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LOCI IMPORTANT FOR APPLE FRUIT QUALITY WHAT IS KNOWN ABOUT THEIR FUNCTIONAL ALLELES? PowerPoint Presentation
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LOCI IMPORTANT FOR APPLE FRUIT QUALITY WHAT IS KNOWN ABOUT THEIR FUNCTIONAL ALLELES?

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LOCI IMPORTANT FOR APPLE FRUIT QUALITY WHAT IS KNOWN ABOUT THEIR FUNCTIONAL ALLELES?

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  1. LOCI IMPORTANT FORAPPLE FRUIT QUALITY WHAT IS KNOWNABOUT THEIR FUNCTIONAL ALLELES? Cameron Peace, Jim Luby, Kate Evans, Susan Brown, Matthew Clark, Yingzhu Guan,Ben Orcheski, Cari Schmitz, Sujeet Verma, Nahla Bassil, Eric van de Weg, Amy Iezzoni

  2. “Fresh Sensation” A region in the apple genome (jewel in the genome) discovered that controls (predicts) crispness, juiciness, & tartness ‘Honeycrisp’ ‘Honeycrisp’ has a great combination for consistent fresh sensation (if stored for ≤6 months)

  3. “Fresh Sensation” APPLICATION: Industry med fresh up to 6 mo ‘Granny Smith’ med fresh up to 6 mo low fresh up to 2 mo high fresh up to 6 mo ‘Gala’ ‘Pink Lady’ med fresh up to 6 mo ‘Honeycrisp’ low fresh up to 3 mo low fresh up to 9 mo ‘Fuji’ ‘Golden Delicious’ Describe genetic potential for achieving great fruit quality… …to develop best management practices without laborious trial and error ‘Red Delicious’

  4. “Fresh Sensation” APPLICATION: Industry med fresh up to 6 mo ‘Granny Smith’ med fresh up to 6 mo low fresh up to 2 mo high fresh up to 6 mo ‘Gala’ ‘Pink Lady’ med fresh up to 6 mo ‘Honeycrisp’ super fresh up to 12 mo low fresh up to 3 mo low fresh up to 9 mo ‘WA 99’ ‘Fuji’ ‘Golden Delicious’ Describe genetic potential for achieving great fruit quality… …to develop best management practices without laborious trial and error – especially for new varieties ‘Red Delicious’

  5. “Fresh Sensation” APPLICATION: Breeding: seedling selection × ‘WA 99’

  6. “Fresh Sensation” APPLICATION: Breeding: parent selection

  7. Supporting the Future GERMPLASM BREEDING INDUSTRY Orchards of the Future Valuable Traits DNA-Informed breeding Rapid response to industry challenges & consumer demands

  8. Outline of Presentation • Apple Fruit Quality & Some Known Trait Loci • Storability: ACS & ACO • Skin Color: Rf • “Fresh Sensation”: Ma

  9. Apple Fruit Quality & Some Known Trait Loci

  10. Components Of Apple Fruit Quality • Flavor • sweetness • acidity • aroma • Texture • firmness • crispness • juiciness • Appearance • color • shape • freedom from defects • Consistency of quality • Maintenance of quality

  11. Some Known Trait Loci Linkage group 1 2 3 4 5 6 7 8 9 Md-AAT1 Rf Md-Exp7 11 12 13 14 15 16 17 Ma 10 Md-ACS1 Md-PG1 Md-ACO1

  12. Storability: ACS & ACO

  13. Md-ACS1 & Md-ACO1 www.rosbreed.org/breeding/jewel-use/apple Apple fruit storability

  14. Md-ACS1 & Md-ACO1 Apple fruit storability

  15. Skin Color: Rf

  16. Rf • Alleles = MYB1 promoter variations, simple PCR • Alleles 2,3 = non-blushed • Alleles 1, 4 = blushed • Allele 5 = red-fleshed 9 0.00 Mb = Md-MYB1/MYB10 Rf 29.48 Mb can be deduced from published information 33.72 Mb

  17. Rf • Alleles = SNP haplotypes from 8K genome scan • Allele “rf” = non-blushed • Allele “Rf” = blushed, dominant 9 0.00 Mb = Md-MYB1/MYB10 Rf 29.48 Mb 33.72 Mb

  18. no. individuals Rf - Predictions 9 “ PercOvrClr” = “% red / overcolor color of skin” Rf rfrf Rfrf RfRf 1 no 2 <25% 5 >75% 3 25-50% 4 50-75%

  19. Rf – Functional Genotypes 9 “ PercOvrClr” = “% red / overcolor color of skin” Rf rfrf Golden Delicious, Granny Smith, Aurora Golden Gala Honeycrisp, Gala, Zestar, Pacific Rose, Braeburn, Pinova, McIntosh, Cripps Pink, Splendour, Cameo, Red Delicious Rfrf RfRf Jonathan, Jonamac, Empire, Scired

  20. Rf – Has a Friend 9 2 Bl • Another locus, on LG2, is nicknamed the “blush” locus (Bl) because on its own it is associated with degree of blushiness vs. stripiness • But the “Bl” locus also interacts with Rfto influence apple skin blush amount (PercOvrClr) – blbl less blush than BlBl Rf blbl BlBl is more often like this is more often like this

  21. no. individuals Rf & Bl - Predictions 9 RfRf, Blbl RfRf, blbl RfRf, BlBl Rfrf, BlBl Rfrl, Blbl rfrf, BlBl Rfrf, blbl Rf rfrf, Blbl rfrf, blbl 1 no 2 <25% 5 >75% 3 25-50% 4 50-75%

  22. “Fresh Sensation”: Ma

  23. The Ma locus • Ma locus first described 1970(J. Verhaeg) • Some populations acidity difference so great that discernible by taste: High/Low • Texture studies in late 90s (C. Maliepaard et al.) found QTLs for acidity there, also QTLs for crispness, juiciness • Sujeet Verma collectively calls these traits “fresh sensation” (crisp, juicy, tart = fresh!) 16 Sujeet Verma - current PhD studies on the Ma locus Ma

  24. Ma haplotyping 16 • SSR dissection at WSU uncovered numerous haplotypes, some allocated to Ma, ma alleles • RosBREED SNP data allowed further refinement, first with 20 SNPs targeted there with GoldenGate assay (late 2010)... CH05c06 Ma ~16 cM Hi04e04

  25. Ma haplotyping 16 CH05c06 Ma ~16 cM Hi04e04

  26. Ma haplotyping 16 • Each cultivar/parent of U.S. breeding germplasm was haplotypede.g. Honeycrisp = H2H7 Braeburn = H2H4 Granny Smith = H1H2 Golden Delicious = H1H4 Red Delicious = H3H4 • Recently, FlexQTL run with various traits from standardized phenotyping efforts... CH05c06 Ma ~16 cM Hi04e04

  27. Ma and its Traits of Influence Acidity (titratable acidity, 10 weeks storage, 2011) 16 CH05c06 Ma ~16 cM Hi04e04

  28. Ma and its Traits of Influence Acidity (sensory 1-5, 10 weeks storage, 2011) 16 CH05c06 Ma ~16 cM Hi04e04

  29. Ma and its Traits of Influence Crispness (sensory 1-5, 10 weeks storage, 2011) 16 CH05c06 Ma ~16 cM Hi04e04

  30. Ma and its Traits of Influence Crispness (Cn, 10 weeks storage, 2011) 16 CH05c06 Ma ~16 cM Hi04e04

  31. Ma and its Traits of Influence Juiciness (sensory 1-5, 10 weeks storage, 2011) 16 CH05c06 Ma ~16 cM Hi04e04

  32. Ma and its Traits of Influence Firmness (sensory 1-5, 10 weeks storage, 2011) 16 CH05c06 Ma ~16 cM Hi04e04

  33. Ma and its Traits of Influence Fruit Weight (g, 10 weeks storage, 2011) 16 CH05c06 Ma ~16 cM Hi04e04

  34. Ma and its Traits of Influence Bitter Pit (sensory 1-5, 10 weeks storage, 2011) 16 CH05c06 Ma ~16 cM Hi04e04

  35. Ma and its Traits of influence • Some example functional haplotypes:Honeycrisp’s H7 Braeburn’s H2 (84-230) (108-224) Acidity lower higherCrispness higherlower Juiciness higherlower Bitter Pit higherlower

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

  37. Questions?