1. LOCI IMPORTANT FOR APPLE FRUIT QUALITY
WHAT IS KNOWN ABOUT 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
‘Granny Smith’
‘Gala’
APPLICATION:
Industry
med fresh up to 6 mo
‘Golden Delicious’
med fresh up to 6 mo
‘Pink Lady’
‘Honeycrisp’
low fresh
up to 2 mo
high fresh up to 6 mo
med fresh up to 6 mo
‘Red Delicious’
‘Fuji’
low fresh
up to 3 mo
low fresh up to 9 mo
Describe genetic potential for achieving great fruit quality…
…to develop best management practices without laborious trial and error

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

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

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

7. Supporting the Future GERMPLASM BREEDING INDUSTRY
3/31/2017
Supporting the Future
GERMPLASM
BREEDING
INDUSTRY
Orchards of the Future
Valuable Traits
DNA-Informed breeding
Rapid response to industry challenges & consumer demands
Template B-curves

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 11 12 13 14 15
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 9 Alleles = MYB1 promoter variations, simple PCR
Alleles 2,3 = non-blushed
Alleles 1, 4 = blushed
Allele 5 = red-fleshed
0.00 Mb
= Md-MYB1/MYB10 Rf
can be deduced from published information
29.48 Mb
33.72 Mb

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

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

19. Rf – Functional Genotypes9
“ PercOvrClr” = “% red / overcolor color of skin” Rf
rfrf
Golden Delicious, Granny Smith, Aurora Golden Gala
Rfrf
Honeycrisp, Gala, Zestar, Pacific Rose, Braeburn, Pinova, McIntosh, Cripps Pink, Splendour, Cameo, Red Delicious
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 Rf to 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. Rf & Bl - Predictions 9 no. individuals RfRf, Blbl RfRf, blbl
Rfrl, Blbl
rfrf, BlBl
Rfrf, blbl Rf
rfrf, Blbl
rfrf, blbl 1 no 2
<25% 3
25-50% 4
50-75% 5
>75%

22. “Fresh Sensation”: Ma

23. The Ma locus 16 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 haplotyped e.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 H (84-230) ( )
Acidity lower higher Crispness higher lower
Juiciness higher lower
Bitter Pit higher lower

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

37. Questions?