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QTL and QTL allele validation in peach Ksenija Gasic

QTL and QTL allele validation in peach Ksenija Gasic. 25 July 2013 ASHS Palm Desert, CA. Outline of Presentation. Choosing the trait and QTL QTL validation – G4Mat maturity QTL allele validation – G4Mat maturity. RosBREED. Choosing the trait and QTL. Choosing the trait and QTL.

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QTL and QTL allele validation in peach Ksenija Gasic

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  1. QTL and QTL allele validation in peach KsenijaGasic • 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 RosBREED

  3. Choosing the trait and QTL

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

  5. Choosing the trait and QTL • SE results for fresh market peaches Sweetness & acidity

  6. Flwg date Ripe date Sugars Fruit size Acidity Acidity Sugars Ripe date Ripe date Sugars Sugars Mealiness Flwg date Skin blush Skin blush Skin blush Browning Mealiness Acidity Bruising Sugars Flwg date Ripe date Ripe date Sugars Bruising Acidity Sugars Mealiness Acidity Bleeding Flwg date Sugars Bruising Some of the known loci in the Prunusgenome G1 G2 G3 G4 G5 G6 G7 G8 Mi D Nl Xap Ma Dw Ps Xap Cs D Ripe date Xap Sf Ag Xap Y E Sc Lb Pcp Pi Sk Gr sharka Fc Xap G Evg Br F-M Dl Peach, Nectarine Almond Apricot • Flwg date S Si B

  7. QTL Validation - confirming the G4Mat QTL really existsin 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 RosBREED

  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 RosBREED

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

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

  12. G4Mat – Maturity Date • 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... APR MAY JUN JUL AUG SEP Maturity date RosBREED

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

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

  15. G4Mat – Maturity Date TX SC AR CA

  16. Other Jewels for Peach

  17. Some Jewels To Tell You About • White vs. yellow flesh • 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 Sweetness & acidity APR MAY JUN JUL AUG SEP Maturity date Fruit texture type Fruit skin color Fruit Xap resistance Nectarine vs. peach RosBREED

  18. Flwg date Ripe date Sugars Fruit size Acidity Acidity Sugars Ripe date Ripe date Sugars Sugars Mealiness Flwg date Skin blush Skin blush Skin blush Browning Mealiness Acidity Bruising Sugars Flwg date Ripe date Ripe date Sugars Bruising Acidity Sugars Mealiness Acidity Bleeding Flwg date Sugars Bruising Loci of interest on Prunusgenome G1 G2 G3 G4 G5 G6 G7 G8 Mi D Nl Xap Ma Dw Ps Xap Cs D Ripe date Xap Sf Ag Xap Y E Sc Lb Pcp Pi Sk Gr sharka Fc Xap G Evg Br F-M Dl Peach, Nectarine Almond Apricot • Flwg date S Si B

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

  20. G4Mat Sweetness APR MAY JUN JUL AUG SEP Maturity date

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

  22. Allele distribution for G3Bl Poster #359 RosBREED

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

  24. Fruit texture type Peach fruit texture type RosBREED

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

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

  27. Allele distribution for G1XapF RosBREED

  28. Allele distribution for G6XapF RosBREED

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

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

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