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 lam87@cornell.edu

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 (s.andrews@cgiar.org)

Credits

Thank you!