OBJ. 1 TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT

1. OBJ. 1 TRAIT AND MARKET SEGMENT BREEDING TARGET ESTABLISHMENT Year 3 Deliverables, Challenges,Year 4 Goals

2. 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 trait loci for the development of DNA diagnostic tools 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 3 Deliverables • What • Grower and market intermediary survey data – relative values of fruit quality and production traits were obtained • To whom • U.S. Rosaceae industry & breeders • Impact • Trait values obtained are being used to prioritize traits for development of DNA diagnostic tools RosBREED

5. Year 3 Deliverables • What • Consumer’s preferences and values for targeted fruit quality attributes – elicited • To whom • U.S. Rosaceae industry & breeders • Impact • Trait values obtained will be used by breeders to assign trait priorities; industry sectors have knowledge of relative consumer values RosBREED

6. Challenges and plans for tackling • Elements in the choice experiment scenarios not absolutely clear (e.g. individual interpretations of flavor and sweetness) use a consensus approach to interpret the data • Logistical challenges in providing apple samples that met criteria for the consumer auction experiment help from the WTFRC(demonstration after lunch!)

7. Year 4 Deliverables • What • Trait priorities for market intermediaries, growers, and consumers of apples - analyzed, interpreted, and communicated • To whom • MAB Team and Rosaceae community Impact intended • DNA diagnostic tools will be developed for the most valuable fruit target trait loci, thereby increasing breeding efficiency for high priority traits

8. Year 4 Deliverables Impact intended • Awareness of marker-assisted breeding by industry sectors will be increased through their participation in this prioritization process and from disseminated summaries • Breeder’s knowledge of trait priorities, along with availability of DNA diagnostic tools, will result in increased likelihood of cultivar release, adoption, enlarged market potential and increased consumption.

9. OBJ. 2 GENOME SCANS AND COMPARATIVE GENOMICS Year 3 Deliverables, Challenges, Year 4 Goals

10. Goal • Genome-wide genotyping platforms for apple, peach, cherry, and strawberry – develop and utilize • Comparative genomics to accelerate identification and validation of Jewels in the Genome

11. Year 3 Deliverables What • Genome-scanning SNP arrays developed and utilized for apple (9K), peach (9K) and cherry (6K) by international RosBREED-led efforts

12. Year 3 Deliverables • To whom • Rosaceae scientific community • Impact • These cost effective commercially available genome scan platforms are not only enabling RosBREED outcomes, but they are and will continue to enable the generation of new knowledge by the international Rosaceae community RosBREED

13. Year 3 Deliverables • What • Genome-wide genetic data obtained for plant material (peach, cherry, and apple completed) • To whom • Rosaceae scientific community • Impact • Analysis of this dataset, combined with pedigree and phenotypic datasets is enabling the identification and validation of Jewels for use in breeding RosBREED

14. Year 3 Deliverables • What • Strawberry genome scan strategy (Affymetrix 90K Axiom® chip) developed by a RosBREED-led international consortium (W309, PAG XXI) • To whom • RosBREED Strawberry Team • Impact • Genotypic data obtained will enable discovery of new trait loci and their validation for conversion into jewels for use in breeding

15. Challenges and plans for tackling • Ensure accessibility of Genomics, Genetics, and Breeding Data – database infrastructure and capacity • Develop a flexible modular structure, submit short read sequences to NCBI • Suitability of the SNP genotyping algorithm to analyze the strawberry SNP array • a two-phase strategy is in place to permit initial testing of the array using the genotyping algorithm

16. Year 4 Deliverables • What • Strawberry 90K Axiom® SNP chip evaluated and utilized to genotype strawberry breeding materials – goal is a minimum of 4000 robust SNP markers • To whom • International strawberry research community • Impact intended • Genome-scan capability for octoploid strawberry enables Jewel discovery RosBREED

17. Year 4 Deliverables • What • Dissemination of genomics, genetic, and breeding data through GDR • To whom • Rosaceae research community • Impact intended • Efficient sustained access to genetics, genomics, and breeding data will enable the use of this knowledge for practical applications and for future discoveries

18. OBJ. 3 PEDIGREE-BASEDBREEDING INFORMATION MANAGEMENT SYSTEM Year 3 Deliverables, Challenges, Year 4 Goals

19. Goal Develop, deliver, and implement software that leverages genomics and phenotypic trait information to maximize breeding efficiency • Involves: • Software teams (Pedigree-Based Analysis [PBA],Breeding Information Management System [BIM System])and all crop breeding teams that provide, collect,and use the data for finding and validating QTLs RosBREED

20. Year 3 Deliverables (PBA) 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 of trait loci, validation of associated markers + Role in the bracelet impact & coherence Impact Jewels available for breeding Information required Pedigree + Genotypic + Phenotypic

21. Year 3 Deliverables (PBA) What • Improved user-friendliness • 10-fold reduction of computation time for massive data sets • New functionality: building SNP haplotype blocks • Software to build integrated genetic maps across multiple mapping populations To whom • Demonstration breeders & trainees, allied scientists Impact • Eased discovery of trait loci • Eased quantification of allele effects

22. Year 3 Deliverables (PBA) What • Familiarity with software & concepts • Training through a 2.5 day workshop • Individual consulting with MSU-based postdoc To whom • Demonstration breeders and trainees, allied scientists Impact • Basic understanding on concepts project-wide • Students are conducting PBA analyses on RB data

23. Challenges and plans for tackling (PBA) • PBA software development • Ease of access to FlexQTL output • Generation of a user-friendly interface • PBA use by breeders – consulting • Awareness of need for scrutinizing pedigree and marker data prior to in-depth QTL characterization • Finalize analyses and interpretation into application-ready deliverables • 2-day workshop (May 2013), online meetings, one-on-one RosBREED

24. Year 4 Deliverables (PBA) What • New software modules and functionalities • Training, consultations To whom • Demonstration breeders & • trainees, allied scientists Impact intended • PBA software better adjusted to massive data sets • PBA-experienced trainees & breeders • Scrutinized pedigree & marker datasets • Discovery of new trait loci and polishing of new jewels

25. Year 3 Deliverables (BIM System) 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

26. Year 3 Deliverables (BIM System) Impact What To • Demo Breeders and Trainees • Database and Capabilities: Delivered during RBIV and through program visits • Understand capability; ability to plan crosses with Cross Assist and other MAB applications Which parents have the jewels? Computer demo: BIM System Which combinations to create? Which seedlings have the jewels?

27. Challenges and plans for tackling (BIM System) • Diversity of Breeder’s own program needs and desires: assess capacities of BIM System 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 IV Annual Project Meeting, web tutorials, live demonstrations RosBREED

28. Year 4 Deliverables (BIM System) • What • All BIM System software modules combined in a single connected system for conducting MAB • To whom • Breeders & allied scientists • Impact intended • Streamlined MAB Pipelining to choose, validate, and quantify utility of Jewels for integration into routine breeding operations RosBREED

29. Year 4 Deliverables (BIM System) • What • BIM System use training: tutorials, web-based instruction, and in-person training provided • To whom • Breeders & allied scientists • Impact intended • Breeders and their supporting scientists are able to use the BIM System to enable the breeding use of DNA information RosBREED

30. Goal (Demonstration Breeding Programs) • Find “shiny rocks”, polish them into Jewels RosBREED Jewel Mining Co • Use Jewels to make breeding programs more efficient

31. Year 3 Deliverables • What • Phenotypic data for apple, peach, cherry, strawberry reference germplasm from 2010 - 2012quality-checked and archived • To whom • BIM System Team (for databasing) • PBA Team & back to Breeding Team • Impact • Ability to discover and validate Jewels in breeding germplasm

32. Year 3 Deliverables • What • New trait loci (shiny rocks) discovered for apple, peach, and cherry by using PBA software, with genome-scan and multi-year phenotypic data on breeding-representative germplasm • To whom • MAB Pipeline Team and breeders • Impact • New trait loci discovered, available for “polishing” in the MAB Pipeline RosBREED

33. Year 3 Deliverables • What • Genetic data from DNA markers for three strawberry Jewels was used to verify & correct parentage in the RosBREED strawberry germplasm • To whom • Strawberry breeders • Impact • Correct parentage information, when combined with genetic and phenotypic data, will enable the validation of jewels in U.S. strawberry germplasm RosBREED

34. Challenges and plans for tackling Confounded germplasm and locations effects in apple and peach  Develop relationship matrices to correct for location Finding reliable commercial labs to routinely run markers in timely fashion for breeders  Test other labs to find timely, accurate and cost-effective options RosBREED

35. Year 4 Deliverables • What • Location and genotype x location effects estimated for traits phenotyped in strawberry reference set (n=960) • To whom • Strawberry breeders • Impact • Location bias removed for more precise estimation of Jewel effects • Strawberry breeders can identify elite germplasm for their individual programs that will perform well in their target regions RosBREED

36. Year 4 Deliverables • What • Work with Genotyping Team to test DNA diagnostics commercial vendors – plant materials chosen, sent and results reviewed • To whom • Demonstration breeders and Genotyping Team • Impact intended • Reliable, accurate, timely, cost-effective DNA diagnostic options identified RosBREED

37. Computer Demonstrations Eric van de Weg Pedigree-Based Analysis software Dorrie Main BIM System CholaniWeebadde Jewels in the Genome in eXtension