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Data Flows in Integrated Breeding

Data Flows in Integrated Breeding. Graham McLaren IBP Annual Meeting 1 st -3 rd June 2011 Wageningen. Principles of DM for Integrated Breeding (IB). IB requires high standards of sample and pedigree identification, it requires integration of field and lab data,

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Data Flows in Integrated Breeding

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  1. Data Flows in Integrated Breeding Graham McLaren IBP Annual Meeting 1st-3rd June 2011 Wageningen

  2. Principles of DM for Integrated Breeding (IB) • IB requires high standards of sample and pedigree identification, • it requires integration of field and lab data, • and quality is of paramount importance. • Data collected during breeding processes has immediate value for breeders and • it also has cumulative value over years and populations.

  3. Compatibility of DM Schemes • Users may have existing DM systems which need to be accommodated. • DM needs to be compatible across all members working on the same project. • Use of analysis and decision support tools and sharing of data with partners requires data to be formatted and stored in defined ways. • Training and support in DM and analysis is essential for IB projects

  4. Breeding Data Flows Breeding Partner 1 Breeding Project 1 Breeding Partner 1 Breeding Partner 2 Breeding Project 2 Breeding Partner 3 Breeding Project 3 Public Crop Information Breeding Partner n Breeding Project n Project data management Breeding data management Copy of Project Database Project database shared Crop lead Center n Public Database Central database < shared and published > Local Breeding Data Public Crop Central Database Project Data Update to project database • Project data curator: • QA for project data • Curation and integration • Distribution to partners • Project Trait Dictionary • Fieldbook Templates • Update to public DB • Download of public DB • Training of partner DMs • Data manager (DM): • Database management • Breeding logistics • Fieldbook preparation • Data entry/checking • Data management • Central DB curator: • QA for public data • Curation and integration • Distribution to projects • Publication on Internet • Global Trait Dictionary • Catalogue of Templates • Training of DMs and • Curators

  5. Interaction of breeding workflow and platform elements Choose parental material based on haplotype values, known genes, traits and adaptation High density genotyping MSL LIMS ST TSL FDM PIM PIM A&DS A&DS A&DS MSL ST LIMS GRSS MSL Develop crossing scheme based on genotype and phenotype compatibility LIMS Phenotypic characterization Breeding Information system Public Crop Information Key Information System ST Genetic Resources TSL FDM Pedigree information updated A&DS Parental Material ST PIM A&DS Sample Tracking Pedigree Information Laboratory Information Field Data Analysis & Decision Support Selection of lines based on QTL analysis / estimation of marker breeding values Crossing Block LIMS High density genotyping PIM Pedigree information updated FDM Phenotypic evaluation Platform Services A&DS Nursery 1 Selection on index of marker values GRSS n cycles of selection and recombination Nursery 2 Marker genotyping Genetic Resource Service Marker Service Trait Service Selection of improved lines based on trait improvement and adaptation MSL Pedigree information updated TSL Multi-location testing GRSS Evaluation Trials TSL ST FDM Cultivars and breeding lines Improved Lines

  6. Project Planning Breeding Decisions Germplasm Management Germplasm Evaluation Molecular Analysis Data Analysis Open Project Specify objectives Identify team Data resources Define strategy Parental selection Crossing Population development Experimental Design Fieldbook production Data collection Data loading Marker selection Fingerprinting Genotyping Data loading Quality Assurance Trait analysis Genetic Analysis QTL Analysis Index Analysis Selected lines Recombines Recombination plans Field Trial Management System Analytical Pipeline Statistical analysis applications and selection indices Trial field book and environment characterization system The IBP Configurable Workflow System Breeding Activities Breeding Project Planning Breeding Management System Genotypic Data Management System Decision Support System MB design tool, Cross prediction and Strategic simulation MABC MAS MARS GWS Breeding nursery and pedigree record management Lab book, quality assurance and diversity analysis Breeding Applications

  7. The Breeding Management System Breeding Management System • Nursery Management • Characterization lists • Pedigree maintenance • Evaluation lists • Seed Inventory Genotypic Data Management System ST Field Trial Management System

  8. ST Sample Tracking

  9. Genotyping Data Management System Genotypic Data Management System Breeding Management System Characterization lists • Planting list • Sample list ST Analytical Pipeline LIMS • Data Transformation • Genotyping Database • Application file formats • Genotyping Data • Quality Assurance

  10. ST Tracking Genotyping Samples

  11. LIMS Genotyping order form

  12. LIMS Genotyping results:

  13. Field Trial Management System Field Trial Management System Breeding Management System Analytical Pipeline Evaluation lists • Fieldbook • preparation Experimental design and randomization • Data Collection • Hand-held devises • Automatic measurement CWS ConfigurationSystem Trait templates • Environmental • characterization • Quality Assurance • Phenotyping data • Data Transformation • Phenotyping Database • Application file formats

  14. The Trial Template

  15. Analytical Pipeline Analytical Pipeline Genotypic Data Management System Decision Support Tools Genotyping data • Genotyping QA • Diversity analysis • Genetic mapping • Phenotyping QA • Single site analysis • Multi site analysis • GxE Analysis • QTL Analysis • QTLxE Analysis Diversity scores Pedigree trees COP matrices Phenotype means Genotype BLUPS Stability measures Adaptation scores Marker scores Genetic distance Genetic maps QTL estimates Field Trial Management System Phenotyping data

  16. LIMS Genotyping scores:

  17. Decision Support and Simulation Decision Support Tools Breeding Decisions Analytical Pipeline Germplasm lists for characterization Foreground markers Background markers Target genotypes Donor germplasm Recipient germplasm Ranked germplasm Selection lists Parental lists Crossing schemes • MBDT • Breeding indices • OptiMas Diversity scores Pedigree trees COP matrices Phenotype means Genotype BLUPS Stability measures Adaptation scores Marker scores Genetic distance Genetic maps QTL estimates Simulation Tools Population sizes Selection intensity Marker densities Crossing schemes Selection schemes Trait selection GE targeting Optimal breeding systems • QuLine • QuHybrid • QuMARS • QuGene Genetic models GE systems Breeding methods

  18. ICIS COP matrix Lower Triangular part of Coefficient of Parentage Matrix ROWID COLID ROWNO COLNO COP Optional Labels 50533 50533 1 1 0.9577 "IR 64" "IR 64" 70125 50533 2 1 0.2231 "IR 72" "IR 64" 70125 70125 2 2 0.9896 "IR 72" "IR 72" 11105 50533 3 1 0.1872 "IR 36" "IR 64" 11105 70125 3 2 0.5108 "IR 36" "IR 72" 11105 11105 3 3 0.9478 "IR 36" "IR 36" Lower Triangular part of Inverse Coefficient of Parentage Matrix ROWID COLID ROWNO COLNO INV-COP Optional Labels 50533 50533 1 1 1.1113776 "IR 64" "IR 64" 70125 50533 2 1 -0.1900738 "IR 72" "IR 64" 70125 70125 2 2 1.4324875 "IR 72" "IR 72" 11105 50533 3 1 -0.1170834 "IR 36" "IR 64" 11105 70125 3 2 -0.7344297 "IR 36" "IR 72" 11105 11105 3 3 1.4739708 "IR 36" "IR 36"

  19. Flapjack QTL Information File Compulsory Fields QTL Chromosome Position Minimum Maximum Trait Experiment Optional Fields AddEffects AddSE Minlog10(P) %VarExplained PosMinFM PosMaxFM LFM RFM

  20. Flapjack Map Data The map file should contain information on the markers, the chromosome they are on, and their position within that chromosome. The markers do not need to be in any particular order as Flapjack will group and sort them by chromosome and distance once they are loaded.

  21. Breeding program designer • Blue/gray – strategy • Green – Generation • Yellow – selection round • Pink/red – trait selection step • To start, open ‘BreedingProgram.jar’ • Can create/drag/drop any new objects anywhere • Use left mouse click to drag any piece and drop on higher hiearchy • Use centre mouse click to zoom • Edit in list/value boxes to set parameters + add new object at next level X delete object clone object Scott Chapman

  22. Integrating the applications of the Configurable Workflow System Breeding Management System Genotypic Data Management System Field Trial Management System Genotypic Data Management System Analytical Pipeline Decision Support Tools • Fieldbook • preparation • Planting list • Sample list • Genotyping QA • Diversity analysis • Genetic mapping • Phenotyping QA • Single site analysis • Multi site analysis • GxE Analysis • QTL Analysis • QTLxE Analysis • MBDT • Breeding indices • OptiMas • Planting list • Sample list • Nursery Management • Characterization lists • Pedigree maintenance • Evaluation lists • Seed Inventory LIMS LIMS • Data Collection • Hand-held devises • Automatic • measurement Simulation Tools • Genotyping Data • Quality Assurance • Genotyping Data • Quality Assurance • Environmental • characterization • Quality Assurance • Phenotyping data • QuLine • QuHybrid • QuMARS • QuGene GMS DMS GEMS

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