • Cross-species markers available on GDR

  • To whom

  • Rosaceae scientific community

  • Intended Impact

  • Genome-scan capability for octoploid strawberry and new Jewels in the Genome...

RosBREED


Obj 1 trait and market segment breeding target establishment

Planned Year 3 Deliverables

  • 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

RosBREED


Obj 1 trait and market segment breeding target establishment

OBJ. 3

PEDIGREE-BASED BREEDING INFORMATION MANAGEMENT SYSTEM

Year 2 Deliverables, Challenges, Year 3 Goals


Obj 1 trait and market segment breeding target establishment

Goal

Develop, deliver, and implement software that leverages genomics and phenotypic trait information to maximize breeding efficiency

Who

  • Software teams (Pedigree-Based Analysis and Toolbox) and breeding teams that provide and collect the data used for analysis

RosBREED


Obj 1 trait and market segment breeding target establishment

Year 2 Deliverables – PBA software team

What

  • New software capable of doing the full range of necessary statistical analysis to include identification and validation of marker-locus-trait associations

To whom

  • Demonstration breeders and trainees

Impact

PBA Analyses

Discovery Jewels markers for traits

+

Role in the bracelet impact & coherence

Impact

Jewels available for breeding

Information Required

Pedigree

+

Genotypic

+

Phenotypic


Obj 1 trait and market segment breeding target establishment

Y2 Deliverables – PBA: new software

What

  • 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

  • To whom

    • Demonstration breeders & trainees, scientists

    Impact

    • Eased discovery of Jewels

    • Eased qualification of their beauty & use

      • Characteristics of individual jewels

      • Contribution to the colier as a whole: coherence


    Obj 1 trait and market segment breeding target establishment

    Y2 Deliverables – PBA implementation

    What

    • 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

    To whom

    • Demonstration breeders and trainees, scientists

    Impact

    • Basic understanding on concepts project wide

    • PhD students have started PBA analyses on RB data


    Obj 1 trait and market segment breeding target establishment

    Challenges, Plans for Tackling, & Solving

    • 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

    RosBREED


    Obj 1 trait and market segment breeding target establishment

    Planned Year 3 Deliverables

    What

    • New software modules and functionalities

    • Trainings, consultations

    To whom

    • Demonstration breeders &

      • trainees, scientists

    Intended Impact

    • PBA software adjusted to massive data sets

    • PBA experienced trainees & breeders

    • Scrutinized marker & pedigree data sets

    • Discovery and polishing of new jewels


    Obj 1 trait and market segment breeding target establishment

    What is the Toolbox?

    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


    Obj 1 trait and market segment breeding target establishment

    Year 2 Deliverables

    Impact

    What

    To

    • Templates for breeding databases compatible with PBA software: Developed

    Breeding Programs able to enter PBA information and own breeding data

    • Demo Breeders and Trainees

    Breeding Databases – parentage information, phenotypic data, performance at multiple locations, genetic data

    RosBREED


    Obj 1 trait and market segment breeding target establishment

    Year 2 Deliverables

    Impact

    What

    To

    • Demo Breeders and Trainees

    • Database and Capabilities: Delivered during RBIII and through program visits

    • Understand capability; ability to plan crosses with Cross Assist and other MAB applications

    Which parents have the jewels?

    Computer Demo:

    Toolbox

    Which combinations to create?

    Which seedlings have the jewels?


    Obj 1 trait and market segment breeding target establishment

    Challenges and plans for tackling

    • 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

    RosBREED


    Obj 1 trait and market segment breeding target establishment

    Planned Year 3 Deliverables

    • DELIVERABLES

    • TOOLBOX V 1.0

    • TOOLBOX V 1.0 demonstrated at RBIII

    • TOOLBOX V 1.5

    • TOOLBOX V 1.5 demonstrated at ASHS meeting

    • 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


    Obj 1 trait and market segment breeding target establishment

    Goal

    • Breeders & Breeding Trainees

    • assist in the finding and polishing of the Jewel in the Genome

    • adopt Marker-Assisted Breeding for these Jewels


    Obj 1 trait and market segment breeding target establishment

    Year 2 Deliverables

    • What

    • Pedigree-linked U.S. reference germplasm sets

    • Standardized phenotyping protocols

    • Year 2

    • Updated germplasm sets and protocols, videos added

    RosBREED


    Obj 1 trait and market segment breeding target establishment

    Year 2 Deliverables

    • What

    • Phenotypic data for apple, peach, cherry and strawberry germplasm sets collected and combined with prior data

    • By whom

    • Demonstration breeders and associates

    • Impact

    • Ability to discover and validate M-L-T associations in relevant germplasm

    RosBREED


    Obj 1 trait and market segment breeding target establishment

    Challenges and plans for tackling

    • Transforming massive amounts of data to format usable for PBA

    • Divide tasks and provide assistance from PBA and genotyping teams

    RosBREED


    Obj 1 trait and market segment breeding target establishment

    Planned Year 3 Deliverables

    • What

    • Phenotypic data for apple, peach, cherry and strawberry germplasm sets collected and combined with prior data and archived

    • Data analysis using software

    • By whom

    • Demonstration breeders, associates, and PBA and Toolbox Teams

    • Intended Impact

    • New Jewels in the Genome….

    RosBREED


    Obj 1 trait and market segment breeding target establishment

    Computer Demonstrations

    Gennaro Fazio

    Toolbox

    Eric van de Weg PBA Software

    Dorrie Main GBrowse

    UmeshRosyara PBA Software

    CholaniWeebadde

    Videos


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