1. Data Flows in Integrated Breeding Graham McLaren IBP Annual Meeting 1 st -3 rd 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. Information Cycle for Crop Improvement Public Crop Information accessible via internet Genetic Resources Information Systems Genomics and Genetics Databases Crop Lead Centers Curation, integration and publication of Public Crop Information Breeding Informatics Community of Practice Institutional CIS National CIS Project CIS Private CIS ARI Local CIS NARS Local CIS Networks Local CIS SMEs Local CIS Shared Information management Practices

4. 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

5. Breeding Partner 1 Breeding Partner 2 Breeding Partner 3 Breeding Partner n Copy of Project Database Data manager (DM): Database management Breeding logistics Fieldbook preparation Data entry/checking Data management Breeding Project n Breeding Project 1 Breeding Project 2 Breeding Project 3 Project data management Project Data Local Breeding Data 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 Update to project database Public Database Public Crop Information Crop lead Center n 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 Breeding data management Project database shared Central database Public Crop Central Database Breeding Data Flows

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

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

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

9. Sample Tracking ST

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

11. Tracking Genotyping Samples ST

12. Genotyping order form LIMS

13. Genotyping results: LIMS

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

15. The Trial Template

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

19. Genotyping scores: LIMS

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

21. 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"

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

23. 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.

24. Trushar Shah

25. 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

26. Available breeding simulation tools QuLine, a computer software that simulates breeding programs for developing inbred lines QuHybrid, a computer software that simulates breeding programs for developing hybrids QuMARS, a computer software that simulates marker-assisted recurrent selection and genome-wide selection Jiankang Wang

27. What can QuLine do? Comparison of genetic gains from different selection methods Change in population mean Change in gene frequency Change in Hamming distance (distance of a selected genotype to the target genotype) Comparison of cross performance Selection history Rogers’ genetic distance Number of lines retained from each cross Comparison of cost efficiency Number of families Individual plants per generation Validation of theories Jiankang Wang

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