An initiative of the CGIAR Generation Challenge Programme (GCP) Breeding Management System Overview of functionalities Photo credit: Isagani Serrano/IRRI

Breeding Management System A suite of interconnected software tools and applications specifically designed to help breeders manage their day-to-day activities: Programme management Customise preferences and monitor programme activities from the Workbench, a dashboard application with integrated tools to manage and query crop information across the system Marker-assisted breeding Select germplasm and design crosses by complementing phenotypic selection with marker technology, for integrated breeding decisions Breeding activities Prepare trials and nurseries, manage seed inventories and keep continuous genealogy records season after season Statistical analysis Analyse field and lab data with powerful statistics and mixed model comparisons of locations and genotypes

A platform for plant breeders – Sept 2014 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 The Breeding Management System is a comprehensive, all-in-one suite of tools to effectively manage your breeding activities throughout all development phases of your programs, from project planning to final decision-making: Breeding Management System

BMS Workbench The Workbench offers access to multiple breeding programs and allows users to add and remove programs as required. A platform for plant breeders – Sept 2014

BMS Workbench Germplasm lists, nurseries, trials and recent activities are shown for the highlighted program A platform for plant breeders – Sept 2014

List Manager

 The List Manager is at the center of all activities in the Breeding Management System: First screen you arrive at after opening your Breeding Program Left navigation menu provides direct access to all tools Easily build and work with the lists that are used in each stage of the breeding cycle A platform for plant breeders – Sept 2014 List Manager

 Key List Manager Features: Ability to browse and modify existing lists Ability to search for lists and germplasm entries Ability to create a new list dynamically by pulling from existing lists or germplasm search results Expanded ability to modify list contents Ability to export lists for use outside of the BMS A platform for plant breeders – Sept 2014

Germplasm Search A platform for plant breeders – Sept 2014

Nursery Management  Breeding Manager comprises four tools which facilitate breeding logistics and population development Crossing Manager Nursery Book Manager Advancement Tool Inventory Manager  Key Features of the Breeding Manager: Uses germplasm lists to make nurseries Uses crossing block nurseries to capture new crosses Advances pedigree nurseries by bulk and selection methods Tracks seed inventory through population development A platform for plant breeders – Sept 2014

Nursery Management: Crossing Tool

Nursery Management: Nursery Book A platform for plant breeders – Sept 2014

Nursery Management: Advance Pedigrees A platform for plant breeders – Sept 2014

Nursery Management: Inventory

Field Testing  Once populations are developed, the breeder wants to set up a trial to evaluate promising lines: describe the trial; select a list of germplasm for testing; specify the trial environment(s); specify the trial design and generate the layout; specify traits to be measured and produce fieldbooks;  and collect data check and store data. A platform for plant breeders – Sept 2014

Describe the Trial A platform for plant breeders – Sept 2014

Select the Germplasm

Specify the Trial Environments A platform for plant breeders – Sept 2014

Specify the trial design and generate the layout A platform for plant breeders – Sept 2014

Specify traits and produce the Fieldbook A platform for plant breeders – Sept 2014

Crop Specific Trait Dictionaries Measurement Variate Trait property Reporting units or scale Measurement method

Trait descriptors / ontology …links to

Labels A platform for plant breeders – Sept 2014

Field Map A platform for plant breeders – Sept 2014

Electronic data capture  Fieldbook connects to Android-based tablet devices for data collection in the field and laboratory

Data capture practicals – Technicians’ Training, Jan 2012, Bamako, Mali. Photo credit: A. Portugal. A platform for plant breeders – Sept 2014

Integrated Breeding Database  Genealogy Management System (GMS) Germplasm nomenclature, chronology, IP and passport data Pedigrees and breeding history  Phenotyping Data Management System (DMS) Germplasm characterization and evaluation data Annotated with Crop Research and Crop Trait Ontologies  Genotypic Data Management System (GDMS) Medium density fingerprinting data Genotyping data for MAS and MABC Genotyping data for Marker-trait association analysis A platform for plant breeders – Sept 2014 Databases fully integrated into BMS workbench

Query Tools  At the outset of a breeding cycle users want to: browse all germplasm information review existing characterization and evaluation search for adapted germplasm perform head to head comparisons A platform for plant breeders – Sept 2014

Head to Head Query A platform for plant breeders – Sept 2014

Management and Analysis of Genotyping Data  The GDMS module allows users to integrate the use of molecular techniques into their breeding programs: Order genotyping services Import genotyping data Search for polymorphic markers Retrieve, view and analyse genotyping data  Key Functions search genotyping data for a set of lines, retrieve and visualize these data and calculate a similarity matrix search genotyping data for parents of a potential cross to confirm there are sufficient polymorphic markers select available SNP markers (including any markers linked to a trait of interest) and create a genotyping order form A platform for plant breeders – Sept 2014

Uploading genotyping data A platform for plant breeders – Sept 2014

Visualization of genotyping data A platform for plant breeders – Sept 2014

Statistical Analysis of Phenotyping Data  Breeding View provides easy access to the high throughput analyses routinely required by breeders The same interface can be used to access procedures in Genstat or R-scripts and allows analyses to be configured  Single site analysis is available for complete and incomplete block designs as well as row-column designs and spatial analysis New designs are being added at each update Analyses can be run in batches over environments and traits  Two-stage multi-site analysis is available for GxE and stability analysis with or without grouping of environments Single pass meta analysis of unbalanced site by season data is being incorporated A platform for plant breeders – Sept 2014

Statistical Analysis of Phenotyping Data

 Single trait linkage analysis (QTL) Quality control phenotypes (summary statistics) Quality control marker data QTL detection – genome wide scan using single and composite IM Output includes profile plots and tables Results available for automatic viewing in Flapjack HTML report of QTL results  Multiple trait sequential analysis QTL results for each trait combined Single Flapjack view for all traits Breeding View - QTL analysis

A platform for plant breeders – Sept 2014

Decision support for marker implementation  OptiMAS Developed at INRA, Le Moulon Implementation of markers in a MARS breeding scheme Identify and track favorable alleles through cycles of recombination and selection  Molecular Breeding Decision Tool (MBDT) Developed by team at ICRISAT Implementation of markers in a MAS and MABC context

Future Directions  Continuous improvement of UI based on user feedback  Additional analysis methods for expanded experimental designs and genetic analysis  Seed inventory management system  Cloud based deployment  Data will be stored in a single shareable database with user access roles  Off-line capability will be supported by a data cache which will synchronize when a connection is available A platform for plant breeders – Sept 2014