lambert, p., 2012
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Séminaire SNP -UGAFL - 19 janvier 2012
Peach Molecular Breeding at the INRAAvignon and links to a new European
initiative to increase fruit breeding efficiencyFP7 KBBE FruitBreedomics
Patrick LAMBERTUR1052 UGAFL INRA Avignon
France
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Peach breeding programmes at INRA Avignon
Two main targets
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
Resistance to pests and diseases
Fruit QualityPowdery mildew
PPV
Green peach aphid
Monilinia
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
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European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Context• Sanitary protection of the orchard: a strong concern • fruit orchards : 21 % of the insecticide market • Green aphid, powdery mildew, plum pox virus, monilinia :
> resistances are available and exploitable
Motivations:• Contribute to lower chemicals to protect the environment and the health of all the actors > producer and consumer• help in the adoption of alternative methods of phytoprotection to support the European fruit production and the fruit producers by the release of resistant and innovative varieties
Stakes:• Development of new tools to obtain improved material via Marker Assisted Breeding
• an innovative collaborative project at the international level begun in 2011� FP7 KBBE FruitBreedomics
Peach Breeding for resistance to pests and diseases
A main objective
Séminaire SNP -UGAFL - 19 janvier 2012
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European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Several sources of resistance are available
but … The agronomical level is low
Selection process slowed and time consuming
Successive crosses are needed to get a commercial agronomical value
But, molecular markers linked to the loci of interest could help to speed up the released of
novel resistant varieties
But….how to reach these objectives?
Implementation of Marker Assisted Breeding (MAB)
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Prunus davidiana (clone P 1908) : resistant to powdery mildew, green peachaphid, monilinia and PPV … but the agronomical level is very low
Wild
species
related
to
peach
and
Rootstocks
peach
Pamirskij5
Rubira
Few sources of resistance available
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Objectives
� novel varieties resistant to Powdery mildew, Green peach aphidPlum pox virus and Monilinia
Selecting novel varieties or elite cultivars with improved resistance > several strategies
For short term :
� by combining several strong monogenic resistance factors in
selected improved cultivars
Powdery mildew + Myzus persicae
For long term :
� Building lasting resistance by combining these monogen ic resistances
with polygenic resistance factors from:
- Prunus davidiana (Powdery mildew, Myzus, Monilinia and sharka)
- old varieties and genetic resources ( cv Bolinha for Monilinia…)
Séminaire SNP -UGAFL - 19 janvier 2012
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European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Overview of the types of resistance carried by the resistance sources used for breeding
P. davidiana: cl. P1908
Backcross
Polygenic
Monogenic
Resistances
Myzus
Powdery mildew
Malo Konare: Vr1
Weeping Flower peach: Rm1
S 2678
Rubira: Rm2
S 2605
Pamirskij 5: Vr2
S 5392
MP.SD-3.1 , MP.SD-5.1
PM.SD-6 , PM.SD8
PPV.RD-2.1, 2.2, 7.1, 7.2 …
Myzus
Powdery mildew
Mono/Poly Pest or disease Origin QTLs/locus (gene) Improved varieties
Gen
etic
var ia
bilit
y
PPV
S 6146
Séminaire SNP -UGAFL - 19 janvier 2012
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A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Fine analysis of mechanisms
Developing tests for selection at early
stages
Integrating molecularmarkers
Finding Resistance sources
Consum
ers
Research
Breeders
� Sowing at a young stage in greenhouse
�Validation under insect-proof tunnel
� And\or in orchard at a grown-up stage
• Genotyping and mapping of segregatingpopulations
•QTL and candidate gene mapping
•Marker assisted Breeding (MAB)
Evaluation of collections and genetic resources
� Resistance scoring
� Classic biological tests
� On leaves and/or fruits
�Inoculations / controlled infestations
� scoring scales in classes (0 - 4)
� Study of the aphid feeding behaviourby electropenetrography ( EPG)
� Analysis of the organic volatile compounds
� Biochemical analyses (polyphenols) . Associated with genetic studies
A pluridisciplinary approach for improving resistance> genetic to functionnal
Fruit grovers
Séminaire SNP -UGAFL - 19 janvier 2012
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European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Time (hour)
P 1908
Malo konare
Summergrand
Rubira
WFP
Example of the resistance to Myzus persicae(1) behaviour on the host tree
0
20
40
60
80
100
0 24h 48h 72h 96h 120h 144h 168
Aph
ids
on th
e le
aves
(%)
Antixenosis
(no colonisation)
Antibiosis
(colonisation but
no reproduction)
MajorGene
Séminaire SNP -UGAFL - 19 janvier 2012
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European COST 873 and ISHS joint meeting
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Signal amplification
Electrode(copper)
V signal
plant
electrode (Copper)
generator
Green peach aphid linked with a golden wire
Diagramme of the electric ciruitry(mod. Tjallingii)
Graph derived from the electricall variations obtained by using the EPG method.The different feeding phases correspond to different i ntensities.
Feeding behaviour
(2) Study of the feeding behaviour of Myzus persicae
by using EPG method
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
Séminaire SNP -UGAFL - 19 janvier 2012
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A G R I C U L T U R E
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European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Segregating populations used for breedingand genetic mapping
Interspecific peach x P.davidiana*Summergrand x P.davidiana (SD): F1 77 ind.*AF (Summergrand x P.davidiana)40: F2 99 ind.*SD40 x Summergrand (BC1= BC1s+BC1r)
(BC1) x Zephir: BC2 162 ind.*Rubira x P.davidiana (RxD)² : F2 190 ind.
Pamirskij 5 x P.davidiana (PxD)² : F1 250 ind.
Malo Konare x P.davidiana (MKxD)² : F1 170 ind.
Intraspecific peach*Pamirskij 5 x Rubira (PxR)²: F1 190 ind.AF Bolinha x Bolinha (B²): F1>170 ind.*(Weeping Flower peach x Pamirskij 5 (WP²) F2 100 ind.
* Genetic maps available anchored to the Prunus reference map
Séminaire SNP -UGAFL - 19 janvier 2012
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A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Targets for the developement of Marker AssistedBreeding (MAB) at UGAFL
Gr
Vr2
Rm2
Rmia
Major gene for Powdery mildew
Major gene for green peach aphid
Major gene for color
QTL Plum pox Virus P. davidiana
QTL Myzus persicae P. davidiana
QTL Powdery mildew P. davidiana
Resistance to pests and diseases
Major gene for nematode
Dicaffeoyl quinic acid
Chlorogenic acid
Fruit Quality and phenolics
Fructose/Glucose content
Position of major genes and QTLs identified from our peach mapping populations
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
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European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Many researches, results, QTLs ….BUTTo date just a few used in selection
(simple traits)Main reasons:- Low marker density (SSR)
� gaps in the genetic maps� weak precision on the QTL mapping
- Lack of information on the allelic diversity- Lack of information on background and
environmental effects- So far, lack of cheap and high throughput
genotyping tools
However, the curent use of markers in selection hasseveral limites
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Laurens F., Aranzana M.J. , Arus P. , Bonany J. , Corelli L. Patocchi A. ,
Peil, A. , Quilot B., Stella A., Troillard V., Velasco R., van de Weg E…….
An integrated approach for
increasing breeding efficiency in
apple and peach
1 March 2011- 31 August 2015
EU-FP7 KBBE large collaborative project
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
To fill in the gap between Genetics/Genomics and
breeding
- By developing and using molecular tools (SNP , Full transcript
chips) through multi-national collaborations
- By improving knowledge about genetics + genomics of major
agronomic traits + allelic diversity
���� By transferring material + tools + methodologies
to breeders
(within and outside the consortium)
AIMS
Séminaire SNP -UGAFL - 19 janvier 2012
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A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Partners
1515
2424
1616
1818
1919 2020
2121
33
44
771414
1717
1313
1212
1010
9988
66
55
1111
China
South Africa
11
Israël
NZ
2222
2222
2222
Close links with
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
WP1 Breeding
1. Breeding strategies
2. Fine mapping of traits
3. Pilot studies
4. MAB Pipeline
5. Data Base interface
WP2 Pre-Breeding
1. Material evaluation
2. Conventional pre breeding
3. Fast prebreeding
European Breeding
Platform
WP1 leader: A. Patocchi
(EVD)
WP2 leader: A. Peil
(JKI)
Aims at the establishment of pre-breeding materialIn a more efficient way by using SNP markers
� 10,000 seedlings for each species�Different crosses with different trait
combinations� Aims at the improvement and application of a fast-breeding system in apple.
The general objective is to develop more efficient breeding programmes applyingmarker assisted reeding.
� WP1 will use the two 9k SNP Illumina Chips developed in the framework of RosBREED
Targets>Monogenic traits>QTLs with strong
effects
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
WP4Exploring the phenotypic and geneticdiversity in collections and exploitation by association genetics approach
Diversity and QTL
mapping
WP3 PBA
3. QTL Fine mapping
2. QTL new traits
5. Wider QTL mining
4. Genet. div . in EU Breeding
6. QTL validation
1. Adaptation Flex Software
WP4 LD/GWA
1. Phen & genet variability
2. Core collection Establish
3. QTL mapping by GWA
WP3 leader: E. van de Weg
(DLO)
WP4 leader: M.J. Aranzana
(IRTA)
WP3Identification and characterisation of QTLBy the pedigree-based analysis approach
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Pedigree Based Analysis
Allelic diversity
Association Genetics
Fine Genetic Mapping
Objective
Find an « association » (correlation)
between the variation of a marker and a trait
Steps:
•Phenotyping
•Genotyping
•Find out associations
markers/phenotypes Rafalski & Morgante, 2004
SNP : Single Nucleotide Polymorphism
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich
Pedigree Based Analysis
Allelic diversity
Association Genetics
Fine Genetic Mapping
CULTIVARSMAPPING POPULATIONSRallsJan
Delicious
W inesap
RomBeauty
Jonathan
M_PRI668-100
GoldenDel
F2_26829-2-2
RedW inter
W agenerap
Prima
Cox
F_X-4598
Anta34.16
F_X-4355
Jefferies
PRI830-101
Clochard
ReiDuMans
GranSmith
F_Ill_#2
O53T136
Fuji
Crandall
PRI14-126
PRI14-152
Idared
KidsOrRed
X-4598
Z185
X-2599
Chantecler
Ill_#2
Rubinette
X-6823
TN_R10A8
PRI668-100
X-3177
PRI612-1
Gala
X-4355
X-3188
PRI672-3
X-6417
X-2771
X-3263
RedWinterX3177
Florina
X-6681
X-6799
Coop-17
X-4638
X-3143
Galarina
X-6564
X-6820
Baujade
X-3259
X-6679
Dorianne
X-6808
X-3318
X-6398
X-6683
X-3305
12_I01
I_CC03
12_K01
12_L01
12_O03
I_BB02
I_J01
12_F01
12_J01
I_W01
I_M01
12_N01
12_P01
Apple30 progenies9K SNP chip
Peach30 progenies9K SNP chip
Apple20-50K SNP chip
Peach9K SNP chip
WP5 New Trait knowledge
1. Biotic stresses: Monilia
2. Fruit quality : texture, fiber
3. Abiotic stresses: chilling
requirement, water stress
WP5 leader: B. Quilot
(INRA)
WP5
Aims at enhancing the knowledge of genetics underlying no vel traits
And providing phenotyping methods by
� developing tools for novel traits determination
�Investigate novel complex traits using « omics » approach a nd modeling
�Make novel trait analysis high throughput applicable for the breeding industry
WP5 New Trait knowledge
2. Fruit quality : texture, fiber
Cell wall biochemicalanalyses
Transcriptomics
New tools
omics
WP5 Trait
knowledge
1. Biotic stresses
2. Fruit quality
3. Abiotic stresses
WP1 Breeding
1. Breeding strategies
2. Fine mapping Traits
3. Pilot studies
4. MAB Pipeline
5. DB interface
WP2 Pre-Breeding
1. Material evaluation
2. Conventional pre breeding
3. Fast prebreeding
European Breeding
Platform
Diversity and QTL
mappingWP3 PBA
3. QTL Fine mapping
2. QTL new traits
5. Wider QTL mining
4. Genet. div . in EU Breeding
6. QTL validation
1. Adaptation FlexWP4 LD/GWA
1. Phen & genet vriability
2. Core collection
3. QTL mapping by GWA
WP6 SNP chips
Low Medium
Low cost MAB
High WP6 leader: R. Velasco
FEM Italy
PFR ARC
WP5 Trait
knowledge
1. Biotic stresses
2. Fruit quality
3. Abiotic stresses
WP1 Breeding
1. Breeding strategies
2. Fine mapping Traits
3. Pilot studies
4. MAB Pipeline
5. DB interface
WP2 Pre-Breeding
1. Material evaluation
2. Conventional pre breeding
3. Fast prebreeding
European Breeding
Platform
Diversity and QTL
mappingWP3 PBA
3. QTL Fine mapping
2. QTL new traits
5. Wider QTL mining
4. Genet. div . in EU Breeding
6. QTL validation
1. Adaptation Flex SoftwareWP4 LD/GWA
1. Phen & genet variability
2. Core collection
3. QTL mapping by GWA
WP7 bioinfo
FruitBreed Data BaseWP7 leader: A. Stella
(PTP) Genome DatabaseFor Rosaceae (GDR)
WP5 Trait
knowledge
1. Biotic stresses
2. Fruit quality
3. Abiotic stresses
WP1 Breeding
1. Breeding strategies
2. Fine mapping Traits
3. Pilot studies
4. MAB Pipeline
5. DB interface
WP2 Pre-Breeding
1. Material evaluation
2. Conventional pre breeding
3. Fast prebreeding
European Breeding
Platform
Diversity and QTL
mappingWP3 PBA
3. QTL Fine mapping
2. QTL new traits
5. Wider QTL mining
4. Genet. div . in EU Breeding
6. QTL validation
1. Adaptation Flex SoftwareWP4 LD/GWA
1. Phen & genet variability
2. Core collection
3. QTL mapping by GWA
WP6 SNP chips
Low Medium
Low cost MAB
High
WP7 bioinfo
FruitBreed Data Base
Tools
WP
8 D
issem
ina
tion
WP
9.
Ma
na
ge
me
nt W
P8
lea
de
r: J. Bo
na
ny
(IRT
A)
WP
9 l
ea
de
r: V
. T
roil
lard
(IT
)
WP5 Trait
knowledge
1. Biotic stresses
2. Fruit quality
3. Abiotic stresses
WP1 Breeding
1. Breeding strategies
2. Fine mapping Traits
3. Pilot studies
4. MAB Pipeline
5. DB interface
WP2 Pre-Breeding
1. Material evaluation
2. Conventional pre breeding
3. Fast prebreeding
European Breeding
Platform
Diversity and QTL
mappingWP3 PBA
3. QTL Fine mapping
2. QTL new traits
5. Wider QTL mining
4. Genet. div . in EU Breeding
6. QTL validation
1. Adaptation Flex SoftwareWP4 LD/GWA
1. Phen & genet variability
2. Core collection
3. QTL mapping by GWA
WP6 SNP chips
Low Medium
Low cost MAB
High
WP7 bioinfo
FruitBreed Data Base
Tools
WP
8 D
issem
ina
tion
WP
9.
Ma
na
ge
me
nt W
P8
lea
de
r: J. Bo
na
ny
(IRT
A)
WP
9 l
ea
de
r: V
. T
roil
lard
(IT
)
Germplasm
curators
Breeding stakeholders
Séminaire SNP -UGAFL - 19 janvier 2012
A L I M E N T A T I O N
A G R I C U L T U R E
E N V I R O N N E M E N T
Peach Breeding aknowledgement
T. Pascal 1, P. Lambert 1, B. Quilot, J.L. Poëssel 1, M. Corre 1, E. Lecerf 1, M.H. Sauge 2, JP. Lacroze 2, F. Pfeiffer 1, M. Staudt 3, Y. Rahbé A. 4, Moing 5
1 INRA, Unité de Génétique et d'Amélioration des Fuits et Légumes, BP 94 - 84143 Avignon - Montfavet Cedex2 INRA, Unité Plante et Système de culture Horticole, Domaine St Paul, Site Agroparc, 84914 Avignon - Mont favet3 Centre d'Ecologie Fonctionnelle et Evolutive - CNRS, 1919, Route de Mende, 34293 Montpellier Cedex,4 INSA - INRA UA 203, Laboratoire de Biologie Appliquéee 406, 20 av. A. Einstein, 69621 Villeurbanne5 INRA, UMR 619 Biologie du Fruit - Plate-forme Metabo lome-Fluxome , BP81, 33883 Villenave d’Ornon
Thanks for your attention
European COST 873 and ISHS joint meeting
14-17 February 2012 Zurich