1. An integrated approach for
increasing breeding efficiency in
apple and peach
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, …
EU-FP7 large collaborative project
1 March 2011- 31 August 2015

2. AIMS
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
(within and outside the consortium)

3. AIMS
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
(within and outside the consortium)

4. Partners
Research SMEs
1 – INRA 3 – ASF
2 – ARO (IL) 4 – B3F
5 – CRA-W 7 – DNV
6 – CRA 14 – NOVADI
8 – ETHZ 17 – RDG
9 – EVD
10 – FEM Management
12 – IRTA 11 – IT 24 China
13 – JKI
15 – PTP
21
16 – RBIPH
18 – DLO 18
5 13
19 – UMIL 4
16
20 – UNIBO
21 – READING + in 2012 : KUL, RCL … 1
11 8 9
22 – ARC (ZA)
3
23 – PFR (NZ) 19 20
14
24 – ZJU (CN) 7
15
17 12 6
10
+ close links with : Rosbreed (WSU),
SLU (Sweeden) 22
23 2
South Africa NZ Israël

5. Structure
WP1 Breeding European Breeding
Platform WP2 Pre-Breeding
WP9. Management
WP8 Dissemination
WP6 SNP chips Tools WP7 bioinfo
Diversity and QTL mapping
WP3 PBA
WP5 Trait
WP4 LD/GWA knowledge

6. Structure
WP1 Breeding European Breeding
1. Breeding strategies Platform
2. Fine mapping
3. Pilot studies
4. Pipeline
5. DB interface
WP1 leader: A. Patocchi
(EVD)
- On 10 000 seedlings on apple + 10 000 peach
- From commercial selection programmes
- Traits : according to the needs of stakeholders
- Selection of ind +/ind-
- Genotyping pipeline

7. Structure
European Breeding WP2 Pre-Breeding
Platform 1. Material evaluation
2. Conventional pre breeding
3. Fast prebreeding
WP2 leader: A. Peil
(JKI)

8. Structure
WP1 Breeding European Breeding
Platform WP2 Pre-Breeding
WP3 leader: E. van de Weg
(DLO)
Diversity and QTL mapping
WP3 PBA
Pedigree Based Analysis
1. Adaptation Flex WP4 leader: M.J. Aranzana
WP4 LD/GA
2. QTL new traits (IRTA)
1. Phen & genet variability
Genome Wide
3. QTL Fine mapping Association
2. Core collection
4. Genet. div . in EU Breeding
3. QTL mapping by GWA
5. Wider QTL mining
6. QTL validation

9. Fine Genetic Mapping
Allelic diversity
Pedigree Based Analysis Association Genetics

10. Fine Genetic Mapping
Allelic diversity
Pedigree Based Analysis Association Genetics
Objective
Find an « association » (correlation)
between the variation of a marker and a trait
Steps:
• Phenotyping
• Genotyping
• Find out associations
markers/phenotypes

11. Fine Genetic Mapping
Allelic diversity
Pedigree Based Analysis Association Genetics
MAPPING POPULATIONS CULTIVARS
RallsJan
Delicious Fuji
X-3318
X-3143
Winesap PRI668-100 X-2771
I_J01
Crandall
RomBeauty
X-6398
Jonathan PRI14-126 Galarina
X-3177
X-3263
M_PRI668-100 PRI14-152 12_F01
X-6564 X-6683
GoldenDel RedWinterX3177
Idared
PRI612-1
F2_26829-2-2
X-3305
X-6820 12_J01
RedWinter KidsOrRed
Florina
Wagenerap
Gala
X-4598 12_I01
Prima Baujade
I_W01
Cox Z185
X-6681
I_CC03
X-4355
F_X-4598
X-3259
X-2599
Anta34.16
I_M01
12_K01
X-6799
F_X-4355 Chantecler
X-3188
X-6679
Jefferies
Ill_#2 12_L01
PRI830-101 12_N01
Coop-17
PRI672-3
Clochard Rubinette Dorianne
12_O03
ReiDuMans
X-6823
12_P01
GranSmith X-6417 X-4638
X-6808
I_BB02
F_Ill_#2 TN_R10A8
O53T136
Apple Peach Apple Peach
30 progenies 30 progenies 20-50K SNP chip 9K SNP chip
?9-20K? SNP chip 9K SNP chip 4 CC 4 CC

12. Structure
WP1 Breeding European Breeding
Platform WP2 Pre-Breeding
Diversity and QTL mapping
WP3 PBA
1. Adaptation FlexQTL
2. QTL new traits
3. QTL Fine mapping
4. Genet. div . in EU Breeding
5. Wider QTL mining
6. QTL validation

13. Structure
WP1 Breeding European Breeding
Platform WP2 Pre-Breeding
Diversity and QTL mapping
WP4 LD/GWA
1. Phen & genet variability
2. Core collection
3. QTL mapping by GWA

14. Structure
WP5 Trait knowledge
WP5 leader: B. Quilot
(INRA)
1. Biotic stresses: Monilia

15. Structure
- Set up infection tests
- Assessment of fruit physical and
biochemical characteristics
- Different sources of resistance
- Modeling /fruit growth
WP5 Trait knowledge
WP5 leader: B. Quilot
(INRA)
1. Biotic stresses: Monilia

16. Structure
Cell wall biochemical Transcriptomics
analyses
WP5 Trait knowledge
2. Fruit quality : texture, fiber

17. Structure
Set up tests to :
- Predict chilling and heat requirement WP5 Trait knowledge
- Evaluate responses to water scarcity
3. Abiotic stresses:

18. Structure
WP1 Breeding European Breeding
1. Breeding strategies Platform WP2 Pre-Breeding
1. Material evaluation
2. Fine mapping
2. Conventional pre breeding
3. Pilot studies
3. Fast prebreeding
4. Pipeline
5. DB interface
WP6 SNP chips
PFR
WP6 leader: R. Velasco
RosBREED
Low Medium High
ARC FEM
Low cost MAB
Diversity and QTL mapping
WP3 PBA
1. Adaptation Flex WP5 Trait
WP4 LD/GWA knowledge
2. QTL new traits
1. Phen & genet variability 1. Biotic stresses
3. QTL Fine mapping
2. Core collection 2. Fruit quality
4. Genet. div . in EU Breeding
3. QTL mapping by GWA 3. Abiotic stresses
5. Wider QTL mining
6. QTL validation

19. Structure
WP1 Breeding European Breeding
1. Breeding strategies Platform WP2 Pre-Breeding
1. Material evaluation
2. Fine mapping
2. Conventional pre breeding
3. Pilot studies
3. Fast prebreeding
4. Pipeline
5. DB interface
WP7 bioinfo
WP7 leader: A. Stella GDR
(PTP) FruitBreed DB RosBREED (US)
Diversity and QTL mapping
WP3 PBA
1. Adaptation Flex WP5 Trait
WP4 LD/GWA knowledge
2. QTL new traits
1. Phen & genet variability 1. Biotic stresses
3. QTL Fine mapping
2. Core collection 2. Fruit quality
4. Genet. div . in EU Breeding
3. QTL mapping by GWA 3. Abiotic stresses
5. Wider QTL mining
6. QTL validation

20. Structure
WP1 Breeding European Breeding
1. Breeding strategies Platform WP2 Pre-Breeding
1. Material evaluation
WP9 leader: V. Troillard (IT)
WP8 leader: J. Bonany (IRTA)
2. Fine mapping
2. Conventional pre breeding
WP9. Management
WP8 Dissemination
3. Pilot studies
3. Fast prebreeding
4. Pipeline
5. DB interface
WP6 SNP chips Tools WP7 bioinfo
Low Medium High FruitBreed DB
Low cost MAB
Diversity and QTL mapping
WP3 PBA
1. Adaptation Flex WP5 Trait
WP4 LD/GWA knowledge
2. QTL new traits
1. Phen & genet variability 1. Biotic stresses
3. QTL Fine mapping
2. Core collection 2. Fruit quality
4. Genet. div . in EU Breeding
3. QTL mapping by GWA 3. Abiotic stresses
5. Wider QTL mining
6. QTL validation

21. Structure
WP1 Breeding European Breeding
1. Breeding strategies Platform WP2 Pre-Breeding
1. Material evaluation
2. Fine mapping
2. Conventional pre breeding
WP9. Management
WP8 Dissemination
3. Pilot studies
3. Fast prebreeding
4. Pipeline
Breeding stakeholders
5. DB interface
WP6 SNP chips Tools WP7 bioinfo
Low Medium High FruitBreed DB
Low cost MAB
Diversity and QTL mapping
WP3 PBA
1. Adaptation Flex WP5 Trait
WP4 LD/GWA knowledge
2. QTL new traits
1. Phen & genet variability 1. Biotic stresses
3. QTL Fine mapping
2. Core collection 2. Fruit quality
4. Genet. div . in EU Breeding
3. QTL mapping by GWA 3. Abiotic stresses
5. Wider QTL mining Germplasm
6. QTL validation curators

22. Contacts with breeding stakeholders
Objective:
to establish collaborations with all EU apple and peach
breeding programs to improve our understanding on
various genetic aspects of breeding
Then, extension to non EU countries and other Rosaceae
species
Steps:
1- Registration to the stakeholder platform
2- Questionnaire/breeding programmes
3- Invitation letter to participate to some research (WP3)
4- Questionnaire on Database/Breeder interface Not yet started

23. Contacts with breeding stakeholders
Questionnaire
• General information
• Selection criteria/ objectives of selection
• Methodology/cycle of selection
• Database/ Breeder interface
• Genitors, funders, genealogy
• ….

24. Contacts with breeding stakeholders
Invitation for participation in some research
of FruitBreedomics (WP3)
Your requested input:
1- Providing genealogy information on your germplasm.
2-(later), providing young leaves of some selected pedigreed germplasm (for DNA
isolation) plus related phenotypic data for some selected traits
In WP3, FruitBreedomics will provide you with:
- Level of representation of your founders in available European breeding germplasm
- Genetic relationships within your germplasm (Pedimap software WUR-DLO)
- Detailed marker data (SNP markers ) on your material
- Report on (in)-consistencies between genealogy and marker data on your material
- Presence and absence of QTL-alleles (identified and characterised in other parts of
FruitBreedomics)
- Functionality of these QTLs in your environment and genetic backgrounds
- Participation in a workshop on Pedigree Based Analyses

25. Contacts with breeding stakeholders
General output for the breeders
• Access to relevant information on the development of the project
• Be eligible for funds to attend training activities and workshops organized by
FruitBreedomics on:
– MAB protocols (WP1, WP6),
– characteristics of new breeding lines or populations made available (WP2),
– PBA software: FlexQTL (WP3), Spring 2013
– genetic resources available for fruit breeding (WP4),
– assessment of new traits (WP5),
– bioinformatics tools (WP7)
• Access to the Database and the Breeder interface (when completed)
• Invitation to the annual stakeholder seminars of the project

26. Acknowledgement to
the FruitBreedomics consortium

27. Go on www.fruitbreedomics.com to get the last news of the project
francois.laurens@angers.inra.fr