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

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

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

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

5. 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 Challenges, Plan for tackling

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

7. 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 Year 3 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)

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

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

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

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

13. 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 Year 2 Deliverables 5954 425476 Total 6855 polymorphic SNPs EUUS Evaluation of Peach 9K Chip

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

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

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

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

18. What Dissemination and comparison of results Scientific discussion tomorrow, Jan 13 th 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 Planned Year 3 Deliverables

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

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

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

22. What To whom Y2 Deliverables – PBA: new software Impact 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 Demonstration breeders & trainees, scientists Eased discovery of Jewels Eased qualification of their beauty & use −Characteristics of individual jewels −Contribution to the colier as a whole: coherence

23. What To whom Y2 Deliverables – PBA implementation Impact 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 Demonstration breeders and trainees, scientists Basic understanding on concepts project wide PhD students have started PBA analyses on RB data

24. 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 Challenges, Plans for Tackling, & Solving

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

26. 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 What is the Toolbox?

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

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

29. 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 Challenges and plans for tackling

30. DELIVERABLES TOOLBOX V 1.0 TOOLBOX V 1.0 demonstrated at RBIII TOOLBOX V 1.5 TOOLBOX V 1.5 demonstrated at ASHS meeting Planned Year 3 Deliverables 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. Breeders & Breeding Trainees assist in the finding and polishing of the Jewel in the Genome adopt Marker-Assisted Breeding for these Jewels Goal

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

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

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

35. 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 Planned Year 3 Deliverables Intended Impact New Jewels in the Genome….

36. Computer Demonstrations Gennaro Fazio Toolbox Eric van de Weg PBA Software Umesh Rosyara PBA Software Dorrie Main GBrowse Cholani Weebadde Videos