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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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Presentation Transcript
slide1

OBJ. 1

TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT

Year 2 Deliverables, Challenges,Year 3 Goals

slide2

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

slide3

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

slide4

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

slide5

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
slide6

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
slide7

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
slide8

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

slide9

OBJ. 2

GENOME SCANS AND COMPARATIVE GENOMICS

Year 2 Deliverables, Challenges, Year 3 Goals

slide10

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
slide11

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

slide12

Year 2 Deliverables

  • What
  • Prior knowledge of Jewels was used to “populate” SNP arrays
  • Validated SNPs
  • RosCOS
  • Candidate genes
slide13

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

slide14

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

slide15

Year 2 Comparative Approaches

  • What
  • Peach reference genome used to choose cherry SNPs
  • RosCOS loci included for each crop

Computer Demo: Peach Gbrowse

& Toolbox

slide16

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

slide17

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

slide18

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

slide19

OBJ. 3

PEDIGREE-BASED BREEDING INFORMATION MANAGEMENT SYSTEM

Year 2 Deliverables, Challenges, Year 3 Goals

slide20

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

slide21

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

slide22

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
slide23

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
slide24

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

slide25

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
slide26

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

slide27

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

slide28

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?

slide29

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

slide30

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
slide31

Goal

  • Breeders & Breeding Trainees
  • assist in the finding and polishing of the Jewel in the Genome
  • adopt Marker-Assisted Breeding for these Jewels
slide32

Year 2 Deliverables

  • What
  • Pedigree-linked U.S. reference germplasm sets
  • Standardized phenotyping protocols
  • Year 2
  • Updated germplasm sets and protocols, videos added

RosBREED

slide33

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

slide34

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

slide35

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

slide36

Computer Demonstrations

Gennaro Fazio

Toolbox

Eric van de Weg PBA Software

Dorrie Main GBrowse

UmeshRosyara PBA Software

CholaniWeebadde

Videos

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