Innovation in plant breeding is imperative to meet the growing demand for staple food crops in developing countries. Modernizing breeding was therefore a major objective of the Generation Challenge Programme (GCP, http://www.generationcp.org). In this endeavor,the GCP createdthe Integrated Breeding Platform (IBP, https://www.integratedbreeding.net),to provide breeding material,knowledge and tools to assist researchers in their work,including custom-built software forreliable data management – the Breeding Management System (BMS Pro).These activities were sustained mainly through funding by the Bill & Melinda Gates Foundation,which ended this last September after 10 years of direct collaboration. The IBP has proven to be agile, adaptable and bold over the years, and is now applying the same spirit and resolve to find revenue from both public and private sources to continue serving its broad basis of stakeholders, among which national programs in Sub-Saharan Africa (SSA) remainfront and center. BMS Pro – a professional-grade software package distributed through LAN or cloud – is being used by close to 700 users in over 30 organizations of different types around the world (17 in SSA). We have learned that digitizing breeding is less about technology than it is about changing mindsets;it requires proper support on the ground,and thatmanagement commits to empower adoption within institutions. Although there is still some way to go before reaching routine adoption, a solid basis has been established and continues to be supported by a new generation of African breeders.Breeding digitization in Africa is well underway.
Presentation made by the GCP Director during the CGIAR Fund Council (FC) visit to CIMMYT (GCP's host), on the sidelines of the FC meeting in Mexico in May 2014.
Presentation made by the GCP Director during the CGIAR Fund Council (FC) visit to CIMMYT (GCP's host), on the sidelines of the FC meeting in Mexico in May 2014.
Dr Jean-Marcel Ribaut presents the GCP case study during the session on Developing World Crops at the CROPS conference, organised in May 2015 by the HudsonAlpha Institute for biotechnology, in Huntsville, Alabama, USA.
Magni Bjarnason, IBP Breeding Specialist, presenting at Stuttgart-Hohenheim Symposium: "The Breeder’s eye, today and tomorrow: Innovations in Plant Breeding"
Introducing the Africa RISING research framework africa-rising
Presented by Joseph Rusike (IITA) at the Africa RISING East and Southern Africa Research Review and Planning Meeting, Arusha, Tanzania, 1-5 October 2012
van Schagen - Walking the impact pathway: The CIALCA Experience in Mobilizing...CIALCA
Presentation delivered at the CIALCA international conference 'Challenges and Opportunities to the agricultural intensification of the humid highland systems of sub-Saharan Africa'. Kigali, Rwanda, October 24-27 2011.
Workstream 1: Technology Platform: Case StudiesHillary Hanson
Scientific and Technical Partnerships in Africa: Technologies, Platforms, and Partnerships in support of the African agricultural science agenda, Abidjan, Cote d'Ivoire, April 4&5, 2017
Jim Hansen, CCAFS Flagship 2 Leader, IRI
Presentation during an event on strengthening regional capacity for climate services in Africa, Victoria Falls,27 October 2015
Innovate, generate, disseminate and adopt improved technologiesHillary Hanson
Scientific and Technical Partnerships in Africa: Technologies, Platforms, and Partnerships in support of the African agricultural science agenda, Abidjan, Cote d'Ivoire, April 4&5, 2017
Africa imperatively needs to increase food and nutritional security to serve a growing population and reduce food importation costs (currently estimated at US$ 35 billion/year). There is considerable potential to raise agricultural productivity through the development of improved cultivars that lift yields, and respond to both local and global market demands. However, and despite decades of major investment in R4D, the impact in farmers’ field remains limited, especially for subsistence crops. Farmers still have difficulty accessing water, fertilizers and phytosanitary products, amongst others, and seed quality and distribution are a major bottleneck in most places. Even if improved germplasm with large genetic potential is available, it often lacks critical or specific local characteristics, or only performs well under optimal conditions. In the African context, some links of the crop value chain are either broken or missing, and only an integrated approach – from crop diversity to production in the field – can have a sustainable impact on agricultural productivity. Improvement toward sustainable change will include the implementation of a demand-led breeding practice, that is based on modern technologies aligned with local reality, and supported by a strong capacity development component (human and infrastructure). Stimulating entrepreneurial spirit to implement local/regional businesses at strategic points down the chain is also a must to succeed. The case for this vision builds on examples and lessons learnt from the Generation Challenge Programme and the Integrated Breeding Platform, after working in R4D, with and for African partners, for more than 15 years.
Dr Jean-Marcel Ribaut presents the GCP case study during the session on Developing World Crops at the CROPS conference, organised in May 2015 by the HudsonAlpha Institute for biotechnology, in Huntsville, Alabama, USA.
Magni Bjarnason, IBP Breeding Specialist, presenting at Stuttgart-Hohenheim Symposium: "The Breeder’s eye, today and tomorrow: Innovations in Plant Breeding"
Introducing the Africa RISING research framework africa-rising
Presented by Joseph Rusike (IITA) at the Africa RISING East and Southern Africa Research Review and Planning Meeting, Arusha, Tanzania, 1-5 October 2012
van Schagen - Walking the impact pathway: The CIALCA Experience in Mobilizing...CIALCA
Presentation delivered at the CIALCA international conference 'Challenges and Opportunities to the agricultural intensification of the humid highland systems of sub-Saharan Africa'. Kigali, Rwanda, October 24-27 2011.
Workstream 1: Technology Platform: Case StudiesHillary Hanson
Scientific and Technical Partnerships in Africa: Technologies, Platforms, and Partnerships in support of the African agricultural science agenda, Abidjan, Cote d'Ivoire, April 4&5, 2017
Jim Hansen, CCAFS Flagship 2 Leader, IRI
Presentation during an event on strengthening regional capacity for climate services in Africa, Victoria Falls,27 October 2015
Innovate, generate, disseminate and adopt improved technologiesHillary Hanson
Scientific and Technical Partnerships in Africa: Technologies, Platforms, and Partnerships in support of the African agricultural science agenda, Abidjan, Cote d'Ivoire, April 4&5, 2017
Africa imperatively needs to increase food and nutritional security to serve a growing population and reduce food importation costs (currently estimated at US$ 35 billion/year). There is considerable potential to raise agricultural productivity through the development of improved cultivars that lift yields, and respond to both local and global market demands. However, and despite decades of major investment in R4D, the impact in farmers’ field remains limited, especially for subsistence crops. Farmers still have difficulty accessing water, fertilizers and phytosanitary products, amongst others, and seed quality and distribution are a major bottleneck in most places. Even if improved germplasm with large genetic potential is available, it often lacks critical or specific local characteristics, or only performs well under optimal conditions. In the African context, some links of the crop value chain are either broken or missing, and only an integrated approach – from crop diversity to production in the field – can have a sustainable impact on agricultural productivity. Improvement toward sustainable change will include the implementation of a demand-led breeding practice, that is based on modern technologies aligned with local reality, and supported by a strong capacity development component (human and infrastructure). Stimulating entrepreneurial spirit to implement local/regional businesses at strategic points down the chain is also a must to succeed. The case for this vision builds on examples and lessons learnt from the Generation Challenge Programme and the Integrated Breeding Platform, after working in R4D, with and for African partners, for more than 15 years.
ICRISAT Global Planning Meeting 2019:Research Program - Innovation Systems fo...ICRISAT
The Global Planning Meeting 2019 focused on an innovation systems approach harnesses the conditions needed to create demand for technologies and creates the knowledge that may be used to bring about such changes…innovations most often emerge from a systems of actors collaborating, communicating and learning, methodologies and tools to create innovations, understand entry points/tradeoffs and leverage actors towards profitable resilient and sustainable agri-food systems at scale and work together to contribute to ICRISAT’s mission.
ICRISAT Global Planning Meeting 2019: Modernising Crop Improvement II (AVISA...ICRISAT
Most public breeding programs in the developing world are 20-30 years behind state-of-art private sector programs due to: Lack of engineering support for mechanization and automation; Primitive data collection, management, and decision support systems; Obsolete and expensive genotyping capacity unsuited to forward breeding; Inadequate selection pressure for yield in multi-location trials; Breeders are not trained, incentivized, or supported to optimize pipelines; Reliance on visual selection; Lengthy breeding cycles, excessive backcrossing, No selection of parents for high breeding value; Obsolete dissemination models designed for the Green Revolution
Dr Jean-Marcel Ribaut, IBP Director, gives the concluding lecture at the 5th International Conference on Next Generation Genomics and Integrated Breeding for Crop Improvement (NGGIBCI-V), which was held on 18-20 February 2015 at ICRISAT Campus, in Hyderabad, India.
See also:
the day in photos: https://www.flickr.com/photos/130732617@N02/sets/
Session 6 2 Monitoring, Evaluation and Learning: Monitoring Uptake for Impact David Ngome
As the ACAI project shifts focus from research-related activities to dissemination activities, it becomes imperative that different results and targets are achieved, and how these results and targets will be monitored and be known to all stakeholders.
The presentation on ME&L highlighted the results to be achieved, targets to be met and methodologies to monitor number of farmers reached with the DSTs, farmers changing practices through use of the DSTs, and farmers benefiting from use of the DSTs.
Farmers reached will be monitored by aggregation of number of farmers who are aware and gain knowledge of ACAI DST per use case, per DST format and per partner dissemination approach.
Farmers changing practices through use of the DSTs will be monitored through panel surveys, which will be done on annually starting in 2019.
Farmers benefiting from use of the DSTs will be monitored by impact survey, which will be conducted at the end of the project.
Rice breeding is both challenged and benefited by the fact that a successful varietal improvement program must embrace both the integration single genes that segregate in a simple Mendelian fashion as well as complex traits that are inherited in more quantitative ways. For decades the rice genetics community has produced a wealth of knowledge about these single genes and has developed markers that allow a breeder to track them in a population. However, marker assisted selection (MAS) alone is insufficient to drive the rates of genetic gain for more complex traits that are equally necessary. This presentation will describe the attempts made in the Favorable Environments Breeding program at IRRI to integrate the selection for single genes appropriate for MAS into a more complex population improvement strategy designed to improve quantitatively inherited traits.
Presenting the Integrated Breeding Platform (IBP) and the IBP Breeding Management System at the Symposium on Crop Breeding Databases, held by
the American Society of Agronomy (ASA), the Crop Science Society of America (CSSA) and the Soil Science Society of America (SSSA) for their Annual Meeting in Minneapolis.
On the IBDB phenotyping data model, mapping to the CHADO natural diversity schema, and accessing data through an API (Application Programming Interface)
Dr Mark Sawkins, IBP Support Manager, gave a demo presentation of Breeding View, a simple graphical interface to conduct statistical analysis of phenotypic and genotypic data. It can access procedures in Genstat or R-scripts, allows analyses to be configured, and is fully integrated into the IBP Breeding Management System (BMS).
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
PAG XVIII - Achievements and lessons after 10 years of digitization in Sub-Saharan Africa - Jean-Marcel Ribaut, IBP
1. 10 years to digitize breeding programs
in Sub-Saharan Africa: achievements,
lessons learned and perspective
Jean-Marcel Ribaut
13 January, 2020
PAG, San Diego
Enabling the Plant Breeding Revolution
2. Where are we coming from
Enabling the Plant Breeding Revolution
3. Challenges: The very big picture
Population growth and urbanization are generating
growing and differentiated food and nutritional needs
Increased emphasis on food for quality and processing
In developing countries, the gap between potential yield
and farm yield is huge (5 to 10 times)
Slow variety replacement in farmers’ fields
It isn’t so much a problem of genetic gain per se, but for what
Without a reasonable crop value chain in place breeding is useless
Informal seed systems might biase the numbers
Time to run Breeding 4 Investment
4. Key drivers of this breeding revolution:
Data Management
Data Management
Increased data quality and cost reduction at the source, thanks
to better performing tools and processes, will boost breeding
programs’ efficiency and make collaboration more effective
80% of a scientist's effort is
spent discovering, acquiring,
documenting, transforming, and
integrating data
Generally below 5% of the
research budget is allocated to
data management, if any. Poor
Institutional data management
policy
The business cost of poor
quality data may be as high
as 15-25% of an
organization's revenue, and
as much as 50% of the typical
IT budget may be spent in
"information scrap and rework".
Enabling the Plant Breeding Revolution
6. Migration
Moving from hand writing to electronic data capture
Moving from excel spreadsheet to relational DB
Integration
Developing workflows across different data sets of a same kind
Combining different kinds of data
Scale-up
Using larger data sets
Using more data sets
Data quality
Automating quality control steps
Standardization of data format and documentation
Analytical power
Running new kinds of analysis
Implementing high throughput analysis
Digital revolution: Key components
Enabling the Plant Breeding Revolution
7. Migration
Moving from hand writing to electronic data capture
Moving from excel spreadsheet to relational DB
Integration
Developing workflows across different data sets of a same kind
Combining different kinds of data
Scale-up
Using larger data sets
Using more data sets
Data quality
Automating quality control steps
Standardization of data format and documentation
Analytical power
Running new kinds of analysis
Implementing high throughput analysis
Digital revolution: Key components
Enabling the Plant Breeding Revolution
8. Data management integration
Specific germplasm
Phenotype
(target)
Trial or nursery
Trial site / Location
Genealogy
Parental crosses
Environment location
- Weather
- Elevation
- Day length
Environment plot
- NDVI
- CT
Physiology
- Chlorophyll
- Sugar content
Haplotype (prediction)
Genetic Diversity
Physical/Sequence map
QTL Map Gene/SNPs
Phenotypic data
Metabolomic
- Proteins
- Enzyme Genotypic data
Gene expression
Haplotype
(target)
Yield components
Secondary traits
SELECTION
GermplasmEnvironment
Physiology
Genetic
Morphology
Enabling the Plant Breeding Revolution
9. Web services
API
Large scale data
(Phenotyping)
(Genotyping)
Shared File Storage
(Genome hub)
(Seed catalogue)
Crop information
system
Breeders
Users of other
systems
Meta data
(GIS)
(Agroecology)
Germplasm
Pedigree
Data
capture
Ontology
Seed Inventory
System
Trial
nursery
Analytics
Crop Modeling
Data capture
Crop data management tools: integration
10. Breeders
(national programmes)
research & breeding
create foundation seeds
PRA - market demand (general traits and value)
Linking the dots down the value chain Integration
seed multiplication certify
and distribute
EvaluationPVS – product evaluation (adapted to demand)
Extension workers
(seed business)
Farmers
(local market and environment)
12. Where are we coming from: IBP in Brief
The Integrated Breeding Platform: A GCP Initiative
Started in 2009, ended September 2019
US$ 40M Initiative (BMGF and GCP)
Primary Targets: Breeding programmes in developing
countries and CG Centers
Support breeding programmes all over the world
Strategic objective: Digitalize breeding programmes
IBP: Your partner for modern breeding
https://www.integratedbreeding.net
13. IBP and the BMS
We are enabling and supporting national programme breeders to
play a leading role in R4D (R 4 Investment) by offering them
access to modern breeding technologies, breeding materials
and related information in a centralised, integrated and
practical manner
Enabling the Plant Breeding Revolution
Steady and growing interest for the BMS
the core product of the IBP
+5000 registered users
And it keeps growing!
IBP Portal
14. In transfer of technology the technical part is the
easiest one, sustainable adoption is the most
challenging one!
Enabling the Plant Breeding Revolution
15. The BMS deployment in SSA
Enabling the Plant Breeding Revolution
Numbers, challenges and conclusions
16. COUNTRY NARS/Institute Started BMS / deployment status
Uganda NaCRRI 2015 Server (Cloud) / Well advanced
Uganda NaSARRI 2015 Server (Cloud) / Well advanced
Tanzania LZARDI 2015 Server (local) / On going
Senegal ISRA/CERAAS 2015 Server (Cloud) / Well advanced
Burkina Faso INERA 2016 Stand alone (+Server IITA-cowpea) / Well
advanced
Ghana CRI 2016 Stand alone / Well advanced
Ghana SARI 2016 Stand alone / On going
Mali IER 2016 Stand alone / Well advanced
Benin INRAB 2017 Stand alone / Beginning
Ivory Coast CNRA 2017 Stand alone / Beginning
Niger INRAN 2017 Server (Cloud) well advanced
Nigeria NACGRAB 2017 Stand alone / Beginning
Rwanda RAB 2017 Server (local) on hold
South Africa ARC 2017 Server (local) /On going
Kenya KALRO 2016-2020 Stand alone/ Server Planning stage
Ethiopia EIAR 2016-2020 Stand alone/ Server Planning stage
Adoption of BMS by African NARS
12 servers, plus 3 servers at universities
17. Modernisation of plant breeding programs is a change management
process; it is not simply a matter of introducing a new technology and
tools and expecting institutions to embrace change
Enforcement and implementation
Big difference between the private and public sectors
Champions, champions and champions, plus the buy-in of upper
management (Commitments letters from 12 African Institutions)
Needs to happen in an integrated context with appropriate resources
and policies:
Dedicate time to learn new things
Data management policy in place and implemented
Resources allocated properly at the project proposal stage
Training embedded in research activities
Only possible if it builds on a rigorous (steps well defined) but
flexible (to be adjusted on a case by case) deployment process
Creating a momentum for change
Enabling the Plant Breeding Revolution
18. Digitizing breeding is a big commitment
Continue capacity development of local focal points is key
Engaging with universities to expose the new generations of
breeders to new tools and technologies
IBPʼs pioneer sustainability model as a Non-Profit
Organization
Enabling the Plant Breeding Revolution
Subsidized users are people
from public institutions in
developing countries
partnering with the IBP
◦ Receive BMS Pro products and
support services at no cost
◦ Costs covered by public funds
(projects, network, etc.).
All non-subsidized users can access
BMS Pro products and services
as paying users.
° Prices and conditions for license and
services are scaled in accordance with the
institution’s nature, size and region
° Income form paying users support tool
development and deployment for
subsidized users
19. Conclusions
Plant breeders are at the forefront of the next food revolution,
most particularly in Africa
Still some way to go from deployment to adoption
Impact indicators: cost and time saving, breeding efficiency, etc
Support and deployment must be ensured in the region and by
local Institutions, creating ownership by users
The tools and technologies to digitize breeding are available to
most, if not all, plant breeders in Africa
It is up to institutions’ management to ensure and commit they have
the capability to access these technologies
It is up to individual plant breeders/ teams, champions, to use the
best available technologies
Implementation of new approaches is as much a managerial
challenge as a scientific and logistical one (cultural change)
So, clearly some challenges must be addressed, but digitizing
plant breeding in Africa is already well advanced
The shift from deployment to adoption will happen through
breeding projects led by Africans