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  • 1. Welcome to the WP1 workshop! Increase efficiency of (marker assisted) breeding 29th March 2011
  • 2. Agenda
    • Organization of WP1 (A. Patocchi, 5min)
    • Presentation of the 5 tasks by the task leaders and discussion:
      • T1.2 SNP development (A. Patocchi, 15min)
      • T1.1 Breeding strategies (F. Laurens, T. Pascal, 30min)
      • T1.3 Pilot studies (F. Laurens, T. Pascal, 30min)
      • T1.4 Genotyping pipeline (S. Tartarini, 15min)
      • T1.5 Specification list of the breeder interface
      • (S. Tartarini, 15min)
    • Proposal of action plan first 12 months (A.Patocchi, 10min)
  • 3. Organization of WP1
    • WP1 leader A. Patocchi, Co-leader T. Pascal
    • Responsible for the coordination of the tasks within WP1 and between WP1 and the other WPs
    • Responsible for submitting the WP1 report but not for writing it!
    • WP1 task leaders (F. Laurens T1.1 and T1.3 apple;
    • T. Pascal T1.1 and T1.3 peach; T1.2 A. Patocchi apple; T.Pascal peach; T1.4 and T1.5 S. Tartarini):
    • Responsible for the coordination of the task or task part
    • Persons of reference for the partners participating to the task
    • Responsible for the collection and check of the reports of the partners
    • Responsible for the submission of the validated report of the task to the WP leader
  • 4. Organization of WP1
    • WP1 partners :
    • Responsible for the execution of the respective work according Annex I (Description of Work, DoW)
    • Responsible for writing their reports and submit them to the task leaders
    • QUESTIONS?
    • WP1 partners are invited to fill the mailing list table
  • 5. Presentation of the tasks and discussion
  • 6. Approach / Methodology
    • Task 1.2: Development and mapping of SNPs tightly associated to selected loci (M1-M24)
    • Leaders: EVD (apple), INRA-Av (peach) Andrea Patocchi and Thierry Pascal
    • Involved partners: ETHZ, UNIBO, JKI, PFR, UMIL, IRTA, INRA-Bo
    • Only done for major genes and QTLs with large effects , mapped before the beginning of the project
    • The goal:
      • 5 SNP markers for the major genes (interval 1cM)
      • 10 SNPs for the QTLs (5 on each side of the QTL peak, interval of 10cM)
    • Traits:
      • Apple:
          • Apple scab ( Vf , Vh2 , Vh4 , Vb , Vbj , Vr2 , Vdurello , Vm , Va1 , QTLs LG17), mildew ( Pl1 and 2 , QTL LG2/13), fire blight (Fb-E, Fb.R5), rosy apple aphid ( Dp-fl )
      • Peach:
          • green peach aphid ( Rm2, QTLs LGs 3/5 ) , powdery mildew ( Vr2 , QTLs LGs 6/8 ), fruit low acidity ( D ), flat/round fruit shape ( S ), peach/nectarine ( G ) yellow/white flesh ( Y ), firm/soft melting flesh ( F/f1/f1 )
  • 7. T1.2 Approach apple
      • Using the apple genome sequence SSR markers in the regions close to the goi will be developed
      • Once SSR markers bracket the goi in about:
        • 1cM interval for major genes (MG)
        • 10cM interval for QTLs
      • 5 SNP markers will be developed for the MG in this interval
      • 10 SNPs will be developed for the QTLs in this interval (about 5 on each side of the QTL peak)
      • Verification of level of polymorphism of the SNPs (in 8 genotypes, which ones? Founders? How polymorphic have the SNPs to be?)
      • As many as possible markers will be included in the apple SNP array (T6.3)
  • 8. T1.2 Approach peach
      • Populations segregating for the goi will be genotyped with a 9k SNP chip (year 2?)
      • SNPs know to derive from the goi region will be mapped
      • Due to the high number of SNPs tested, it is expected that SNP markers tightly linked to goi will be “automatically” identified
      • As for the apple:
        • 5 SNP markers will be identified for the MG in about 1cM interval
        • 10 SNPs will be identified for the QTLs in a 10cM interval (about 5 on each side of the QTL peak)
        • Verification of high level of polymorphism of the SNPs (in 8 genotypes, which ones? Founders? How polymorphic have the SNPs to be?)
  • 9. T1.2 Milestones and deliverables
    • Milestones
      • MS4: markers tightly linked to the loci of interest identified (M28; but SNP markers used in the pilot studies have to be delivered at latest by M24 , coordination with T1.3 required)
    • Deliverables
      • D1.3 Submitted manuscripts on the fine mapping of selected major genes or QTLs (M28) (EVD, INRA-Av + all partners involved )
  • 10. Partner vs traits/loci
    • Apple :
    • ETHZ : Rvi6 ( Vf ), Rvi15 ( Vr2 ) (apple scab), Fb-E , Fb-R5 (fire blight)
    • EVD (+ PRF): Rvi2 ( Vh2 ), Rvi4 ( Vh4 ), Rvi11 ( Vbj ), Rvi12 ( Vb ), QTL F/D LG17 (scab) , Pl2 (mildew)
    • UNIBO: Rvi5 ( Vm ), Rvi13 ( Vdurello ) (scab), QTL LG2/13 (mildew), Dp-fl (rosy apple aphid)
    • JKI: Va1 (scab), Pl1 (mildew)
    • Peach :
    • INRA-Av: Rm2, QTLs LGs 3+5 (green peach aphid), Vr2 and QTLs LGs 6+8 (powdery mildew)
    • INRA-Bo: D (fruit low acidity), S (flat/round fruit shape)
    • IRTA: G (peach/nectarine), Y (yellow/white flesh)
    • UNIML: F/f1/f1 (firm/soft melting flesh)
    • THESE ARE THE ONLY TRAITS/LOCI FOR WHICH MAB CAN BE APPLIED IN THE APPLE AND PEACH PILOT STUDIES (AT M24)!
    + ACIDITY, FIRMNESS?
  • 11. Approach / Methodology
    • Task 1.1: Breeding strategies (M1-M48)
    • Leaders: INRA (Angers/apple-François; Avignon/peach-Thierry)
    • Involved partners: DLO, EVD, UNIBO, UMIL, IRTA, Novadi, B3F, ASF, RDG, DNV
    • My view (3 steps):
    • 1- definition of breeding objectives (François, Thierry)
    • 1- Review of apple and peach breeding programmes : objectives, methodologies, … current “ideotypes”
    • - Pilot studies participants
    • - European breeders : updated breeder list, bibliography (start from existing data [Apple: YL 2005; JKI, 2011; Peach ?], new questionnaire
    • 2- needs of the fruit chain : profesionnal litterature, contact with representatives of the fruit chain (supermarket, wholesalers, extension services, growers, consummers ?, ….)
    • Definition of ideotypes… => index for Pilot studies (task 1.3)
    • Milestone
        • MS1. Ideotypes and relative breeding scheme including MAB described (month 12)
    • Deliverable
        • D1.1 Description of ideotypes and breeding schemes (month 12)
    • We will report at 12 months as planned but the review will be carried on afterwards…
    Name of the participants
  • 12. Approach / Methodology
    • Task 1.1: Breeding strategies (M1-M48) following…
    • 2- Review of breeding strategies in other crops or animals (Marco)
    • 3- “Evaluation” of GWS in apple and peach breeding programmes (Marco)
    • Milestones
      • MS2. Evaluation of applicability of GWS to apple and peach (month 12)
      • MS3. Evaluation of breeding strategies used in other crops (month 30)
    • Deliverable
        • D1.2 Evaluation of breeding strategies used in other crops (GWS included) (month 30)
  • 13. Approach / Methodology
    • Task 1.3: Pilot studies (M1-M48)
    • Leaders: INRA (Angers/apple-François; Avignon/peach-Thierry)
    • Involved partners: EVD, UNIBO, UMIL, IRTA, Novadi, B3F, ASF, RDG, DNV
    • Input from :
    • T1.1 => selection schemes
    • T1.2 + T3.2 + T3.3 => mapping of SNP markers tightly linked associated to selected traits/loci
    • T1.4 => genotyping pipeline
    • + (WP5 = phenotyping)
  • 14. Approach / Methodology
    • Task 1.3: Pilot studies (M1-M48) following…
    • Description of the work:
    • Apple : EVD, UNIBO, Novadi B3F: 2500/partner
    • Peach : UMIL, IRTA, ASF, RDG, DNV: 1600/partner
    • 1- Selection of the progenies (today up to next annual meeting(?)
    • - Research Institutes: new crosses pyramidizing Resistance major genes and QTLs
    • - Private companies: fruit quality /harvest and in storage (+ field resistance (?))
    • 2- DNA sampling
    • 3- selection on the basis of the markers => ind +/ind -/ind random
    • 4- phenotyping on selected individuals (+, -, Random) (≥ 50ind/each class)
    • For resistance: glasshouse tests + field tests (Y4 and Y5)
    • 5- comparison
    • Milestone
        • MS1. Ideotypes and relative breeding scheme including MAB described (month 12)
    • Deliverable
        • D1.1 Description of ideotypes and breeding schemes (month 12)
    • We will report at the stage we are but the review will be carried on afterwards…
  • 15. Approach / Methodology
    • Task 1.3: Pilot studies (M1-M54) following…
    • Milestone
        • MS7. Pilot studies performed, including MAB and validation of the results (month 54)
    • Deliverable
        • D1.4 Submitted manuscript of the results of the pilot studies (month 54)
    • ???: start of the MAB = depends on the marker delivery (T1.2, T3.2, T3.3)
  • 16. Selection of the progenies Let’s discuss few minutes about the progenies proposed …
  • 17. Size ? New crosses ? Apple crosses in Bologna Year Code Genitori Totale 87 87403 Perleberg 3 x Florina 287 88 88419 Gelata x Red Chief 97 89 89401 Red Chief x Florina 99 89 89404 Royal Gala x Florina 200 89 89412 Royal Gala x B1R7T1 115 89 89414 Royal Gala x Gelata 147 89 89415 Royal Gala x Red Chief 193 91 91401 Belgolden x Braeburn 278 91 91405 Fuji houfu1 x Florina 89 91 91410 Stark Splendor x Royal Gala 241 95 95409 Durello di Forlì x Fiesta 209 96 96401 Discovery x Durello di Forlì 153 96 96405 Gold Chief x Durello di Forlì 170 96 96407 79410002 x Durello di Forlì 126 96 96409 GoldRush x 79410002 169 96 96412 Primiera x Abbondanza rossa 96 96 96415 Primiera x Pink Lady 93 96 96421 Fuji Aki-Fu 1 x Gold Chief 147 96 96424 Gold Chief x Pink Lady 169 96 96434 Gala x Golden 185 98 98427 GoldRush x PI 172612 99 98 98428 GoldRush x Russian 113 98 98430 GoldRush x White Angel 111 99 99401 Durello di Forlì x Golden Delicious 310 99 99402 Durello di Forlì x Granny Smith 201 99 99406 Harmonie x Murray 119 99 99411 Renetta Grigia di Torriana x Golden Delicious 155 99 99412 Renetta Grigia di Torriana x GoldRush 197 00 00403 GoldRush x Discovery 201 00 00404 GoldRush x Realka 142 00 00405 GoldRush x Amasya 94 03 03408 Ariwa x Pinova 146 05 05403 Golden x Murray 231 5382
  • 18. 1) Parent 313 (Gala x Braeburn) x Fuji 2542 individuals in different planting seasons   No selection on seedling level Trait is quality : appeal, texture, good balance sweet-acid and storability. Selection at better3fruit will be focused on appeal and taste. Approximately 5 % will be harvested. Keep ind. for FBO 2)Braeburn x Pri2482-100 400 individuals ; 2 different plantations?   Trait: Vm resistance: AS-MGs Rvi5 Selection on seedling level with artificial infection: classes 0-1-2 retained. Susceptible selections not available. Selection at Better3fruit: all accessions will be harvested and described. Selection on quality: firmness, texture, storability, harvest time. No first selection on appeal 3) Parent 313 (Gala x Braeburn) x Alkmène 814 individuals ; 2 planting seasons   Trait: Polygenic resistence (Alkmene) Selection on seedling level with artificial scab infection. Susceptible selections are not available 442 selections -planted in 2011- were planted in an unsprayed field. Field resistance observations will be possible. (257 plants budded in 2010 will be sprayed) Selection at Better3fruit: appeal, quality and storability: Less than 5 % will be harvested. Apple progenies proposed by B3F
  • 19. 1) Pinova x INRA hyb Vf 1255 individuals but planted in 5 different sites ( ≈400 in 1 site + ≈ 200 in the 4 other sites)   selection for scab on seedling level Segregating fruit traits: attractivenes, fruit quality, 2 nd flowering… 2) INRA hyb Vf x Choupette 915 (+184) individuals not selected for scab in greenhouse, to be planted in 1 site + 1438 selected for Vf (greenhouse test) to be planted in 5 sites ( 475 in the same site as above) Segregating fruit traits: attractivenes, fruit quality, 2 nd flowering… Polygenic (?) resistance   Apple progenies proposed by Novadi Others existing or new crosses … (on request)
  • 20. Peach progenies proposed by UMIL PROGENY GOAL CROSS YEAR SDLGS N° NOTES ON SEGREGATION BO 96016208 self MONI 02 359 F2 of Contender x Ambra : brown rot on fruit, glabrous skin, fruit quality; genotyped SOLEADA * GLOHAVEN MONI 02 115 Brown rot on fruit Soleada * MAYCREST QUAL 02 134 Brown rot on fruit, ripening date BIG TOP * BIG BANG BGTP 04 93 Fruit quality, ripening date and flesh texture BO 93030045 * DIAMOND BRIGHT BGTP 04 164 Fruit quality, ripening date and flesh texture BO 93041003 self HABI 04 110 Growth habit and fruit size and quality BO 96016097 * MAY GLO MONI 04 178 Brown rot on fruit ELEGANT LADY self MAPPA 04 95 Glabrous skin and ripening date GLOHAVEN * GF 677 MAPPA 04 92 Back cross from almond x peach hybrid ; fruit size and quality, ripening date, tree vigour GUERRIERA * BO 96003028 BGTP 04 125 Fruit quality and ripening date, flesh texture MAX 10 * BO 96003028 BGTP 04 246 Fruit quality and ripening date, flesh texture RED MOON * CONTENDER MONI 04 117 Brown rot on fruit, fruit quality and ripening date S 6699 * BORDO' AFIDI 04 309 Green aphid resistance, fruit quality and ripening date S 6699 * DIAMOND BRIGHT AFIDI 04 256 Green aphid resistance, fruit quality and ripening date STARK RED GOLD * BO 96003028 BGTP 04 98 Fruit quality and ripening date, flesh texture BO 92038046 self MAPPA 05 97 Brown rot on fruit BO 92038071 * SUPEACHSIX MONI 05 112 Brown rot on fruit D 41-62 self STHA 05 151 All seedlings stony hard and same ripening date DIAMOND RAY * BO 89015029 QUAL 05 165 Fruit quality and ripening date NADIA (BO 82015079) * BO 00025004 MONI 05 115 Brown rot on fruit, fruit quality and ripening date ORION * DIAMOND BRIGHT QUAL 05 136 Fruit quality and ripening date SOLEADA * S 6699 AFIDI 05 165 Green aphid resistance, fruit quality and ripening date BO 02028017 self MAPPA 06 110 F2 of MORSIANI 90 x EARLY SILVER; glabrous skin, fruit quality and ripening date BO 92050007 self MAPPA 06 91 F2 of NJ WEEPING (PI 91459) x BOUNTY; growth habit, flesh texture (melting-non melting), fruit quality and ripening date BO 92050010 self MAPPA 06 128 F2 of NJ WEEPING (PI 91459) x BOUNTY; growth habit, flesh texture (melting-non melting), fruit quality and ripening date HONEY GLO * BO 96028059 BGTP 06 1060 Fruit quality, ripening date and flesh texture ALITOP * RUBY RICH BGTP 07 150 Fruit quality, ripening date and flesh texture ALIX * RED MOON QUAL 07 103 Fruit quality, ripening date and flesh texture BO 88008037 * FRANCESCA MONI 07 211 Fruit quality and brown rot on fruit BO 92038046 self MAPPA 07 126 F2 of Contender x Elegant Lady ; Fruit quality and brown rot on fruit BO 92038071 self MAPPA 07 280 F2 of Contender x Elegant Lady; Fruit quality and brown rot on fruit BO 92038140 self MAPPA 07 250 F2 of Contender x Elegant Ladys; Fruit quality and brown rot on fruit
  • 21. Peach progenies proposed by UMIL (following) PROGENY GOAL CROSS YEAR SDLGS N° NOTES ON SEGREGATION BO 96013007 self BGTP 07 209 F2 of Bolero x Rich Lady ; Flesh texture and fruit quality BO 96027023 self MAPPA 07 107 F2 of SPLENDOR x TOP LADY s; fruit quality, flesh colour and quality DIALONA * RITA STAR QUAL 07 509 Fruit quality DIAMOND BRIGHT * ALICE QUAL 07 162 Fruit quality DORIS * BO 88008091 QUAL 07 494 Fruit quality GUERRIERA * HONEY ROYAL BGTP 07 902 Fruit quality, flesh texture and ripening date HONEY GLO * ALEXA BGTP 07 715 Fruit quality, flesh texture and ripening date HONEY GLO * BORDO' BGTP 07 1256 Fruit quality, flesh texture and ripening date HONEY GLO * DIAMOND RAY BGTP 07 989 Fruit quality, flesh texture and ripening date MARIA DORATA * HONEY ROYAL PC 07 324 Fruit quality ORION * SD 75 PPV 07 358 Back cross from peach x Prunus davidiana; Flesh colour and fruit quality SWEET FIRE * GARCICA BGTP 07 1051 Fruit quality and flesh texture SWEET LADY * HONEY ROYAL BGTP 07 269 Fruit quality and flesh texture SWEET SILVER * GARCICA BGTP 07 451 Fruit quality and flesh texture TARDIBELLE * SPRINGBELLE QUAL 07 152 Ripening date and fruit quality VISTA RICH * BO 02009066 BGTP 07 133 Flesh texture, fruit quality and brown rot on fruit NADIA (BO 82015079) * BO 92038173 MONI 08 130 Fruit quality and brown rot on fruit CONTENDER * ELEGANT LADY MONI 92 200 Brown rot on fruit, ripening date and fruit quality; genotyped BOLERO * ORO A OIDIO 96 183 Powdery mildew, ripening date and flesh texture; genotyped
  • 22. WP1 - T1.4 Genotyping pipeline 29th March 2011
  • 23. T-1.4 – Genotyping pipeline
      • MAIN AIM: Definition of the best MAB protocol to be used to perform the pilot studies
      • TIME FRAME: M23-M30
    • Responsibility: UNIBO supported by EVD, INRA, UMIL, Novadi, B3F, ASF, DRG, DNV, IRTA
  • 24.
      • Brainstorming on each genotyping pipeline STEP:
      • Preliminary phenotypic selection
      • Plant samples collection
      • Sample tracking along the pipeline
      • DNA extraction
      • Technique for genotyping
      • Scoring of the genotyping results
      • Final Selection Decision
    T-1.4 – Genotyping pipeline
  • 25.
      • T1.4 has strong links with other WP1 Tasks:
      • Traits selected in T1.2 (resistances vs fruit quality traits) and segregating in the pilot studies as defined in T1.3
      • Markers identified for selected traits in T1.2 (i.e. only SNPs or SNP/SSR)
    T-1.4 – Genotyping pipeline
  • 26.
      • No activity are planned before month 23
      • BUT
      • in the first year the Workflow has to be planned:
      • - Survey on the genotyping pipelines used in other species
      • Links with the genotyping pipeline under construction in RoseBreed
    T-1.4 – Genotyping pipeline
  • 27. WP1 - T1.5 Specification list of the breeding interface 29th March 2011
  • 28. T-1.5 – Breeder interface definition
      • MAIN AIM: Definition of the list of information to be included in the breeder-interface site
      • TIME FRAME: M1-M30
    • Responsibility: UNIBO supported by ETHZ, EVD, CRA-W, INRA, JKI, DLO, FEM, UMIL, Novadi, CRA, B3F, ASF, DRG, DNV, IRTA
  • 29.
      • Brainstorming among different expertise from the whole breeding and genotyping pipeline (breeders, molecular geneticist, statisticians, database designer) to provide useful information to the breeder interface designers in WP7 (T7.1)
      • A “wishing list” to help future breeders
      • Stakeholders meeting will provide the first information
    T-1.5 – Breeder interface definition
  • 30.
      • Organization of different sections?
      • List of traits and genes sources
      • Where to find useful genes/genotypes
      • Possible pedigrees inclusion
      • Markers for traits/gene selection and interpretation of MAS results (both for seedling and parent marker-assisted selection)
      • Definition of the accessibility rules for the breeder-interface and genotypes
    T-1.5 – Breeder interface definition
  • 31.
    • OTHER SUGGESTIONS?
  • 32. Action plan WP1 first 12 months
  • 33. Proposed action plan first 12M WHAT WHO HOW DL
      • T1.1 Breed. strategies
      • Identification of most important traits and assignment of weights (ranking)
      • Definition of ideotypes and breeding schemes
      • Evaluation applicability of GWS to apple + peach
    Breeders: EVD, UNIBO, UMIL, IRTA, Novadi, B3F, ASF, DRG, DNV Workshop of Thursday afternoon and/or stakeholder survey? Definition of breeding schemes including MAB specific for each site 12 Del T1.2 SNPs Develop SNP markers half/all of the loci assigned to the specific partrner EVD, UNIBO, ETHZ, JKI? Peach? Start M7
    • Using the apple genome sequence,
    • locus bracketed with SSRs, then SNP development in the interval
    • Genotyping of seg.
    • pop, mapping of SNPs, test of polymorphism
    12
  • 34. Proposed action plan first 12M WHAT WHO HOW DL T1.3 Pilot studies Select fruiting population or perform crosses for pilot studies (according ideotype defined in T1.1) Breeders: EVD, UNIBO, UMIL, IRTA, Novadi, B3F, ASF, DRG, DNV Breeding companies evaluate own pop. Breeding institutes perform crosses 12
      • T1.4 Genotyping
      • Start searching for systems to track plants samples and efficiently collect leaf samples
    UNIBO supported by: EVD, INRA, UMIL, Novadi, B3F, ASF, DRG, DNV, IRTA Study what it is done in other crops where MAB is more used 12 T1.5 Breeder interface Collect first whishes from breeders and stackholders UNIBO Workshop of Thursday afternoon and/or stakeholder survey? 12
  • 35.
    • Thank you for attending the workshop!