Amy Iezzoni James Luby Chengyan Yue Doreen Main Gennaro Fazio Eric van de Weg Nahla Bassil Cholani Weebadde James McFerson Cameron Peace Dept Horticulture, Michigan State University Dept Horticultural Science, Univ. Minnesota Dept Applied Economics, Univ. Minnesota Dept Horticulture & LA, Washington State Univ. Pullman USDA-ARS Cornell Univ. Geneva Plant Research International, Netherlands USDA-ARS NCGR, Corvallis Dept Horticulture, Michigan State University Washington Tree Fruit Research Commission Dept Horticulture & LA, Washington State Univ. Pullman

THE ROSACEAE FAMILY OF HORTICULTURAL CROPS STONE FRUIT POME FRUIT BERRIES (some) rose

GENOMICS 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? (USA) Total: OPPORTUNITIES AVAILABLE OPPORTUNITIES EXPLOITED

THE CHASM MARKER-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 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 CHASM Marker-trait associations MAB routine use

RosEXEC: U.S. Rosaceae Genomics, Genetics, & Breeding Executive Committee BRIDGING THE CHASM The Rosaceae Specialty Crops Planning Workshop (22-23 June 2007) Requires lots of: IDEAS PLANNING STAKEHOLDER BUY-IN

COMMUNITY 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 programs Many research programs, industry & international partners PI: B ERT A BBOTT ( CLEMSON UNIV ) $5.0 mil

COMMUNITY 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 #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: A MY I EZZONI ( MICHIGAN STATE UNIV ) 17 breeding programs Many research programs, industry & international partners $6.0 mil + equal matching

COMMUNITY 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 #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: A MY I EZZONI ( MICHIGAN STATE UNIV ) 12 core breeding programs Tech transfer to rest Many research programs, industry & international partners $7.2 mil + equal matching

COMMUNITY 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 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 Apple  Susan Brown  Kate Evans  Jim Luby Strawberry  Jim Hancock  Chad Finn  Tom Davis Peach  John Clark  Dave Byrne  Ksenija Gasic  Tom Gradziel Cherry  Nnadozie Oraguzie  Amy Iezzoni Executive Committee Cameron Peace Nahla Bassil Gennaro Fazio Jim Luby Dorrie Main Eric van de Weg Cholani Weebadde Chengyan Yue Project Director Amy Iezzoni RosBREED MANAGEMENT WSU U Minn Cornell U UC Davis Clemson U U Arkansas Texas A&M MSU UNH USDA-ARS Corvallis WSU MSU Rosaceae RosBREED CORE BREEDING PROGRAMS

RosBREED 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 UtilityValidation Improved 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 ACTIVITIES MAB Routine Use MASS Trial Use MASS Cost Efficiency & Logistics MAPS Decisions UtilityValidation Improved 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 SCANS Scans 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, and interpreting 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 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 UtilityValidation Improved 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