The document outlines the challenges and reform strategies for modernizing crop improvement and seed systems, particularly in developing countries, emphasizing the importance of genetic gain and the need for improved breeding practices. It introduces the AVISA initiative, focusing on enhancing crop performance, establishing integrated breeding support systems, and addressing socio-economic and gender-responsive seed delivery. The document also details innovative approaches for overcoming barriers in seed production and highlights the necessity for collaboration among various stakeholders in the agricultural sector.

1. Modernising Crop
Improvement II
AVISA
Dr. Jan Debaene
Global Head – Breeding

2. Perspective from our major funder…

3. © 2012 Bill & Melinda Gates Foundation | 3
Key metrics for Gates Foundation investments
in crop improvement and seed systems:
February 12, 2019
▪ Rate of genetic gain delivered to farmers’ fields
– Intermediate metrics are set out in the Breeding Program Assessment Tool
(BPAT)
▪ Average area-weighted age of varieties in farmers’ fields
– Metric developed by Byerlee and applied by Melinda Smale
Affecting these metrics will require massive reform of the
breeding and seed systems serving smallholders along
the lines of commercial breeding

4. © 2012 Bill & Melinda Gates Foundation | 4February 12, 2019
▪ 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
Most public breeding programs in the developing world are 20-30
years behind state-of-art private sector programs due to:

5. © 2012 Bill & Melinda Gates Foundation | 5February 12, 2019
▪ 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
Most public breeding programs in the developing world are 20-30
years behind state-of-art private sector programs due to:

6. AVISA is focused on 5 primary outcomes:
1) The rate of genetic gain for performance in mandate crops
accelerated to an estimated 1.5% annually.
2) Integrated CGIAR/NARS Program anchored by an integrated
breeding decision and informatics support system.
3) Legume and cereal crop improvement, seed production and
delivery systems aligned for gender-responsiveness and end-
user demands and preferences.
4) Increased and equitable rate of varietal turnover.
5) Efficient project management and reporting.
AVISA
(Accelerated Varietal Improvement and Seed Delivery
of Legumes and Cereals in Africa)

7. Legend
Chickpea
Cowpea
Groundnut
Common bean
Sorghum
Pearl Millet
AVISA Geographies
Burkina Faso
Ghana
Nigeria
Ethiopia
Tanzania
Mali
Uganda
AVISSA Crops & Geographies: 5 Crops in 7 Countries

8. The EiB approach
Provide access to:
Cutting-edge tools, services and best
practices, application-oriented training
and practical advice to augment
breeding program performance
From where?
CGIAR, ARIs, private sector
Benefit to:
Public and private sector breeding
programs targeting low- and middle-
income countries

9. What does EiB provide?
Technical consultancy to CGIAR &
NARS breeding programs to enable
adoption and implementation of
improved practices as a part of a culture
of continuous improvement
A Platform for development of and
access to shared services and tools
across CGIAR breeding programs
A way to articulate shared goals
(communication with funders)

10. Structure
Breeding program
excellence
Optimizing
breeding schemes
Toolbox
Genotyping /
sequencing
Phenotyping
technologies &
assessments
Bioinformatics
and data
management
Tools&services

11. 1. Breeding program excellence
Enable breeding programs to implement:
1. Standardized product profiles
2. A stage gate process “from breeding cross to farm”
3. Routine genetic gains assessment
4. Optimized breeding schemes commensurate with level of
investment, product profile, tools and traits available
5. Lower-cost, well targeted genotypic data supporting larger,
more cost-effective programs
6. Lower-cost, well targeted phenotypic data supporting larger,
more cost-effective programs
7. Bioinformatics tools that support automation, data integration
and decision making
Identified based on feedback from AFS CRPs & the
Genebank Platform

12. • By aggregating demand for tools and services
economies of scale can be achieved
• Can only be achieved if CGIAR breeding is
coordinated and commits to the use of shared
services
• HTPG is a successful example of benefits from
this approach
Shared Services

13. Creating
synergies to
accelerate
genetic gains of
breeding
programs
targeting the
developing
world
Five focus areas = Modules
• Breeding program managementModule 1
• Optimizing breeding schemesModule 2
• Genotyping / sequencing
• tools and servicesModule 3
• Phenotyping tools and servicesModule 4
• Bioinformatics, biometry and data management
• tools and servicesModule 5
The Toolbox
The
“What”
The
“How”
TOOLS

14. • AVISA participatory CG centers will act as liaisons between the
NARS and EiB.
• Multi-stakeholder workshops will be organized in collaboration
with EiB to guide and mediate the design of PPs for each crop
with inputs from multidisciplinary teams (Module 1).
• Instituting a clearly regimented stage-gate system for crop
improvement activities (Module 1).
• EiB module 2 Leads in close collaboration with a development
team and breeders will design tools to calculate efficiencies and
to optimize breeding schemes.
• EiB module 4 Leads will conduct assessments of research
stations and consult on modernization upgrades of facilities and
equipment in order of priority and value.
Collaboration Between AVISA and EiB

15. Systemic bottlenecks in GL & DC seed systems
• Profitability/value of new GL & DC crop varieties
• Are the varieties superior/good enough?
• Are value chain actors aware of them?
• Is there sufficient seed to supply if demanded?
• Need for robust data on profitability of new varieties?
• Estimating markets and demand for seed
• Erratic demand that does not drive investment
• Market aggregation and demand structure
• limited data for informed decision making about market
segmentation
• Limitations in policy support
• complex regulations by Governments

16. Innovative approaches for cracking the EGS Code
• Decentralizing EGS production of public varieties
• private sector participation through licensing; sufficient size, capacity
and ambition to produce their own foundation seed
• performance-based time-bound exclusive rights
• Partnership with EGS producing private foundation seed companies
• Compulsory or Self-Regulation?
• Compulsory or Voluntary certification (SANSOR model; TLS model)?
• Maintenance breeding
• Quality/purity of EGS
• Variety release by Seed company
• Co-development with research centers
• Seed revolving fund
• Farmer-produced-breeder-managed EGS production

17. drivers and barriers
(cultural and gender factors)
of adoption:
inform breeders for
developing relevant product
profiles (varietal traits)
access to seed of improved
varieties and ICM practices
among wo/men farmers
Socio-economic and gender
analysis to create and
measure impacts.
Integration of social sciences into Seed Systems

18. The product profile process
The product profile functions as a contract between all stakeholders
in a network to design and deliver market-focused products
* Breeding teams and clients may include
CGIAR, NARS, Private sector, NGOs, etc.

19. SEED CATALOGUE (SEARCH)
GPS Coordinates
of the Plot Image of the
plot
Performance
Info
DIGITAL SEED ROADMAP TOOL
Variety | Geo | Target | Allocation | Track
Field Staff
Uses the M&E mobile
application to enter the
variety trial output data
(YIELD info)
M&E TOOL (MEASURE)
M&E (MEASURE) Dashboard (TRIAL
DATA)
Seeds Spl
Uses the
Seed
Roadmap to
generate,
allocate,
track seed
production
details
CLOUD SERVER
Digital MLE, Seed Catalogue and Production Roadmap

20. New Elements of Seed Systems in AVISA
• Hybrid Parents Research Consortia (HPRC) for sorghum
(ESA/WCA) and millet (WCA) established and strengthened.
• Participatory foresight analysis to estimate the magnitude and
geographical distribution of future demand and customer profiles
• Product profile development and approval process formalized
and regularly reviewed to replace existing varieties.
• Behavior change interventions designed to incentivize the choice
of improved varieties and quality seed in place of ‘informal
sources’

21. Stage-gates in functional, market-
oriented public breeding programs
Stage 1
Stage 2
Stage 3
Stage 4
Stage 5
Stage 6
Product design
Breeding strategy & optimization
Product development & testing #1
Product testing #2
Product multiplication
Product introduction
FromModule1feedback

22. Stage-gates link projects to programs
Trait
discovery
Trait
deployment
Core
Breeding 1 2 3 4 5 6
1 2 3 4 5 6
1 2 3 4 5 6
TRAIT PIPELINE
GERMPLASM PIPELINE
PRODUCT PIPELINE
TECHNICAL
OPERATIONS

23. The Module 1 approach
Understanding
Client Needs
Market-driven
product profile
contracts
Well-designed
breeding programs
Well-designed
product testing &
delivery
Annual
review
process

24. Product Profile Contract
An agreement to deliver a product to the beneficiary within 5 years
– The breeder is the "promisor”
– The funder is the "promisee"
– The client is the beneficiary
• Breeder also has an agreement with the pre-breeding
Traits
• “Basic” or “Essential” Traits - Traits present in the leading variety
targeted for replacement
• “Value Added” – Improved traits targeted for the replacement
variety that would allow it to replace the leading variety in the
market
Key definitions

25. Breeding programs will be driven by Product Profiles (PPs)
• PPs will be designed with input from NARS, market experts,
climatologists, socio-economic scientists, gender specialists,
nutritionists and breeders.
• PPs will be based on realistic prioritized objectives, with
quantifiable trait targets, with the aim to replace the
predominant variety in the market or introduce new product.
• Once initial PPs are generated, a feedback system using stages
and gateways to ensure agile response to customers needs with
the greatest potential impact on livelihoods.
• Team meetings by breeders with complementary disciplines, i.e.
plant pathologists, physiologists, genomic scientists, etc., to
strategize on how to execute on effective delivery of the PPs.
Develop Product Profiles for Each Crop/Geography

26. Continuous improvement
• A new way of working and philosophy, implemented
at all levels with management support
• Breaking the breeding program down into stage-
gate processes (both traits and products)
• Linking different products into a whole-breeding
program perspective
• Entered on the annual product advancement and
review process

27. Removing Bias From The Process
• Recent Product Design Workshops at ICRISAT
• Participants (SMEs)
– Value Chain; Socio-Economics; Gender/Youth; Seed
specialist; Private Sector Marketing
– Technical Experts (Validators of Delivery)

28. Shortened breeding cycle
Increased selection accuracy
Increased selection intensity
Optimizing breeding schemes

29. Genetic Gain
Δ𝐺 𝑦𝑒𝑎𝑟 =
i 𝑟𝐴𝐼 σ 𝐴
𝐿
𝐢 = Selection intensity
𝒓 𝑨𝑰 = Accuracy
𝝈 𝑨 = Genetic variance
𝑳 = Generation interval
Time:
• Reducing generation interval =
increases slope of the line
• Denominator = Largest effect
Traitvalue
0 1 4
Existing
value
Target
value
2 3
Trait value
Trait value
Trait value
Trait value
Trait value
Time

30. 30
Trends in breeding to drive genetic gain
Widen
Shorten
Shorten
More accurate
More efficient ($$$)

31. Shortening breeding cycle
• Rapid generation advance
• Contra cycle nurseries to multiply seed (seed based
crops)
• Sufficient early stage testing
• Early selection of parents
• Make crosses early and cull populations
• Contra season disease and quality testing
• Genomic Selection (for programs that are ready)

32. Panel of chickpea lines (ICAR) Sorghum and groundnut

33. Accelerated breeding pipelines using Speed-
breeding / Rapid generation turnover methods
• RGT accelerates the fixing of
lines.
• Using RGT prior to GS scheme
allow faster predictions to be
made about new recombinants,
“the more homozygous the
plants are, the more accurate
the genomic predictions will
be”.

34. Panel of chickpea lines (ICAR)
Sorghum and groundnut
Transformative strategies for accelerated breeding pipelines using
Speed-breeding / Rapid generation turnover methods
• Rapid introgression of genes/
haplotypes into elite lines
using marker-assisted
selection.
• Deploying RGT for rapid
development of RIL’s for
molecular marker discovery
and MAS allow efficient and
cost effective screening for
‘make or break’ traits.

35. Increasing selection intensity
• Start applying selection to larger populations
– Apply more selection pressure to whole populations
allowing larger population sizes
• Effective parent development strategy
– Increases effective population size
• Implement MAS (where appropriate)
– Increases effective population size

36. Separating pre-breeding from
breeding
• These activities should be very clearly
separated
• Each individual should clearly know their
role and expectations to fulfill that role
• Resources should be allocated
appropriately

37. Compartmentalize Breeding ActivitiesTraitvalue
0 1 4
Existing
value
Target
value
2 3
Trait value
Trait value
Trait value
Trait value
Trait value
Time
Core Breeding
(elite x elite)
Pre-Breeding
(elite x landrace
Or elite x
introgression)
Discovery or
Wide
Hybridization
(genebank
sources or
new
collections)
3 – 5 years 5 – 10 years 10 + years

38. Core breeding
• For the purpose of replacing varieties in the
market place
• Exclusively dealing with populations from elite x
elite parental combinations
• Continuous population improvement and
extraction of products from elite populations
being improved

39. A two-part strategy for genomic selection in crops
John M Hickey,
Chris Gaynor and Gregor Gorjanc
www.alphagenes.roslin.ed.ac.uk

40. Module 3 - Genotyping
• Quality control (parents, germplasm,
hybridization)
• Marker assisted selection (MAS)
• Genomic selection (GS)

41. Module 4 - Phenotyping
• More accurate data
• Lower cost, higher throughput data
• More relevant and representative data
(i.e. site selection)
• Likely to involve capital and infrastructure
considerations

42. Module 5 – Data management and
biometrics
• All data, pedigrees, trial designs, etc. to
be managed in a purpose built database
• Current best practice trial designs and
analyses implemented

43. AVISA Kick-off Meeting 25-27 February

44. Thank You