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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.

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Presentation on theme: "LOCI IMPORTANT FOR APPLE FRUIT QUALITY WHAT IS KNOWN ABOUT THEIR FUNCTIONAL ALLELES? Cameron Peace, Jim Luby, Kate Evans, Susan Brown, Matthew Clark, Yingzhu."— Presentation transcript:

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 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

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

4 Honeycrisp Granny Smith Gala Pink Lady Fuji Golden Delicious high fresh up to 6 mo low fresh up to 2 mo med fresh up to 6 mo low fresh up to 9 mo Red Delicious low fresh up to 3 mo WA 99 super fresh up 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

5 WA 99 APPLICATION: Breeding: seedling selection × Fresh Sensation

6 APPLICATION: Breeding: parent selection Fresh Sensation

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

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 Md-ACO1 Md-Exp7 Md-AAT1 Md-ACS1 Ma Rf Md-PG1

12 Storability: ACS & ACO

13 Md-ACS1 & Md-ACO1 Apple fruit storability

14 Md-ACS1 & Md-ACO1 Apple fruit storability

15 Skin Color: Rf

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

17 Rf = Md-MYB1 / MYB Mb Mb 0.00 Mb Alleles = SNP haplotypes from 8K genome scan Allele rf = non-blushed Allele Rf = blushed, dominant

18 Rf - Predictions Rf 1 no 2 <25% % % 5 >75% PercOvrClr = % red / overcolor color of skin RfRfrfrfRfrf no. individuals

19 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

20 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 Rf to influence apple skin blush amount (PercOvrClr) – blbl less blush than BlBl blblBlBl is more often like this

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

22 Fresh Sensation: Ma

23 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!)

24 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

25 Ma haplotyping Ma CH05c06 Hi04e04 ~ 16 cM

26 Ma haplotyping Ma CH05c06 Hi04e04 ~ 16 cM 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...

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

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

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

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

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

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

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

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

35 Ma and its Traits of influence Some example functional haplotypes: Honeycrisps H7Braeburns H2 (84-230) ( ) Acidity lowerhigher Crispness higherlower Juiciness higherlower Bitter Pit higherlower

36 Acknowledgements This project is supported by the Specialty Crop Research Initiative of USDAs National Institute of Food and Agriculture

37 Questions?


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