1. DISCOVERIES AND BREEDING DATABASES FOR THE FRUIT RESEARCH COMMUNITY 1 August 2012 ASHS, Miami, Florida

2. Outline of Presentation  The RosBREED Project  Resource Development  MAB Enablement  Workshop Presentations

3. The RosBREED Project

4. 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

5. RosBREED Mission Statement We will develop and apply 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 cultivar adoption. 4 yrs $7.2M federal $7.2M matching Amy Iezzoni, Michigan State Univ. Cameron Peace, Wash. State Univ. This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture

6. RosBREED designed to bridge this chasm Genomics Resources Marker- assisted breeding Genomics knowledge More efficient development of new cultivars

7. WSU U Minn Cornell U UC Davis Clemson U U Arkansas Texas A&M MSU UNH USDA-ARS Corvallis WSU MSU Rosaceae Four Crop Groups

8. Demonstration Breeding Programs

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 Ksenija Gasic Jim Luby Dorrie Main Jim McFerson Eric van de Weg Cholani Weebadde Chengyan Yue Project Director Amy Iezzoni RosBREED’s ManagementRosBREED Project Participants

10. RosBREED’s International Partners Plant Research Intl., The Netherlands East Malling Research, United Kingdom INRA – Bordeaux, Avignon & Angers, France CRA-FRU Rome, IASMA, Italy Andres Bello University, Chile ARC, South Africa Plant & Food Research, New Zealand

11. Focus on fruit quality

12. RosBREED is utilizing improved knowledge Courtesy David Byrne, Texas A&M Univ.) of industry values and consumer preferences to select target traits for Marker-Assisted Breeding (MAB) Impacts: increase new cultivar adoption enlarge market potential

13. RosBREED has developed tools Marker-assisted breeding in application For those traits that have value for producers, market intermediaries and consumers

14. Marker-Assisted Breeding Which parents to use? Which combinations to create? Which seedlings to progress? Which selections to trial? Which advanced selections to commercialize? Increased breeding efficiency

15. Analogy of Jewels in the Genome An individual’s genome is the full complement of genetic information that it inherited from its parents. Within this vast repertoire of genetic information, individuals genes are being discovered that control critical production and fruit quality traits. Jewels = valuable genetic discoveries that are put into breeding application

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

17. Resource Development

18. BREEDING PEDIGREE SETS Reference Germplasm Minnesota BP Set (n=160) Washington BP Set (n=160) New York BP Set (n=160) Any breeder’s additional germplasm with data 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. SNP Genome Scans Illumina Infinium® II SNP arrays: developed 2010, first used in 2011 9K8K +1K 6K Verde et al. 2012 PLoS One 7(4): e35668 Chagne et al. 2012 PLoS One 7(2):e31745 Peace et al. (Submitted, PLoS One)

21. 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)

22. Jewel Discovery SNP genome scans Standardized phenotyping Pedigree- Based Analysis QTL discovery

23. MAB Enablement

24. 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

25. 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

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

27. PBA: crop - wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme Trial MASS Efficient, precise, creative breeding The MAB Pipeline Seedling selection scheme

28. Examples of Jewels

29. New generations enriched for favorable alleles Genetic information used to inform both MAPS and MASS marker-assisted parent selection marker-assisted seedling selection

30. 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)

31. 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 Breeders Toolbox (www.rosaceae.org) What parents have the jewels? What crosses to make? Which seedlings have the jewels?

33. http://uniquefloristtampa.com/PageTemplates/ShoppingCart.aspx?PageID=133&Virt ualCatalogProductID=1529910 Workshop Presentations

34. What are the Jewels? How can you access this ‘Treasure Chest’?

35. Workshop Presentations  Describe germplasm, phenotypic and genetic data used for Jewel finding and polishing  Describe Jewels, including knowledge useful for scientists seeking to understand these biological processes  Describe available pedigree-based and decision based breeding software designed to address the problem of data overload

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

37. Questions? www.rosbreed.org