29 gx e interactions-f. laurens

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29 gx e interactions-f. laurens

  1. 1. Environmental effects and Genotype x Environment Interaction in apple F. Laurens, F. Dupuis, … and colleagues who collected the data for Novadi and HiDRAS Preliminary studies from 2 datasets: - INRA-Novadi Breeding programme - cultivars from the European Project HiDRAS -
  2. 2. FAO, 2011
  3. 3. EUFRIN-FruitBreedomics Lleida Feb. 2013 Dr. U. Mayr/Dr. R. Stehr Apple varieties in Germany in Production Northern GermanyLake Konstanz region
  4. 4. German apple production Altes Land Bodensee my notes from K. Klopp and M. Buchele presentations in Interpoma 2012
  5. 5. seeds crosses seedlings resistant to the scab test G l a s s h o u s e young trees with good behaviour against scab and mildew Elite Selections Own root or grafting Nursery Selection process for new scab resistant apple cultivars 1 new cultivar O r c h a r d Year 0 Year 6-8 Year 15-25… Variety testing Fruit Q Yield…
  6. 6. Few studies on GxE on apple in the litterature • New Zealand (Alspach et al, 2002, Oraguzie et al 2003, Kumar et al, 2010): Open pollinated progenies x 3 sites x 4 years – Low GEI for tree and fruit traits; higher for mineral content, fruit disorder, browning and powdery mildew susceptibility • Canada (Hampson et al, 2008): 12 genotypes x 4 sites x 7 years – High environmental effect but no significant GEI for tree vigour, harvest time – Significant for fruit attractiveness, firmness
  7. 7. Study of « environmental » effects in the French INRA-Novadi dessert apple breeding programme. Practical and Methodological outcomes from a commercial breeding programme F. Laurens*, A. Kouassi*, F. Lebreton** and C. Pitiot** * UMR GenHort INRA Angers – France ** Novadi , Lyon-France D I E T A G R I C U L T U R E E N V I R O N M E N T XIIth Eucarpia conference on Fruit Breeding and Genetics
  8. 8. 1 1 2 5 6 3 4Individuals in 1 = 6 Individuals in 2 = 5 Individuals in 3 = 4 INRA-Novadi Dessert Apple Breeding Programme Location of the 6 nursery sites Series 98, 99, 00, 01: each ind duplicated
  9. 9. INRA-Novadi Dessert Apple Breeding Programme Analysis on series 1998, 1999, 2000 • Experimental sites : 6 (1-6) in 3 pairs • Families : 24 • Years of planting : 3 (98, 99, 00) • Tree ages : 6 (2…7 years old) • Years of observation : 7 (2000, …2006) Anova model : Y = µ + Site + Family + Tree Age + Obs. Year + Site * Family + e => 62 600 data
  10. 10. INRA-Novadi Dessert Apple Breeding Programme ANOVA on a subset of 24 families DF F values Source Firmness Texture Flavour Juice Ac/ sugar Global Taste Site 5 31 244 413 281 27 113 Family 24 15 7 11 12 13 9 Year 6 8 5 6 7 6 17* Age 5 3NS 0 NS 3(5%) 1NS 2NS 4(1%) Site x family 94 5 6 7 7 4 7 * DF=4  Very High Site effect; Family effect significant but <<
  11. 11. INRA-Novadi Dessert Apple Breeding Programme ‘Site’ effect • Climate, soil, …. • ‘Human factor’ (harvesting, tasting, …) • Other factors (storage facilities, …)
  12. 12. INRA-Novadi Dessert Apple Breeding Programme Study of the ‘site’ effect 226 ind from 6 progenies Site 1 Site 6 Site 2 Site 5 Site 3 Site 4 Taste at Harvest time by each site 37 41 35
  13. 13. Site 4 Site 3 discarded selected discarded 1 4 selected 0 11 Site 6 Site 1 discarded selected discarded 9 18 selected 0 6 Site 5 Site 2 discarded selected discarded 0 1 selected 0 8 2 5 1 6 3 4 INRA-Novadi Dessert Apple Breeding Programme Results of the selection based on the sensory assessment performed at harvest at each site j
  14. 14. Site 4 Site 3 discarded selected discarded 1 4 selected 0 11 Site 6 Site 1 discarded selected discarded 9 18 selected 0 6 Site 5 Site 2 discarded selected discarded 0 1 selected 0 8 2 5 1 6 3 4 INRA-Novadi Dessert Apple Breeding Programme Results of the selection based on the sensory assessment performed at harvest at each site
  15. 15. Phenotypic correlations between sites within each pair 1-6 2-5 3-4 Attractiveness 0,41 0,54 0,32 Size 0,12 - 0 Firmness 0,52 0,2 0,11 Texture -0,26 0,60 0,29 Flavour -0,03 0,1 0 Global Taste -0,28 - -0,17 Juiciness 0,42 0,41 -0,34 Ac/sugar 0,27 -0,40 0,26 INRA-Novadi Dessert Apple Breeding Programme Results of the selection based on the sensory assessment performed at harvest in each site P<0.01 P<0.05 NS or neg
  16. 16. Site 1 Site 6 Site 2 Site 5 Site 3 Site 4 Instrumental Measurements Colorimetry Penetrometry Sugar content Acidity content ‘Sensory’ tasting Taste at Harvest time by each site assessment at INRA 10-20 fruit samples/ind sent to INRA INRA-Novadi Dessert Apple Breeding Programme Study of the ‘site’ effect After2months instorage
  17. 17. 2 5 1 6 3 4 INRA-Novadi Dessert Apple Breeding Programme Results of the selection based on the sensory assessment performed at INRA after 2 months Site 4 Site 3 discarded ?? selected discarded 25 5 0 ?? 0 6 1 selected 1 1 2 Site 6 Site 1 discarded ?? selected discarded 22 2 1 ?? 3 3 0 selected 4 2 2 Site 2 Site 5 discarded ?? selected discarded 22 3 2 ?? 3 1 1 selected 0 0 0
  18. 18. Phenotypic correlations between sites within each pair 1-6 2-5 3-4 Attractiveness 0,46 0,308 0,34 Firmness 0,63 0,264 0,42 Texture 0,004 0,18 0,30 Flavour 0,20 0,35 0,13 Juiciness 0,23 0,64 0,43 Ac/sugar 0,61 0,50 0,53 Global Taste 0,25 0,39 0,52 P<0.01 P<0.05 NS / 41 hyb / 34-35 hyb / 36-37 hyb INRA-Novadi Dessert Apple Breeding Programme Results of the selection based on the sensory assessment performed at INRA after 2 months
  19. 19. Few concluding remarks (1) Selection is dependant on both environmental and « testor » effects Big importance of site effects and GxE in selection: ranking of the cultivars can be different from one site to the other Few practical questions for the breeders: - what is their scope : worldwide cultivars or regional ones ? - Is it better to get less genotypes but duplicated or more genotypes not duplicated ?
  20. 20. HiDRAS High-Quality Disease Resistant Apples for a Sustainable Agriculture 2003 - 2006 Aim: to get a better knowledge of the genetic bases of apple quality
  21. 21. HiDRAS- WP1 « phenotyping » Plant material/ Fruit quality • ≈450 progenitors = 30 « common » cvars + 420 specific • 28 F1 progenies: • Fuji x Mondial Gala (200 ind) : UniBo • 27 progenies from : – INRA : 13 (11 x 50 ind + 2 x 25 ind) : 600 ind – SGGW : 4 (4 x 50 ind) : 200 ind – RIPF : 4 (4 x 50 ind) : 200 ind – BAZ : 3 (1 x100 ind + 2x 50 ind) : 200 ind – RCL : 3 (1 x100 ind + 2x 50 ind) : 200 ind 26 cvars for this study
  22. 22. WP1 – Fruit quality traits – Sensory evaluation – Instrumental measurements
  23. 23. Observation/sensory evaluation % of russet Cracking Bitter pit Watercore Harvest time Yield Eearly fruit drop Fruit,size Colour (ground colour, overcolour, - %, type) Attractiveness Fruit Shape Firmness Crispness Quality of theTexture Juiciness Sweetness Acidity Aroma Global Taste WP1 – Fruit quality traits
  24. 24. Instrumental measurements • Penetrometry firmness • Sugar content • Acidity content WP1 – Fruit quality traits
  25. 25. 4 dates of measurement: - Harvest (optimal maturity) - In storage: + 2 months + 4 months - « Shelf life »: after 2 monts in storage + 10-12 jours in the lab (+/- 20°C) WP1 – Fruit quality assessment for 3 years : 2003, 2004, 2005
  26. 26. 6 Experimental sites University of Bologna INRA Angers East Malling BAZ Dresden SGG Warsaw RIPF Skierniewice
  27. 27. Results
  28. 28. 1 2 3 4 5 6 2345678 lieux F2 D IT GB FR PO2 PO1 Elstar Golden De Mutsu Priscilla Discovery Illustration the GxE interaction Firmness Sites F2(Firmness) Mutsu Golden Del. Elstar
  29. 29. 1 2 3 4 5 6 2345678 lieux F2 D IT GB FR PO2 PO1 Elstar Golden De Mutsu Priscilla Discovery Illustration the GxE interaction Firmness Sites F2(Firmness) Mutsu Golden Del. Elstar Priscilla
  30. 30. Estimation of the GxE = « Ecovalence »; Wricke (1962) • Wricke Ecovalence = Wi = Σ(Yij - Yi. - Y.j + Y..)2 • Where Wi = ecovalence of the cvar i, • Yij = value of genotype i in year j, • Yi. = mean effect of the genotype i • Y.j = mean effect of year j • Y.. = general mean (all genotypes, all years) • Relative ecovalence = % ecovalence for 1 cvar or 1 site. Low Wi => high stability High Wi => low stability
  31. 31. Ecovalence of cvars for the instrumental traitsFiesta GranSmit Clivia Pilot IngMarie Braeburn Elstar Jonathan Idared Jonamac Prima Monroe Rubin Mutsu Topaz JamesGr Deliciou Gloster Pinova Discover Spartan Elan Akane Priscill GoldenDe Gala acidite inst Ecovalence 0.0 0.5 1.0 1.5 2.0 2.5 GranSmit Mutsu Clivia Fiesta Gala Discover Pilot Pinova Monroe Braeburn Jonamac Gloster Jonathan Spartan GoldenDe IngMarie Topaz Elan Priscill JamesGr Prima Akane Rubin Elstar Idared sucre inst Ecovalence 0.0 0.2 0.4 0.6 0.8 1.0 1.2 Discover Topaz Priscill Elan Pilot Fiesta Akane GranSmit JamesGr Braeburn Pinova Jonathan Clivia Gala Prima Deliciou Spartan Gloster Idared GoldenDe IngMarie Rubin Monroe Jonamac Mutsu Elstar variable F2 Ecovalence 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4
  32. 32. Ecovalence of cvars for the instrumental traitsFiesta GranSmit Clivia Pilot IngMarie Braeburn Elstar Jonathan Idared Jonamac Prima Monroe Rubin Mutsu Topaz JamesGr Deliciou Gloster Pinova Discover Spartan Elan Akane Priscill GoldenDe Gala acidite inst Ecovalence 0.0 0.5 1.0 1.5 2.0 2.5 GranSmit Mutsu Clivia Fiesta Gala Discover Pilot Pinova Monroe Braeburn Jonamac Gloster Jonathan Spartan GoldenDe IngMarie Topaz Elan Priscill JamesGr Prima Akane Rubin Elstar Idared sucre inst Ecovalence 0.0 0.2 0.4 0.6 0.8 1.0 1.2 Discover Topaz Priscill Elan Pilot Fiesta Akane GranSmit JamesGr Braeburn Pinova Jonathan Clivia Gala Prima Deliciou Spartan Gloster Idared GoldenDe IngMarie Rubin Monroe Jonamac Mutsu Elstar variable F2 Ecovalence 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 0 5 10 15 20 25 GranSmit Fiesta Clivia Pilot Discover Braeburn Topaz Pinova Mutsu Jonathan IngMarie JamesGr Elan Monroe Priscill Jonamac Akane Elstar Prima Gala Gloster Spartan Idared Rubin GoldenDe Ecovalencesrelatives acidité sucrosite penet Cvar relative ecovalences
  33. 33. 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 D FR GB IT PO1 PO2 0.00 0.50 1.00 1.50 2.00 2.50 D FR GB IT PO1 PO2 0.00 0.50 1.00 1.50 2.00 2.50 3.00 2003 2004 2005 fermeté croquant jutosité arome sucrosité acidité texture note globale 0.00 0.20 0.40 0.60 0.80 1.00 1.20 1.40 2003 2004 2005 acidité inst sucre inst penetromètrie Cumul of relative ecovalences / Year / Site /Sensorydata/Instrumentaldata
  34. 34. 1- ANOVA => GxE values Firmness ~ Genotype + site + Genotype : Site 2- PCA => Principal components on the GxE Interaction data Additive Main effects and Multiplicative Interaction (AMMI)
  35. 35. -0.5 0.0 0.5 -0.50.00.5 composante 1 (65.3 % ) composante2(15.9%) Akane Braeburn Clivia Deliciou DiscoverElan Elstar Fiesta GalaGlosterGoldenDe GranSmit IdaredIngMarie JamesGr Jonamac Jonathan Monroe Mutsu Pilot PinovaPrima Priscill Rubin Spartan Topaz -10 -5 0 5 10 -10-50510 D FR ITGB PO1 PCA of the interaction (AMMI) :
  36. 36. -0.5 0.0 0.5 -0.50.00.5 composante 1 (45.1 % ) composante2(32.6%) Akane Braeburn Clivia Deliciou Discover Elstar Fiesta Gala Gloster GoldenDeGranSmit Idared IngMarie JamesGr Jonamac Jonathan Monroe Mutsu Pilot Pinova Prima PriscillRubin Spartan -4 -2 0 2 4 -4-2024 D FR GB PO1 PO2 PCA of the interaction (AMMI) without Italian data:
  37. 37. Discover Topaz Priscill Elan Pilot Fiesta Akane GranSmit JamesGr Braeburn Pinova Jonathan Clivia Gala Prima Deliciou Spartan Gloster Idared GoldenDe IngMarie Rubin Monroe Jonamac Mutsu Elstar Variable Pénétromètrie Ecovalence 0.0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 IT D PO1-FR Correspondance lieux Effect of environments on the ecovalence of genotypes Cvars which ecovalence is mainly due to: Italy Germany Poland + France
  38. 38. Conclusions-Perspectives Importance of environmental effects but also GxE => Main issue for the breeders  Difficult/impossible to predict so far  Needs for variety testing network as EUFRIN We need more information on G x E:  merge breeding , variety testing (EUFRIN) , … data and perform common statistical analyses work with ecophysiologists to improve our understanding in GxE ( models including environmental factors)
  39. 39. 1 2 3 4 5 6 2345678 lieux F2 D IT GB FR PO2 PO1 Elstar Golden De Mutsu Topaz
  40. 40. PCA on the sensory data -0.4 -0.2 0.0 0.2 0.4 -0.4-0.20.00.20.4 composante 1 (71,4 % ) composante2(16,1%) Akane Braeburn Clivia Deliciou Discover Elan Elstar Fiesta Gala Gloster GoldenDe GranSmit Idared IngMarie JamesGr Jonamac Jonathan Monroe Mutsu Pilot Pinova Prima Priscill Rubin Spartan Topaz -4 -2 0 2 4 -4-2024 ferm croc jut gout sucr acid text PC 1 (71.4%) PC2(16.1%)
  41. 41. Idared 7% Red D. 6.5% Elstar 4.4% Braeburn 3% Granny S. 3% Shampion 2.9% Fuji 2.2% Cripps Pink 1.5% Golden D. 24% Gala 10%Jonagold 8.5% European apple production FAOstat
  42. 42. Granny Smith 12% Braeburn 6% Red Del 4.8% Fuji 3.7% Canada 2.7% Belchard 2.6% Elstar 1% Golden D. 34% Gala 16% French apple production ANPP 2011
  43. 43. Braeburn 8.8% Boskoop 6.3% Holst.cox 5.5% Jonagold 32% Elstar 29%
  44. 44. Braeburn 8.8% Boskoop 6.3% Holst.cox 5.5% Jonagold 32% Elstar 29% German(Altes land) apple production
  45. 45. Braeburn 8.8% Boskoop 6.3% Holst.cox 5.5% my notes from K. Klopp presentation in Interpoma 2012 Jonagold 32% Elstar 29% German(Altes land) apple production
  46. 46. Braeburn 10% Golden 5%Idared 6% Gala 10% Boskoop 3% Cox Or. 1% Jonagold 30% Elstar 16%
  47. 47. Braeburn 10% Golden 5%Idared 6% Gala 10% Boskoop 3% Cox Or. 1% Jonagold 30% Elstar 16% German(Bodensee) apple production
  48. 48. INRA-Novadi Dessert Apple Breeding Programme Assessed traits in orchards • Harvest date • Fruit set • # fruits/cluster • Fruit drop • Firmness • Texture quality • Juice • Ratio Acidity/Sugar • Flavour • Global Taste • Fruit size • Overcolour • % colouring • Ground-colour • Type of colouring • Attractiveness • Bitter Pit • Russeting • Water core • Cracking • Susc. P. mildew • Susc. other diseases Tree/harvesting Attractiveness Fruit Quality Disease Susceptibility Physiological disorders Ordinal scale : 1 (low, bad) – 5 (high, very good)

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