Luis Augusto Becerra presents an overview of Flagship Project 1 'Enhanced genetic resources' of the CGIAR Research Program on Roots, Tubers and Bananas (RTB), during the 18th Triennial Symposium of the International Society of Tropical Roots Crops (ISTRC) in October 2018.

1. S E P T E M B E R 2 0 1 8
Flagship Project 1:
Enhanced Genetic
Resources
LUIS AUGUSTO BECERRA • RTB ISC ANNUAL F2F MEETING

2. OUTLINE
• Flagship overview
• Key scientific achievements 2018
• Looking ahead: opportunities and challenges

3. Flagship overview
The objective of Flagship project 1 (FP1) is to develop and apply leading-edge
science toward faster and more precise development of user-demanded
varieties, and to enhance the long-term conservation and use of genetic
diversity.

4. Clusters and Cluster Leaders
Dr Ted Carey
DI1.1 – Breeding Community of
Practices
Dr Marc Ghislain
DI1.3 – Game-changing Traits
Dr Ehsan Dulloo and Dr Michael Abberton
DI1.4 – Tapping into RTB genetic
diversity
Dr Ismail Rabbi
DI1.2 – NextGen Breeding

5. Level of funding by window and cluster : FP1
- 1 2 3 4 5 6 7 8 9
DI 1.4
DI 1.3
DI 1.2
D I1.1
0.9
0.6
1.3
1.0
0.2
0.7
1.7
1.1
0.2
0.4
1.5
0.8
0.2
0.1
0.0
Millions
Cluster
Funding by Cluster
W1&2 W3 BILATERAL OWN FUNDS
W1&2
35%
W3
34%
BILATERAL
27%
OWN FUND
4%
Funding by Window
W1&2 W3 BILATERAL OWN FUND TOTAL
FP1 3.8 3.8 2.9 0.4 10.9

6. Key scientific achievements 2017-18

7. DI1.1 RTB Breeding Community of
Practice

8. RTB Interactions with EiB
• EiB Module 1
• StageGate system for breeding pipelines-
inputs from Ted Carey and M Friedmann on
RTB crop issues of specific traits, bulking of
planting material for advancement, etc.
• EiB Module 2
• Portal to share strategies and tools-to
coordinate with RTB BCoP portal
• Breeding program optimization;
workflows-to adjust to RTB crops as well
• EiB Module 3
• Access to genotyping platforms- being
used by RTB Scientists (cassava, potato,
and yam).
• EiB Module 4
• NIRS experiences from RTB scientists and
looking into ground penetrating radar for
early bulking trait screening
• EiB Module 5
• RTB databases (eg cassavabase,
sweetpotatobase) and contributions to
BrAPI for database inter-operability.

9. Integrating gender: trait preferences for cassava

10. DI1.2 Next Generation Breeding for
root, tubers and bananas

11. Consequences of interspecificity and structural variations on chromosome
segregation and recombination in A/B allopolyploid bananas
BANANA

12. Proof of Concept of Marker-Assisted Selection (Cassava) put
forward to the cassava community by IITA
• Tier 1 traits: Pest and disease resistance, micronutrient density and dry
matter content
• Resistance to CMD (6 SNPs)
• Resistance to CBSD (NaCRRI – Uganda) (not finalized yet)
• Resistance to CGM (NRCRI) (14 SNPs)
• Provitamin A content (17 SNPs)
• Dry matter content (15 SNPs)
• CIAT is currently working on developing and validating molecular
markers to whiteflies resistant and complementing the work by IITA on
the high accumulation of β-carotene.
• CIAT through partnership with Leibniz Institute DSMZ-German Collection
of Microorganisms and Cell Cultures (Dr Winter) sources of CBSD
immunity has been found – currently developing segregating progenies
for both CBSD and CMD
CASSAVA

13. CASSAVA

14. DI1.3 Game changing traits

15. Cross-cutting: Stewardship and regulation
of biotech products
Results from a DI1.3 workshop (Nairobi, September, 2017)
Biotech potato and Banana
Project / Product issues:
• Quality control: for both crops, tools are available to ensure product integrity
• Regulatory strategy: country by country approvals by CG and NARS
• Market confusion: difficult to maintain susceptible variety, but new trait / new variety
• Crop cultivation and utilization: NARS will have to take monitoring & compliance responsibility
Organizational / Operational issues:
• Competencies: train CG and NARS and take on achievable responsibilities
• Integrating regulatory and stewardship requirements: clear instructions to responsible staff
• Tracking / inventory: establish a traceability system
• Documentation / Archiving: assign resources to safeguard archives
• Contractual obligations: stewardship compliance included in MTA, agreements, contracts
Genome editing
• During research and product development, CG and NARS will have to handle gene-edited crops as
genetically engineered crops
• Approval and release will be dictated by national legislation.

16. Genome Editing at IITA
BANANA

17. Genome Editing to Remove a Selectable Marker Gene from Late
Blight Resistant Potato for Africa
Joseph Kpakpo Quaye, Jens Boch
Leibniz Universität Hannover
Design of the editing tools (sgRNAs ) of target sequence - nptII
CRISP/Cas9 in vitro cleavage analyses
• 4 sgRNAs came out as promising candidates
• Next step is to do it on protoplasts of a good lead transgenic
event and regenerate potato plants
Figure: sgRNAL14, lane + has all components and show
cleavage while other lack 1, 2, or 3 = negative controls)
POTATO

18. Genome Editing at CIAT
CASSAVA

19. DI1.4 Genetic Diversity

20. Rapid Appraisal of diversity in hotspots of RTB crops

21. Cassava agrobiodiversity of the Yanesha communities of
Peru
• Rapid diversity assessment
surveys nearly complete
• 300 hh, 12 communities Zona baja
Nuevo Progreso
Hanswald
San Juan de Pachitea
Huacamayo
Zona media
Centro Esperanza
Pampa Cocha
Loma Linda
Santo Domingo
Zona alta
Gramazu
Miraflores
Alto Yurinaki
El Milagro

22. RTB-DI1.4.2.2 : Seed storage behavior of wild banana seeds

23. Potato Cryobank at CIP

24. Looking ahead: opportunities and
challenges

25. OPPORTUNITIES AND CHALLENGES
• Opportunities
• A wealth of genomic resources has been generated for RTBs
germplasm (approx. 25% of what's available in Germplasm Banks -
GB). This resource can be used to unravel and exploit heterosis.
• Great advances on phenotyping approaches have been made (e.g.,
consumer preference). This will allow characterizing genomic region
(genes discovery) for traits of economic and agronomic importance
• Genome editing approaches for gene(s) involve in climate
adaptation and those that will improve use of natural resources
• Challenges
• Agree on a common analytical platform (genotypic and phenotypic)
• Find resources to complete the sequence characterization of RTB-GB
• Improve phenotypic platform for RTBs
• Find to increase financial investment in this area

26. Thank you