04 wp3 progresses&results-20130221

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Text of 04 wp3 progresses&results-20130221

  • 1. WP3 Results achieved since the beginning of the project and plans for 2013
  • 2. Main objectives of WP3 1. Extend software for pedigree based QTL analyses 2. Discovery of QTL for fruit quality traits and disease resistance. 3. Validation of QTL-alleles over climatic regions and harvest dates 4. Assessment of genetic diversity as exploited within European breeding programs
  • 3. Results: PBA software T3.1 Intro: FlexQTLTM software Used to search for markers linked to traits. Designed for low marker densities SSR, AFLP... High densities (SNP): computation time too long Needs: Approaches reducing computation time
  • 4. Results: FlexQTLTM Approaches: More efficient algorithm implemented: -25% Option to sample marker info less frequently: -10x Windows -> version Linux platform : - 5x
  • 5. Results: PBA software II Intro-II SNP calling is performed using Genome Studio software Easily creates > million data points Issue: preparation of input data files for PBA software Approach Script developed that converts Genome Studio output to a Pedimap (FlexQTLTM) input file
  • 6. Intro III Visual interpretation easier than inspection of large tables Approach Important QTL results are presented in figures R-scripts have been added or improved for Trace plots of QTL positions along the genome Bin-wise posterior probabilities of QTL Posterior mean estimates of QTL effects Posterior probabilities of QTL genotypes of individuals Results: PBA software III
  • 7. Intro IV FlexQTLTM results are presented in a large series of output files. Not user friendly for occasional users. Approach A Interface is under development. Test version is un use.
  • 8. PBA software: Visual FlexQTL
  • 9. PBA software: Visual FlexQTL
  • 10. PBA-Software: Integrated maps Intro V QTL mapping requires markers to be in correct order. LG, succession in within Linkage group Physical map not adequate: 15% SNP misplaced Need Markers correctly positioned on linkage map Approach Protocols developed for the generation of integrated genetic linkage maps over multiple families
  • 11. PBA-software Summary - Better adopted to high marker densities - Reductions in computation time - Additional new functionalities - Increased user friendliness - Interface Acknowledgements RosBREED project USDA-SCRI www.RosBREED.org Amy Iezzoni Cameron Peace
  • 12. Results: Training on PBA software T3.7 Workshop Aim: Intro to FlexQTLTM & Pedimap Participants: Partners WP3-Peach Date: Feb 17-18, 2013 Instructors: IRTA: Diego Micheletti DLO: Marco Bink Eric van de Weg
  • 13. Results: Discovery QTL T3.2-T3.2 Background 1. Fruit related Traits Maturity time Fruit Size Flesh color Firm/soft melting Flesh adherence, Titrable acidity Total sugar Flowering time Flowering intensity White anthers Monilinia resistance 3. Phenotypic data Historic: EU-Projects, National projects 2. Segregating germplasm 18 families , 1500 individuals 5 breeding programs, 3 countries 4. Marker Data: next slide Peach 3. Phenotypic data New : 2011 & 2012 season Uploaded to DataBase Results
  • 14. Peach Marker data 9K SNP array Filtered for robust SNP Marker maps generated for each family
  • 15. Genotyping performance Assayed SNPs = 8144 Polymorphic: 67.1% Robust and informative 53.8% Null Allele/preferencial annealing 2.9% Paralogous regions 10.1% Non-Polymorphic 32.9% False SNP 9.6% Failed 23.3%
  • 16. Genetic mapping Comparison of the genetic map of chromosome 3 for two crosses Belbinette x Nectalady (IF7319828 x P. ferganensis) x IF7310828 High colinearity between genetic map and genome No need to create an integrated genetic for the PBA
  • 17. PBA Preliminary results Peach FlexQTL confirms known QTLs both for Flowering intensity & time Peaks in Green FlexQTL gives some evidence for additional minor QTL peaks in black G 8 Flowering Time G 4 Flower intensity
  • 18. Fruit Quality Taste Firmness Juiciness Crispness Total Sugar Acidity Storability Shelf life Harvest date Fruit size Skin Color Resistance to Nectria Apple 1. Fruit Quality Traits: > 10 3. Phenotypic data HiDRAS 3 Years, Multiple time moments Harvest, Storage 2 & 4M Shelf Life: 2wks - 2M storage National projects 2. Segregating germplasm 24 families , 1600 individuals 6 breeding programs, 6 countries 4. Genotyping: next slide Results: Discovery QTL T3.2-T3.2 Results Background
  • 19. Genotyping Infinium 20K SNP Available Jan 16, First 2x96 individuals tested Jan 19 Jonathan x Prima High quality data! High number of polymorphic markers
  • 20. Genotyping: 1st SNP results High number of polymorphic markers 70% (1820/2598) excluded: same segregation pattern 700 800 Unique segregation patterns, 45/LG 3 SNP / Focal Point Jonathan # # Left Prima # # Left J+P # J+P # Left Total Filtered 3000 2958 2400 Similarity -JM -1549 1409 Ungrouped -33 1376 Excluded 1081 -271 1105 Similarity map -317 764 -303 764 Unique patterns 764 802
  • 21. Mapped easily J1 P1 J2 P2 J3 P3 J4 P4 J5 P5 J6 P6 J7 P7 J8 P8 J9 P9 J10 P10 J11 P11 J12 P12 J13 P13 J14 P14 J15 P15 J16 P16 J17 P17 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 Some ends of chromosomes need to be checked +P7
  • 22. Graphical genotyping: Error added
  • 23. Graphical genotyping: High quality maps!
  • 24. Results genetic diversity EU breeding programs T3.4 Peach: SSR study Presentation Maria Jose Stakeholdersday Apple Results for 2 breeding programs (Y1) Y2: No activities Urgent need to progress
  • 25. Publications Peach: Planned Title WP Responsible Participants Application of PBA in peach: PBA to identify major genes* 3 IRTA All WP3-Peach Genetic diversity as exploited in EU apple and peach breeding. 3 DLO DLO+IRTA AG and PBA: characters related to climate change *(blooming/flowering/maturity) 3-4 INRA tbd AG? and PBA to detect QTLs of characters related to disease resistance 3-4 INRA tbd AG and PBA to detect QTLs of characters related to fruit quality 3-4 UNIMI-CRA tbd
  • 26. Publications Apple: Published 1. Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. 2012, BMC Genomics 25;13:203. Antanaviciute L, Fernndez-Fernndez F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ 2. PEDIMAP: Software for the visualization of genetic and phenotypic data in pedigrees. 2012, Journal of Heredity. Voorrips RE, Bink MCAM, Van de Weg WE
  • 27. Publications Apple: Planned 13 - 14 1. Procedures for construction of Integrated Genetic linkage using multiple families. Jansen et al. DLO, IASMA, PFR 2. Procedures for filtering and calling of SNP markers. DiGuardo et al. DLO, IASMA 3. Integrated genetic linkage map of apple using 24 families. DiGuardo et al. DLO, IASMA, .....? 4. QTLs for Nectria resistance in apple Koehorst et al. DLO, IASMA
  • 28. Main challenges for 013 - Peach Extend PBA to the 18 subpopulations (starting from March) Normalization of phenotypic data from 5 different location in Europe: INRA - Avignon (F), INRA- Bordeaux (F), IRTA (E), CRA- FRU (I), and University of Milan (I) Evaluation of the construction of SNP haplotypes (to use as multi-allelic markers, more informative than single SNPs) Correction of the genetic/physic position of some misplaced SNPs
  • 29. Main challenges for 2013 - Apple 1. Apple: Integrated genetic linkage map Needed to get started with QTL analyse