Genetic mapping and MAS of

resistance genes
in stone fruit and nut trees
at INRA

COST 873 meeting 18-19 February 2010 Barcelona

Plan of the presentation

INRA: Centers involved in fruit species researches

Examples of resistance genes analyzed on fruit species at INRA

Unit de Recherche sur les Espces Fruitires (UREF)
Research programs
Genetic Resources Center of INRA Bordeaux

Two examples developed with the collaboration of the UREF

Resistance to Xanthomonas campestris pv Juglandis in walnut
Root-knot nematode (RKN) resistance in Prunus rootstocks

COST 873 meeting 18-19 February 2010 Barcelona

Apple
Peach -Apricot
Sweet cherry-Peach strawberry
Prunus rootstock (walnut, chesnut)
Citrus

Apple- Apricot

Different levels of development

Exemples at the INRA

Evaluation of the resistance

Resistance to Xanthomonas campestris pv Juglandis in walnut
UREF-INRA Bx

Genetic mapping
Resistance to Phytophthora in Fagaceae (Castanea)
collaboration : UMR Biogeco Bx Pierroton: C. Robin
UREF: T Barrreneche
Resistance to Monilia in peach
UGAFL Avignon: B Quilot
SAM in progress
Resistance to the sharka virus in apricot
UGAFL Avignon: JM Audergon
UMR GDPP Bordeaux: V Decroocq
SAM already use
Nematode resistance in Prunus rootstock
collaboration : UMR IBSVSophia Antipolis, D. Esmenjaud
UREF Bordeaux , E. Dirlewanger
COST 873 meeting 18-19 February 2010 Barcelona

LUnit de Recherche sur les Espces Fruitires UREF

UREF
Aquitaine Region
Gironde dpartement
Villenave dOrnon, at 10 kms from Bordeaux

30 people

Breeding programs
Genetic and genomic: peach, Prunus rootstocks, strawberry
Fruit quality and disease resistance

UREF

Genetic and genomic

Breeding programs for sweet cherry,
strawberry and Prunus rootstock
Traits affected by climatic changes (chilling
requirement, blooming date)

2008

UREF: Genetic Resources Center for Prunuswalnut and chesnut

INRA CRG GAP-INRA for plants

7

Genetic Resources Center of INRA Bordeaux

Species

Accessio
ns Nb.

Phenotyping

Genotyping

Cherry

P.avium
P.cerasus

497

Phenology
+ Morphology

SSR

Plum

P.domestica

138

Phenology
+ Morphology

SSR
cpDNA

Peach

P.persica

608

Phenology

SSR

186

Phenology
+ Morphology

SSR
cpDNA

200

Phenology
+ Fruit
morphology

SSR

129

Morphology

SSR

55

Phenology
+ Fruit
morphology

SSR

Prunus related sp.

Walnut

J.regia

Walnut related sp.

Chestnut

C.sativa
C.mollisima
C.crenata

Total: 1813 accessions

Photos H. Christmann (INRA)

Resistance to Xanthomonas campestris pv Juglandis in

walnut

Bacterial disease is the main disease in walnut and can

be responsible of a loss of 50% of the production
No variety is resistant but differences of susceptibility
are observed
Symptoms on leaves, branches and fruits

COST 873 meeting 18-19 February 2010 Barcelona

Symptoms on leaves, branches and fruits

COST 873 meeting 18-19 February 2010 Barcelona

10

Objectives of the program INRA-UREF for resistance

to Xanthomonas campestris in walnut

Development of an early test for Xaj and for CVS (Chancre vertical
suintant- Deep bark cancer)

Use phenolic markers with simple determinism as Juglone, chalcone

synthase, myricitrine: antibacterial molecules (juglone)
Juglans nigra (resistant to Xanthomonas campestris): high amount
of myricitrine in leaves
Juglans regia (16 studied varieties): low amount in myricitrine

Identify variability for the susceptibility in several crosses

COST 873 meeting 18-19 February 2010 Barcelona

11

Parents (Juglans regia)

observed
Hybrids

Susceptibility to bacteria on fruit %

Null

Very low

Low
(Fa)

Intermedi
ate
(M)

High
(Fo)

Very
high

Franquette (Fa) x Payne (Fo)

129

10.9

10.9

32.6

33.3

8.5

3.9

Franquette (Fa) x Pedro (Fo)

62

27.4

22.6

29.0

17.7

3.2

0.0

Franquette (Fa) x Ashley (TFo)

80

11.3

21.3

32.5

27.5

6.3

1.3

Franquette (Fa) x Howard (M)

35

0.0

40.0

40.0

11.4

8.6

0.0

Franquette (Fa) x Lara (M)

99

33.3

29.3

27.3

9.1

1.0

0.0

Franquette (Fa) x Chandler (TFo)

72

12.5

41.7

22.2

18.1

4.2

1.4

Meylannaise (Fa) x Payne (Fo)

83

20.5

31.3

28.9

13.3

6.0

0.0

Meylannaise (Fa) x Pedro (Fo)

45

15.6

26.7

33.3

24.4

0.0

0.0

Solze(Fa) x Lara (M)

118

29.7

28.8

25.4

14.4

1.7

0.0

Solze(Fa) x Chandler (TFo)

38

0.0

26.3

28.9

26.3

15.8

2.6

Adams 10(TFa) x Lara (M)

96

17.7

34.4

25.0

18.8

4.2

0.0

Adams 10(TFa) x Chandler (TFo)

48

2.1

27.1

45.8

18.8

6.3

0.0

Grosvert (Fa) x Lara (M)

108

38.0

42.6

14.8

3.7

0.9

0.0

Grosvert (Fa) x Chandler (TFo)

66

3.0

18.2

56.1

18.2

4.5

0.0

Marbot (Fa) x Lara (M)

83

28.9

49.4

15.7

3.6

2.4

0.0

R de Montignac (Fa) x Chandler (TFo)

28

28.6

28.6

28.6

10.7

3.6

0.0

Chandler (TFo) x Lara (M)

36

0.0

13.9

52.8

27.8

5.6

0.0

Lara (M) x Chandler (TFo)

62

0.0

16.1

41.9

27.4

11.3

3.2

Fernette (Fa) x Chandler (TFo)

37

2.7

24.3

40.5

21.6

8.1

2.7

Fernette (Fa) x Serr (M)

67

4.5

29.9

43.3

20.9

1.5

0.0

H 96-26 (M) (Meylannaise X Pedro) x Serr (M)

25

0.0

44.0

44.0

12.0

0.0

0.0

Fernor (Fa) x Chico (Fo)

27

0.0

18.5

33.3

33.3

14.8

0.0

1444

13,0

28.5

33.7

18.7

5.4

0.7

Total number of hybrids

COST 873 meeting 18-19 February 2010 Barcelona

12

Susceptibility to bacteria on fruit %

Observed
hybrids

Null

Very
low

Low
(Fa)

Intermedi
ate
(M)

High
(Fo)

Very
high

Early

42

4.8

11.9

38.1

31.0

9.5

4.8

Intermediate

236

3.0

17.8

37.7

31.8

8.1

1.7

Intermediate-late

403

8.2

27.8

37.7

19.6

6.0

0.7

Late

321

13.4

32.7

32.1

18.1

3.7

0.0

Very late

345

34.5

32.8

20.9

9.0

2.3

0.6

Extremely late

94

36.2

38.3

21.3

3.2

1.1

0.0

1441

16.5

28.7

31.4

18.0

4.7

0.8

Bud break

Total

More bud break is delayed, less the trees are susceptible to bacteria.
This may be the wettest periods in early bud which would foster the growth of bacteria.
Gradually, as the production increases, severity increases: certainly du to the volume of the
canopy and fruit density.
COST 873 meeting 18-19 February 2010 Barcelona

13

Additional crosses.

Gniteurs

Observed
hyrides

Sensibilit la bactriose sur fruit en %

Nulle

Trs
faible

Faible
(Fa)

Moyenn
e
(M)

Forte
(Fo)

Trs
forte

Fernor (Fa) x Adams 10(TFa) (3me feuille)

(40 nont pas fructifi)

80

45

15

25

12.5

2.5

Lara (M) x Grand jefe (M) (3me feuille)

47

44.6

10.6

17.0

21.3

4.2

Franquette (Fa) x UK 6-2 (Fo) (5me feuille) (18)

(2me feuille) (22)

105

0
22.7

0
18.2

0
18.2

39
22.7

17
13.6

44
0

3 years of fructification are needed to evaluate the susceptibility on fruits

and wood

COST 873 meeting 18-19 February 2010 Barcelona

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Next interesting steps.

Associate hyper susceptibility to Cherry Leaf Roll Virus (CLRV) and

Xaj resistance by BC with Juglans regia.

Juglans nigra

Juglans regia

Juglans regia

resistant to Xaj, monogenic

hyper susceptibility to CLRV, monogenic

tolerant to CLRV
good fruit quality

Use phenolic markers for early selection

COST 873 meeting 18-19 February 2010 Barcelona

15

Root-knot nematode (RKN) resistance in

Prunus rootstocks

Nematodes from the Meloidogyne genus

- RKN species with the highest

economical impact :
M. arenaria
M. incognita
M. javanica
(M. floridensis)

16

RKN resistance
Resistance spectrum of main Prunus rootstocks
Rootstock

M. arenaria M. incognita M. javanica M. floridensis

Common peach, almond or plum

Ma

Rjap

R/S

Prunophora
Myrobalan plum

Japanese plum

Amygdalus
Peach

P.2175
P.1079
P.2980
J222

Nemared
Nemaguard
Shalil

Almond x Peach GF.557

Almond

Alnem 1.88.201

RMja

RMia
RMia

RMja

Ma1/ma
(Lecouls et al.
1977)

RMia/rmia
(Claverie et
al. 2004a)
RMja/RMja(Kochba and
Spiegel-Roy1975)

17

RKN resistance : RMia and Ma localisation

Claverie et al. 2004, Dirlewanger et al. 2004

G1

G2

G3

G4

G5

G6

G7

G8

RMia

Ma

COST 873 meeting 18-19 February 2010 Barcelona

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RKN resistance : RMja almond, Rjap in Japenese

plum

Almond-peach
TxE
(LG7)

Japenese plum
J.222
Myrobalan plum
P.2175

Almond
Alnem1
CPPCT022

CPPCT022

CPPCT022
SCAN12

SCAN12
3.5

Pchgms6
0/29
0/29
1/29
2/29
3/29

RMja 2.3

CPSCT026

Pchgms6

Ma

Rjap

Pchgms6

CPSCT026
Pchgms6

7.2
33

CPSCT026
UDP98-405
UDP98-405

20
11.8
CPPCT033

CPPCT033

CPPCT033

CPPCT033

Van Ghelder et al , TGG 2009

COST 873 meeting 18-19 February 2010 Barcelona

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RKN resistance : Ma map base cloning

Fine mapping: BSA-AFLP

Transformation of AFLPs into SCARs
Sceening a large progeny with the SCAR markers
Construction of a BAC library
Screening the BAC library
Sequencing the two BAC clones containing each alleles R/S

Gene prediction analyses

To be done
Validation: transformation
COST 873 meeting 18-19 February 2010 Barcelona

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Cloning of Ma gene: 3 TNLs candidats

TNL: TIR-NBS-LRR

Ma (54 kb)
TNL 1
10kb

TNL 1
tnl1

TNL 2

TNL 3

7 ORF

LRR/ retro. E

8kb

TNL 2 TNL 3
tnl2

tnl3

=R
=S

21

Thanks for your invitation

UREF
22