MSU Amy Iezzoni (PD) Jim Hancock Dechun Wang Cholani Weebadde WSU Cameron Peace Dorrie Main

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

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

3. The RosBREED Project

4. The RosBREED Project • 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 RosBREED

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

6. The RosBREED Project • Mission We will create a dynamic, sustained program in research, infrastructure establishment, training, and outreachfor developing and applying marker-assisted breeding based on improved knowledge of industry value and consumer preferences to accelerate and increase the efficiency of rosaceous cultivar release and successful cultivaradoption. RosBREED

7. RosBREED’s Objectives • 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 = techtransfertomorebreeders & engageotherstakeholders RosBREED

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

9. RosBREED’s Management • 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 • Project Assistant Genomics Team Leader: Dorrie Main Extension Team Leader: Cholani Weebadde Breeding Team Leader Jim Luby Genotyping Team Leader: Nahla Bassil • Apple • Jim Luby • Susan Brown • Kate Evans • Peach • Ksenija Gasic • John Clark • Dave Byrne • Tom Gradziel Socio- Economics Team Leader: Chengyan Yue • Strawberry • Chad Finn • Jim Hancock • Tom Davis Pedigree- Based Analysis Team Leader: Eric van de Weg • Cherry • Amy Iezzoni • Nnadozie Oraguzie MAB Pipeline Team Leader BIMS Team Leader: Gennaro Fazio Cameron Peace

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

11. Demonstration Breeding Programs RosBREED

12. Resource Development

13. 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 Household data analysis 2010; consumer survey 2012 Producer survey Fall 2011- Winter 2012 Market Intermediary survey Fall 2010- Winter 2011 Breeder survey 2010 Trait Values RosBREED

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

15. SNP Genome Scans Illumina Infinium® II SNP arrays: developed 2010, used 2011 9K 8K 6K +1K Verde et al. 2012 PLoS One, accepted Chagne et al. 2012 PLoS One 7(2):e31745 Peace et al. manuscript in prep. RosBREED

16. SNP Genome Scans 9K 8K 6K sweet cherry sour cherry every 4th-5th detected SNP chosen, so spacing varies over genome 40-60 kb intervals SNP SNP SNP SNP SNP STRATEGY SNP SNP SNP 100-200 kb intervals SNP SNP SNP P. avium genome P. fruticosa genome SNP SNP Avg 27 kb/SNP Avg 446 kb/cluster Avg 38 kb/SNP RESULTS Avg 84% SNPs polymorphic Avg 72% SNPs polymorphic Avg SNPs polymorphic = 32% (sweet), 36% (sour) Avg 94% clusters polymorphic RosBREED

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

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

19. Standardized Phenotyping • Reference Germplasm Sets Public: 480 individuals Additional: +480 individuals • Standardized phenotypingat 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) RosBREED

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

21. Jewel Discovery SNPgenome scans Pedigree-Based Analysis QTL discovery Standardized phenotypic data RosBREED

22. MAB Enablement

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

24. MAB Successes So Far “Cross Assist” MAPS marker-assisted parent selection New generations enriched for favorable alleles “Seedling Select” MASS marker-assisted seedling selection RosBREED

25. MAB Successes So Far • Two jewels polished in RosBREED, put to routine use in demo breeding programs “Cross Assist” “Seedling Select” RosBREED

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

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

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

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

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

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

32. RosBREED: Filling the Treasure Chest for Rosaceae Breeders

33. International Context

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

35. Critical International Partnerships 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 + 2 Scientific Advisory Panel members (Spain, New Zealand)

36. Future Funding... We are seeking funding beyond Aug 2013 Proposalsubmission= Jan 2013 Must be newobjectives Ideas are coalescing now • crops? • traits? • approaches? • resources? • partners? RosBREED

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