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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. State of the art: World apple production
~70 Mt
FAOstat

3. State of the art: European apple cvars
2009: 11 Mt
Golden D.
24%
Gala
Jonagold 10%
8.5%
10 cvars ~ ¾ EU production
FAOstat

4. State of the art: Main issues for the EU apple industry
• All the commercial apple cultivars are susceptible to most of the pests
and diseases
⇒ chemical sprays
• High labor farm cost (pruning, harvest, thinning)
• Slowly decreasing fruit consumption
• Keeping fruit quality ALAP in storage
• …
Breeding programmes

5. State of the art: Fruit breeding programmes
– Numerous
– Similar objectives
– Low genetic variability within genitor pool
– Empirical approaches
– Similar selection processes: long and expensive

6. State of the art: Genetic studies on fruit species
– Mapping of major genes and QTLs :
• Resistance
• Fruit quality
• Tree architecture
• …
– Functional genomics
• Candidate genes (ACO, ACS, Exp7, Araf…)
• cDNA chips
– Gene cloning (Rvi6-Vf/apple; …)
…. Whole genome sequences available for apple,
peach, and … strawberry

7. State of the art: limits of the use of markers in selection
Many researches, results, QTLs ….BUT
No (few) use in selection
Main reasons:
- Low marker density (SSR)
gaps
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

8. An integrated approach for
increasing breeding efficiency in
apple and peach

9. 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)

10. 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
13
19 – UMIL 5
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

11. First results of the FruitBreedomics
apple breeding questionnaire
to get a better knowledge of the apple breeding
programs and understand the needs and requests of
apple breeders

12. Context of the questionnaire
- September- December 2011
- 31 answers at all 29 European fresh fruit breeding
programs analysed
- Questions related to:
- Administrative information
- Selection traits
- Selection methodology
- Use of Molecular markers
- Interest in FruitBreedomics output

13. Some administrative data…
Starting year of the breeding
programmes
6
5
4
3
2
1
0
1890' 1900' 1910' 1920' 1930' 1940' 1950' 1960' 1970' 1980' 1990' 2000'
• Most ancient program: Agroscope Changins-Wädenswil (end of XIXth century)
• Most recent program: Centro Ricerche Produzioni Vegetali Soc. Coop. (2009)
• Acceleration of the initialization of the breeding programmes after 1940’s

14. description of the organizations
Other; 6,1% University;
18,2%
Commercial
company; 21,2%
Research
Institute; 54,5%
• About 50% of research institutes
• 60% of the organizations are public

15. Summary: ranking of the listed traits
rank trait average score
1 Apple scab 8,5
2 Storability 8,3 rank trait average score
3 Juiciness 8,2 22 Russeting 6,0
4 Crispness 8,0 23 Pre-harvest fruit drop 5,9
5 Firmness 7,9 24 Scald 5,9
6 Productivity 7,9 25 Watercore 5,8
7 Shelf life 7,8 26 Fruit skin bicolour 5,6
8 Fruit homogeneity 7,6 27 Mealiness 5,6
9 Storage diseases 7,4 28 Fruit skin yellow colour 5,5
10 Fruit size 7,3 29 Nectrian canker 5,4
11 Aroma 7,2 Extended harvest
12 Sweetness 7,2 30 season 5,1
13 Bitter pit 7,2 31 Single fruit per cluster 5,0
14 Fruit skin red colour 7,0 32 Tree vigour 4,5
15 Powdery mildew 6,8 33 Aphids 4,3
16 Harvest date 6,7 34 Red flesh colour 4,0
17 Fruit set 6,7 35 Fruit skin green colour 3,9
18 Cracking 6,6 36 Cold stress 3,8
19 Fruit shape 6,3 37 Lenticelosis 3,8
20 Cracking 6,3 38 Heat stress 3,0
21 Acidity 6,2 39 Bloom time 2,9
40 Drought stress 2,6
41 Chilling requierement 2,1
42 Self fertility 1,5

16. Bottlenecks
Fundings Time/ space Club variety Available
labour pollen germplasm
availability novel traits
10 5 6 1 1
Tests for Tests for Widening Markers for Climatic
resistance quality genetic basis resistance factors
assessment assessment for resistance genes
2 1 2 1 1
Main bottlenecks are related to lack of funding (fundings ss, time/labour, space)

17. Are molecular markers being used currently in your
breeding program?
Among the 21 breeders who answered this
question, 9 are using MAS

18. ethylene
aroma Which traits markers
4%
storage/shelf life 4%
4%
fruit quality
are used for?
4%
allergens
4% scab
malic acid 37%
3%
columnar
3%
mildew
11%
texture fire blight
11% 15%
• Main target: biotic stress resistance 63%
• mainly for apple scab

19. What are the reasons for not using molecular
markers in the breeding program ?
No added value
6%
Non economically
viable No training in
39% usage of molecular
markers for
breeding purposes
11%
No markers No technology
available for traits available
of interest 22%
22%
• 44% need for further development or improvement of MAS
• 39% funding

20. 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

21. 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)

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

23. 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

24. Fine Genetic Mapping
Allelic diversity
Pedigree Based Analysis Association Genetics
MAPPING POPULATIONS CULTIVARS
RallsJan
De licious Fuji
X-3 318
X-314 3
Winesap PRI668-100 X-2771
I_J01
Cranda ll
RomBe auty
X-6 398
Jo nathan PRI14-126 Galarina
X-3177
X-3263
M_PRI668-100 PRI14-152 12_F01
X-656 4 X-6 683
GoldenDel Red WinterX31 77
Idared
PRI612-1
F2_2682 9-2-2
X-3 305
X-682 0 12_J0 1
RedW inter KidsOrRed
Florina
W agenerap
Gala
X-4 598 12_I01
Prima Baujad e
I_ W01
Cox Z185
X-6681
I_ CC03
X-4355
F_X-4598
X-325 9
X-2 599
Anta34 .16
I_M01
1 2_K01
X-6799
F_X-4355 Chantecler
X-3188
X-667 9
Je fferies
Ill_#2 12_L 01
PRI83 0-101 12 _N01
Coop-17
PRI672-3
Clochard Rub in ette Do rianne
12_O03
ReiDuMans
X-6 823
12_P0 1
GranSmith X-6417 X-4638
X-680 8
I_BB02
F_Ill_#2 TN_R10A8
O53T1 36
Apple Peach Apple Peach
30 progenies 30 progenies 20-50K SNP chip 9K SNP chip
20K SNP chip 9K SNP chip 4 CC 4 CC

25. 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

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

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

28. 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

29. Contacts with stakeholders
Objective:
to establish links with all kinds of stakeholders to:
1- collect the needs and requirements of the whole fruit chain
2- provide the breeders with solutions (plant material, tools, methodologies,
skills, …) to fill in these expectations
1st steps:
1- Contacts and collaboration with apple and peach breeders and germplasm
curators
2- Extension to other species
3- Contacts with other fruit chain actors (questionnaire)

30. Acknowledgement to
the FruitBreedomics consortium