1. MSU Amy Iezzoni (PD) Jim Hancock Dechun Wang Cholani Weebadde WSU Cameron Peace Dorrie Main Kate Evans Karina Gallardo Vicki McCracken Nnadozie Oraguzie Former WSU Raymond Jussaume 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. Acknowledgements This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture

3. 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 International Collaborators + 2 Scientific Advisory Panel members (Spain, New Zealand)

4. Discovering a QTL A major milestone or a stepping-stone into practical marker-assisted breeding? Cholani Weebadde 25 July 2013 ASHS, Palm Desert, CA

5. Outline of Presentation  How does QTL discovery inform MAB?  The RosBREED MAB pipeline - a strategy to put DNA knowledge into practical application  Workshop presentations

6. How does QTL discovery inform Marker-Assisted Breeding (MAB)?

7. Which wild germplasm to use? Which traits to target? Which parents & combinations to create? Which seedlings to progress? Which selections to trial? Which advanced selections to commercialize? What is Marker-Assisted Breeding? Use of DNA information to support breeding decisions

8. What published QTLs look like  A bump on the chromosome  What does it tell the breeder??? Nothing much really! Just that there may be a gene in the “bump region” of the chromosome that is associated with the trait

9. Known QTLs and their application  Hundreds of published QTLs are currently available for Rosaceae crops  Of these, only a few were being used for MAB

10. RosBREED has bridged this chasm Genomics Resources Marker- assisted breeding 100s of QTLs published More efficient development of new cultivars RosBREED is dedicated to putting DNA knowledge into practical application to increase the efficiency of rosaceous crop breeding

11. 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

12. Demonstration Breeders & Breeding Trainees

13. The RosBREED MAB Pipeline: a strategy to put DNA knowledge into practical application…. How we bridged the Chasm….

14. Find An individual’s genome is the full complement of genetic information that it inherited from its parents. Within this vast repertoire of genetic information, individual’s genes are being discovered that control critical production and fruit quality traits. Put into application in breeding Jewels = valuable genetic discoveries ready for breeding application = marker-locus-trait associations validated in a breeding program Polish Jewels in the genome analogy

15. Lots of Shiny Rocks! So What?!! Each breeder needs to appraise for themselves all these “gemstones”… …to decide which ones are worth polishing… www.rocktumbler.com …to find the “jewels”!

16. Socio-Economics Surveys (example for apple) Breeders Market Intermediaries Michigan Producers Washington Producers % of respondents  MOST important traits LEAST important traits So that resources for development of genetic tests (polishing the shiny rocks) can be directed to traits with the highest importance to stakeholders….

17. Integrate DNA information with conventional breeding, systematically (8-stage MAB Pipeline) RosBREED MAB Pipeline

18. “Jewels in the Genome” Available Now!

19. Information on the jewels on eXtension “RosBREED Jewels are now featured in eXtension”

20. Workshop presentations

21. Breeding markers DNA testing services QTL priorities Crossing schemes Trial MASS Simple validation Allele effects & distributions Seedling selection schemes RosBREED success stories: QTL and QTL allele validation in Cherry, Apple and Peach 1.Amy Iezzoni – Cherry 2.Sujeet Verma – Apple 3.Ksenija Gasic - Peach

22. Breeding markers DNA testing services QTL priorities Crossing schemes Trial MASS Simple validation Allele effects & distributions Seedling selection schemes Marker-Assisted Breeding for Apple: Experiences from University of Minnesota and Washington State University Jim Luby RosBREED Breeding Team Lead