01 introduction-f. laurens-20130221

Laurens F., Aranzana M.J. , Arus P. , Bonany J. , Corelli L., Durel C.E., Micheletti D., Patocchi A. , Pascal T., Peil, A. , Quilot B., Stella A., Troggio M., Troillard V., Velasco R., van de Weg E, …

1 March 2011- 31 August 2015

EU-FP7 large collaborative project

www.fruitbreedomics.com 2nd annual meeting

Lleida

http://www.fruitbreedomics.com/

15

Research 1 – INRA 2 – ARO (IL) 5 – CRA-W 6 – CRA 8 – ETHZ 9 – EVD 10 – FEM 12 – IRTA 13 – JKI 15 – PTP 16 – RBIPH 18 – DLO 19 – UMIL 20 – UNIBO 21 – READING 22 – ARC (ZA) 23 – PFR (NZ) 24 – ZJU (CN)

25 – KUL 26 – RCL

SMEs 3 – ASF 4 – B3F 7 – DNV 14 – NOVADI 17 – RDG

Management 11 – IT

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23

24

16

18

19 20

21

3

4

7 14

17

13

12

10

9 8

6

5

2

11

Israël NZ

China

South Africa

1

+ close links with :

Rosbreed (WSU), SLU (Sweeden)

Partners

25

+ contacts in Russia:

VNIISPK (Orel)

SKZNIISIV (Krasnodar) North Caucasia

To fill in the gap between Genetics/Genomics and breeding

- Development + use of molecular tools (SNP , Full transcript chips) /international collaboration

- Better knowledge / genetics + genomics of major agronomic traits + allelic diversity Material + tools + methodologies /breeders

AIMS

WP5 Trait knowledge

WP1 Breeding/MAB WP2 Pre-Breeding European Breeding Platform

Diversity and QTL mapping WP3 PBA

WP4 LD/GWA

WP6 SNP chips WP7 bioinfo Tools

WP

8 D

issem

inatio

n W

P9

. Man

age

me

nt

A. Patocchi (EVD) A. Peil (JKI)

E. van de Weg (DLO)

Pedigree Based Analysis

Genome Wide Association

M.J. Aranzana (IRTA)

B. Quilot (INRA)

A. Stella (PTP) R. Velasco (FEM)

V. T

roill

ard

(IT

) J. B

on

ani (IR

TA)

Test the efficiency of the use of molecular markers in current breeding programmes

WP1 Breeding/MAB

1. Breeding strategies

2. Fine mapping

3. Pilot studies

4. Pipeline

5. DB interface

WP1 highlights 2012 + perspectives 2013

- Apple and peach Questionnaires, meetings

priorities - Breeding criteria - Breeding schemes

SNP markers tighted to most of

the targeted genes

Selection of the apple pilot progenies

In progress - Test of SNP based low cost

genotyping platforms for MAB and GWS

- pipeline… to be discussed at the WP1 workshop

Decision to move towards GWS

-> MAB for MG -> GWS for Q traits

WP1 Breeding/MAB

WP8

1. Breeding strategies

2. Fine mapping

3. Pilot studies

4. Pipeline

5. DB interface


- Apple and peach Questionnaires, meetings

priorities - Breeding criteria - Breeding schemes

SNP Markers tighted to most of

the targeted genes

Selection of the apple pilot progenies

In progress - Test of SNP based low cost

genotyping platforms for MAB and GWS

- pipeline… to be discussed at the WP1 workshop

Decision to move towards GWS

-> MAB for MG -> GWS for Q traits

WP1 Breeding/MAB

MAB GWS

On apple and peach

Ms on fine mapping of selected major genes or QTLs

WP2 Pre-Breeding


To prepare new genitors (progenitors) for the future breeding programmes Selection time

1. Material evaluation

2. Conventional pre breeding

3. Fast prebreeding


Plant material evaluated for resistance

and fruit traits

New progenies created to pyramide genes of

interest

New early apple flowering lines carrying resistance genes (fire

blight, powdery mildew) produced and pollinated

WP2 Pre-Breeding

1. Material evaluation

2. Conventional pre breeding

3. Fast prebreeding


Plant material evaluated for resistance

and fruit traits

New progenies created to pyramide genes of

interest

New early apple flowering lines carrying resistance genes (fire

blight, powdery mildew) produced and pollinated

WP2 Pre-Breeding

Phenotype and genotype new

progenies

Put data in DB

Solve some issues about FB early flowering lines

Diversity and QTL fine 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 WP4 LD/GA

1. Phen & genet variability

2. Core collection

3. QTL mapping by GWA

Pedigree Based Analysis


WP3 PBA

3. QTL Fine mapping

2. QTL new traits

5. Wider QTL mining


6. QTL validation

1. Adaptation Flex Pedigree Based Analysis

Peach progenies genotyped with the 9K

IPSC SNP array

FlexQTLTM

Interface computation time New functionalities


first peach QTL mapping

analyses in progress

Apple 20K SNP array

WP6

WP3 PBA

3. QTL Fine mapping

2. QTL new traits

5. Wider QTL mining


6. QTL validation

1. Adaptation Flex Pedigree Based Analysis

Peach progenies genotyped with the 9K

IPSC SNP array

FlexQTLTM

Interface computation time New functionalities


Apple 20K SNP array

Peach QTL mapping analyses

completed

Apple QTL mapping analyses

Integrated linkage map

List of EU-founders and indications on their level of exploitation in breeding. (Del 3.1)

WP6

Organization of the PBA training session

WP8

WP4 LD/GA


Genetic structure of apple and peach

germplasm. Preliminary GWA studies on peach

Apple and peach phenotypic data

in FB DB


WP1

WP7

Define core collection D4.1

Test panel with 48 accessions

genotyped with 20K SNP chip

WP6

WP4 LD/GA


Genetic structure of apple and peach

germplasm. Preliminary GWA studies on peach

Apple and peach phenotypic data

in FB DB


WP1 WP7

Define core collection D4.1

Test panel with 48 accessions

genotyped with 20K SNP chip

WP6

Peach GWA studies

completed

Apple genotyping (choice of the

genotyping tool)

then GWA

WP6

WP5 Trait knowledge

1. Biotic stresses: Monilia

2. Fruit quality : texture, fiber

3. Abiotic stresses


and test of tools and protocols

Start transcriptomics approach

/Fruit quality

WP5 Trait knowledge

1. Biotic stresses: Monilia

2. Fruit quality : texture, fiber

3. Abiotic stresses


and test of tools and protocols

Start transcriptomics approach

/Fruit quality

Select highthrouput phenotyping tools

Select /stop

New tests in

2013

Analysis of the data

WP6 SNP chips Tools

Tests of low density chips for

WP1

20k Illumina Infinium Apple SNP

Chip available


Test apple 20k Illumina Infinium on 48

genotypes

WP4 WP1 WP3

WP6 SNP chips Tools

Tests of low density chips for

WP1

20k Illumina Infinium Apple SNP

Chip available

Selection of a genotyping tool for apple WP4 in

progress (GBS or arrays ?)


Test apple 20k Illumina Infinium on 48

genotypes

WP4

Protocols to be used for large

germplasm genotyping

WP1 WP3

WP4 WP4

Final choice = Feb 2013

WP7 bioinfo Tools

Structure of phenotypic DB for apple and peach

completed User Interface

completed


Excel template Apple and

peach data in the DB

WP7 bioinfo Tools

Structure of phenotypic DB for apple and peach

completed

Need to standardize

names (ontology)

Search tool in phenotypic

database

User Interface completed


Enter and use genotypic data

Resequencing data

Excel template Apple and

peach data in the DB

WP8 Dissemination


Design and management of

the Website

Contacts with stakeholders (meetings, questionnaires)

1st Newsletter

Training sessions

WP8 Dissemination


Design and management of

the Website

Contacts with stakeholders (meetings, questionnaires)

1st Newsletter

2nd Newsletter

Transfer of technology to stakeholders

01 introduction-f. laurens-20130221

Technology

Transcript of 01 introduction-f. laurens-20130221