01 introduction-f. laurens-20130221
DESCRIPTION
TRANSCRIPT
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
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
22
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
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
MAB GWS
On apple and peach
Ms on fine mapping of selected major genes or QTLs
WP2 Pre-Breeding
WP2 highlights 2012 + perspectives 2013
To prepare new genitors (progenitors) for the future breeding programmes Selection time
1. Material evaluation
2. Conventional pre breeding
3. Fast prebreeding
WP2 highlights 2012 + perspectives 2013
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
WP2 highlights 2012 + perspectives 2013
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
Genome Wide Association
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 Pedigree Based Analysis
Peach progenies genotyped with the 9K
IPSC SNP array
FlexQTLTM
Interface computation time New functionalities
WP3 highlights 2012 + perspectives 2013
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
4. Genet. div . in EU Breeding
6. QTL validation
1. Adaptation Flex Pedigree Based Analysis
Peach progenies genotyped with the 9K
IPSC SNP array
FlexQTLTM
Interface computation time New functionalities
WP3 highlights 2012 + perspectives 2013
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
Genome Wide Association
Genetic structure of apple and peach
germplasm. Preliminary GWA studies on peach
Apple and peach phenotypic data
in FB DB
WP4 highlights 2012 + perspectives 2013
WP1
WP7
Define core collection D4.1
Test panel with 48 accessions
genotyped with 20K SNP chip
WP6
WP4 LD/GA
Genome Wide Association
Genetic structure of apple and peach
germplasm. Preliminary GWA studies on peach
Apple and peach phenotypic data
in FB DB
WP4 highlights 2012 + perspectives 2013
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
WP5 highlights 2012 + perspectives 2013
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
WP5 highlights 2012 + perspectives 2013
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
WP6 highlights 2012 + perspectives 2013
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 ?)
WP6 highlights 2012 + perspectives 2013
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
WP7 highlights 2012 + perspectives 2013
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
WP7 highlights 2012 + perspectives 2013
Enter and use genotypic data
Resequencing data
Excel template Apple and
peach data in the DB
WP8 Dissemination
WP8 highlights 2012 + perspectives 2013
Design and management of
the Website
Contacts with stakeholders (meetings, questionnaires)
1st Newsletter
Training sessions
WP8 Dissemination
WP8 highlights 2012 + perspectives 2013
Design and management of
the Website
Contacts with stakeholders (meetings, questionnaires)
1st Newsletter
2nd Newsletter
Transfer of technology to stakeholders