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RosBREED

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

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RosBREED

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  1. 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 Amy Iezzoni James Luby Chengyan Yue Doreen Main Gennaro Fazio Eric van de Weg Nahla Bassil Cholani Weebadde James McFerson Cameron Peace RosBREED RosBREED Enabling marker-assisted breeding in Rosaceae

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

  3. 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

  4. OPPORTUNITIES AVAILABLE OPPORTUNITIES EXPLOITED HOW MUCH IS BEING APPLIED? (USA) Total: 117 317 58 11 6 3

  5. MARKER-ASSISTED BREEDING THE CHASM Marker-trait associations MAB routine use Breeding Genomics Programs Research In reality, there is no connection It’s quite simple, isn’t it? If we look closer at the translation of research to application, we discover… Genomics Resources More efficient development of new cultivars D

  6. MAB routine use THE CHASM Marker-trait associations Some reasons the chasm exists 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 Breeding Genomics Programs Research

  7. MAB routine use BRIDGING THE CHASM Marker-trait associations Breeding Genomics Programs Research

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

  9. MAB routine use COMMUNITY PROPOSAL #1 Submitted Feb 2008 to USDA-CSREES National Research Initiative Marker-trait associations RosCAP PI: BERT ABBOTT (CLEMSON UNIV) $5.0 mil Breeding Genomics Programs Research Targeted traits specified but diverse (highest priority for each crop) 9 breeding programs Many research programs, industry & international partners

  10. MAB routine use COMMUNITY PROPOSAL #1 Marker-trait associations RosCAP Subfamily teams on high-priority traits, “ready-to-use breeders’ toolkits” Breeding Genomics REVIEW: No detail on “breeders’ toolkits” Phenotyping, Genotyping Programs Research Webportal & database (GDR) Pedigree-Based Analysis Outreach platform Education - undergrad & grad

  11. MAB routine use COMMUNITY PROPOSAL #2 Submitted Aug 2008 to USDA-CSREES Specialty Crops Research Initiative Marker-trait associations RosBREED PI: AMY IEZZONI (MICHIGAN STATE UNIV) $6.0 mil + equal matching Breeding Genomics Programs Research “Trait neutral” – highest priority traits to be decided for each crop 17 breeding programs Many research programs, industry & international partners

  12. MAB routine use COMMUNITY PROPOSAL #2 Marker-trait associations RosBREED Explicit focus on MAB pipeline components Breeding Genomics Phenotyping, Genotyping Programs Research REVIEW: Outreach not enough to convince breeders to change operations. Expensive! Webportal & database (GDR) Pedigree-Based Analysis Outreach platform Education - breeding trainees

  13. MAB routine use COMMUNITY PROPOSAL #3 Submitted Apr 2009 to USDA-CSREES Specialty Crops Research Initiative Marker-trait associations RosBREED PI: AMY IEZZONI (MICHIGAN STATE UNIV) $7.2 mil + equal matching Breeding Genomics Programs Research Fruit quality as common high priority “trait” for demonstration 12 core breeding programs Tech transfer to rest Many research programs, industry & international partners

  14. MAB routine use COMMUNITY PROPOSAL #3 Marker-trait associations RosBREED 8-stage MAB Pipeline infrastructure & implementation “Recommended for funding” Breeding Genomics Phenotyping, Genotyping Programs Research Webportal & database (GDR) Pedigree-Based Analysis Outreach platform Education - breeding trainees SNP genome scans Socio-economics

  15. RosBREED OBJECTIVES • 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

  16. RosBREED CORE BREEDING PROGRAMS Clemson U WSU Texas A&M UC Davis U Minn U Arkansas Rosaceae Cornell U MSU WSU MSU USDA-ARS Corvallis UNH RosBREED MANAGEMENT • Executive Committee • Cameron Peace • Nahla Bassil • Gennaro Fazio • Jim Luby • Dorrie Main • Eric van de Weg • Cholani Weebadde • Chengyan Yue • Project Director • Amy Iezzoni • Project Assistant Genomics Team Leader: Dorrie Main Extension Team Leader: Cholani Weebadde Breeding Team Leader Jim Luby Genotyping Team Leader: Nahla Bassil • Apple • Susan Brown • Kate Evans • Jim Luby • Peach • John Clark • Dave Byrne • Ksenija Gasic • Tom Gradziel Socio- Economics Team Leader: Chengyan Yue • Strawberry • Jim Hancock • Chad Finn • Tom Davis Pedigree- Based Analysis Team Leader: Eric van de Weg • Cherry • Nnadozie Oraguzie • Amy Iezzoni MAB Pipeline Team Leader BIMS Team Leader: Gennaro Fazio Cameron Peace

  17. TRAIT & MARKET CLASS BREEDING TARGET ESTABLISHMENT Seedling Selection Efficiency Tool PEDIGREE-BASED BREEDING INFORMATION MANAGEMENT SYSTEM Genome Database Resources Available M-T Associations Warehouse Selection Target Identifier Crop Reference & Breeding Pedigree Germplasm Databases Cross Planning Tool Technology Portfolio RosBREED OVERVIEW GENOME SCANS & COMPARATIVE GENOMICS Available M-T Associations Genetic Screening Efficiency MAB Routine Use MASS Cost Efficiency & Logistics MAPS Decisions MASS Trial Use Improved Markers Prioritization Validation Utility

  18. TRAIT & MARKET CLASS BREEDING TARGET ESTABLISHMENT Seedling Selection Efficiency Tool PEDIGREE-BASED BREEDING INFORMATION MANAGEMENT SYSTEM Genome Database Resources Available M-T Associations Warehouse Selection Target Identifier Crop Reference & Breeding Pedigree Germplasm Databases Cross Planning Tool Technology Portfolio RosBREED ACTIVITIES MAB PIPELINE IMPLEMENTATION GENOME SCANS & COMPARATIVE GENOMICS • 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 GENOME SCANS GENOME SCANS SOCIO-ECONOMICS COMPARATIVE GENOMICS • 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 • 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 • 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 • 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 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 Available M-T Associations Genetic Screening Efficiency MAB Routine Use MASS Cost Efficiency & Logistics MAPS Decisions MASS Trial Use Improved Markers Prioritization Validation Utility

  19. TRAIT & MARKET CLASS BREEDING TARGET ESTABLISHMENT Seedling Selection Efficiency Tool PEDIGREE-BASED BREEDING INFORMATION MANAGEMENT SYSTEM Genome Database Resources Available M-T Associations Warehouse Selection Target Identifier Crop Reference & Breeding Pedigree Germplasm Databases Cross Planning Tool Technology Portfolio RosBREED ACTIVITIES GENOME SCANS & COMPARATIVE GENOMICS 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 Available M-T Associations Genetic Screening Efficiency MAB Routine Use MASS Cost Efficiency & Logistics MAPS Decisions MASS Trial Use Improved Markers Prioritization Validation Utility Extension Platform

  20.  Routine marker-assisted breeding enabled for U.S. Rosaceae crops (not just hoped for)

  21. RosBREED RosBREED Enabling marker-assisted breeding in Rosaceae Vision Coordination Funding Action

  22. RosBREED IS HERE!

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