29 gx e interactions-f. laurens
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Transcript of 29 gx e interactions-f. laurens
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 -
FAO, 2011
EUFRIN-FruitBreedomics Lleida Feb. 2013 Dr. U. Mayr/Dr. R. Stehr
Apple varieties in Germany in Production
Northern Germany Lake Konstanz region
German apple production
Altes Land Bodensee
my notes from K. Klopp and M. Buchele presentations
in Interpoma 2012
seeds
crosses
seedlings resistant
to the scab test
Glasshouse
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
Orchard
Year 0
Year 6-8
Year 15-25…
Variety testing
Fruit Q
Yield…
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
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
1
1 2
5 6
3
4 Individuals 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
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
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 <<
INRA-Novadi Dessert Apple Breeding Programme
‘Site’ effect
• Climate, soil, ….
• ‘Human factor’ (harvesting, tasting, …)
• Other factors (storage facilities, …)
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
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
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
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
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 A
fter 2
mo
nth
s
in s
tora
ge
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
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
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 ?
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
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
WP1 – Fruit quality traits
– Sensory evaluation
– Instrumental measurements
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
Instrumental measurements
• Penetrometry firmness
• Sugar content
• Acidity content
WP1 – Fruit quality traits
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
6 Experimental sites University of Bologna
INRA Angers
East Malling
BAZ Dresden
SGG Warsaw
RIPF Skierniewice
Results
1 2 3 4 5 6
23
45
67
8
lieux
F2
D IT GB FR PO2 PO1
ElstarGolden DeMutsuPriscillaDiscovery
Illustration the GxE interaction Firmness
Sites
F2 (
Firm
ne
ss)
Mutsu
Golden Del.
Elstar
1 2 3 4 5 6
23
45
67
8
lieux
F2
D IT GB FR PO2 PO1
ElstarGolden DeMutsuPriscillaDiscovery
Illustration the GxE interaction Firmness
Sites
F2 (
Firm
ne
ss)
Mutsu
Golden Del.
Elstar
Priscilla
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
Ecovalence of cvars for the instrumental traits Fi
esta
Gran
Smit
Clivi
aPi
lotIn
gMar
ieBr
aebu
rnEl
star
Jona
than
Idar
edJo
nam
acPr
ima
Mon
roe
Rubin
Mut
suTo
paz
Jam
esGr
Delic
iouGl
oste
rPi
nova
Disc
over
Spar
tan
Elan
Akan
ePr
iscill
Golde
nDe
Gala
acidite inst
Ecov
alen
ce
0.0
0.5
1.0
1.5
2.0
2.5
Gran
Smit
Mut
suCl
ivia
Fies
taGa
laDi
scov
erPi
lotPi
nova
Mon
roe
Brae
burn
Jona
mac
Glos
ter
Jona
than
Spar
tan
Golde
nDe
IngM
arie
Topa
zEl
anPr
iscill
Jam
esGr
Prim
aAk
ane
Rubin
Elst
arId
ared
sucre inst
Ecov
alen
ce
0.0
0.2
0.4
0.6
0.8
1.0
1.2
Dis
cove
rTo
paz
Pris
cill
Ela
nP
ilot
Fies
taA
kane
Gra
nSm
itJa
mes
Gr
Bra
ebur
nP
inov
aJo
nath
anC
livia
Gal
aP
rima
Del
icio
uS
parta
nG
lost
erId
ared
Gol
denD
eIn
gMar
ieR
ubin
Mon
roe
Jona
mac
Mut
suE
lsta
r
variable F2
Eco
vale
nce
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1.4
Ecovalence of cvars for the instrumental traits F
iesta
Gra
nS
mit
Cliv
iaP
ilot
IngM
ari
eB
raeburn
Els
tar
Jonath
an
Idare
dJonam
ac
Pri
ma
Monro
eR
ubin
Muts
uT
opaz
Jam
esG
rD
elic
iou
Glo
ste
rP
inova
Dis
cover
Spart
an
Ela
nA
kane
Pri
scill
Gold
enD
eG
ala
acidite inst
Eco
va
len
ce
0.0
0.5
1.0
1.5
2.0
2.5
Gra
nS
mit
Muts
uC
livia
Fie
sta
Gala
Dis
cover
Pilo
tP
inova
Monro
eB
raeburn
Jonam
ac
Glo
ste
rJonath
an
Spart
an
Gold
enD
eIn
gM
ari
eT
opaz
Ela
nP
riscill
Jam
esG
rP
rim
aA
kane
Rubin
Els
tar
Idare
d
sucre inst
Eco
va
len
ce
0.0
0.2
0.4
0.6
0.8
1.0
1.2
Dis
cover
Topaz
Pri
scill
Ela
nP
ilot
Fie
sta
Akane
Gra
nS
mit
Jam
esG
rB
raeburn
Pin
ova
Jonath
an
Cliv
iaG
ala
Pri
ma
Delic
iou
Spart
an
Glo
ste
rId
are
dG
old
enD
eIn
gM
ari
eR
ubin
Monro
eJonam
ac
Muts
uE
lsta
r
variable F2
Eco
va
len
ce
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1.4
0
5
10
15
20
25
Gra
nSm
it
Fie
sta
Cliv
ia
Pilo
t
Dis
cove
r
Bra
eb
urn
Top
az
Pin
ova
Mu
tsu
Jon
ath
an
IngM
arie
Jam
esG
r
Elan
Mo
nro
e
Pri
scill
Jon
amac
Aka
ne
Elst
ar
Pri
ma
Gal
a
Glo
ste
r
Spar
tan
Idar
ed
Ru
bin
Go
lde
nD
e
Ecovalences relatives
acidité
sucrosite
penet
Cvar relative ecovalences
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
/ Se
nso
ry d
ata
/In
stru
me
nta
l dat
a
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)
-0.5 0.0 0.5
-0.5
0.0
0.5
composante 1 (65.3 % )
com
posante
2 (
15.9
%)
Akane
Braeburn
Clivia
Deliciou
DiscoverElan
Elstar
Fiesta
GalaGlosterGoldenDe
GranSmit
IdaredIngMarie
JamesGr
Jonamac
Jonathan
MonroeMutsu
Pilot
PinovaPrima
PriscillRubinSpartan
Topaz
-10 -5 0 5 10
-10
-50
510
D
FR
ITGB
PO1
PCA of the interaction (AMMI) :
-0.5 0.0 0.5
-0.5
0.0
0.5
composante 1 (45.1 % )
com
posante
2 (
32.6
%)
Akane
Braeburn
Clivia
Deliciou
Discover
Elstar
Fiesta
Gala
Gloster
GoldenDeGranSmitIdared
IngMarie
JamesGr
Jonamac
Jonathan
Monroe
Mutsu
Pilot
Pinova
PrimaPriscillRubin
Spartan
-4 -2 0 2 4
-4-2
02
4
D
FRGB
PO1
PO2
PCA of the interaction (AMMI) without Italian data:
Dis
cover
Topaz
Priscill
Ela
nP
ilot
Fie
sta
Akane
Gra
nS
mit
Jam
esG
rB
raeburn
Pin
ova
Jonath
an
Cliv
iaG
ala
Prim
aD
elic
iou
Spart
an
Glo
ste
rId
are
dG
old
enD
eIn
gM
arie
Rubin
Monro
eJonam
ac
Muts
uE
lsta
r
Variable Pénétromètrie
Eco
va
len
ce
0.0
0.2
0.4
0.6
0.8
1.0
1.2
1.4
ITDPO1-FR
Correspondance lieux
Effect of environments on the ecovalence of genotypes
Cvars which ecovalence is mainly due to: Italy Germany Poland + France
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)
1 2 3 4 5 6
23
45
67
8
lieux
F2
D IT GB FR PO2 PO1
ElstarGolden DeMutsuTopaz
PCA on the sensory data
-0.4 -0.2 0.0 0.2 0.4
-0.4
-0.2
0.0
0.2
0.4
composante 1 (71,4 % )
com
posante
2 (
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
-4-2
02
4
fermcroc jut gout
sucr
acid
text
PC 1 (71.4%)
PC
2 (
16
.1%
)
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
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
Braeburn
8.8%
Boskoop
6.3%
Holst.cox
5.5%
Jonagold 32%
Elstar
29%
Braeburn
8.8%
Boskoop
6.3%
Holst.cox
5.5%
Jonagold 32%
Elstar
29%
German(Altes land) apple production
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
Braeburn 10%
Golden
5% Idared
6%
Gala 10%
Boskoop
3%
Cox Or.
1%
Jonagold 30%
Elstar
16%
Braeburn 10%
Golden
5% Idared
6%
Gala 10%
Boskoop
3%
Cox Or.
1%
Jonagold 30%
Elstar
16%
German(Bodensee) apple production
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)