Integrated Breeding Platform (IBP) and the Breeding Management System (BMS) Tools to support modern Breeding Programs General overview

Overview  The context  What is IBP?  IBP solutions: ◦Breeding Management System (BMS) ◦Breeding services & products ◦Support services  Perspectives and conclusions IBP & BMS – General Overview

The Context IBP & BMS – General Overview

Need to Increase Agricultural Production  Innovation in plant breeding is imperative to meet global challenges such as population growth and climate change. IBP & BMS – General Overview

Need to Increase Agricultural Production  The world population is ~7.3 billion people today, and is estimated to reach around 9.7 billion by Image modified from ‘World Population Growth’ by Lauren Manning on Flickr, Oct.27, 2008 IBP & BMS – General Overview

Need to Accelerate Yield Increase and Genetic Gain  Boosting yield in farmers‘ fields is needed to meet increase in demand for food and feed.  In developing countries, the gap between potential yield and farm yield is large, and the genetic gain/year is low in most breeding programs. IBP & BMS – General Overview

Need to Improve Breeding Programs  Many NARS breeding programs have fallen behind their private sector counterparts over the last 20+ years in terms of: ◦implementing best practices ◦adopting new approaches and technologies ◦delivering genetic gains to smallholder farmers IBP & BMS – General Overview

What is the Integrated Breeding Platform (IBP) ? IBP & BMS – General Overview

Principles and core offer  Plant breeders are at the forefront of the next food revolution, most particularly in developing countries. The IBP provides them the tools and knowledge they need to rise to a new level of breeding innovation: ◦SOFTWARE: an suite of integrated applications – the IBP Breeding Management System – partner plugins, and a directory of third-party solutions; ◦SERVICES: a network of service providers for genotyping, phenotyping, location analysis, climate maps and more ◦PRODUCTS: breeding materials and related information for a broad range of crops, including germplasm, trait dictionaries and predictive markers ◦SUPPORT: breeding and technical support, social networks, community spaces, and some funding opportunities ◦KNOWLEDGE: training courses & workshops, e-modules, technical documentation and tutorials, and online resources  It aims to be the most comprehensive source for best practices in plant breeding: IBP & BMS – General Overview

IBP & BMS – General Overview

Principles and core offer  We are here to enable breeders to play a leading role in R4D  Our primary target are breeders in developing countries, both in the public and private sectors  We target sustainable deployment at the institutional level  We promote the adoption of the entire platform (products, services and networks) We believe that this level of adoption would initiate a tangible revolution for breeders..! IBP & BMS – General Overview

Value Proposition  Breeders: ◦Increase data quality, documentation and exchange ◦Savings in time and cost to run breeding activities ◦Increased genetic progress per each crop cycle ◦Enhanced certainty in crop breeding outcomes  Institutions: ◦Improved institutional data management ◦Better product at a lower price (efficiency and effectiveness) ◦Improve the value proposition to attract funding  Society: ◦Improved crops (quality and yield) in farmers’ fields ◦More income for smallholder farmers ◦More and better food to feed the world IBP & BMS – General Overview

Evolution of the Platform  Phase I ◦ : Development  Phase II ◦ : Development + Deployment  Phase III + ◦2019-???: Development + Deployment + Maintenance  Key milestones: ◦Breeding Management System (BMS) Evolution BMS v1: Stand-alone, June 2013 BMS v2: Improved processing, functionality and UI, Jan 2014 BMS v3: Official Release Oct 2014 BMS v4: Web-based application, November 2015 BMS v5: Commercial-grade application, June 2016 ◦2014: IBP from GCP, new governance ◦2014: Establishment of Regional Hubs ◦ : Implementation of Business Plan IBP & BMS – General Overview

Deployment & Early Adopters  East and South Africa ◦1 Hub (BecA in Kenya) ◦+46 identified champions, across 14 programmes and 8 institutions  West and Central Africa ◦3 Hubs (IITA in Nigeria; AfricaRice in Benin; CERAAS in Senegal) ◦+53 identified champions, across 17 programmes and 10 institutions  South & South East Asia ◦3 Hubs (BIOTEC in Thailand; CAAS in China; ICRISAT in India) ◦+35 identified champions, across 27 programmes and 6 institutions  Rest of the world + Commercial activities ◦Central Team, VSNi ◦In discussion with +5 companies for deployment of commercial beta version  Users: ◦CGIAR Centers, selected institutions, NARS, Universities, a show of interest in the private sector ◦About 1500 unique downloads (v3.x) ◦About committed early adopters worldwide (used in daily routines) IBP & BMS – General Overview

Our Deployment Team IBP & BMS – General Overview

IBP Regional Hubs IBP & BMS – General Overview

IBP Solutions Breeding Management System (BMS) IBP & BMS – General Overview

Breeding Management System (BMS) IBP & BMS – General Overview

BMS Product Concept  Simple and easy-to-use application containing all informatics tools needed by a breeder  Seamless flow of data between mutually compatible applications  Accumulation, sharing and re-use of breeding data ◦As of mid 2015, twelve crop-specific databases with historical data: bean, cassava, chickpea, cowpea, groundnut, lentil, maize, pearl millet, rice, sorghum, soybean and wheat ◦Up next: barley, potato and sweet potato ◦Unified DB available for all crops ◦Phenotyping DB schema: Chado Natural Diversity Module  Targets routine breeding activities, in complementarity with research tools IBP & BMS – General Overview

BMS Product Concept  Allow integration of users’ own tools into the system through a publicly accessible API  Implementable as a standalone system ◦Merged DB  Will also be available as a cloud-based system ◦For computationally intensive analyses or large data storage needs ◦For large and/or decentralized teams Version 4.0 (web) to be released: end 2015 IBP & BMS – General Overview

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 IBP & BMS – General Overview

Core applications Programme & information management WorkBench (dashboard view) Study Browser Breeder Queries Ontology Manager (9 crops) Germplasm import tool Data import wizard Breeding activities Germplasm List Manager Crossing Manager Nursery Manager, with Seed Inventory Trial Manager Field maps and label printing Statistical analysis – Breeding View: Single-site analysis Multi-site analysis Multi-year multi-site analysis; Single trait (single environment) QTL analysis Marker-assisted breeding Integrated Breeding Planner Genotypic data management MBDtool: introgress QTL in back-crossing projects OptiMAS ​ : increase the frequency of favorable alleles over successive generations IBP & BMS – General Overview

BMS Workbench The Workbench offers access to multiple breeding programs and allows users to add and remove programs as required. IBP & BMS – General Overview

Crossing Manager IBP & BMS – General Overview

Database at the foundation of the BMS ICIS CHADO IBP & BMS – General Overview

Crop Ontology …links to IBP & BMS – General Overview

Linking to other Plant Breeding Systems  Plant Breeding API (BRAPI) ◦Partners in the definition of a standard Application Programming Interface (API) for plant breeding ◦BMGF is supporting development  Will serve to: ◦Facilitate data exchange among different initiatives ◦Expand the range of tools available to IBP clients ◦Reduce unnecessary duplication of tasks / More efficient use of resources ◦Increase communication among programmers working on similar projects (CoP) IBP & BMS – General Overview

Current members of BRAPI BRAPI KDDart (Diversity Arrays Technology) BMS (IBP) Triticeae Toolbox (T-CAP) Cassavabase (Cornell/BTI) B4R (IRRI) Flapjack, Germinate (JHI) GOBI (Cornell) Other interested parties IBP & BMS – General Overview

IBP Solutions Breeding Services and Products IBP & BMS – General Overview

Breeding services & products IBP & BMS – General Overview

Genotyping services  A fruitful partnership with LGC ◦Over 33 million data points generated for our partners ◦Preferential rates for IBP members ◦2 dedicated LGC project managers to manage IBP work orders. ◦Expedited timelines can be arranged for individual projects  All accessible through the IBP website: ◦Estimating a project with the Cost Calculator ◦Getting a quotation and/or submit a work order ◦Requesting a plant collection kit – free of charge with the purchase of LGC services. ◦Accessing KASP™ validated SNP markers for 11 key crops IBP & BMS – General Overview

More partner services  A network of service providers to facilitate the implementation of various stages of a breeding program.  Registered users can obtain some of these services at concessionary fees: ◦Breeding: Genotyping Phenotyping Location analysis and climate maps ◦Informatics: BMS plugins (partner applications, complementary to the BMS) Third party software Coming soon: hardware options (barcodes, printers, tablets, lasers, etc.) IBP & BMS – General Overview

Breeding products  Compilation of products derived from tangible outputs of research: germplasm, markers, genomics resources and informatics: ◦Crop information & genomics ​ research results directly applicable to plant breeding, and high-quality germplasm and evaluation data ◦Diagnostic markers & Germplasm resources Public & validated for traits such as drought, pest, disease, etc. for over 10 crops, and directly available to use in your breeding program IBP & BMS – General Overview

IBP Solutions Support Services IBP & BMS – General Overview

Support Services  Technical Support (IT): ◦Level 1 – Installation: downloading, installing and getting started with the BMS and related tools ◦Level 2 – Operational: day-to-day use of the BMS and related tools  Professional Support (Breeders): ◦Customized breeding support primarily in developing countries ◦Capacity building for training in using the tools ◦Interaction with peers through social networks and peer communities To promote adoption and ensure sustainability IBP & BMS – General Overview

Technical documentation & tutorials IBP & BMS – General Overview

More support resources IBP & BMS – General Overview

Perspectives and conclusions IBP & BMS – General Overview

Perspectives  Better data management: ◦Quality, safety and documentation improved thanks to electronic data capture tools with predefined templates ◦Knowledge and resource sharing across teams ◦In line with requirements of many donors  A change management process: ◦Down-to-Top: People are drivers of change (championing) ◦Top-Down: Buy-in, ownership and policy are key for enforcement and implementation  Evolve along with IT and internet access: ◦Different infrastructure models (stand alone, LAN, Cloud) ◦Build on cell phone technology IBP & BMS – General Overview

A solution for National Programs  A comprehensive suite, interconnecting all your breeding tools in one place: ◦Flexible standalone or network application ◦Support multiple crops within one system ◦Statistical tools for data analysis and quantitative genetics ◦Applications for a gradual transition into integrating genotypic data ◦Easily integrates with external technologies  Improved data management: ◦More security and preservation / legacy ◦Standardized documentation and quality control ◦Easier and faster retrieval and sharing ◦All in one place, from the field to the lab, thanks to electronic data capture capabilities  Dedicated support: ◦Adapted, from small workgroups to big scale breeding programs ◦Local assistance and training opportunities, to ensure your success in implementing new technology  Impact: ◦Better rates of genetic gain per crop cycle ◦Savings in time and cost to bring new crop varieties ◦More efficiency in your national program can contribute to a larger-scale impact on regional economy and food security. IBP & BMS – General Overview

A solution for Universities  A comprehensive suite, interconnecting breeding tools in one place: ◦Support multiple crops within one system ◦Statistical tools for data analysis and quantitative genetics ◦Applications for a gradual transition into integrating genotypic data ◦All in one place, from the field to the lab, thanks to electronic data capture capabilities ◦Easily integrates with external technologies  Meeting educational and research objectives: ◦Online educational resources to help integrate breeding theory with cutting-edge breeding technologies ◦Customizable educational materials to integrate into a plant breeding curriculum ◦IBP staff to assist with structuring workshops and curricula  Dedicated support: ◦Adapted, from small workgroups to big scale breeding programs ◦Collaboration with international institutions, professionals and academics in extended communities and networks ◦Training opportunities, capacity building initiatives and professional services  Impact: ◦More efficiency in breeding programs (genetic gain, time and cost savings) will contribute to a larger-scale impact on regional economies and food security ◦Students learn now how to use breeding software: added value for prospective employers IBP & BMS – General Overview

A solution for Enterprises  A comprehensive suite, interconnecting all your breeding tools in one place: ◦LAN solution for a decentralized enterprise (cloud solution also coming soon) ◦Support multiple crops within one system ◦Manages breeding information as well as workflow ◦Powerful data visualization tools, and advanced analytics and decision support tools for better breeding outcomes ◦Easily integrates with external technologies  Improved data management: ◦More security and preservation / legacy ◦Standardized documentation and quality control ◦Easier and faster retrieval and sharing ◦All in one place, from the field to the lab, thanks to electronic data capture capabilities  Dedicated support: ◦Adapted, from small workgroups to big scale breeding programs ◦Affordable professional support and training for change management ◦Dedicated relationship: we know your business and understand your local needs  Impact: ◦Better rates of genetic gain per crop cycle ◦Savings in time and cost to bring new crop varieties ◦Further your Corporate Social Responsibility (CSR) objectives IBP & BMS – General Overview

Conclusions  Huge potential impact: ◦crop research data management, ◦crop improvement ◦ultimately, on food security  Igniting a crop breeding revolution in developing countries  People drive change: need to encourage a new culture  Champions + buy-in of upper management  Partnerships: building a solid and vibrant breeding community  New operational model for R4D: thinking out of the box IBP & BMS – General Overview

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