lambert, p., 2012

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







Peach breeding programmes at INRA Avignon

Two main targets





Resistance to pests and diseases

Fruit QualityPowdery mildew

PPV

Green peach aphid

Monilinia









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







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)







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







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…)







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







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







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







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










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







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







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







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







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







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







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







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







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







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


2. Fine mapping Traits

3. Pilot studies

4. MAB Pipeline

5. DB interface

WP2 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


6. QTL validation

1. Adaptation FlexWP4 LD/GWA

1. Phen & genet vriability

2. Core collection


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



3. Pilot studies

4. MAB Pipeline

5. DB interface

WP2 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


6. QTL validation

1. Adaptation Flex SoftwareWP4 LD/GWA


2. Core collection


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



3. Pilot studies

4. MAB Pipeline

5. DB interface

WP2 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


6. QTL validation



2. Core collection


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



3. Pilot studies

4. MAB Pipeline

5. DB interface

WP2 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


6. QTL validation



2. Core collection


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

Go to www.fruitbreedomics.com

[email protected]

To get the latest news of the project

And





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



lambert, p., 2012

Documents

material evaluation

marker assisted

material evaluation

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agronomical

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fruit quality