Data Management for Integrated Breeding Graham McLaren

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.

Three Types of Data for IB parents 1) Genealogy or pedigree data unique identification of germplasm through Germplasm IDs (GID) names

3 Types of Data 2) Phenotypic data observable characteristics or traits 3 Types of Data 2) Phenotypic data environmental data across studies are linked via controlled trait vocabularies / standard terms

3 Types of Data 3) Genotypic data genetic composition  usually with reference to a specific trait under consideration

Sh. A. R. P. Importance of Data Management Data that are properly managed are: Sh. A. R. P.

Sh = Shareable Importance of Data Management Data that are properly managed are: Sh more accessible to research partners national and global sharing & linking of data

A Importance of Data Management Data that are properly managed are: = Available enables reliable analysis & conclusions leads to better science & more sophisticated research

R Importance of Data Management Data that are properly managed are: = Re-usable more likely to be used again for different purposes

P Importance of Data Management Data that are properly managed are: = Preservable  important for historically significant data  scientific method changed to: hypothesize , then look up answer in database

Sh A R P Importance of Data Management Data that are properly managed are: Sh areable A vailable R e-usable P reservable

Information Cycle for Crop Improvement Genetic Resources Information Systems Genomics and Genetics Databases Public Crop Information accessible via internet Crop Lead Centers Curation, integration and publication of Public Crop Information Institutional CIS National CIS Project CIS Private CIS Community of Practice Breeding Informatics Shared Information management Practices ARI Local CIS NARS Local CIS Networks Local CIS SMEs Local CIS

< shared and published > Breeding Data Flows Breeding Partner 1 Breeding Partner 1 Breeding Project 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 Data manager (DM): Database management Breeding logistics Fieldbook preparation Data entry/checking Data management 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 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

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

The IBP Configurable Workflow System Breeding Applications Breeding Activities Open Project Specify objectives Identify team Data resources Define strategy Project Planning Parental selection Crossing Population development Germplasm Management 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 Breeding Project Planning 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 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

A Simple Workflow for the Cassava Tutorial 1. Search for Germplasm Search a particular germplasm by name from the database Understand the information about germplasm entries contained in the ICASS database. 2. Import Parental Lists MALE2009 FEMALE2009 Set of 12 female parents and 12 male parents (some repeated) with high protein content and CMD Resistance There were will be two lists created. One for female parents and another one for male parents 3. F1 Nursery NR2009F1 (2008-11-15) F1s planted 12 crosses made from the female and male parents   4. Clonal Propagation NR2010C1 283 plants developed through clonal propagation Derive 284 plants from the F1 through clonal propagation 5. Selected Clones NR2011V1 25 selected from the initial list of clones Select 25 individuals from the initial clones for traditional clonal increase 6. Field Trial The selected clones will be tested in the field for evaluation There will be 3 locations and 3 reps in RCBD

Running the Cassava Tutorial