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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