loci important for apple fruit quality what is known about their functional alleles?

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?