1. Agricultural Biotechnology in Africa: Fostering Innovation
Current Biotechnology tools for crop improvement – how does Africa benefit?
Santie de Villiers
ICRISAT
Agricultural Biotechnology in Africa: Fostering Innovation
Addis Ababa May 2001

2. Outline Needs in crop improvement Biotechnology – current status
Applications in crop improvement
Cost and complexity/constraints
What should be established in Africa?
What do we have access to and how can it be best exploited?
ICRISAT Biotechnology

3. Key Areas for crop improvement
Increased yields through
Biotic and abiotic stress tolerance.
Hybrid varieties.
Yield and plant architecture.
Product quality and human nutrition.
The main need in crop improvement is increased yield in order to feed the growing world population within a changing climate on the currently available land. This can be achieved through breeding crops with
Increased stress tolerance
hybrids
improved plant architecture such as root structure for better water use efficiency
improved nutrition

4. Biotechnology tools Tissue culture Genetic engineering Genomics tools
Consist mainly of these three technologies, which I will discuss in more detail, but for the purpose of this presentation, I will focus mostly on Genomics tools as these currently develops the fastest and is posing the biggest questions on what can and should be done in Africa.

5. Tissue culture Disease free plants of vegetatively propagated crops
Mass propagation of endangered species
Conservation through in vitrogenebanks
Plant transformation
The most widely used applications of tissue culture are
Production of disease free plants such as the very successful deployment of tissue culture bananas in eastern Africa
Mass propagation of endangered species, with strong emphasis on medicinal plants
Gene banks for vegetatively propagated crops that cannot be conserved through seeds
- Integral part of virtually all plant transformation protocols

6. Genetic engineering/GMO crops
Traits not available in compatible germplasm
Commercial products
Bt maize, cotton
Herbicide resistant soybean and oil seed rape
Virus resistant papaya
Public sector products
Golden rice
Wilt-resistant banana
Pod borer-resistant cowpea
Biofortified sorghum
These crops represents an essential technology which enables transfer of traits across the sexual compatibility barrier, which cannot be done through conventional breeding.
Even though there are not many GMO traits released, they have been incredibly successful.
I will not go into more details, only to mention that apart from the commercial events that have been released over the past 13 years, some public sector products are also nearing completion and will be available in 1 to 7 years.

7. Infrastructure in Africa – yes!
Tissue culture
relatively inexpensive
low-technology options
Genetic engineering
Biosafety considerations
BL2 requirement
Expensive to develop
Local products
Do we and should we have infrastructure for these technologies in Africa and the answer is a definite yes.
Tissue culture operations are relatively inexpensive and some good, low technology options are available.
Genetic engineering requires a greater monetary investment as it needs to comply with rigorous biosafety requirements. It is also highly recommended to produce products locally that address issues of importance to Africa

8. What is genomics?
Industrialization of molecular biology to address complex biological questions
Integrates biology, engineering and statistics to solve the sequence of a complex genome and then mine the sequence data to obtain biological insights.
As I mentioned before, I want to spend more time to discuss Genomics and the recent developments in this field and the implications thereof for Africa.
DNA sequence is simply the starting point for large-scale genome analysis.

9. Genomics approaches Structural Functional Bioinformatics
DNA sequence (genomic, cDNA)
Molecular mapping (SNPs, SSR, AFLP, etc.)
Genotyping and fingerprinting
Functional
Gene expression analysis (RNA, proteins)
Gene function analysis (knockouts, mutations, biochemical assays)
Gene interactions
Bioinformatics
Data storage, compilation and analysis

10. Why genomics?
Enables rapid and efficient discovery of important genes related to crop quality and improvement.
Genomics approaches enables the exploration and understanding of complex traits and pathways.

11. Exploit weeds/wild relatives as sources for desirable traits
Ancient farmers selected for major, visible desirable traits over thousands of years (domestication)
Modern breeding improved these traits in high input environments

12. Weeds/wild relatives as sources for desirable traits
Genomics enable identification of genes and gene networks responsible for traits such as
Stress response (pests, pathogens, abiotic and water/nutritional)
Growth/development (suckering, flowering, maturity)
Pave the way to reintroduce new and “lost” traits

13. Molecular markers Points of difference on chromosomes
Among varieties
Different forms of genes/traits
Focus on markers derived from DNA differences such as
- Short sequence repeats (SSRs) in non-coding DNA
- Single nucleotide polymorphisms (SNPs) in all areas of DNA
DNA array/chip technologies which show up differences between individuals/populations/varieties
Most genomics applications in crop improvement uses molecular markers.
These are “labels” that indicate points of difference between chromosomes of individuals – among varieties or different forms of genes/traits
SSRs – the number of repeats differ amongst individuals enabling detection
SNPs differentiate on the basis of single nucleotide differences
Genome- and next generation sequencing contribute to rapid development in this field

14. Molecular markers in Africa
Apply SSRs and SNPs for diversity assessment and faster, more efficient breeding
-Molecular tools development
- Quantitative Trait Loci (QTL) mapping and association mapping
Marker assisted breeding (MAB) and marker- assisted recurrent selection (MARS) to introgress QTL-based traits
Genetic diversity and gene flow studies
Genetic identity and purity testing
SNP analyses are outsourced e.g
IlluminaKBioscience
SSR genotyping at BecA

15. Molecular breeding protocol
Collection and phenotyping of germplasm for important target traits
Characterization with molecular markers e.g. SSRs, SNPs
Statistical analysis (diversity, genetic clustering)
Identifying molecular markers associated with target trait and map QTLs
- Markers enable faster, more precise breeding through MAB and MARS
- Further studies to isolate causative genes and mechanism
Drought tolerant
Weevil & multiple borers resistance
QPM
Extra early & early maturing lines
Collection and characterization of germplasm for important traits e.g. Reaction to drought/disease/pests and yield
Germplasm fingerprinting with molecular markers e.g. Microsatellites, SNPs ...
Statistical analysis (diversity, genetic clustering...)
Identifying molecular markers associated with trait of interest
-Markers associated with trait is used speed up breeding process and increase breeding precision
-Further studies to isolate causative gene and mechanism carried out

16. MAB to farmer preferred varieties
Donor variety with target trait QTL is crossed with FPV
Subsequent generations back-crossed to FPV
Use markers to:
ensure that the QTL are introgressed (FG selection)
select for recovery of FPV characteristics (BG selection)

17. New technologies Genome-wide selection Genotyping by sequencing
technically simple
highly multiplexed
high throughput
low cost platform
simultaneous marker discovery and genotyping by sequencing (GBS).
Population studies, germplasm characterization, breeding and trait mapping in diverse organisms.

18. Constraints: cost and complexity
Expensive infrastructure e.g sequencers, genotyping platforms
High throughput requirement
Dedicated personnel
Consumables
Rapid development renders equipment obsolete

19. What can/should be in Africa?
Using genomics tools entail
Selection of germplasm/appropriate populations
Phenotyping
Sampling
DNA extraction
Genomic analysis (outsourcing is cheaper, quicker and better)
Data analysis and Bioinformatics
Feedback into breeding program ✔ ✔ ✔ ✔✗ ✔✗ ✔ ✔

20. ICRISAT projects in Africa at BecA
QTL introgression through marker-assisted breeding
Strigatolerance in sorghum(BMZ, ASARECA)
Staygreen drought tolerance in sorghum (SFSA, ASARECA)
QTL mapping of midge resistance in sorghum(RF)
Gene flowstudies in sorghum (USAID, BMGF)
Finger millet blast and drought resistance mapping (BioInnovate)
Diversity assessment: Sorghum (BecA, RF, GCP)
Pigeonpea (Irish Aid)
Groundnut (Irish Aid)
Finger millet (BMGF)

21. MAB of Striga resistance QTL into farmer preferred sorghum varieties
Mali, Kenya, Sudan, Eritrea, Rwanda and Tanzania
Field trials on-station and on-farm - Kenya, Sudan, Mali, Eritrea
Materials have 1-3 QTLs introgressed
Selections for multi- location trials and seed multiplication for release in Sudan and Mali

22. Gene flow in sorghum
Population genetics to assess gene flow for GMO risk assessment
Mali, Niger, Burkina Faso and Kenya through collections of cultivated and wild varieties and genotyping
Implications for future release of GM sorghum
Inform regulatory authorities
K=4

23. Capacity building Post graduate students Training courses
Ph.D
M.Sc
Training courses
Visiting scientists

24. ICRISAT partner countries in Biotechnology

25. In conclusion All Biotechnology tools are accessible
Not all aspects need to be done in-house, especially for Genomics
Capacity building of paramount importance – train scientists well
Balance needed between technology in Africa and appropriate outsourcing for maximum benefit
Experimental design, sampling, DNA extraction and Bioinformatics capabilities
Networks and collaborations

26. Thank you