Mark Sawkins' presentation at the Symposium on Crop Breeding Databases - November 2015
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Transcript of Mark Sawkins' presentation at the Symposium on Crop Breeding Databases - November 2015
IBP Breeding Management SystemAn Integrated Software Product to Manage a Modern Plant Breeding Program
Mark Sawkins and IBP TeamSymposium--Crop Breeding Databases2015 Annual Meeting, 15-18 November 2015, Minneapolis
Outline
Introduction to the Integrated Breeding Platform (IBP)
The IB & Genotyping databases IBP Breeding Management System (BMS) Ontology Management System (OMS) Linkage to other public crop breeding
initiatives BMS deployment strategy
Mark Sawkins’ presentation of the BMSASA, CSSA, SSSA Annual Meetings – 15-18 November 2015
Integrated Breeding Platform (IBP)
Conceived during phase II of the Generation Challenge Programme (GCP)
Improve the efficiency of plant breeding programmes in developing countries
Enable plant breeders to access modern breeding technologies, breeding materials and related information in a centralised, integrated and practical manner
www.integratedbreeding.net
Mark Sawkins’ presentation of the BMSASA, CSSA, SSSA Annual Meetings – 15-18 November 2015
Integrated Breeding Platform (IBP) Software tools
◦ Breeding Management System (BMS) Breeding services and products
◦ Genotyping Support Services (GSS) supporting first time users from developing country breeding programs;
◦ Trait and metabolite, drought phenotyping and other phenotyping services;
◦ Location analysis and climate resources online Professional support
◦ Establishment of regional Hubs to support and promote use of IBP software and services.
◦ Breeding support; capacity building, social networks and Communities of Practice
Mark Sawkins’ presentation of the BMSASA, CSSA, SSSA Annual Meetings – 15-18 November 2015
BMS FeaturesProgram & Information Management• WorkBench (dashboard view) • Study Browser• Breeder Queries• Ontology Manager (10 crops)• Germplasm Import Tool• Data Import Tool
Breeding activities• Germplasm List Manager• Crossing Manager• Nursery Manager, with Seed
Inventory• Trial Manager
Statistical Analysis – Breeding View:• Single-Site Analysis• Multi-Site Analysis• Multi-Year Multi-Site Analysis; • Breeding View Standalone for
QTL• Quality Assurance
Marker-Assisted Breeding• Genotypic Data Management
System (GDMS)• QTL Analysis Tools• Molecular Breeding Design Tool
(MBDT)• OptiMAS
Integrated Breeding Database
Mark Sawkins’ presentation of the BMSASA, CSSA, SSSA Annual Meetings – 15-18 November 2015
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
Integrated Breeding Database
Mark Sawkins’ presentation of the BMSASA, CSSA, SSSA Annual Meetings – 15-18 November 2015
International Crop Information Database (ICIS)◦ “open-source” “open-license” generic crop information system under
development since the early 1990’s by researchers from CGIAR and non CGIAR partners
Review of ICIS in 2013◦ Current system suffers performance and complexity problems◦ Current model is not intuitive◦ Desire an optimum phenotyping database which meets user
needs in the most efficient way Initial mapping of sample problems to the Chado with ND extensions
showed a good fit◦ Natural Diversity Module is an extension to the Chado schema to better support
natural diversity data (phenotypic) Take an “additive approach” to table inclusion, no need to include all Chado
tables
Integrated Breeding DatabaseDetails of the database at the foundation of the BMS:
ICISCHADO
Ontology Management System
Preloaded with crop, location and breeding ontologies
Elizabeth Arnaud and team at Bioversity
Customizable Effort to streamline and reconcile
the ontologies this year Current crops
◦ Bean, Cassava, Chickpea, Cowpea, Groundnut, Maize, Rice, Sorghum, Soybean, and wheat.
Next Crops◦ Yam, Pearl millet, Barley,
Sunflower, Sweet potato, Oat Future crops
◦ Cocoa, Coffee, forages, Musa, Potato, Tef...
...and “Your Crop” (Trait Dictionary template v5 (TDv5) Mark Sawkins’ presentation of the BMS
ASA, CSSA, SSSA Annual Meetings – 15-18 November 2015
IBP Breeding Management System (BMS)
BMS WorkbenchThe Workbench offers access to multiple breeding programs and allows users to add and remove programs as required.
List Manager
Germplasm Search
Crossing Manager
Nursery Manager
Trial Manager
Technicians’ Training, Jan 2012, Bamako, Mali. Photo credit: A. Portugal (IBP).
Support for electronic data capture Field Book (Kansas
State University) KD Smart (Diversity
Arrays) FieldLab (IRRI) .csv files
Breeding View – Statistical Analysis Simple graphical
Interface for phenotypic and genotypic analysis
◦ Single site◦ G x E◦ QTL detection
Choice of Genstat or R-scripts
Developed with partners at WUR and VSNi
Current Analysis Pipelines
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
Linking to other Plant Breeding Systems Plant Breeding API (BRAPI)
◦ Definition of a standard API to be implemented by interested parties (http://docs.brapi.apiary.io/#)
◦ BMGF supported development of an open, shared Application Programming Interface (API) for crop breeding
◦ Facilitate data exchange among different initiatives◦ Expand the range of tools available to IBP clients◦ Reduce duplication of effort and support more
efficient use of resources◦ Contact Lukas Mueller [email protected]
Mark Sawkins’ presentation of the BMSASA, CSSA, SSSA Annual Meetings – 15-18 November 2015
Members of the collaboration
BRAPI
KDDart (Diversity
Arrays Technology)
BMS(IBP)
Triticeae Toolbox(T-CAP)
Cassavabase(Cornell/BTI)
B4R(IRRI)
Flapjack, Germinate
(JHI)
GOBI(Cornell)
Mark Sawkins’ presentation of the BMSASA, CSSA, SSSA Annual Meetings – 15-18 November 2015
Other interested
parties
BMS Deployment In December 2014 an adoption strategy and
roadmap was developed, including the establishment of regional hubs◦ ESA (East and South Africa)◦ WCA (West and Central Africa)◦ SSA (South & South East Asia)
First BMS conversion started with the National Agricultural Research organization (NARO) Uganda in February 2015
Mark Sawkins’ presentation of the BMSASA, CSSA, SSSA Annual Meetings – 15-18 November 2015
IBP Regional Hubs
For more information
Licensing questions: Stewart Andrews ([email protected])
Credits
Thank you!