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Convegno la mela nel mondo   interpoma bz - 17-11-2012 4 - francois laurens
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Convegno la mela nel mondo   interpoma bz - 17-11-2012 4 - francois laurens Convegno la mela nel mondo interpoma bz - 17-11-2012 4 - francois laurens Presentation Transcript

  • An integrated approach forincreasing breeding efficiency inapple and peachLaurens 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
  • State of the art: World apple production ~70 Mt FAOstat
  • State of the art: European apple cvars 2009: 11 Mt Golden D. 24% Gala Jonagold 10% 8.5% 10 cvars ~ ¾ EU production FAOstat
  • 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
  • State of the art: Fruit breeding programmes – Numerous – Similar objectives – Low genetic variability within genitor pool – Empirical approaches – Similar selection processes: long and expensive
  • 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
  • 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
  • An integrated approach forincreasing breeding efficiency inapple and peach
  • AIMS To fill in the gap between Genetics/Genomics and breeding- Development + use of molecular tools (SNP , Full transcriptchips) /international collaboration- Better knowledge / genetics + genomics of major agronomictraits + allelic diversity Material + tools + methodologies /breeders (within and outside the consortium)
  • PartnersResearch SMEs1 – INRA 3 – ASF2 – ARO (IL) 4 – B3F5 – CRA-W 7 – DNV6 – CRA 14 – NOVADI8 – ETHZ 17 – RDG9 – EVD10 – FEM Management12 – IRTA 11 – IT 24 China13 – JKI15 – PTP 2116 – RBIPH18 – DLO 18 1319 – UMIL 5 4 1620 – UNIBO21 – READING + in 2012 : KUL, RCL … 1 11 8 922 – ARC (ZA) 323 – PFR (NZ) 19 20 1424 – ZJU (CN) 7 15 17 12 6 10+ close links with : Rosbreed (WSU), SLU (Sweeden) 22 23 2 South Africa NZ Israël
  • First results of the FruitBreedomics apple breeding questionnaire to get a better knowledge of the apple breedingprograms and understand the needs and requests of apple breeders
  • 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
  • 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
  • description of the organizations Other; 6,1% University; 18,2% Commercialcompany; 21,2% Research Institute; 54,5% • About 50% of research institutes • 60% of the organizations are public
  • Summary: ranking of the listed traitsrank 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 5,510 Fruit size 7,3 29 Nectrian canker 5,411 Aroma 7,2 Extended harvest12 Sweetness 7,2 30 season 5,113 Bitter pit 7,2 31 Single fruit per cluster 5,014 Fruit skin red colour 7,0 32 Tree vigour 4,515 Powdery mildew 6,8 33 Aphids 4,316 Harvest date 6,7 34 Red flesh colour 4,017 Fruit set 6,7 35 Fruit skin green colour 3,918 Cracking 6,6 36 Cold stress 3,819 Fruit shape 6,3 37 Lenticelosis 3,820 Cracking 6,3 38 Heat stress 3,021 Acidity 6,2 39 Bloom time 2,9 40 Drought stress 2,6 41 Chilling requierement 2,1 42 Self fertility 1,5
  • 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 factorsassessment assessment for resistance genes 2 1 2 1 1Main bottlenecks are related to lack of funding (fundings ss, time/labour, space)
  • Are molecular markers being used currently in your breeding program? Among the 21 breeders who answered this question, 9 are using MAS
  • ethylene aroma Which traits markers 4% storage/shelf life 4% 4% fruit quality are used for? 4% allergens 4% scabmalic acid 37% 3%columnar 3% mildew 11% texture fire blight 11% 15% • Main target: biotic stress resistance 63% • mainly for apple scab
  • 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
  • Structure WP1 Breeding European Breeding Platform WP2 Pre-BreedingWP9. Management WP8 Dissemination WP6 SNP chips Tools WP7 bioinfo Diversity and QTL mapping WP3 PBA WP5 Trait WP4 LD/GWA knowledge
  • Structure WP1 Breeding European Breeding 1. Breeding strategies Platform 2. Fine mapping 3. Pilot studies 4. Pipeline 5. DB interfaceWP1 leader: A. Patocchi (EVD)
  • Structure European Breeding WP2 Pre-Breeding Platform 1. Material evaluation 2. Conventional pre breeding 3. Fast prebreeding WP2 leader: A. Peil (JKI)
  • Structure WP1 Breeding European Breeding Platform WP2 Pre-BreedingWP3 leader: E. van de Weg (DLO) Diversity and QTL mapping WP3 PBAPedigree 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
  • Fine Genetic Mapping Allelic diversity Pedigree Based Analysis Association GeneticsMAPPING 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-3263M_PRI668-100 PRI14-152 12_F01 X-656 4 X-6 683 GoldenDel Red WinterX31 77 Idared PRI612-1F2_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
  • Structure- Set up infection tests- Assessment of fruit physical andbiochemical characteristics- Different sources of resistance- Modeling /fruit growth WP5 Trait knowledge WP5 leader: B. Quilot (INRA) 1. Biotic stresses: Monilia
  • Structure Cell wall biochemical Transcriptomics analyses WP5 Trait knowledge 2. Fruit quality : texture, fiber
  • StructureSet up tests to :- Predict chilling and heat requirement WP5 Trait knowledge- Evaluate responses to water scarcity 3. Abiotic stresses:
  • Structure WP1 Breeding European Breeding 1. Breeding strategies Platform WP2 Pre-Breeding 1. Material evaluation 2. Fine mapping 2. Conventional pre breedingWP9. 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
  • Contacts with stakeholders Objective:to establish links with all kinds of stakeholders to:1- collect the needs and requirements of the whole fruit chain2- 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 germplasmcurators2- Extension to other species3- Contacts with other fruit chain actors (questionnaire)
  • Acknowledgement tothe FruitBreedomics consortium