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OBJ. 1 TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT

OBJ. 1 TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT Year 2 Deliverables, Challenges, Year 3 Goals. Socio-Economics Team Goal. Help accelerate and increase efficiency of cultivar development and adoption by identifying valuable breeding trait targets.

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OBJ. 1 TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT

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  1. OBJ. 1 TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT Year 2 Deliverables, Challenges,Year 3 Goals

  2. Socio-Economics Team Goal • Help accelerate and increase efficiency of cultivar development and adoption by identifying valuable breeding trait targets • Objectively identify important breeding trait targets • Prioritize the most valuable target traits for marker-assisted breeding development RosBREED

  3. We like firm tart cherries that pit well! What trait is my next breeding target? We like disease resistant apple trees! I like tasty strawberries! Processors Producer survey Fall 2011/ Winter 2012 Market Intermediary survey Spring 2011 Household data analysis 2010; consumer survey 2012 Breeder survey 2010 Trait Values RosBREED

  4. Year 2 • What • Grower Clicker Survey developed and given across U.S. (14) • To Whom • U.S. Rosaceae industry • Impact • Trait values will be known and will be used to prioritize traits for development of DNA diagnostics RosBREED

  5. Challenges, Plan for tackling • Motivate the crop producers to participate in the mail-in grower survey • Work with breeding and extension teams to deliver integrated information to industry by emphasizing utility of the integrated knowledge gained • Clicker surveys used to familiarize growers with forthcoming mail in grower survey and encourage their participation

  6. Year 3 • What • Surveys of trait priorities for breeders, market intermediaries and growers analyzed and interpreted • To whom • MAB Team and Rosaceae community Intended Impact • Knowledge of trait priorities and economic values for traits by breeders, market intermediaries and growers used to objectively define selection targets

  7. Year 3 • What • Survey of trait priorities for consumers of apples, peaches, cherries, and strawberries developed and disseminated • To whom • U.S. Rosaceae industries, U.S. Rosaceae genomics, genetics, and breeding community • Intended Impact • Knowledge of trait priorities and economic values for traits by consumers used to objectively define selection targets

  8. Summary • The search for Jewels in the Genome will be prioritized for identified high impact traits • How are we doing? Cross-check of available Jewels in the Genome with industry trait values (talk later today) RosBREED

  9. OBJ. 2 GENOME SCANS AND COMPARATIVE GENOMICS Year 2 Deliverables, Challenges, Year 3 Goals

  10. Year 2 Goals • Genome-wide genotyping platforms for apple, peach, cherry and strawberry – development & utilization • Comparative genomics to accelerate identification and validation of Jewels in the Genome

  11. Year 2 Deliverables • What • Infinium SNP arrays designed and commercially available (8K apple, 9K peach, and 6K cherry) • To whom • International Rosaceae scientific community • Impact • Research community has access to reasonably priced high-throughput genome scan technology RosBREED

  12. Year 2 Deliverables • What • Prior knowledge of Jewels was used to “populate” SNP arrays • Validated SNPs • RosCOS • Candidate genes

  13. Year 2 Deliverables • What • Genome-wide genetic data obtained for plant material (peach and cherry completed, apple ~90% completed) • Informativeness of genetic data assessed for the three crops EU US 5954 425 476 Total 6855 polymorphic SNPs Evaluation of Peach 9K Chip

  14. Year 2 Deliverables • What • Strawberry High-Throughput Platform Strategy • Re-sequencing bin population and identifying segregating SNPs • Synthetic octoploid pilot study (using peach) BB AA 2:6 1:7 1:5 1:3

  15. Year 2 Comparative Approaches • What • Peach reference genome used to choose cherry SNPs • RosCOS loci included for each crop Computer Demo: Peach Gbrowse & Toolbox

  16. Challenges, Plan for tackling • Genome-scan strategy for strawberry (octoploid) difficult • Robust flexible database infrastructure that suits diverse needs of genomics, genetics, and breeding communities 2011

  17. Planned Year 3 Deliverables • What • Dissemination and comparison of genotyping results • High-throughput genome scans of strawberry • Cross-species markers available on GDR • To whom • Rosaceae scientific community • Intended Impact • Genome-scan capability for octoploid strawberry and new Jewels in the Genome... RosBREED

  18. Planned Year 3 Deliverables • What • Dissemination and comparison of results • Scientific discussion tomorrow, Jan 13th • Two talks at PAG (Chagne et al. & Gasic et al.in Fruits/Nuts Workshop) • Three manuscripts: • - Apple – accepted • - Peach – very advanced stage of preparation • - Cherry – advanced stage of preparation RosBREED

  19. OBJ. 3 PEDIGREE-BASED BREEDING INFORMATION MANAGEMENT SYSTEM Year 2 Deliverables, Challenges, Year 3 Goals

  20. Goal Develop, deliver, and implement software that leverages genomics and phenotypic trait information to maximize breeding efficiency Who • Software teams (Pedigree-Based Analysis and Toolbox) and breeding teams that provide and collect the data used for analysis RosBREED

  21. Year 2 Deliverables – PBA software team What • New software capable of doing the full range of necessary statistical analysis to include identification and validation of marker-locus-trait associations To whom • Demonstration breeders and trainees Impact PBA Analyses Discovery Jewels markers for traits + Role in the bracelet impact & coherence Impact Jewels available for breeding Information Required Pedigree + Genotypic + Phenotypic

  22. Y2 Deliverables – PBA: new software What • Improved user friendliness • Ease data handling (align with GenomeStudio output) • Ease interpretation output • Reduction of computation time for massive data sets • New functionalities: Pipeline for filtering most robust markers To whom • Demonstration breeders & trainees, scientists Impact • Eased discovery of Jewels • Eased qualification of their beauty & use • Characteristics of individual jewels • Contribution to the colier as a whole: coherence

  23. Y2 Deliverables – PBA implementation What • Familiarity with software & way of thinking • Training through a 2½ day workshop; • Individual consulting with MSU-based post-doc • Bi-weekly conference calls on marker issues To whom • Demonstration breeders and trainees, scientists Impact • Basic understanding on concepts project wide • PhD students have started PBA analyses on RB data

  24. Challenges, Plans for Tackling, & Solving • PBA Software development • – Dealing with massive data sets of new marker type • Explore expertise of a wide range of colleagues • PBA implementation • – Transfer of experience in PBA analyses • workshops, conference calls, one-on-one support • PBA Use in breeding • – Integrate results in the various Breeders Tools • Regular conference calls among teams RosBREED

  25. Planned Year 3 Deliverables What • New software modules and functionalities • Trainings, consultations To whom • Demonstration breeders & • trainees, scientists Intended Impact • PBA software adjusted to massive data sets • PBA experienced trainees & breeders • Scrutinized marker & pedigree data sets • Discovery and polishing of new jewels

  26. What is the Toolbox? RosBREED and Affiliated Breeding Programs produce TRILLIONS of DATA POINTS! How do we facilitate the application of all this? The Toolbox: a user-friendly database and tools that leverage genomics information for maximum utility within the Marker-Assisted Breeding (MAB) Pipeline, including functions to aid breeding decision-making

  27. Year 2 Deliverables Impact What To • Templates for breeding databases compatible with PBA software: Developed Breeding Programs able to enter PBA information and own breeding data • Demo Breeders and Trainees Breeding Databases – parentage information, phenotypic data, performance at multiple locations, genetic data RosBREED

  28. Year 2 Deliverables Impact What To • Demo Breeders and Trainees • Database and Capabilities: Delivered during RBIII and through program visits • Understand capability; ability to plan crosses with Cross Assist and other MAB applications Which parents have the jewels? Computer Demo: Toolbox Which combinations to create? Which seedlings have the jewels?

  29. Challenges and plans for tackling • Diversity of Breeder’s own program needs and desires • Assess the capacities of Toolbox team to fulfill as many priorities as possible • Complexity, Enormity – Break into workable chunks and communicate through web and file sharing. • Gaining breeder’s understanding – Present at RosBREED III Annual Project Meeting, Web Tutorials, Live Demonstrations RosBREED

  30. Planned Year 3 Deliverables • DELIVERABLES • TOOLBOX V 1.0 • TOOLBOX V 1.0 demonstrated at RBIII • TOOLBOX V 1.5 • TOOLBOX V 1.5 demonstrated at ASHS meeting • INTENDED IMPACT • Plan crosses using Cross Assist based on PBA data and work through the MAB pipeline from discovered QTL to marker development, genotyping, validation, and utility assessment in own breeding program. • Understanding of TOOLBOX through demos and tutorials

  31. Goal • Breeders & Breeding Trainees • assist in the finding and polishing of the Jewel in the Genome • adopt Marker-Assisted Breeding for these Jewels

  32. Year 2 Deliverables • What • Pedigree-linked U.S. reference germplasm sets • Standardized phenotyping protocols • Year 2 • Updated germplasm sets and protocols, videos added RosBREED

  33. Year 2 Deliverables • What • Phenotypic data for apple, peach, cherry and strawberry germplasm sets collected and combined with prior data • By whom • Demonstration breeders and associates • Impact • Ability to discover and validate M-L-T associations in relevant germplasm RosBREED

  34. Challenges and plans for tackling • Transforming massive amounts of data to format usable for PBA • Divide tasks and provide assistance from PBA and genotyping teams RosBREED

  35. Planned Year 3 Deliverables • What • Phenotypic data for apple, peach, cherry and strawberry germplasm sets collected and combined with prior data and archived • Data analysis using software • By whom • Demonstration breeders, associates, and PBA and Toolbox Teams • Intended Impact • New Jewels in the Genome…. RosBREED

  36. Computer Demonstrations Gennaro Fazio Toolbox Eric van de Weg PBA Software Dorrie Main GBrowse UmeshRosyara PBA Software CholaniWeebadde Videos

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