Peach Molecular Breeding at the INRA      Avignon and links to a new European initiative to increase fruit breeding effici...
Peach breeding programmes at INRA Avignon                                                             Two main targets   R...
Peach Breeding for resistance to pests and diseases                                                         A main objecti...
But….how to reach these objectives?                   Several sources of resistance are available                         ...
Few sources of resistance available   Wild species related                                                                ...
Selecting novel varieties or elite cultivars with improved                           resistance > several strategies   Obj...
Overview of the types of resistance carried by the                          resistance sources used for breeding          ...
A pluridisciplinary approach for improving resistance                                      > genetic to functionnalEvaluat...
Example of the resistance to Myzus persicae                                                         (1) behaviour on the h...
(2) Study of the feeding behaviour of Myzus persicae                                                               by usin...
Segregating populations used for breeding                                and genetic mapping   Interspecific peach x P.dav...
Targets for the developement of Marker Assisted                       Breeding (MAB) at UGAFL  Position of major genes and...
However, the curent use of markers in selection has                                              several limites    Many r...
An integrated approach for    increasing breeding efficiency in    apple and peachLaurens F., Aranzana M.J. , Arus P. , Bo...
AIMS        To fill in the gap between Genetics/Genomics and                              breeding   - By developing and u...
Partners                                                                                                                 2...
WP1 Breeding              European Breeding        1. Breeding strategies           Platform                 WP2 Pre-Breed...
Diversity and QTL                                           mapping                    WP3 PBA                           W...
Fine Genetic Mapping                                    Allelic diversity      Pedigree Based Analysis                    ...
Fine Genetic Mapping                                                                                      Allelic diversit...
WP5 New Trait knowledge       WP5 leader: B. Quilot             (INRA)   1. Biotic stresses: Monilia   2. Fruit quality : ...
TranscriptomicsCell wall biochemical      analyses                                omics                          WP5 New T...
WP1 Breeding             European Breeding       1. Breeding strategies          Platform                      WP2 Pre-Bre...
WP1 Breeding             European Breeding       1. Breeding strategies           Platform                    WP2 Pre-Bree...
WP1 Breeding                 European Breeding                                1. Breeding strategies               Platfor...
WP1 Breeding                 European Breeding                                1. Breeding strategies               Platfor...
francois.laurens@angers.inra.fr                 AndTo get the latest news of the project     Go to www.fruitbreedomics.com
Peach Breeding aknowledgement T. Pascal 1, P. Lambert 1, B. Quilot, J.L. Poëssel 1, M. Corre1, E. Lecerf 1, M.H. Sauge 2, ...
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Lambert, P., 2012.

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Lambert, P., 2012.

  1. 1. Peach Molecular Breeding at the INRA Avignon and links to a new European initiative to increase fruit breeding efficiency FP7 KBBE FruitBreedomics Patrick LAMBERT UR1052 UGAFL INRA Avignon France ALIMENTATIONEuropean COST 873- and ISHS joint meeting Séminaire SNP AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  2. 2. Peach breeding programmes at INRA Avignon Two main targets Resistance to pests and diseases Fruit Quality Powdery mildew Monilinia PPV Green peach aphid ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  3. 3. Peach Breeding for resistance to pests and diseases A main objective Context • Sanitary protection of the orchard: a strong concern • fruit orchards : 21 % of the insecticide market • Green aphid, powdery mildew, plum pox virus, monilinia : > resistances are available and exploitable Motivations: • Contribute to lower chemicals to protect the environment and the health of all the actors > producer and consumer • help in the adoption of alternative methods of phytoprotection to support the European fruit production and the fruit producers by the release of resistant and innovative varieties Stakes: • Development of new tools to obtain improved material via Marker Assisted Breeding • an innovative collaborative project at the international level begun in 2011 FP7 KBBE FruitBreedomics ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  4. 4. But….how to reach these objectives? Several sources of resistance are available but … The agronomical level is low Successive crosses are needed to get a commercial agronomical value Selection process slowed and time consuming But, molecular markers linked to the loci of interest could help to speed up the released of novel resistant varieties Implementation of Marker Assisted Breeding (MAB) ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  5. 5. Few sources of resistance available Wild species related Pamirskij5 to peach andRootstocks peach Rubira Prunus davidiana (clone P 1908) : resistant to powdery mildew, green peach aphid, monilinia and PPV … but the agronomical level is very low ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  6. 6. Selecting novel varieties or elite cultivars with improved resistance > several strategies Objectives novel varieties resistant to Powdery mildew, Green peach aphid Plum pox virus and Monilinia For short term : by combining several strong monogenic resistance factors in selected improved cultivars Powdery mildew + Myzus persicae For long term : Building lasting resistance by combining these monogenic resistances with polygenic resistance factors from: - Prunus davidiana (Powdery mildew, Myzus, Monilinia and sharka) - old varieties and genetic resources (cv Bolinha for Monilinia…) ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  7. 7. Overview of the types of resistance carried by the resistance sources used for breeding t y ili b ria Weeping Flower peach: Rm1 va S 2678 ic Myzus et en Rubira: Rm2 G S 2605 Monogenic Malo Konare: Vr1 S 5392 Powdery mildew Resistances Pamirskij 5: Vr2 Myzus S 6146 MP.SD-3.1 , MP.SD-5.1 Polygenic PPV P. davidiana: PM.SD-6 , PM.SD8 cl. P1908 PPV.RD-2.1, 2.2, Backcross Powdery mildew 7.1, 7.2 …Mono/Poly Pest or disease Origin QTLs/locus (gene) Improved varieties ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  8. 8. A pluridisciplinary approach for improving resistance > genetic to functionnalEvaluation of collections and genetic resources Resistance scoring Study of the aphid feeding behaviour Classic biological tests by electropenetrography ( EPG) On leaves and/or fruits Analysis of the organic volatile compounds Inoculations / controlled infestations Biochemical analyses (polyphenols) scoring scales in classes (0 - 4) . Associated with genetic studies Consumers Fine analysis of Research Finding Resistance mechanisms sources Breeders Developing tests Fruit grovers for selection at early Integrating molecular stages markers • Genotyping and mapping of segregating Sowing at a young stage in greenhouse populations Validation under insect-proof tunnel •QTL and candidate gene mapping Andor in orchard at a grown-up stage •Marker assisted Breeding (MAB) ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  9. 9. Example of the resistance to Myzus persicae (1) behaviour on the host tree 100 Antibiosis Aphids on the leaves (%) 80 (colonisation but P 1908 no reproduction) 60 Malo konare 40 Summergrand Antixenosis 20 Rubira (no colonisation) Major WFP Gene 0 0 24h 48h 72h 96h 120h 144h 168 Time (hour) ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  10. 10. (2) Study of the feeding behaviour of Myzus persicae by using EPG method Feeding behaviour generator plant Signal amplification Electrode (copper) electrode (Copper) V signal Diagramme of the electric ciruitry Green peach aphid linked with a (mod. Tjallingii) golden wire Graph derived from the electricall variations obtained by using the EPG method. The different feeding phases correspond to different intensities. ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - ALIMENTATION A G GR IIC CL U R E T U R E A R U TU L UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT ENVIRONNEMENT 2012
  11. 11. Segregating populations used for breeding and genetic mapping Interspecific peach x P.davidiana *Summergrand x P.davidiana (SD): F1 77 ind. *AF (Summergrand x P.davidiana)40: F2 99 ind. *SD40 x Summergrand (BC1= BC1s+BC1r) (BC1) x Zephir: BC2 162 ind. *Rubira x P.davidiana (RxD)² : F2 190 ind. Pamirskij 5 x P.davidiana (PxD)² : F1 250 ind. Malo Konare x P.davidiana (MKxD)² : F1 170 ind. Intraspecific peach *Pamirskij 5 x Rubira (PxR)²: F1 190 ind. AF Bolinha x Bolinha (B²): F1>170 ind. *(Weeping Flower peach x Pamirskij 5 (WP²) F2 100 ind. * Genetic maps available anchored to the Prunus reference map ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  12. 12. Targets for the developement of Marker Assisted Breeding (MAB) at UGAFL Position of major genes and QTLs identified from our peach mapping populations Rmia Vr2 Gr Rm2 Resistance to pests and diseases Major gene for Powdery mildew Major gene for green peach aphid Fruit Quality and phenolics Major gene for color Major gene for nematode Fructose/Glucose content QTL Powdery mildew P. davidiana Chlorogenic acid QTL Myzus persicae P. davidiana Dicaffeoyl quinic acid QTL Plum pox Virus P. davidiana ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  13. 13. However, the curent use of markers in selection has several limites Many researches, results, QTLs ….BUT To date just a few used in selection (simple traits) Main reasons: - Low marker density (SSR) gaps in the genetic maps 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 ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  14. 14. An integrated approach for increasing breeding efficiency in apple 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 KBBE large collaborative project 1 March 2011- 31 August 2015 ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  15. 15. AIMS To fill in the gap between Genetics/Genomics and breeding - By developing and using molecular tools (SNP , Full transcript chips) through multi-national collaborations - By improving knowledge about genetics + genomics of major agronomic traits + allelic diversity By transferring material + tools + methodologies to breeders (within and outside the consortium) ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  16. 16. Partners 24 China 22 NZ 21 18 5 13 22 4 16 1 11 8 9 South Africa 3 19 20 14 7 15 22 Close links with 17 12 6 10 Israël ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  17. 17. WP1 Breeding European Breeding 1. Breeding strategies Platform WP2 Pre-Breeding 1. Material evaluation 2. Fine mapping of traits Targets 2. Conventional pre breeding >Monogenic traits 3. Pilot studies 3. Fast prebreeding >QTLs with strong 4. MAB Pipeline effects 5. Data Base interface WP1 leader: A. Patocchi WP2 leader: A. Peil (EVD) (JKI) The general objective is to develop more Aims at the establishment of pre-breeding material efficient breeding programmes applying In a more efficient way by using SNP markers marker assisted reeding. 10,000 seedlings for each species WP1 will use the two 9k SNP Illumina Chips Different crosses with different trait developed in the framework of RosBREED combinations Aims at the improvement and application of a fast-breeding system in apple. ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  18. 18. Diversity and QTL mapping WP3 PBA WP4 LD/GWA 1. Adaptation Flex Software 2. QTL new traits 3. QTL Fine mapping 1. Phen & genet variability 4. Genet. div . in EU Breeding 2. Core collection Establish 5. Wider QTL mining 3. QTL mapping by GWA 6. QTL validation WP3 leader: E. van de Weg WP4 leader: M.J. Aranzana (DLO) (IRTA) WP3 WP4 Identification and characterisation of QTL Exploring the phenotypic and genetic By the pedigree-based analysis approach diversity in collections and exploitation by association genetics approach ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  19. 19. Fine Genetic Mapping Allelic diversity Pedigree Based Analysis Association Genetics Objective Find an « association » (correlation) between the variation of a marker and a trait SNP : Single Nucleotide Polymorphism Steps: •Phenotyping •Genotyping •Find out associations markers/phenotypes Rafalski & Morgante, 2004 ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012
  20. 20. Fine Genetic Mapping Allelic diversity Pedigree Based Analysis Association Genetics MAPPING POPULATIONS CULTIVARS RallsJan De licious Fuji X-3 318 X-314 3 W inesap PRI668-10 0 X-2771 I_J01 Cranda ll RomBe auty X-6 398 Jo nathan PR I14-126 Galarina X-3177 X-3263 M_PRI668-100 PR I14-152 12_F01 X-656 4 X-6 683 GoldenDel Red WinterX31 77 Idared PRI612-1 F2_26829-2-2 X-3 305 X-682 0 12_J0 1 RedW inter KidsOrRed Florina W agenerap Gala X-4 598 12_I01 Prima Baujade 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 inette Dorianne 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 progeniesEuropean COST 873 and ISHS joint meeting Séminaire SNP - A 20-50K ISNP chip LIMENTAT ON 9K SNP chip 9K 14-1719chip 20129K SNP chip SNP janvier UGAFL - February Zurich AGRICULTURE ENVIRONNEMENT 2012
  21. 21. WP5 New Trait knowledge WP5 leader: B. Quilot (INRA) 1. Biotic stresses: Monilia 2. Fruit quality : texture, fiber chilling 3. Abiotic stresses: requirement, water stressWP5Aims at enhancing the knowledge of genetics underlying novel traitsAnd providing phenotyping methods by developing tools for novel traits determination Investigate novel complex traits using « omics » approach and modeling Make novel trait analysis high throughput applicable for the breeding industry
  22. 22. TranscriptomicsCell wall biochemical analyses omics WP5 New Trait knowledge New tools 2. Fruit quality : texture, fiber
  23. 23. WP1 Breeding European Breeding 1. Breeding strategies Platform WP2 Pre-Breeding 1. Material evaluation 2. Fine mapping Traits 2. Conventional pre breeding 3. Pilot studies 3. Fast prebreeding 4. MAB Pipeline 5. DB interface WP6 SNP chipsPFRARC WP6 leader: R. Velasco Low Medium High FEM Italy Low cost MAB Diversity and QTL WP3 PBA WP5 Trait mapping1. Adaptation Flex knowledge WP4 LD/GWA2. QTL new traits 1. Phen & genet vriability 1. Biotic stresses3. QTL Fine mapping 2. Core collection 2. Fruit quality4. Genet. div . in EU Breeding 3. QTL mapping by GWA 3. Abiotic stresses5. Wider QTL mining6. QTL validation
  24. 24. WP1 Breeding European Breeding 1. Breeding strategies Platform WP2 Pre-Breeding 1. Material evaluation 2. Fine mapping Traits 2. Conventional pre breeding 3. Pilot studies 3. Fast prebreeding 4. MAB Pipeline 5. DB interface WP7 bioinfoWP7 leader: A. Stella (PTP) FruitBreed Data Base Genome Database For Rosaceae (GDR) Diversity and QTL WP3 PBA mapping1. Adaptation Flex Software WP5 Trait WP4 LD/GWA knowledge2. QTL new traits 1. Phen & genet variability3. QTL Fine mapping 1. Biotic stresses 2. Core collection4. Genet. div . in EU Breeding 2. Fruit quality 3. QTL mapping by GWA5. Wider QTL mining 3. Abiotic stresses6. QTL validation
  25. 25. WP1 Breeding European Breeding 1. Breeding strategies Platform WP2 Pre-BreedingWP9 leader: V. Troillard (IT) 1. Material evaluation WP9. Management WP8 leader: J. Bonany (IRTA) 2. Fine mapping Traits 2. Conventional pre breeding WP8 Dissemination 3. Pilot studies 3. Fast prebreeding 4. MAB Pipeline 5. DB interface WP6 SNP chips Tools WP7 bioinfo Low Medium High FruitBreed Data Base Low cost MAB Diversity and QTL WP3 PBA mapping 1. Adaptation Flex Software WP5 Trait WP4 LD/GWA knowledge 2. QTL new traits 1. Phen & genet variability 3. QTL Fine mapping 1. Biotic stresses 2. Core collection 4. Genet. div . in EU Breeding 2. Fruit quality 3. QTL mapping by GWA 5. Wider QTL mining 3. Abiotic stresses 6. QTL validation
  26. 26. WP1 Breeding European Breeding 1. Breeding strategies Platform WP2 Pre-BreedingWP9 leader: V. Troillard (IT) 1. Material evaluation WP9. Management WP8 leader: J. Bonany (IRTA) 2. Fine mapping Traits 2. Conventional pre breeding WP8 Dissemination 3. Pilot studies 3. Fast prebreeding 4. MAB Pipeline Breeding stakeholders 5. DB interface WP6 SNP chips Tools WP7 bioinfo Low Medium High FruitBreed Data Base Low cost MAB Diversity and QTL WP3 PBA mapping 1. Adaptation Flex Software WP5 Trait WP4 LD/GWA knowledge 2. QTL new traits 1. Phen & genet variability 3. QTL Fine mapping 1. Biotic stresses 2. Core collection 4. Genet. div . in EU Breeding 2. Fruit quality 3. QTL mapping by GWA 5. Wider QTL mining Germplasm 3. Abiotic stresses 6. QTL validation curators
  27. 27. francois.laurens@angers.inra.fr AndTo get the latest news of the project Go to www.fruitbreedomics.com
  28. 28. Peach Breeding aknowledgement T. Pascal 1, P. Lambert 1, B. Quilot, J.L. Poëssel 1, M. Corre1, E. Lecerf 1, M.H. Sauge 2, JP. Lacroze 2, F. Pfeiffer 1, M. Staudt 3, Y. Rahbé A. 4, Moing 5 1 INRA, Unité de Génétique et dAmélioration des Fuits et Légumes, BP 94 - 84143 Avignon - Montfavet Cedex 2 INRA, Unité Plante et Système de culture Horticole, Domaine St Paul, Site Agroparc, 84914 Avignon - Montfavet 3 Centre dEcologie Fonctionnelle et Evolutive - CNRS, 1919, Route de Mende, 34293 Montpellier Cedex, 4 INSA - INRA UA 203, Laboratoire de Biologie Appliquéee 406, 20 av. A. Einstein, 69621 Villeurbanne 5 INRA, UMR 619 Biologie du Fruit - Plate-forme Metabolome-Fluxome , BP81, 33883 Villenave d’Ornon Thanks for your attention ALIMENTATIONEuropean COST 873 and ISHS joint meeting Séminaire SNP - AGRICULTURE UGAFL - 19 janvier 2012 Zurich 14-17 February ENVIRONNEMENT 2012

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