1. QTL and QTL allele validation in peach Ksenija Gasic 25 July 2013 ASHS Palm Desert, CA

2. Outline of Presentation Choosing the trait and QTL QTL validation – G4Mat maturity QTL allele validation – G4Mat maturity

3. Choosing the trait and QTL

4. -4 breeding programs -Fresh market and processing peach Choosing the trait and QTL

5. -SE results for fresh market peaches

6. Some of the known loci in the Prunus genome Y F-M B Evg Mi Nl D Br Dl Pi Pcp Cs Ag Fc Lb Sk G D Sc Gr Ps Ma S Sf E Si Ripe date Skin blush Flwg date Sugars Skin blush Ripe date Acidity Sugars Ripe date Acidity Sugars Flwg date Ripe date Acidity Sugars Bruising Flwg date Fruit size Ripe date Skin blush Sugars Acidity Bleeding Mealiness Browning Sugars sharka Dw G6G5G4G3G2G1G8G7 Peach, Nectarine AlmondApricot AlmondApricot Xap Ripe date Flwg date

7. QTL Validation - confirming the G4Mat QTL really exists in peach breeding germplasm

8. Peach Material ~980 individuals (cultivars, ancestors, founders, breeding lines, selections, and seedlings Genotyped genome-wide with SNP markers Phenotyped in 2010-12 for fruit quality and other high-impact traits

9. Crop Reference Sets 478 individuals (cultivars, ancestors, founders, breeding lines, selections, and seedlings) Peach related: P. davidiana, P. mira Almond related: P. argentea, P. scoparia

10. G4Mat – Maturity Date CA AR TX SC 73% PVE 77% PVE 56% PVE (phenotypic variance explained) 64% PVE

11. QTL Allele Validation - detecting and valuing G4Mat alleles in peach breeding germplasm

12. G4Mat – Maturity Date APRMAYJUNJULAUGSEP 4 SNPs 8 haplotypes distinguished Labeled VE (very early), E, M, L, VL1, VL2, XL, alm 36 possible genotypes (allelic combinations) Uneven allele distribution in populations...

13. G4Mat – Maturity Date AR Pop1 x 182 ±6 200 ±6 207 ±7 222 ±8 40 days!

14. G4Mat – Maturity Date SC Pop0823 164 ±0 192 ±5 194 ±4 210 ±5 45 days! TX Pop3 140 ±2 150 ±8 152 ±9 191 ±7 50 days! CA Pop8-3 192 ±11 211 ±5 212 ±7 233 ±5 41 days!

15. G4Mat – Maturity Date CA AR TX SC

16. Other Jewels for Peach

17. Some Jewels To Tell You About -D – acidity -G – fruit type (p/n) -Y – flesh color -F-M flesh texture & adhesion -G4Mat – maturity date -G4Mat – SSC -G3Bl – blush -G1Xap & G6Xap - bacterial spot resistance APRMAYJUNJULAUGSEP

18. Loci of interest on Prunus genome Y F-M B Evg Mi Nl D Br Dl Pi Pcp Cs Ag Fc Lb Sk G D Sc Gr Ps Ma S Sf E Si Ripe date Skin blush Flwg date Sugars Skin blush Ripe date Acidity Sugars Ripe date Acidity Sugars Flwg date Ripe date Acidity Sugars Bruising Flwg date Fruit size Ripe date Skin blush Sugars Acidity Bleeding Mealiness Browning Sugars sharka Dw G6G5G4G3G2G1G8G7 Peach, Nectarine AlmondApricot AlmondApricot Xap Ripe date Flwg date

19. AR Pop1 G4Mat – SSC 14.4 13.8 13.9 16.4 TX all pops 11.9 10.6 11.3 14.0 o Brix 22% PVE 15% PVE AR=38%, CA=21%, SC=28%

20. G4Mat VE-BBBAArrington, Bradley, CAF2, Hesse, Westbrook, A672, Saturn, Tropic Beauty, Yumyeong, Zin Dai E-ABBBA672, Saturn, Tropic Beauty M-ABBAElberta, JHHale, O'Henry, Dr Davis, Halford, White County, Winblo L-BBAABolinha, A773 VL1-AAAAWhite County VL2-AAABChinese Cling, Elberta, JHHale, O'Henry, 40A17, Peento, Vilmos, Yumyeong, Zin Dai XL-BAABWinblo alm-BBBBall almonds, 2000,2-8, persicaxdavidiana APRMAYJUNJULAUGSEP

21. Red color in apple, cherry and peach Cherry G3 MYB1/10 Fruit skin & flesh color Peach G3 Cs locus (red color around stone) & QTL for flesh bleeding Apple L9 MYB1/10 Fruit skin & flesh color MYB1/10 Fruit skin color

22. Allele distribution for G3Bl Poster #359

23. CAPS markers for G3Bl Fig. 3 Functional alleles associated with blush in peach. Frequency of each allele in peach germplasm shown in brackets. A B BlBl Blbl blbl

24. Fruit texture type Peach fruit texture type

25. (www.rosbreed.org/ breeding/jewel-use) peach fruit texture type Tables of functional genotypes Example here is for

26. ? G1XapF & G6XapF Bacterial spot resistance SUSU RE M alm R SU RE M alm R RE R SU Clayton, Westbrook, WhiteCounty, WhiteRiver, OHenry, Blazeprince, Flordaprince, Contender, Elberta, Early Crawford, Georgia Belle, Loring, Redhaven, Tropic Beauty, Winblo UFGold, Candor, Bailey, Arrington JH Hale, Mayfire, RioOsoGem Springold, Lovell, LateCrawford Almond Susceptibility Resistance M al m Moderate Yang et al. 2012 TGG ? Chinese cling a b/d c e f

27. Allele distribution for G1XapF

28. Allele distribution for G6XapF

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

30. MSU Amy Iezzoni (PD) Jim Hancock Dechun Wang Cholani Weebadde WSU Cameron Peace Dorrie Main Kate Evans Karina Gallardo Vicki McCracken Nnadozie Oraguzie Former WSU Raymond Jussaume Mykel Taylor Cornell Susan Brown Kenong Xu Clemson Ksenija Gasic Gregory Reighard Texas A&M Dave Byrne Univ. of CA-Davis Tom Gradziel Carlos Crisosto Univ. of New Hamp. Tom Davis Univ. of Minnesota Jim Luby Chengyan Yue Oregon State Univ. Alexandra Stone Plant Research Intl, Netherlands Eric van de Weg Marco Bink USDA-ARS Nahla Bassil Gennaro Fazio Chad Finn Univ. of Arkansas John Clark