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13 aranzana

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2015 International FruitBreedomics Conference

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13 aranzana

  1. 1. YOUR LOGO Exploring and exploiting phenotypic and genetic diversity in peach: identification of major genes and QTLs by GWAS. XIV EUCARPIA symposium on Fruit Breeding and Genetics. Maria José Aranzana
  2. 2. YOUR LOGO Exploring and exploiting phenotypic and genetic diversity in peach: identification of major genes and QTLs by GWAS. XIV EUCARPIA symposium on Fruit Breeding and Genetics. Maria José Aranzana
  3. 3. YOUR LOGO Partners involved Ignazio Verde Sabrina Micalli Valeria Aramini M.Teresa Dettori Daniele Bassi Laura Rossini Igor Pacheco Stefano Foschi Alessandra Estella Nelso Nazzicari Andrea Caprera Michela Troggio Elisa Banchi Pere Arús Maria José Aranzana Diego Micheletti José Ramón Hernández Ignasi Iglesias Quim Carbó Sanshan Gao Xionwei Li Li-rong Wang Rui-juan Ma Teresa Barreneche Thierry Pascal Bénédicte Quilot Patrick Lambert François Laurens
  4. 4. YOUR LOGO Partners involved Ignazio Verde Sabrina Micalli Valeria Aramini M.Teresa Dettori Daniele Bassi Laura Rossini Igor Pacheco Stefano Foschi Alessandra Estella Nelso Nazzicari Andrea Caprera Michela Troggio Elisa Banchi Sanshan Gao Xionwei Li Li-rong Wang Rui-juan Ma Teresa Barreneche Thierry Pascal Bénédicte Quilot Patrick Lambert François Laurens Pere Arús Maria José Aranzana Diego Micheletti José Ramón Hernández Ignasi Iglesias Quim Carbó
  5. 5. YOUR LOGO • Select those more interesting accessions within each germplasm collection (200-300) Exploring phenotypic diversity in peach Approach INRA UNIMI CRA-RomeIRTA ZJU (China)
  6. 6. YOUR LOGO • Select those more interesting accessions within each germplasm collection (200-300) Italy France Spain China • Collect all phenotypic information acquired for years • Design the template of a common database for available and common scales for new data Approach Exploring phenotypic diversity in peach
  7. 7. YOUR LOGO 1580 accessions: • Local • Old (founders) • Commercial from breeding programs • Few non-persica Exploring phenotypic diversity in peach Common accessions with phenotypic data between locations
  8. 8. YOUR LOGO Numberofaccessionswithphenotypicdata UMIL ZJU CRA INRA IRTA (1) IRTA (2) Years Data available for several years in many of the accessions Exploring phenotypic diversity in peach
  9. 9. YOUR LOGO Exploring phenotypic diversity in peach Distribution of data on qualitative traits
  10. 10. YOUR LOGO (r2= 0.60- 0.80) (r2= 0.97-0.98) Exploring phenotypic diversity in peach Data correlation between years
  11. 11. YOUR LOGO (r2= 0.38- 0.68) Data correlation between years Exploring phenotypic diversity in peach
  12. 12. YOUR LOGO Mean # days to full blossom IRTA-Mas Badia Mean#daystofull blossomIRTA-Gimenells Mean # days to ripen IRTA-Mas Badia Mean#daysto ripenIRTA-Gimenells Mean ºBRIX IRTA-Mas Badia MeanºBRIXIRTA- Gimenells MeanacidityIRTA- Gimenells Mean acidity IRTA-Mas Badia y = 47.4 + 0.39 x r2= 0.18 y = 3.9 + 1.04 x r2= 0.91 y = 6.5 + 0.49 x r2= 0.39 y = 13.43 + 1.2 x r2= 0.77 Exploring phenotypic diversity in peach Data correlation between locations
  13. 13. YOUR LOGO Exploring and exploiting phenotypic and genetic diversity in peach: identification of major genes and QTLs by GWAS. XIV EUCARPIA symposium on Fruit Breeding and Genetics. Maria José Aranzana
  14. 14. YOUR LOGO • 1580 accessions geotyped with the 9K SNP chip No Call <5%, three genotypes Null allele or preferential annealing Duplicated sequences/genes FalseSNPs Failed Exploring genetic diversity in peach 4330 53% 25%
  15. 15. YOUR LOGO 115 28 17 4 2 2 2 2 0 1 2 3 4 5 6 7 8 9 10 11 # accessions with identical genotype (clones) • SNPs identified 473 clones (173 groups with 2 or more clons) Exploring genetic diversity in peach
  16. 16. YOUR LOGO 115 28 17 4 2 2 2 2 0 1 2 3 4 5 6 7 8 9 10 11 # accessions with identical genotype • SNPs identified 473 clones (173 groups with 2 or more clons) • 92% of accessions with the same name where identical Exploring genetic diversity in peach
  17. 17. YOUR LOGO Exploring genetic diversity in peach Oriental (Chinese) Occidenal Breeding Occidental non-breeding Occidenal Breeding Occidental non-breeding Oriental (Chinese)
  18. 18. YOUR LOGO Exploring genetic diversity in peach Occ Breed Occ non-Breed Oriental Admixed Minor allele Frequency
  19. 19. YOUR LOGO Exploring genetic diversity in peach 1.4 Mb 1 Mb 1.8 Mb 0.8 Mb Occidental Breeding Occidental Local varieties Oriental Occidental varieties show SNPs in LD in the flesh color (Y) region Chromosome 1 Occidental Breeding Occidental Local Oriental Admixed Linkage disequilibrium (LD)
  20. 20. YOUR LOGO Exploring and exploiting phenotypic and genetic diversity in peach: identification of major genes and QTLs by GWAS. XIV EUCARPIA symposium on Fruit Breeding and Genetics. Maria José Aranzana
  21. 21. YOUR LOGO Exploiting genetic diversity in peach: GWAS Sub-acid Peach/nectarine Melting/non-melting Leaf gland White/yellow fruit flesh Flat/round fruit Flower type
  22. 22. YOUR LOGO 0 200 400 600 800 1000 Hap97 Hap98 Hap36 Hap5 Acid Subacid  23 SNPs associated  Region 1.8 Mb  99 haplotypes  4 haplotypes associated Exploiting genetic diversity in peach: GWAS
  23. 23. YOUR LOGO  21 SNPs associated  Region of 5.2 Mb  152 haplotypes  6 haplotypes associated Exploiting genetic diversity in peach: GWAS  3 causal alleles  SSR  TE  SNP
  24. 24. YOUR LOGO 152 haplotypes 6 significant haplotypes Ho 0.76 1.00 0.86 1.00 0.92 1.00 SSR +TE Set of SNPs associated in haplotypes tested in WP1-pilot studies Exploiting genetic diversity in peach: GWAS
  25. 25. YOUR LOGO China Exploiting genetic diversity in peach: GWAS
  26. 26. YOUR LOGO Spain Exploiting genetic diversity in peach: GWAS
  27. 27. YOUR LOGO Ignazio Verde Sabrina Micalli Valeria Aramini M.Teresa Dettori Daniele Bassi Laura Rossini Igor Pacheco Stefano Foschi Alessandra Estella Nelso Nazzicari Andrea Caprera Michela Troggio Elisa Banchi Pere Arús Maria José Aranzana Diego Micheletti José Ramón Hernández Ignasi Iglesias Quim Carbó Sanshan Gao Xionwei Li Li-rong Wang Rui-juan Ma Teresa Barreneche Thierry Pascal Bénédicte Quilot Patrick Lambert François Laurens Thanks for your attention

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