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?. 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. “Fresh Sensation”. - PowerPoint PPT PresentationTRANSCRIPT
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
“Fresh Sensation”
‘Honeycrisp’ has a great combination for
consistent fresh sensation(if stored for ≤6 months)
‘Honeycrisp’
A region in the apple genome (jewel in the genome) discovered that controls (predicts) crispness, juiciness, & tartness
APPLICATION:Industry
‘Honeycrisp’
‘Granny Smith’
‘Gala’
‘Pink Lady’
‘Fuji’
‘Golden Delicious’
high fresh up to 6 mo
low freshup to 2 mo
med fresh up to 6 mo
med fresh up to 6 mo
med fresh up to 6 mo
low fresh up to 9 mo ‘Red
Delicious’
low freshup to 3 mo
Describe genetic potential for achieving great fruit quality…
…to develop best management practices without laborious trial and error
“Fresh Sensation”
‘Honeycrisp’
‘Granny Smith’
‘Gala’
‘Pink Lady’
‘Fuji’
‘Golden Delicious’
high fresh up to 6 mo
low freshup to 2 mo
med fresh up to 6 mo
med fresh up to 6 mo
med fresh up to 6 mo
low fresh up to 9 mo ‘Red
Delicious’
low freshup to 3 mo‘WA 99’
super freshup to 12 mo
APPLICATION:Industry
Describe genetic potential for achieving great fruit quality…
…to develop best management practices without laborious trial and error – especially for new varieties
“Fresh Sensation”
‘WA 99’
APPLICATION:Breeding: seedling selection
×
“Fresh Sensation”
APPLICATION:Breeding: parent selection
“Fresh Sensation”
Valuable Traits DNA-Informed breeding
Rapid response to industry challenges &
consumer demands
Orchards of the
Future
GERMPLASM BREEDING INDUSTRY
Supporting the Future
Outline of Presentation
Apple Fruit Quality & Some Known Trait Loci
Storability: ACS & ACO
Skin Color: Rf
“Fresh Sensation”: Ma
Apple Fruit Quality
& Some Known Trait Loci
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
Some Known Trait Loci
Md-ACO1
Md-Exp7
Md-AAT1
Md-ACS1
Ma
Rf
Md-PG1
Storability:
ACS & ACO
Md-ACS1 & Md-ACO1
www.rosbreed.org/breeding/jewel-use/apple
Apple fruit storability
Md-ACS1 & Md-ACO1
Apple fruit storability
Skin Color:
Rf
Rf
• Alleles = MYB1 promoter variations, simple PCR
• Alleles 2,3 = non-blushed
• Alleles 1, 4 = blushed
• Allele 5 = red-fleshed
Rfcan be deduced from published information
= Md-MYB1/MYB1029.48 Mb
33.72 Mb
0.00 Mb
Rf
Rf = Md-MYB1/MYB1029.48 Mb
33.72 Mb
0.00 Mb
• Alleles = SNP haplotypes from 8K genome scan
• Allele “rf” = non-blushed
• Allele “Rf” = blushed, dominant
Rf - Predictions
Rf
1no
2<25%
325-50%
450-75%
5>75%
“ PercOvrClr” = “% red / overcolor color of skin”
RfRfrfrf Rfrf
no. individuals
Rf – Functional Genotypes
Rf“ PercOvrClr” = “% red / overcolor color of skin”
Golden Delicious, Granny Smith, Aurora Golden Gala
Honeycrisp, Gala, Zestar, Pacific Rose, Braeburn, Pinova, McIntosh, Cripps Pink, Splendour, Cameo, Red Delicious
Jonathan, Jonamac, Empire, Scired RfRf
rfrf
Rfrf
Rf – Has a Friend
Rf
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
blbl BlBlis more often
like thisis more often like this
RfRf, BlBl
RfRf, Blbl
RfRf, blbl
Rfrf, blbl
Rfrl, Blbl
Rfrf, BlBl
rfrf, blbl
rfrf, Blbl
rfrf, BlBl
Rf & Bl - Predictions
Rf
1no
2<25%
325-50%
450-75%
5>75%
no. individuals
“Fresh Sensation”:
Ma
The Ma locus
Ma
Sujeet Verma- current PhD studies
on 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!)
Ma haplotyping
• 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)...
Ma
CH05c06
Hi04e04
~16 cM
Ma haplotyping
Ma
CH05c06
Hi04e04
~16 cM
Ma haplotyping
Ma
CH05c06
Hi04e04
~16 cM
• Each cultivar/parent of U.S. breeding germplasm was haplotypede.g. Honeycrisp = H2H7
Braeburn = H2H4Granny Smith = H1H2Golden Delicious = H1H4Red Delicious = H3H4
• Recently, FlexQTL run with various traits from standardized phenotyping efforts...
Ma and its Traits of Influence
Ma
CH05c06
Hi04e04
~16 cM
Acidity (titratable acidity, 10 weeks storage, 2011)
Ma and its Traits of Influence
Ma
CH05c06
Hi04e04
~16 cM
Acidity (sensory 1-5, 10 weeks storage, 2011)
Ma and its Traits of Influence
Ma
CH05c06
Hi04e04
~16 cM
Crispness (sensory 1-5, 10 weeks storage, 2011)
Ma and its Traits of Influence
Ma
CH05c06
Hi04e04
~16 cM
Crispness (Cn, 10 weeks storage, 2011)
Ma and its Traits of Influence
Ma
CH05c06
Hi04e04
~16 cM
Juiciness (sensory 1-5, 10 weeks storage, 2011)
Ma and its Traits of Influence
Ma
CH05c06
Hi04e04
~16 cM
Firmness (sensory 1-5, 10 weeks storage, 2011)
Ma and its Traits of Influence
Ma
CH05c06
Hi04e04
~16 cM
Fruit Weight (g, 10 weeks storage, 2011)
Ma and its Traits of Influence
Ma
CH05c06
Hi04e04
~16 cM
Bitter Pit (sensory 1-5, 10 weeks storage, 2011)
Ma and its Traits of influence
• Some example functional haplotypes:
Honeycrisp’s H7 Braeburn’s H2 (84-230) (108-224)Acidity lower higher
Crispness higher lowerJuiciness higher lowerBitter Pit higher lower
Acknowledgements
This project is supported by the Specialty Crop Research Initiative of USDA’s
National Institute of Food and Agriculture
Questions?