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


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 <<


‘Site’ effect

• Climate, soil, ….

• ‘Human factor’ (harvesting, tasting, …)

• Other factors (storage facilities, …)


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


discarded 9 18

selected 0 6

Site 5


discarded 0 1

selected 0 8

2

5

1

6

3

4


Results of the selection based on the sensory

assessment performed at harvest at each site

j

Site 4


discarded 1 4

selected 0 11

Site 6


discarded 9 18

selected 0 6

Site 5


discarded 0 1

selected 0 8

2

5

1

6

3

4



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



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


Study of the ‘site’ effect A

fter 2

mo

nth

s

in s

tora

ge

2

5

1

6

3

4



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


discarded 22 2 1

?? 3 3 0

selected 4 2 2

Site 2


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



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


Instrumental measurements

• Penetrometry firmness

• Sugar content

• Acidity content


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


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)

29 gx e interactions-f. laurens

Technology