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Current Biotechnology tools for crop improvement – how does Africa benefit ?

Current Biotechnology tools for crop improvement – how does Africa benefit ?. Santie de Villiers ICRISAT Agricultural Biotechnology in Africa: Fostering Innovation Addis Ababa 12-15 May 2001. Outline. Needs in crop improvement Biotechnology – current status

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Current Biotechnology tools for crop improvement – how does Africa benefit ?

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  1. Current Biotechnology tools for crop improvement –how does Africa benefit? Santie de Villiers ICRISAT Agricultural Biotechnology in Africa: Fostering Innovation Addis Ababa 12-15 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.

  4. Biotechnology tools • Tissue culture • Genetic engineering • Genomics tools

  5. Tissue culture • Disease free plants of vegetatively propagated crops • Mass propagation of endangered species • Conservation through in vitrogenebanks • Plant transformation

  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

  7. Infrastructure in Africa – yes! Tissue culture • relatively inexpensive • low-technology options Genetic engineering • Biosafety considerations • BL2 requirement • Expensive to develop • Local products

  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. • DNA sequence is simply the starting point for large-scale genome analysis.

  9. Genomics approaches Structural 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 relativesas 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 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 SSR genotyping at BecA SNP analyses are outsourced e.g IlluminaKBioscience

  15. Drought tolerant 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 QPM Weevil & multiple borers resistance Extra early & early maturing lines

  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 • 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

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