This document summarizes research from two datasets on the environmental effects and genotype-environment interaction in apple. It finds a very high site effect on traits like firmness, texture, and flavor compared to the family/genotype effect. Phenotypic correlations between sites within pairs ranged from non-significant to highly significant depending on the trait. Analysis of a subset of families found significant selection differences between sites for the same individuals. The study concludes that apple selection is highly dependent on environmental and tester effects, with rankings of cultivars differing between sites.
Environmental effects and Genotype x Environment Interaction in apple breeding programme
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
-
5. seeds
crosses
seedlings resistant
to the scab test
G
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a
s
s
h
o
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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. 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. 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. 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. 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. 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 <<
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. 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. 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. 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. 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. 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. 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. 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 ?
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
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
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. 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. 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. 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. 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
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. -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. -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:
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.
40. 1 2 3 4 5 6
2345678
lieux
F2
D IT GB FR PO2 PO1
Elstar
Golden De
Mutsu
Topaz
41. 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%)
42. 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
43. 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
49. 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)