MSUAmy Iezzoni (PD)

Jim HancockDechun Wang

Cholani Weebadde

WSUCameron Peace

Dorrie MainKate Evans

Karina Gallardo Raymond Jussaume

Vicki McCracken Nnadozie Oraguzie

Mykel Taylor

CornellSusan BrownKenong Xu

Clemson Ksenija Gasic

Gregory Reighard

Texas A&MDave Byrne

Univ. of CA-DavisTom Gradziel

Carlos Crisosto 

Univ. of New Hamp.Tom Davis

Univ. of MinnesotaJim Luby

Chengyan Yue

Oregon State Univ.Alexandra Stone

Plant Research Intl, Netherlands

Eric van de WegMarco Bink

USDA-ARSNahla Bassil

Gennaro FazioChad Finn

Univ. of ArkansasJohn Clark

Outline of Presentation

RosBREED

The RosBREED Project

The Need for RosBREED

Objectives and Major Activities

Advances in Enabling MAB

The RosBREED

Project

RosBREED

• PI: Amy Iezzoni, MICHIGAN STATE UNIVERSITY

• 4 years, SEP 2009 – AUG 2013

• Funded by SCRI (USDA-NIFA’s Specialty Crop Research Initiative)

• $14.4 M ($7.2 M SCRI, $7.2 M in-kind Partners)

The RosBREED Project

RosBREED

• U.S.-wide and international collaboration

• 10 Teams

• 32 members of 3 Advisory Panels (STAKEHOLDER, EXTENSION, SCIENTIFIC)

The RosBREED Project

SOCIO-ECONOMICS

INDUSTRY

BREEDING

PEDIGREE-BASED ANALYSIS

ADMINISTRATION

BREEDERS’ TOOLBOX

GENOMICS

GENOTYPING

MAB PIPELINEEXTENSION

• Centered on breeders & breeding programsThe RosBREED Project

Project Director,Amy Iezzoni

-breeder (tart cherry)-geneticist-genomicist-leader

RosBREED

Integration of modern genomics tools with traditional breeding approaches will transform crop improvement in Rosaceae, significantly improving profitability and sustainability of U.S. rosaceous crop industries and contributing to increased consumption and enjoyment of these fruit, nut, and floral products.

The RosBREED Project

Vision

SELECTION TARGETS

SELECTION STRATEGIES

Objectively define

Optimize

DNA information

Socio-economics information

RosBREED

The RosBREED Approach

The Need for RosBREED

The Chasm

Bridging the Chasm

Genome scan

capability

Public

reference

germ

plasm

sets

New QTLs

Comprehensive fru

it

phenotyp

ic database

PBA training

MAB

Pipelin

e

Objectives & Major

Activities

RosBREED

1) Enhance new cultivar adoption, enlarge market potential, increase consumption– socio-economics knowledge of trait values

2) Establish sustainable infrastructure for MAB in Rosaceae– genome scanning capability, new QTLs (“jewels”)

3) Integrate socio-econ and genomics resources into breeding– breeding information management system

4) Conduct MAB in demo breeding programs, fruit quality focus– MAB implementation

5) Enhance sustainability of cultivar development– MAB tech transfer to breeders & engage other stakeholders

Project Objectives

TRAIT & MARKET SEGMENT BREEDING TARGET ESTABLISHMENT

GENOME SCANS

GENOME RESOURCES INTERFACE

New QTLs discovered

PBA: crop-wide

PBA: breeding program

Breeding markersScr

eenin

g

serv

ices

Mar

ker

prior

ities

Cross

ing

sche

me

Trial

MASSBREEDERS’

TOOLBOX DEVELOPMENT

Socio-economics

information

DNA information

Efficient routine breeding operations

Better fruit!

MA

B P

IPE

LIN

ING

MA

B P

IPE

LIN

ING

Overview of Activities

Seedli

ng

selec

tion

sche

me

REFERENCE GERMPLASM CHOICE

STANDARDIZED PHENOTYPING

Advances in Enabling

MAB

RosBREEDSocio-Economics Team

will determine trait values

Breeder survey 2010

Producer survey Fall 2011-

Winter 2012

Market Intermediary survey Fall 2010-

Winter 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

0 5 10 15 20 0 5 10 15 20 25

Challenges faced when determining priorities

RosBREED

Cumulative of mean 1-10 score Cumulative of mean 1-10 score

Technical challenges Socio-economic challenges

RosBREED

Phenotype Databasesfor Valuable Fruit Traits of Reference Germplasm

• Reference Germplasm SetsPublic: 480 individuals

• Standardized Phenotyping at multiple locations (www.rosbreed.org)

• Data collected 2010 & 2011

• Available at Genome Database for Rosaceae (www.rosaceae.org/resources/fruit-evaluation)

Now playing: Apple

Coming soon: Peach, Cherry, Strawberry

1

2

3

4

5

RosBREED

Pedimap

for visualizing pedigrees (with IBD, alleles, traits)

FlexQTLTM

for discovering QTLsRallsJan Delicious Winesap RomBeauty Jonathan M_PRI668-100 GoldenDel F2_26829-2-2

Fuji Crandall PRI14-126

PRI668-100

X-2771

X-3143

X-3318

Fruit firmness in apple

Pedigree-Based Analysis Team

Flow of a specific linkage block

RosBREED

Pedigree-Based Analysis Team

Software training

RosBREED

Genomics

Genotype obtained for screened sweet cherry germplasm

SNP failed

Illumina Infinium® arrays:

Peach: 9K Apple: 8K Cherry: 6K

“SNP chip”

SNP genotyping

Cherry array success

Example use:

peach mapping

Peach & Cherry

genome scan strategy

Apple genome scan

strategy

RosBREED

GenotypingHigh quality DNA extraction 3 x 1000 samples

PCR for SSRS(QTL-flanking & CG)

Genotype calling- SSRs

- 9K, 8K, 6K SNP genome scans

RosBREED

MAB Pipeline

RosBREED

MAB Pipeline“Fast-tracked

pipelining” of available

jewels

Tables of functional genotypes

Peach fruit texture type

Apple fruit storability

RosBREED

MAB Pipeline

“How To” diagrams

Breeders’ Toolbox Modules

* * **

* **

“Technology Portfolio”

“Selection Target Identifier”

“Genome Database Resources”

“Crop Reference & Breeding Pedigree Germplasm Databases”

“Cross Assist”

“Seedling Select”

“Marker-Locus-Trait Association Warehouse” *

RosBREED

Breeders’ Toolbox

Step 1. Specify data source

Step 2. Select up to 5 target traits

Step 3. Enter trait weights, heritabilities, and max. co-parentage, or use defaults, or Calculate from data

Step 4. Click Generate Parents List

(prototype)

Identifies efficient crossing schemes by mobilizing all available data

Cross Assist

Our outreach is all about staying connected with our stakeholders and project participants

Various ways:

Website www.rosbreed.org

Quarterly Newsletters

Presentations at professional meetings

Community Breeders Page

RosBREED

Extension

!!

!!

RosBREED

Extension: Coming soon…Participation in grower meetings near you! (2011-2012)

TITLE: Tell us what you want! Quantifying your priorities for new cultivars

Visits to U.S. Rosaceae breeding programs (2011-2012)- to enable MAB, share successful approaches

RosBREED Participatory Workshop (30 July 2012) - just a day prior to ASHS 2012 in Miami, Florida

!

!

!

RosBREED

Evaluation of Outreach

Surveys and interviews to:- Gather project feedback- Monitor changes in Rosaceae breeding programs

Acknowledgements

This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture

3 posters

Peach #144Apple #145

Cherry #146

RosBREED MAB postersTues 1:15-2:00, Kona Ballroom