The Breeder’s eye, today and tomorrow: Innovations in Plant Breeding

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

Magni Bjarnason and the IBP Team Symposium: “The Breeder’s eye, today and tomorrow: Innovations in Plant Breeding” Stuttgart-Hohenheim, Germany 19 November 2015

Our discussion today

The context What is IBP? IBP solutions:

◦ Breeding Management System (BMS) ◦ Breeding services & products ◦ Support services

Perspectives and conclusions

IBP & BMS Overview – Magni Bjarnason Stuttgart-Hohenheim, Germany, 19 November 2015

The Context



Need to Increase Agricultural Production

Innovation in plant breeding is imperative to meet global challenges such as population growth and climate change.

The world population is ~7.3 billion people today, and is estimated to reach around 9.7 billion by 2050.


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.


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

What is the Integrated Breeding Platform (IBP) ?


Principles and core offer Plant breeders are in the forefront of the efforts to increase food production,

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 tutorials and related information for a broad range of crops, including germplasm information, 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: www.integratedbreeding.net


http://www.integratedbreeding.net/


www.IntegratedBreeding.net

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..!


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


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 300-500 committed early adopters worldwide (used in daily routines)


IBP Regional Hubs


Our Deployment Team


IBP Solutions Breeding Management System (BMS)


Breeding Management System (BMS)

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


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


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

Core applications

Programme & information management • WorkBench (dashboard view) • Study Browser • Breeder Queries • Ontology Manager(TD v5,9

crops) • Germplasm import tool • Data import tool

Breeding activities • Germplasm List Manager • Crossing Manager • Nursery Manager, with Seed

Inventory • Trial Manager • Integrated Breeding FieldBook

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 • Integrated Breeding Planner • Genotypic Data Management

System (GDMS) • QTL Analysis Tools • Molecular Breeding Design Tool

(MBDT) • OptiMAS

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

Crossing Manager

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)


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 Solutions Breeding Services and Products


Breeding services & products

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 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 1000-2000 KASP™ validated SNP markers for 11 key

crops


Bean products KASPas SNP

◦ 1497 markers ◦ Map position known

Diagnostic markers for four diseases ◦ Angular Leaf Spot Resistance ◦ Bacterial Blight Resistance ◦ Bruchid Resistance ◦ Mosaic Virus Resistance

Trait Dictionary ◦ English, French, Spanish and Portuguese ◦ About 70 traits

Crop community ◦ 249 members


Bacterial Blight Resistance

Bacterial Blight Resistance

IBP Solutions Support Services


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


Technical documentation & tutorials

More support resources

Perspectives and conclusions


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


A solution for Universities Statistical tools for data analysis and quantitative genetics Adapted support, 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 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 Learn now how to use breeding software:

added value for prospective employers


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 Partnerships: building a solid and vibrant breeding

community Champions + buy-in of upper management New operational model for R4D: thinking out of the box


Credits

Thank you! For more information: Magni Bjarnason [email protected] www.IntegratedBreeding.net

mailto:[email protected]

Science

The Breeder’s eye, today and tomorrow: Innovations in Plant Breeding