OBJ. 1TRAIT AND MARKET SEGMENT

BREEDING TARGET ESTABLISHMENT

Year 3 Deliverables, Challenges,Year 4 Goals

RosBREED

• Objectively identify important breeding trait targets

• Prioritize the most valuable target trait loci for the development of DNA diagnostic tools

Help accelerate and increase efficiency of cultivar development and adoption by identifying valuable

breeding trait targets

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 and market intermediary survey data –

relative values of fruit quality and production traits were obtained

To whom• U.S. Rosaceae industry & breeders

Year 3 Deliverables

Impact• Trait values obtained are being used

to prioritize traits for development of DNA diagnostic tools

RosBREED

What• Consumer’s preferences and

values for targeted fruit quality attributes – elicited

To whom• U.S. Rosaceae industry & breeders

Year 3 Deliverables

RosBREED

Impact• Trait values obtained will be used by breeders to

assign trait priorities; industry sectors have knowledge of relative consumer values

Elements in the choice experiment scenarios not absolutely clear (e.g. individual interpretations of flavor and sweetness) use a consensus approach to interpret the data

Logistical challenges in providing apple samples that met criteria for the consumer auction experiment help from the WTFRC(demonstration after lunch!)

Challenges and plans for tackling

What• Trait priorities for market intermediaries, growers, and

consumers of apples - analyzed, interpreted, and communicated

To whom• MAB Team and Rosaceae community

Year 4 Deliverables

• DNA diagnostic tools will be developed for the most valuable fruit target trait loci, thereby increasing breeding efficiency for high priority traits

Impact intended

Year 4 Deliverables

• Awareness of marker-assisted breeding by industry sectors will be increased through their participation in this prioritization process and from disseminated summaries

• Breeder’s knowledge of trait priorities, along with availability of DNA diagnostic tools, will result in increased likelihood of cultivar release, adoption, enlarged market potential and increased consumption.

Impact intended

OBJ. 2GENOME SCANS AND

COMPARATIVE GENOMICS

Year 3 Deliverables, Challenges, Year 4 Goals

• Genome-wide genotyping platforms for apple, peach, cherry, and strawberry – develop and utilize

• Comparative genomics to accelerate identification and validation of Jewels in the Genome

Goal

• Genome-scanning SNP arrays developed and utilized for apple (9K), peach (9K) and cherry (6K) by international RosBREED-led efforts

Year 3 DeliverablesWhat

To whom• Rosaceae scientific community

Year 3 Deliverables

Impact• These cost effective commercially available genome

scan platforms are not only enabling RosBREED outcomes, but they are and will continue to enable the generation of new knowledge by the international Rosaceae community

RosBREED

What• Genome-wide genetic data obtained for plant material

(peach, cherry, and apple completed)

To whom• Rosaceae scientific community

Year 3 Deliverables

Impact• Analysis of this dataset, combined with pedigree and

phenotypic datasets is enabling the identification and validation of Jewels for use in breeding

RosBREED

What• Strawberry genome scan strategy (Affymetrix 90K

Axiom® chip) developed by a RosBREED-led international consortium (W309, PAG XXI)

Year 3 Deliverables

To whom• RosBREED Strawberry Team

Impact• Genotypic data obtained will enable discovery of

new trait loci and their validation for conversion into jewels for use in breeding

Ensure accessibility of Genomics, Genetics, and Breeding Data – database infrastructure and capacity

• Develop a flexible modular structure, submit short read sequences to NCBI

Suitability of the SNP genotyping algorithm to analyze the strawberry SNP array

• a two-phase strategy is in place to permit initial testing of the array using the genotyping algorithm

Challenges and plans for tackling

What• Strawberry 90K Axiom® SNP chip evaluated and

utilized to genotype strawberry breeding materials – goal is a minimum of 4000 robust SNP markers

To whom• International strawberry research community

Year 4 Deliverables

Impact intended• Genome-scan capability for octoploid strawberry

enables Jewel discovery

RosBREED

What• Dissemination of genomics, genetic, and breeding

data through GDR

To whom• Rosaceae research community

Impact intended• Efficient sustained access to genetics, genomics, and

breeding data will enable the use of this knowledge for practical applications and for future discoveries

Year 4 Deliverables

OBJ. 3PEDIGREE-BASED

BREEDING INFORMATION MANAGEMENT SYSTEM

Year 3 Deliverables, Challenges, Year 4 Goals

RosBREED

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

Goal

Involves:Software teams (Pedigree-Based Analysis [PBA],Breeding Information Management System [BIM System])and all crop breeding teams that provide, collect,and use the data for finding and validating QTLs

What

To whom

Year 3 Deliverables (PBA)

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 requiredPedigree

+Genotypic

+Phenotypic

PBA analysesDiscovery of trait loci,

validation of associated markers

+Role in the bracelet impact & coherence

ImpactJewels

available for

breeding

What

To whom

Impact

• Improved user-friendliness • 10-fold reduction of computation time for massive data sets• New functionality: building SNP haplotype blocks• Software to build integrated genetic maps across multiple

mapping populations

• Demonstration breeders & trainees, allied scientists

• Eased discovery of trait loci• Eased quantification of allele effects

Year 3 Deliverables (PBA)

What

To whom

Impact

• Familiarity with software & concepts−Training through a 2.5 day workshop− Individual consulting with MSU-based postdoc

• Demonstration breeders and trainees, allied scientists

• Basic understanding on concepts project-wide• Students are conducting PBA analyses on RB data

Year 3 Deliverables (PBA)

RosBREED

Challenges and plans for tackling (PBA)

• PBA software development - Ease of access to FlexQTL output Generation of a user-friendly interface

• PBA use by breeders – consulting - Awareness of need for scrutinizing pedigree and marker data prior to in-depth QTL characterization

- Finalize analyses and interpretation into application-ready deliverables

2-day workshop (May 2013), online meetings, one-on-one

What

To whom

Year 4 Deliverables (PBA)

Impact intended

• New software modules and functionalities• Training, consultations

• Demonstration breeders & trainees, allied scientists

• PBA software better adjusted to massive data sets• PBA-experienced trainees & breeders• Scrutinized pedigree & marker datasets• Discovery of new trait loci and polishing of new jewels

What To

Year 3 Deliverables (BIM System)

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 ToYear 3 Deliverables (BIM System)

ImpactUnderstand

capability; ability to plan crosses with Cross Assist and

other MAB applications

Demo Breeders

and Trainees

Database and Capabilities:

Delivered during RBIV and through

program visits

Computer demo:BIM System

Which parents have the jewels?

Which combinations to create?

Which seedlings have the jewels?

• Diversity of Breeder’s own program needs and desires: assess capacities of BIM System 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 IV Annual Project Meeting, web tutorials, live demonstrations

Challenges and plans for tackling (BIM System)

RosBREED

What• All BIM System software modules combined in a

single connected system for conducting MAB

To whom• Breeders & allied scientists

Year 4 Deliverables (BIM System)

Impact intended• Streamlined MAB Pipelining to choose, validate, and

quantify utility of Jewels for integration into routine breeding operations

RosBREED

What• BIM System use training: tutorials, web-based

instruction, and in-person training provided

To whom• Breeders & allied scientists

Year 4 Deliverables (BIM System)

Impact intended• Breeders and their supporting scientists are able to

use the BIM System to enable the breeding use of DNA information

RosBREED

• Find “shiny rocks”, polish them into Jewels

Goal (Demonstration Breeding Programs)

RosBREED

Jewel

Mining Co

• Use Jewels to make breeding programs more efficient

What• Phenotypic data for apple, peach, cherry, strawberry

reference germplasm from 2010 - 2012quality-checked and archived

To whom• BIM System Team (for databasing)• PBA Team & back to Breeding Team

Year 3 Deliverables

Impact• Ability to discover

and validate Jewels in breeding germplasm

Phenotypic Data from 2010 - 2012 Seasons>587,000 phenotypic observations

Crop No. Locations

No. Traits No. Observations

Strawberry 5 35 190,000Peach 4 25 94,000Apple 3 135 251,000Sweet Cherry 1 23 34,000Tart Cherry 1 35 18,000

What• New trait loci (shiny rocks) discovered for apple,

peach, and cherry by using PBA software, with genome-scan and multi-year phenotypic data on breeding-representative germplasm

To whom• MAB Pipeline Team and breeders

Year 3 Deliverables

RosBREED

Impact• New trait loci discovered, available for “polishing”

in the MAB Pipeline

What• Genetic data from DNA markers for three strawberry

Jewels was used to verify & correct parentage in the RosBREED strawberry germplasm

To whom• Strawberry breeders

Year 3 Deliverables

RosBREED

Impact• Correct parentage information, when combined with

genetic and phenotypic data, will enable the validation of jewels in U.S. strawberry germplasm

Challenges and plans for tackling

RosBREED

Confounded germplasm and locations effects in apple and peach Develop relationship matrices to correct for location

Finding reliable commercial labs to routinely run markers in timely fashion for breeders Test other labs to find timely,

accurate and cost-effective options

What• Location and genotype x location effects estimated for

traits phenotyped in strawberry reference set (n=960)To whom

• Strawberry breeders

Year 4 Deliverables

RosBREED

Impact• Location bias removed for more precise estimation of

Jewel effects • Strawberry breeders can identify elite germplasm for

their individual programs that will perform well in their target regions

What• Work with Genotyping Team to test DNA diagnostics

commercial vendors – plant materials chosen, sent and results reviewed

To whom• Demonstration breeders and Genotyping Team

Year 4 Deliverables

Impact intended• Reliable, accurate, timely, cost-effective DNA

diagnostic options identified

RosBREED

Computer Demonstrations

Eric van de Weg Pedigree-Based

Analysis software

Dorrie Main BIM System

Cholani WeebaddeJewels in the Genome in eXtension