MSU

Amy Iezzoni (PD)Jim Hancock

Dechun WangCholani 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

Resource Development

MAB Enablement

International Context

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)

• Collaboration U.S.-wide and international

The RosBREED Project

• Centered on breeders & breeding programsThe RosBREED Project

Project Director,Amy Iezzoni

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

We will create a dynamic, sustained program in research, infrastructure establishment, training, and outreach for developing and applying marker-assisted breeding based on improved knowledge of industry value and consumer preferences to accelerate and increase the efficiency of rosaceous cultivar release and successful cultivar adoption.

RosBREED

The RosBREED Project

Mission

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= pedigree-based breeding information management system

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

5) Enhance sustainability of cultivar development= tech transfer to more breeders & engage other stakeholders

RosBREED’s Objectives

QTL discovery(looks promising...)

MAB Pipelining(polishing...)

Breeding(assembling into masterpieces)

RosBREED

“Jewels in the Genome”- discovering, polishing, applying

Project Assistant

Extension Team Leader: Cholani Weebadde

Genomics Team Leader: Dorrie Main

Genotyping Team Leader: Nahla Bassil

BIMS Team Leader: Gennaro Fazio

Socio- Economics Team

Leader: Chengyan Yue

MAB Pipeline Team Leader

Cameron Peace

Pedigree- Based Analysis Team Leader: Eric van de Weg

Breeding Team LeaderJim Luby

Apple· Jim Luby· Susan Brown· Kate Evans

Strawberry· Chad Finn· Jim Hancock· Tom Davis

Peach· Ksenija Gasic· John Clark· Dave Byrne· Tom Gradziel

Cherry· Amy Iezzoni· Nnadozie Oraguzie

Executive CommitteeCameron Peace Nahla BassilGennaro FazioJim Luby Dorrie MainJim McFersonEric van de WegCholani WeebaddeChengyan Yue

Project DirectorAmy Iezzoni

RosBREED’s Management

WSU

U Minn

Cornell U

UC Davis

Clemson U

U Arkansas

Texas A&M

MSU

UNHUSDA-ARS

Corvallis

WSU MSU

Rosaceae

Demonstration Breeding Programs

Demonstration Breeding Programs

RosBREED

Resource Development

RosBREEDTrait 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

RosBREEDAroma

PhytonutrientShape

TartnessJuiciness

SizeOther fruit quality attributes

Storage lifeDisease resistance

No storage disordersExternal appearance

Sugar/acid balanceSweetness/soluble solids

Shelf life at retailFruit firmnessExterior colorFruit crispness

Fruit flavor

0 20 40 60 80 100

2

2

27

9676

1543

33

5

13

335

2610

23

54

777

7

2341

Socio-Economics Surveys (example for apple)

Breeders Market Intermediaries

Michigan Producers

Washington Producers

% of respondents

MOST

important

traits

LEAST

important

traits

SNP Genome Scans

RosBREED

Illumina Infinium® II SNP arrays:developed 2010, used 2011

9K 8K

+1K

6K

Verde et al. 2012 PLoS One, accepted

Chagne et al. 2012 PLoS One 7(2):e31745

Peace et al. manuscript in prep.

SNP Genome Scans

RosBREED

9K 8K 6K

40-60 kb

intervals

sweet cherry

P. avium genome

sour cherry

SNP

SNP

SNP100-200 kb

intervals

SNP

SNP

SNP

SNPSNPSNP

SNPSNPSNP

SNP

Avg 446 kb/clusterAvg 72% SNPs polymorphicAvg 94% clusters polymorphicR

ES

ULT

SS

TRAT

EG

Y

P. fruticosa genome

Avg 27 kb/SNPAvg 84% SNPs

polymorphic

every 4th-5th detected SNP chosen, so spacing varies over genome

Avg 38 kb/SNPAvg SNPs polymorphic =

32% (sweet), 36% (sour)

RosBREED

McIntosh

LivelRasp

F_Spartan

Starr

Delicious

Cox

GoldenDel

RomBeauty

Mflor821

Jonathan

F_P21R4A30

Frostbite

NorthSpy

JerseyBla

F_Gingergold

F_JamesGr

Wealthy

F_IngMarie

Tetofsky

YelTransp

Longfield

DuchOlden

F_PattenGr

Edgewood

WorcPearm

RallsJan

Mavis

BenDavis

Gravenstein

Close

PRI643-11

Jongrimes

Wagener

FrancRus

LadyWill

BlushiGol

F_Undine

Indo

Malinda

Glockenapfel

DrOldenbu

F_Helios

F_EdGoulGol

F_Sandow

Lundbytrop

A28/39

A849-5

BeautBath

VKrakers

BelHerm

PRI2059-101

F_Brina

Scarlet

NJ381049

StarkEarl

Linda

X4598

X3174

AnanasRei

AutGold

BaumanRei

BernRos

Boskoop

BrixPlatt

Calamari

Calvilla

CrimsSnow

Croncels

DallaRosa

EarlyGold

Edelb

Fiamma

Freedom

GelEdel

Gewurz

Hampshire

HarbRei

Limoncini

Magre

MN1628

Napoleone

Ontario

PermainDor

RedFiled

RenCanada

RenChamp

Robusta5

RosBian

RosdiCal

RosDop

RotStett

SanLugano

Sila

Stayman

TavBian

TirSpitz

WeisW int

Melba

Spartan

OR38T610

KidsOrRed

Sonora

F1_9433-2-2

F1_9433-2-8

P21R4A30

Keepsake

M_MN1764

F_Honeycrisp

Melrose

Macoun

PRI54-12

GingerGold

JamesGr

NJ130o

IngMarie

NJ31

Monroe

Mantet

Oriole

Sharon

Fireside

PattenGr

F_Goodland

M_MolliesDel

NJ14

NJ19237

Crandall

NJ35437

CrownPR

Clivia

Splendour

Braeburn

Ambrosia

Cameo

Fuji

NJ35934

F_NJ15

Cortland

F_MolliesDel

PRI1469-100

Delcorf

Idared

Maigold

Akane

Sundowner

CrippsPink

Delblush

Undine

Orin

Shizuka

Toko

F_MN1764

Haralson

Telamon

M_Sunrise

PCF-3-120

Hatsuaki

Jonagold

M_NY632

Gloster

PRI69-52

Alkmene

Helios

Apollo

Empire

Akagi

EdGoulGol

PRI1956-6

Sandow

SchonNord

GranSmith

Delgollune

Dolgo

Angold

Ariwa

Discovery

Belgica

Rafzubin

GoldPink

Brina

Pop_GDxSc

Creston

Delearly

Ligol

Dalinette

Jolana

F_Williams

Gala

NJ67634

F2_26829-2-2

Prima

Honeycrisp

sibLiberty

Liberty

F_Delfloki

NJ117637

NJ12

Elstar

NY88

StateFair

Goodland

NJ440249

M2439

Lambourne

NJ15

NJ303955

MolliesDel

XIIA277

KAZ95-17-14

KAZ95-18-07

KAZ96-05-04

Pilot

Pinova

Senshu

PitmPine

MN1764

MN1702

Monark

Honeygold

Sunrise

Arlet

NY632

Fiesta

52-05-26

Zonga

Piros

Fortune

Shinsekai

GoldenOr

Summerfree

Sabina

WSU46

B_TxBB

Nicogreen

Delcoros

Snowsweet

Kerr

Williams

PRI14-126

PRI14-226

PRI14-644

Winesap

F_Ill_#2

NY65707-19

NJ123249

NJ27

Sonya

NY752

MN1691

NJ37848

PRI47-147

NJ88

Rubin

Vanda

Nicola

WSU2

Chinook

PacQueen

PacRose

AurGoldGa

BC-8S-27-2

BC-8S-31-56

BC-SPA493

NJ136055

Suncrisp

PRI2482-100

Zari

Bellida

Civni

Ecolette

Milwa

Kanzi

Nicoter

NZ_RGxBB

LaFlam

Nevson

Sansa

Scifresh

Scilate

WSU24

WSU37

GMAL4591

GMAL4593

GMAL4595

CIVG198

Dalitron

Ped-PinxCam

ShinGold

WSU34

25-120-9928

Pop_HCxCP

Ped-HCxPit(692)

Ped_HCx1764

MPop_HCx1702

MPop_HCxMon

Silken

Merlijn

NY75414-1

Tunda

WSU35

4-159-9926

Pop_ArlxCP

N_PxF

E_FxGD

E_FxGlo

Murray

NJ53

PRI612-1

Ill_#2

PRI668-100

NY913

PRI610-2

PRI855-102

NY241

Zestar

PCFW 2-134

PRI669-205

PRI1235-100

NJ109

Rubinola

Rubinstep

Rucla

Topaz

WSU17

WSU36

Pop_BBxPR

4-27-0019

5-87-0019

5-90-0019

6-73-0019

4A-100-0013

4A-38-0013

Pop_AurxHC

WSU22

WSU30

NJ90

NJ8

NJ110037

Florina

PRI1661-1

PRI1661-2

Coop-17

Grifer

Coop-15

Priscilla

Coop-10

Camuzat

Jonafree

Ped-SonxNY241

MN1914

Ped-HCxZest

CrimsCrisp

Saturn

NJ24

Julyred

Raritan

PRI1018-101

P7R25A27

Enterprise

Goldrush

Delfloki

Delorina

Pop_GaxC15

Santana

Pristine

Ped_HCxJonf

Jerseymac

Redfree

Ariane

WSU38

Ped-GoldrxNY913

Galmac

Reference Germplasm

CROP REFERENCE

SETn=480

BREEDING PEDIGREE SETS

Any breeder’s additional germplasm with data

RosBREED

Reference GermplasmMinnesota

BP Set(n=160)

Washington BP Set

(n=160)

New York BP Set(n=160)

CROP REFERENCE

SETn=480

RosBREED

Standardized Phenotyping• Reference Germplasm Sets

Public: 480 individualsAdditional: +480 individuals

• Standardized phenotypingat multiple locations,esp. for fruit quality (www.rosbreed.org)

• Evaluations 2010 & 2011(2012 next)

• Available at Genome Database for Rosaceae (www.rosaceae.org/breeders_toolbox)

FlexQTLTM

for QTLdiscovery, validation, characterization

RosBREED

RallsJan 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 (HiDRAS data)

Pedigree-Based Analysis

Flow of a specific linkage block

Pedimap for visualizing pedigrees

(with alleles, traits,Identity-By-Descent)

Jewel Discovery

SNPgenome scans

RosBREED

Standardized phenotypic data

Pedigree-Based Analysis

QTL discovery

MAB Enablement

PBA: crop-wide

PBA: breeding program

Breeding markersScre

ening

servi

ces

Marker

priori

ties

Crossin

g

sche

me

Trial

MASS

Socio-economics information

DNA information

Efficient, precise, creative breeding

Systematic QTL Validation– The MAB Pipeline

Seedli

ng

selec

tion

sche

mesupported by RosBREED’s in-developmentBreeding Information Management System

RosBREED

“Cross Assist”

“Seedling Select”

New

gen

erat

ions

enr

iche

d fo

r fav

orab

le a

llele

s

MAB Successes So Far

MAPS

MASS

marker-assisted parent selection

marker-assisted seedling selection

Two jewels polished in RosBREED, put to routine use in demo breeding

programs

RosBREED

“Cross Assist”

“Seedling Select”

MAB Successes So Far

RosBREED

Routine Use of QTLs in Breeding

allele 1 carriers

allele 2carriers

Use of QTLs: does not predict definitive differences, but enriches for favorable alleles. Brave breeders!

frequ

ency

trait level

Predicted to belarge-fruited (& self-

fertile)

Thousands of inferior seedlings culled- est. $180K saved!

Improved efficiency in seedling evaluationsince fall 2010 in RosBREED breeding programs

Routine MAB with QTLs

(WSU’s apple and sweet cherry breeding programs)

RosBREED

Tables of functional genotypes

(www.rosbreed.org/breeding/jewel-use)

peach fruit texture type

“How To” for Rosaceae Breeders

Example here is for

RosBREED

“How To” for Rosaceae Breeders

Peach fruit texture type

RosBREED

Apple fruit storability

“How To” for Rosaceae Breeders

RosBREED

Cherry fruit size

“How To” for Rosaceae Breeders

RosBREED: Filling the Treasure Chest for Rosaceae Breeders

International Context

RosBREED

The International Rosaceae Genomics, Genetics, & Breeding Community

Plant Research International, NetherlandsEast Malling Research, UKCRA-FRU, Rome, ItalyIASMA, Trento, ItalyINRA (Bordeaux, Avignon, Angers), France

Andres Bello University, Chile Plant & Food Research, New Zealand

ARC, South Africa

RosBREED participant

location

Critical International Partnerships

+ 2 Scientific Advisory Panel members (Spain, New Zealand)

Future Funding...

-crops?-traits?-approaches?-resources?-partners?

RosBREED

We are seeking funding beyond Aug 2013

Proposalsubmission= Jan 2013

Must be newobjectives

Ideas are coalescing now

Acknowledgements

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

Questions?

www.rosbreed.org