THE ROSACEAE FAMILYTHE ROSACEAE FAMILYOF HORTICULTURAL CROPSOF HORTICULTURAL CROPS

STONE FRUIT

POME FRUIT

BERRIES (some)

rose

GENOMICS IN ROSACEAEGENOMICS IN ROSACEAE

Genomics Resources

Genomics Research

Whole genome seqs

Genetic maps

Marker systems

Expressed gene libraries

DNA fragment libraries

Transformation systems

Stats & programs

Databases

Structural Genomics

Comparative Genomics

Functional Genomics

….identify loci controlling horticultural traits

Benefits not yet delivered

HOW MUCH IS BEING APPLIED?HOW MUCH IS BEING APPLIED?

(USA)

Total: 117 317 58 11 6 3

OPPORTUNITIES

AVAILABLE OPPORTUNITIES

EXPLOITED

THE CHASMTHE CHASMMARKER-ASSISTED BREEDINGMARKER-ASSISTED BREEDING

Genomics Resources

It’s quite simple, isn’t it?

More efficient development of new cultivars

In reality, there is no connection

MAB routine

use

Marker-trait associations

D

If we look closer at the translation of research to application, we discover…

THE CHASMTHE CHASM

Marker-trait associations

MAB routine

use

Trait low priority

Different germplasm

Unknown functional alleles

Weak linkage

Unknown genetic action

Unknown environ. effects

Unknown linkage drag

No local genotyping

Not cost efficient

No training in routine MASS

Some reasons the chasm exists

BRIDGING THE CHASMBRIDGING THE CHASM

Marker-trait associations

MAB routine

use

RosEXEC: U.S. Rosaceae Genomics, Genetics, &

Breeding Executive Committee

BRIDGING THE CHASMBRIDGING THE CHASM

The Rosaceae Specialty Crops Planning Workshop (22-23 June 2007)

Requires lots of:

IDEAS

PLANNING

STAKEHOLDER BUY-IN

COMMUNITY PROPOSAL #1COMMUNITY PROPOSAL #1

Marker-trait associations

MAB routine

use

Submitted Feb 2008 to USDA-CSREES National Research Initiative

Targeted traits specified but diverse (highest priority for each crop)

9 breeding programsMany research programs,

industry & international partners

PI: BERT ABBOTT (CLEMSON UNIV)

$5.0 mil

COMMUNITY PROPOSAL #1COMMUNITY PROPOSAL #1

Marker-trait associations

MAB routine

use

Education - undergrad & grad

Pedigree-Based Analysis

Phenotyping, Genotyping

Subfamily teams on high-priority traits, “ready-to-use breeders’ toolkits”

Outreach platform

Webportal & database (GDR)REVIEW: No detail on “breeders’ toolkits”

COMMUNITY PROPOSAL #2COMMUNITY PROPOSAL #2

Marker-trait associations

MAB routine

use

Submitted Aug 2008 to USDA-CSREES Specialty Crops Research Initiative

“Trait neutral” – highest priority traits to be decided for each crop

PI: AMY IEZZONI (MICHIGAN STATE UNIV)

17 breeding programsMany research programs,

industry & international partners

$6.0 mil + equal matching

COMMUNITY PROPOSAL #2COMMUNITY PROPOSAL #2

Marker-trait associations

MAB routine

use

Education - breeding trainees

Outreach platform

Pedigree-Based Analysis

Phenotyping, Genotyping

Webportal & database (GDR)

Explicit focus on MAB pipeline components

REVIEW: Outreach not enough to convince

breeders to change operations.

Expensive!

COMMUNITY PROPOSAL #3COMMUNITY PROPOSAL #3

Marker-trait associations

MAB routine

use

Submitted Apr 2009 to USDA-CSREES Specialty Crops Research Initiative

Fruit quality as common high priority “trait” for demonstration

PI: AMY IEZZONI (MICHIGAN STATE UNIV)

12 core breeding programsTech transfer to rest

Many research programs, industry & international partners

$7.2 mil + equal matching

COMMUNITY PROPOSAL #3COMMUNITY PROPOSAL #3

Marker-trait associations

MAB routine

use

Education - breeding trainees

Outreach platform

Pedigree-Based Analysis

Phenotyping, Genotyping

Webportal & database (GDR)

8-stage MAB Pipeline infrastructure & implementation

SNP genome scans

Socio-economics

“Recommended

for funding”

RosBREED OBJECTIVESRosBREED OBJECTIVES

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

2) Establish sustainable infrastructure for MAB in Rosaceae– MAB Pipeline components

3) Integrate breeding and genomics information- breeding information management system (incl. PBA)

4) Conduct MAB in core breeding programs, fruit quality– MAB Pipeline implementation

5) Enhance sustainability of cultivar development– MAB tech transfer, engage other stakeholders

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 Leader

Jim Luby

AppleSusan BrownKate EvansJim Luby

StrawberryJim HancockChad FinnTom Davis

PeachJohn ClarkDave ByrneKsenija GasicTom Gradziel

CherryNnadozie OraguzieAmy Iezzoni

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

Project DirectorAmy Iezzoni

RosBREED MANAGEMENTRosBREED MANAGEMENT

WSU

U Minn

Cornell U

UC Davis

Clemson U

U Arkansas

Texas A&M

MSU

UNHUSDA-ARS

Corvallis

WSU MSU

RosaceaeRosaceae

RosBREED RosBREED CORE BREEDING PROGRAMSCORE BREEDING PROGRAMS

RosBREED OVERVIEWRosBREED OVERVIEW

TRAIT & MARKET CLASS BREEDING TARGET ESTABLISHMENT

GENOME SCANS & COMPARATIVE GENOMICS

PEDIGREE-BASED BREEDING INFORMATION MANAGEMENT SYSTEM

Available M-T Associations Warehouse

Selection Target

Identifier

Genome Database

Resources

Crop Reference & Breeding Pedigree

Germplasm Databases

Cross Planning

Tool

Technology Portfolio

Seedling Selection Efficiency

Tool

MAB Routine

Use

MASS Trial Use

MASS Cost Efficiency & Logistics

MAPS Decisions

UtilityValidationImproved Markers

Genetic Screening Efficiency

Prioritization

Available M-T

Associations

TRAIT & MARKET CLASS BREEDING TARGET ESTABLISHMENT

GENOME SCANS & COMPARATIVE GENOMICS

PEDIGREE-BASED BREEDING INFORMATION MANAGEMENT SYSTEM

Available M-T Associations Warehouse

Selection Target

Identifier

Genome Database

Resources

Crop Reference & Breeding Pedigree

Germplasm Databases

Cross Planning

Tool

Technology Portfolio

Seedling Selection Efficiency

Tool

RosBREED ACTIVITIESRosBREED ACTIVITIES

MAB Routine

Use

MASS Trial Use

MASS Cost Efficiency & Logistics

MAPS Decisions

UtilityValidationImproved Markers

Genetic Screening Efficiency

Prioritization

Available M-T

Associations

SOCIO-ECONOMICS• Surveys, interviews, and auctions to determine trait

economic weights• Compare to more subjective traditional trait rankings

Economically weighted and objectively defined selection targets for breeding and research

Development

• Existing and de novo SNPs, gene-based• SNP Detection Panels (at least 7-10 indiv per crop)• Focus on fruit quality and family-wide genes• Physical mapping (using whole genome sequences)• Genetic mapping (bin-mapping to ~2 cM intervals)

Choose genome-wide SNPs for at least one segregating gene-based marker per 5 cM for any random cross

GENOME SCANSScans

• SNP Platform Summit (early 2010) to decide best approach•Genome scan each crop

• Crop Reference Set for each crop (n=480)• Breeding Pedigree Set for each breeding program

SNP genotypic data publicly available Integrated with phenotypic & pedigree data

using Pedigree-Based Analysis

GENOME SCANS

• SNP-tagged genes will often be common across crops

• Much opportunity for comparative genomics:

• Chromosome alignment across crops

• Many individuals available for comparisons

• Focus on specific genes and genomic regions

Functional connections among Rosaceae crops and researchers created and enhanced

COMPARATIVE GENOMICS

BIMS• Stats programs, databases, and decision-support tools with

seamless interfacing• Includes PBA (PRI team – needs assessment, training,

support)• Stepwise introduction of BIMS to breeders

Streamlined collection, archiving, conducting, andinterpreting integrated breeding & genomics data

MAB PIPELINE IMPLEMENTATION• Put the 8-stage MAB Pipeline into practice• Demonstrate MAB with high-impact targets• Achieve routine MAB by core breeding programs• Technology transfer to all interested U.S. Rosaceae breeders

Routine marker-assisted breeding for U.S. Rosaceae

RosBREED ACTIVITIESRosBREED ACTIVITIES

EXTENSION PLATFORM

TRAIT & MARKET CLASS BREEDING TARGET ESTABLISHMENT

GENOME SCANS & COMPARATIVE GENOMICS

PEDIGREE-BASED BREEDING INFORMATION MANAGEMENT SYSTEM

Available M-T Associations Warehouse

Selection Target

Identifier

Genome Database

Resources

Crop Reference & Breeding Pedigree

Germplasm Databases

Cross Planning

Tool

Technology Portfolio

Seedling Selection Efficiency

Tool

MAB Routine

Use

MASS Trial Use

MASS Cost Efficiency & Logistics

MAPS Decisions

UtilityValidationImproved Markers

Genetic Screening Efficiency

Prioritization

Available M-T

Associations

EXTENSION• Participatory workshops, Regional workshops, and annual meetings• Breeding trainee mentoring – a unique educational experience• Platforms: eXtension PBG Community of Practice, PBGworks to

create a Community of Interest

Engage, educate, and train stakeholders on socio-economics and genomics research & application

Routine marker-assisted breeding enabled for U.S. Rosaceae crops

(not just hoped for)

Action

Vision

Coordination

Funding