1. MSU Amy Iezzoni (PD) Jim Hancock Dechun Wang Cholani Weebadde WSU Cameron Peace Dorrie Main Kate Evans Karina Gallardo Raymond Jussaume Vicki McCracken Nnadozie Oraguzie Mykel Taylor Cornell Susan Brown Kenong Xu Clemson Ksenija Gasic Gregory Reighard Texas A&M Dave Byrne Univ. of CA-Davis Tom Gradziel Carlos Crisosto Univ. of New Hamp. Tom Davis Univ. of Minnesota Jim Luby Chengyan Yue Oregon State Univ. Alexandra Stone Plant Research Intl, Netherlands Eric van de Weg Marco Bink USDA-ARS Nahla Bassil Gennaro Fazio Chad Finn Univ. of Arkansas John Clark

2. Outline of Presentation  The RosBREED Project  Resource Development  MAB Enablement  International Context

3. The RosBREED Project

4. PI: Amy Iezzoni, Michigan State University 4 years, Sep 2009 – Aug 2013 Funded by SCRI (USDA-NIFA’s Specialty Crop Research Initiative) $14.4 M ($7.2 M SCRI, $7.2 M in-kind Partners) Collaboration U.S.-wide and international The RosBREED Project

5. Centered on breeders & breeding programs The RosBREED Project Project Director, Amy Iezzoni -breeder (tart cherry) -geneticist -genomicist -leader

6. The RosBREED Project Mission

7. 1)Enhance new cultivar adoption, enlarge market potential, increase consumption = socio-economics knowledge of trait values 2) Establish sustainable infrastructure for MAB in Rosaceae = genome scanning capability, new QTLs (“jewels”) 3) Integrate socio-econ and genomics resources into breeding = pedigree-based breeding information management system 4) Conduct MAB in demo breeding programs, fruit quality focus = MAB implementation 5) Enhance sustainability of cultivar development = tech transfer to more breeders & engage other stakeholders RosBREED’s Objectives

8. QTL discovery (looks promising...) MAB Pipelining (polishing...) Breeding (assembling into masterpieces) “Jewels in the Genome” - discovering, polishing, applying

9. 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  Jim Luby  Susan Brown  Kate Evans Strawberry  Chad Finn  Jim Hancock  Tom Davis Peach  Ksenija Gasic  John Clark  Dave Byrne  Tom Gradziel Cherry  Amy Iezzoni  Nnadozie Oraguzie Executive Committee Cameron Peace Nahla Bassil Gennaro Fazio Jim Luby Dorrie Main Jim McFerson Eric van de Weg Cholani Weebadde Chengyan Yue Project Director Amy Iezzoni RosBREED’s Management

10. WSU U Minn Cornell U UC Davis Clemson U U Arkansas Texas A&M MSU UNH USDA-ARS Corvallis WSU MSU Rosaceae Demonstration Breeding Programs

12. Resource Development

13. Trait Values Breeder survey 2010 Producer survey Fall 2011- Winter 2012 Market Intermediary survey Fall 2010- Winter 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

14. Socio-Economics Surveys (example for apple) Breeders Market Intermediaries Michigan Producers Washington Producers % of respondents  MOST important traits LEAST important traits

15. SNP Genome Scans Illumina Infinium® II SNP arrays: developed 2010, used 2011 9K8K +1K 6K Verde et al. 2012 PLoS One, accepted Chagne et al. 2012 PLoS One 7(2):e31745 Peace et al. manuscript in prep.

16. SNP Genome Scans 9K8K6K 40-60 kb intervals sweet cherry P. avium genome sour cherry SNP 100-200 kb intervals SNP Avg 446 kb/cluster Avg 72% SNPs polymorphic Avg 94% clusters polymorphic RESULTS STRATEGY P. fruticosa genome Avg 27 kb/SNP Avg 84% SNPs polymorphic every 4 th -5 th detected SNP chosen, so spacing varies over genome Avg 38 kb/SNP Avg SNPs polymorphic = 32% (sweet), 36% (sour)

17. Reference Germplasm CROP REFERENCE SET n=480 BREEDING PEDIGREE SETS

18. Any breeder’s additional germplasm with data Reference Germplasm Minnesota BP Set (n=160) Washington BP Set (n=160) New York BP Set (n=160) CROP REFERENCE SET n=480

19. Standardized Phenotyping Reference Germplasm Sets Public: 480 individuals Additional: +480 individuals Standardized phenotyping at multiple locations, esp. for fruit quality (www.rosbreed.org) Evaluations 2010 & 2011 (2012 next) Available at Genome Database for Rosaceae (www.rosaceae.org/breeders_toolbox)

20. FlexQTL TM for QTLdiscovery, validation, characterization Fruit firmness in apple (HiDRAS data) Pedigree-Based Analysis Flow of a specific linkage block Pedimap for visualizing pedigrees (with alleles, traits, Identity-By-Descent)

21. Jewel Discovery SNP genome scans Standardized phenotypic data Pedigree- Based Analysis QTL discovery

22. MAB Enablement

23. PBA: crop - wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme Trial MASS Efficient, precise, creative breeding Systematic QTL Validation – The MAB Pipeline Seedling selection scheme supported by RosBREED’s in-development Breeding Information Management System

24. New generations enriched for favorable alleles MAB Successes So Far marker-assisted parent selection marker-assisted seedling selection

25. Two jewels polished in RosBREED, put to routine use in demo breeding programs MAB Successes So Far

26. Routine Use of QTLs in Breeding allele 1 carriers allele 2 carriers Use of QTLs: does not predict definitive differences, but enriches for favorable alleles. Brave breeders! frequency  trait level 

27. Predicted to be large-fruited (& self-fertile)  Thousands of inferior seedlings culled - est. $180K saved! Improved efficiency in seedling evaluation since fall 2010 in RosBREED breeding programs Routine MAB with QTLs (WSU’s apple and sweet cherry breeding programs)

28. Tables of functional genotypes (www.rosbreed.org/ breeding/jewel-use) peach fruit texture type “How To” for Rosaceae Breeders Example here is for

29. “How To” for Rosaceae Breeders Peach fruit texture type

30. Apple fruit storability “How To” for Rosaceae Breeders

31. Cherry fruit size “How To” for Rosaceae Breeders

32. RosBREED: Filling the Treasure Chest for Rosaceae Breeders

33. International Context

34. The International Rosaceae Genomics, Genetics, & Breeding Community

35. Plant Research International, Netherlands East Malling Research, UK CRA-FRU, Rome, Italy IASMA, Trento, Italy INRA ( Bordeaux, Avignon, Angers ), France Andres Bello University, Chile Plant & Food Research, New Zealand ARC, South Africa RosBREED participant location Critical International Partnerships + 2 Scientific Advisory Panel members (Spain, New Zealand)

36. Future Funding... -crops? -traits? -approaches? -resources? -partners? We are seeking funding beyond Aug 2013 Proposal submission = Jan 2013 Must be new objectives Ideas are coalescing now

37. Acknowledgements This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture

38. Questions? www.rosbreed.org