1.
IBP Breeding Management System
An Integrated Software Product to Manage a
Modern Plant Breeding Program
Mark Sawkins and IBP Team
Symposium--Crop Breeding Databases
2015 Annual Meeting,
15-18 November 2015, Minneapolis

2.
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 BMS
ASA, CSSA, SSSA Annual Meetings – 15-18 November 2015

3.
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 BMS
ASA, CSSA, SSSA Annual Meetings – 15-18 November 2015

4.
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 BMS
ASA, CSSA, SSSA Annual Meetings – 15-18 November 2015

5.
BMS Features
Program & 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

6.
Integrated Breeding Database
Mark Sawkins’ presentation of the BMS
ASA, 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

7.
Integrated Breeding Database
Mark Sawkins’ presentation of the BMS
ASA, 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

8.
Integrated Breeding Database
Details of the database at the foundation of the
BMS:
ICIS
CHADO

9.
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

10.
IBP Breeding Management System (BMS)

11.
BMS Workbench
The Workbench offers access to multiple breeding programs and
allows users to add and remove programs as required.

12.
List Manager

13.
Germplasm Search

14.
Crossing Manager

15.
Nursery Manager

16.
Trial Manager

17.
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

18.
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

19.
Current Analysis Pipelines

20.
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

21.
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 lam87@cornell.edu
Mark Sawkins’ presentation of the BMS
ASA, CSSA, SSSA Annual Meetings – 15-18 November 2015

22.
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 BMS
ASA, CSSA, SSSA Annual Meetings – 15-18 November 2015
Other
interested
parties

23.
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 BMS
ASA, CSSA, SSSA Annual Meetings – 15-18 November 2015

24.
IBP Regional Hubs

25.
For more information
Licensing questions: Stewart Andrews (s.andrews@cgiar.org)

26.
Credits

27.
Thank you!