1. Cameron Peace, Kate Evans, Nnadozie Oraguzie, Dorrie Main, Daniel Edge-Garza, Yingzhu Guan, Murali Bellamkonda, Sujeet Verma, Eric van de Weg, Jim McFerson, Amy Iezzoni, Fred Bliss

2. Outline of Presentation Our MAB Team Vital Ingredient: Local Industry Support Breeding Decisions DNA-Informed Breeding

3. Outline of Presentation cont’d Integration into Routine Breeding Operations – Examples in our breeding programs The MAB Pipeline Moving Ahead

4. Our MAB Team

5. Molecular Geneticist (Cameron Peace) Apple Breeder (Kate Evans) Sw. Cherry Breeder (Nnadozie Oraguzie) Advisors (GGB Teams, Industry Advisory Committees) Genetic Screening Service (Pacific Northwest Tree Fruit Genotyping Lab)

6. Local Industry Support

7. Vital Ingredient: Local Industry Support for… Science-based innovation Breeding program but.. Industry support only comes with industry relevance

8. Breeding Decisions

9. Which traits to target? Which parents to use? Which combinations to create? Which seedlings to progress? Which selections to trial? Which advanced selections to commercialize?

10. DNA-Informed Breeding

11. Synonym for Marker-Assisted Breeding DNA information = decision support

12. Many forms of decision support: -Trait choice and manipulation -Parental germplasm choice -Population creation -Crossing method assessment -Parentage verification -Seedling selection -Genetic potential description -Identity confirmation DNA-Informed Breeding Many forms of decision support: -Trait choice and manipulation -Parental germplasm choice -Population creation -Crossing method assessment -Parentage verification -Seedling selection -Genetic potential description -Identity confirmation trait locus markers any markers

13. DNA-Informed Breeding Nice, but not necessary Gene sequence MTL or QTL Linkage group Trait locus SSR, SCAR SSR All that’s needed SSR

14. Examples

15. Marker-Assisted Parent Selection Integration into Routine Breeding Operations - Examples 2 QTLs for storability (gene-based SCARs) -Ethylene biosynthesis genes Md-ACS1 and Md-ACO1 All parents genotyped, ongoing Crosses in recent years have avoided homozyg. poor, made more homozyg. good

16. Integration into Routine Breeding Operations - Examples MTL for self-fertility (gene-based SCAR) -S locus (SRNase / SFB) on G6, targeting S 4 ' allele Also used to avoid incompatible crosses All parents genotyped, ongoing Since 2004, used for all crosses Marker-Assisted Parent Selection

17. FRUIT SIZE 2010 FRUIT SIZE 2009 Integration into Routine Breeding Operations - Examples QTL for fruit size (1 nearby SSR) -Cell number locus on G2. Also QTL for firmness, flavor All parents genotyped, ongoing Since 2010, crosses have emphasized populations enriched for large fruit alleles Marker-Assisted Parent Selection FRUIT SIZE 2010 FRUIT SIZE 2009

18. Integration into Routine Breeding Operations - Examples Any locus markers genotyped on parents Confirm (& refute) parentage of selections Not cost-efficient to use at seedling stage (unless culling, e.g. eliminate outcrosses or selfs) Parentage Verification

19. Integration into Routine Breeding Operations - Examples Parentage of WSU selections: Parentage of ‘WA 2’: Parentage Verification 32 confirmed 2 refuted 1 deduced ‘Splendour’ OP  ‘Splendour’ x ‘Gala’

20. Integration into Routine Breeding Operations - Examples Any locus markers genotyped on populations Determine how often get intended parentage We see 5 - 70% outcrossing Change method? Accept but be aware? Influences quantitative genetics parameters! Crossing Method Success

21. Integration into Routine Breeding Operations - Examples S-genotypes used as primary check, trait locus markers supplement 243 seedlings (22 families) Imported pollen – Did it work? (Yes) Crossing Method Success Intended parentage 68% Self 10% Outcross 11% Does not belong 11%

22. Integration into Routine Breeding Operations - Examples Use spreadsheet that models breeding programs’ numbers, costs, and timing -Identifies cost-eff. & logistically feasible MASS schemes Marker-Assisted Seedling Selection

23. $4 $2 $0 $6 $2 $4 Savings per initial seed

24. Integration into Routine Breeding Operations - Examples Md-ACS1 and Md-ACO1 Trials on 2600 sdlgs in 2008-2009 -Then used to cull 1690 before spring planting in 2010 Routine on 5300 sdlgs in 2010 -Culled 2900 at optimal stage (before expensive grafting) Net resource savings: $62K ($10K spent) Marker-Assisted Seedling Selection

25. Integration into Routine Breeding Operations - Examples Fruit size QTL and Self-fertility (Trial &) Routine on 834 sdlgs in 2010 -Culled 500 before fall planting Net resource savings: $25K ($2.5K spent) Marker-Assisted Seedling Selection

26. Integration into Routine Breeding Operations - Examples High-throughput = high pressure, relatively expensive  MASS gets much attention in MAB press But MAPS is more efficient, more impactful when used to avoid / minimize MASS Marker-Assisted Seedling Selection

27. MTL and QTL markers used to describe genetic potential of advanced selections – inform advancement decisions, enhance industry adoption decisions ‘WA 5’ has Md-Exp7-214 allele – likely has scab resistance Genetic Potential Description Integration into Routine Breeding Operations - Examples

28. ‘WA 2’ and ‘WA 5’ have ++/-- and ++/++ functional genotypes for storability ( Md-ACS1 / Md-ACO1 ) – so expect ‘WA 5’ better Verifying/deducing parentage also useful Genetic Potential Description Integration into Routine Breeding Operations - Examples

29. Integration into Routine Breeding Operations - Examples S-genotypes and QTL markers used 12 selections made by phenotype in 2009. Genotyping refined it to 7 (self-fertile, large fruit) S-genotypes usually given for new releases – example of industry-used genotyping Genetic Potential Description

30. Integration into Routine Breeding Operations - Examples 2 SSRs to confirm identity of selections undergoing repropagation 2 SSRs to resolve nursery mix-up Unique fingerprint reported for ‘WA 2’ release – discourage theft Identity Confirmation

31. The MAB Pipeline

32. MAB routine use Available DNA information MASS Trial Use MASS Cost Efficiency & Logistics MAPS Decisions UtilityValidation Improved Markers Genetic Screening Efficiency Prioritization Used for trait loci Socio- economics information DNA information Routine Breeding Operations

33. Socio- economics information DNA information Routine Breeding Operations The MAB Pipeline Intended impacts I MMEDIATE : Confidence that crosses are aimed more at desired targets and planted seedlings will be better on average M EDIUM - TERM : Greater efficiency of breeding L ONG - TERM : Ongoing superior new cultivars providing industry sustainability and consumer satisfaction, health, enjoyment

34. DNA information The Pipeline’s Eight Stages Socio- economics information Routine Breeding Operations

35. Socio- economics information DNA information Routine Breeding Operations MAB Pipelining at WSU Modest infrastructure, but flowing!

36. Socio- economics information DNA information Routine Breeding Operations Building Pipeline Infrastructure

37. Using New Rosaceae Genomics Knowledge Socio- economics information DNA information Rosaceae fruit quality (Iezzoni – RosBREED) Rosaceae phenology (Dirlewanger) Sweet cherry fruit quality (Quero-Garcia) Peach chilling injury res. (Vizoso) (Nilo) Peach texture (Trainotti) Apple polyphenolics (Chagné) Apple color (Allan) (Chagné) Apple fruit quality (Soeker) Apple Vit C (Davey) Apple biennial bearing (Guitton) Almond bitterness (Sanchez-Perez) Strawberry fruit quality (Deoyes-Rothan) Apple tree arch. & phenology (Celton) Peach chilling requirement (Zhebentyayeva) Raspberry heat tolerance, prickles, growth habit (Molina-Bravo) Prunus hypoxia (Rubio-Cabetas) Strawberry drought stress (Surbanovski) (Razavi) Sweet cherry self- compatibility (Cachi) Rose disease res. (Debener) Prunus PPV resistance (Decroocq) (Zhebentyayeva)) Apple fire blight res. (Durel) Apple disease res. (Malnoy) (Durel) Apple scab res. (Gardiner) Prunus graft incompat. (Pina) Apple texture (Costa) (Zhu) Routine Breeding Operations

38. Moving Ahead

39. Rosaceae industry support More M-L-T associations More people on the Pipeline More breeders willing to take risks Your continued support of RosBREED

40. Moving Ahead We can all have justified expectations that DNA information will be applied …as long as efforts are targeted and coordinated …and details of what it takes (MAB Pipeline) are not underestimated

41. Acknowledgements Terry Rowland and the rest of the PNW Tree Fruit Genotyping Lab Deven See (Western Regional Small Grains Genotyping Lab) Technical staff of the Washington Apple Breeding Program Technical staff of the PNW Sweet Cherry Breeding Program Bruce Barritt Jim Olmstead Yanmin Zhu and other members of our advisory GGB Teams Sue Gardiner and David Chagné Marco Bink RosBREED participants and Advisory Panel members NRI apple texture project participants