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Cassava Research in Nigeria - September 2012

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Presentation by Dr Emmanuel Okogbenin, National Root Crops Research Centre, Umudike, Nigeria …

Presentation by Dr Emmanuel Okogbenin, National Root Crops Research Centre, Umudike, Nigeria
Delivered at the B4FA Media Dialogue Workshop, Ibadan, Nigeria - September 2012
www.b4fa.org

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  • 1. A case study of using molecular markers to link African cassava farmers to the crop’s center of origin for increased diversity and productivity Okogbenin E., Fregene, M, Ceballos H., Egesi, C. Fulton T., and Alves, A.
  • 2. Outline Cassava Challenges Centre of origin Molecular marker tools Marker-assisted breeding Release of varieties Conclusion
  • 3. INTRODUCTION
  • 4. Cassava originated in Latin America and has been grown by the native Indian population for at least 4000 years
  • 5. 17 millions hectares Basic food for more than 500 million people in the tropics Cassava In Africa, Nigeria, the DRC, and Ghana alone account for two-thirds of total production on the continent
  • 6. The Plant Foliage: A Tropical vegetable Stems: Planting materials (source of cellulose) Roots: Unique starch properties
  • 7. Key Commercial Traits Yield Dry matter Starch Protein Beta carotene Delayed post harvest deterioration
  • 8. Recent projections forecast even higher dependence for food security and poverty alleviation Cassava Modified Starch Pharmaceuticals, Processing inputs Livestock feed Processed foods Industrial Starch (e.g., drilling) EthanolFlour Glue
  • 9. Pilot plant for artificial drying of cassava roots and leaves Flours from roots and/or leaves Animal feed Dry extraction of starch Direct production of dextrines Direct production of adhesives
  • 10. Yellow Garri White Garri Light Yellow Garri Yellow Garri Yellow garri has higher price premium than white or intermediate colour garri by 30-60% in Nigeria! Great Potentials for Cassava Products in Nigeria
  • 11. Fried cassava chips Frozen croquettes High value-added products with excelent potential in the export markets Healthy (less fat than equivalent products) Exotic Organic
  • 12. Cassava in BrazilCassava in Brazil Starch – “tapioca”, “farinha de tapioca”, “beiju ”, etc AACA-28Apr2005Photos: A. Alves
  • 13. CHALLENGES
  • 14. • Drought toleranceDrought tolerance
  • 15. Westwards and Southwards Expansion of the Severe Cassava Mosaic Disease Pandemic (Africa) • EACMV • ACMV • EACMV-Ug Cassava Belt Known CMD pandemic Threatened areas CMD ‘crisis’ zones Cassava Belt Known CMD pandemic Threatened areas CMD ‘crisis’ zones Emerging Threats
  • 16. Cassava mosiac diease CMD is a serious disease in Africa and parts of Asia (India) It does not exist in Latin America. Latin American cassava are highly susceptible
  • 17. C. Fauquet
  • 18. CBB scoring scale (1 = no symptoms) 3 3 2 4 5
  • 19. PPD evaluation procedure
  • 20. Cassava breeding and evaluation schemes currently used at CIAT Elite germplasm recombined trough sexual crosses (hand or open pollinations). Thousands of botanical seeds are produced each year. Seedlings from botanical seed are grown in screenhouses and then transplanted to the field. Plants from botanical seed are grown (avoiding selection) for 10 months and 7-8 stakes are produced from each plant. One row plot with 7 or 8 plants/plot One replication – One location 2-rows plot with 10 plants 3 replications – one location 5-rows plot with 30 plants. 3 replications – 2-3 locations F1 [ 6000 GENOTYPES] Clonal Evaluation Trial [4000] Preliminary Yield trial [800] Advanced Yield Trial [300] Regional Trial [90] 4-rows plot with 20 plants 3 replications – one location Shipment to Target Environment Centro Internacional de Agricultura Tropical International Center for Tropical Agriculture
  • 21. The challenges for Nigeria: Solving problems and adding useful traits to the crop Sustaining steady and stable yield levels Enhancing cassava nutritional quality in vitamins and protein contents for the malnourished poor Creating an export-market driven cassava industry Transforming cassava into a major player for economic development and wealth creation
  • 22. CENTRE OF ORIGIN Source of genetic diversity (genetic variation)
  • 23. Brazil (160) Mean = 2.9 % COL / VEN (184) Mean = 3.0 % PER / ECU (87) Mean = 2.2 % PAR / ARG (8) Mean = 3.1 % Caribbean (8) Mean = 2.9% Central America (26) Mean = 4.8 % MEX / USA (13) Mean = 3.5 % Frequencies for protein content in the roots from landraces in the germplasm collection
  • 24. Commonly reported protein levels 0 2 4 6 8 10Crudeproteincontent(%) MGUA91 MCOL2436 MGUA86 MCOL219 SM734-5 CM3236 MGUA76 MCOL2694 MCOL2459 MBRA300 MGUA79 MBRA101 MMEX108 SM1406-1 MMEX95 MCOL678 SM673-1 Crude protein content (%) in selected clones measured in 1999 and 2005 1999:quantification in Australia 2005: quantification in Colombia
  • 25. Yield potential in cassava Cultivar: SM 1433-4 Yield: 84 t/ha Area: 9.5 ha Location: Ciénaga de Oro (Córdoba) The challenge is to turn this into the rule, not the exception In every Department
  • 26. M. tomentosa M. irwinii M. anomala M. dichotoma Mining wild gene pools
  • 27. Traits that we hope to generate and identify variation for: Starch quality: Low or no amylose Low or no amylopectin Different granule size Change in P-bound starch “Sugary” cassava Variation in starch quality and distribution in cassava roots from Brazilian landraces
  • 28. MOLECULAR TOOLS Molecular markers for gene tagging and to explore genetic variation
  • 29. “Diversity”: What does it mean? Variability among living organisms Biological Diversity, genetic diversity Genomic diversity - on a whole genome scale Cowpea at IITA, Nigeria
  • 30. Levels of diversity Among species; within ecosystems Within a species: among populations or individuals Intra-species variation (within a species) Inter-species variation (between species)
  • 31. Allelic diversity Alleles are variants of a particular gene or DNA segment Example: eye color Image from Discovermagazine.com
  • 32. Gregor Mendel In >30,000 crosses, Mendel studied the inheritance of 7 traits In Peas (Pisum sativum)
  • 33. DNA: the most basic level of diversity Each DNA strand is composed of a string of nucleotides, which are formed from a pentose sugar, a phosphate group, and either adenine, guanine, thymine or cytosine (abbreviated as A, G, T, or C). The order of the four bases in the DNA sequence of each individual organism is unique. It carries all the genetic information needed for the organism to function. These illustrations from the Human Genome Project Information site (http://www.doegenomes.org/) show two views of the structure of DNA.
  • 34. Morphological markers versus Molecular markers I. Morphological markers • mutations normally in exons • usually gene knockouts • often deleterious • usually recessive (lose half information for genome mapping) • attached to function ª epistasis a problem • low natural polymorphism, often mono-allelic II. Molecular markers microsatellites polymorphism among maize inbreds Chlorophyll mutant in pepper • any part of genome • often neutral • codominant (maximum info for mapping) • usually no function attached • no epistasis • high natural variation, multi allelic mC A C IN/DEL
  • 35. Molecular markers -- detection of genetic variation at the protein or DNA level Protein level: • Isozymes analysis using non-denaturing gel electrophoresis and enzyme activity stains DNA level: •Restriction fragment length polymophism (RFLP) •Random amplified polymorphic DNA (RAPD) •Amplified fragment length polymorphism (AFLP) •Microsatellites (simple sequence repeat, SSR) detection •Cleaved amplified polymorphisms (CAP); also called Sequence characterized amplified polymorphisms (SCAR) •Single stand conformational polymorphism (SSCP)/ Denaturing gradient Gel electrophoresis (DGGE) •Denaturing high pressure liquid chromotography (cHPLC) •Single nucleotide polymorphism (SNP) detection • DNA chips (allele specific arrays) •Taqman assays •Invader technology •DNA TILLING
  • 36. Scoring bands Individuals Genotypes M Locus A A1A1 A1A2 A2A2 Gel 1 2 3 1,0 1,1 0,1Locus A M 1 2 3 Example of one marker
  • 37. The complete set of DNA that an individual inherits from its parents The genotype of an individual remains unchanged throughout its life, regardless of the environment surrounding and affecting it Although DNA is the basis of a genotype, we can study genotypes without knowing the DNA sequence Genotype
  • 38. ManihotManihot esculentaesculenta • Genome : 770Mbp • Genetic resources • Extensive knowledge on the genetic diversity • Different tools : - genetic maps - markers - BAC librairies - ESTs, microarrays - transformation - silencing (VIGS) • Pests and diseases Cassava : crop of the futureCassava : crop of the future
  • 39. RAPD Bulk Segregant Analysis of Resistance to Whitefly RR11 SS11 RR22 SS22 RR33 SS33 RR44 RR55 R1 and S1: CG 489-34 x MCol 2026 R2 and S2: MBra 12 x MCol 2026 R3 and S3: CG 489-34 x MCol 1505 R4: Ecu 72; R5:Ecu 72 progeny.
  • 40. 2SSR and 2 SCAR marker explains between 90 - 100% of phenotypic variance for CMD resistance Dist Marker cM Name rGY115 7.9 rGY9 15.6 rGY1 16.1 rSSRY28 11.3 Ai19 CMD2 R CMD Resistance F1 progeny CMD Susceptible F1 progeny 150bp RP/SP/RB/SB 200bp 175bp Akano et al 2001 Theor and Appl Genet 105:521-525 Gene Tagging: Resistance to the Cassava Mosaic Disease (CMD) Funding: Rockefeller Foundation
  • 41. MARKER-ASSISTED BREEDING (MAB) Crosses and segregation in plant population developed
  • 42. 144 F1s144 F1s Resistant to ACMV Resistant to CBB Early Bulking Resistant to ACMV Resistant to CBB Early Bulking Good Cooking Quality Resistant to CBB High Photosynthesis Good Cooking Quality Resistant to CBB High Photosynthesis XX TMS30572TMS30572 Female ParentFemale Parent Male ParentMale Parent CM2177-2CM2177-2
  • 43. Male flowers Female flowers Inflorescence Racime
  • 44. Segregation in carotene contents in roots from clone CM4919-1
  • 45. MAB Marker-assisted selection (MAS) for CMD
  • 46. MAS for CMD Resistance at CIAT Sexual Seeds Embryo Rescue PCR Amplificatión Shipment to partners To Breeding scheme S S S R S S R R S R S S S S R S S S S R S S R S R R R R S S S S R C R R S S R S S S R S R R R R R S R R R R S S S S S S R R R R S R S R S S R R R S S S S S R R S R S R S S Progenies of TME3 x CIAT Elite parents
  • 47. Access to Highthroughput Labs
  • 48. MAS: CMD and CGM SCAR in agarose gel NS 158 in acrilamide 1014NO15RS MCOL 2206C-243CR53-411 1013YES14RR MCOL 2206C-243CR53-310 1012NO13SR MCOL 2206C-243CR53-29 1010NO12S´C-243SM1219-9CR-52B-18 1009YES11RRSM1219-9C-243CR52A-437 1007YES9RRSM1219-9C-243CR52A-416 1006YES8RRSM1219-9C-243CR52A-405 1005YES7RRSM1219-9C-243cr52a-394 1004NO6SRSM1219-9C-243CR52A-383 1003YES5RRSM1219-9C-243CR52A-372 998NO1S-SM1219-9C-243CR52A-321 TEJIDO CAMPO/ENVI ONo.SCAR RME 1SSRY 158FRASCOS CC CÓDIGOPARAPOSOEVALUACIÓN EVALUACIÓ NNÚMERODEPADREMADRECODIGOITEM PLACANo9CMD EVALUACI ÓN:FORMATOEVALUACIÓNPARA MAS. 1014NO15RS MCOL 2206C-243CR53-411 1013YES14RR MCOL 2206C-243CR53-310 1012NO13SR MCOL 2206C-243CR53-29 1010NO12S´C-243SM1219-9CR-52B-18 1009YES11RRSM1219-9C-243CR52A-437 1007YES9RRSM1219-9C-243CR52A-416 1006YES8RRSM1219-9C-243CR52A-405 1005YES7RRSM1219-9C-243cr52a-394 1004NO6SRSM1219-9C-243CR52A-383 1003YES5RRSM1219-9C-243CR52A-372 998NO1S-SM1219-9C-243CR52A-321 TEJIDO CAMPO/ENVI ONo.SCAR RME 1SSRY 158FRASCOS CC CÓDIGOPARAPOSOEVALUACIÓN EVALUACIÓ NNÚMERODEPADREMADRECODIGOITEM PLACANo9CMD EVALUACI ÓN:FORMATOEVALUACIÓNPARA MAS. CoP has effectively integrate MAS with field-based strategies
  • 49. A SCAR marker RME1 and an SSR marker, NS158, could predict CMD resistance >90% of the time MAS provides an efficiency gain of up to 20% over phenotypic selection, could be much higher where disease pressure is lower MAS for CMD Resistance: S S S R S S R R S R S S S S R S S S S R S S R S R R R R S S S S R C R R S S R S S S R S R R R R R S R R R R S S S S S S R R R R S R S R S S R R R S S S S S R R S R S R S S
  • 50. MAB Introduction MAS germplasm from Latin America to Africa
  • 51. Facilities
  • 52. Mock Plantlets undergoing hardening
  • 53. From conventional to MAB schemes Figure 1. Germplasm selection scheme of cassava Crossing Block(s) Source population for target ecology Seedling nursery 50,000-100,000 seedlings (no replication) Clonal evaluation 500-3,000 clones (1 replication) Preliminary yield trial 100-200 clones (2 replications) Advanced yield trial about 50 clones (4 replications) Uniform yield trial 15-25 clones (4 replications) On-farm trials (2-5 elite clones), multiplication and release NARS Year 5 Year 4 Year 3 Year 2 Year 1 NARS Screen for: resistance to diseases and pests, root conformation (pre- and post-harvest handling) and plant characteristics Further screen for: resistance to diseases and pests, root conformation (pre- and post-harvest handling) and plant characteristics Evaluate for yield and food quality characteristics Further screen for: resistance to diseases and pests, root conformation (pre- and post-harvest handling) and plant characteristics Further evaluate for yield and food quality characteristics Evaluate for yield, food quality and adaptation in multilocations Selection scheme Feedback
  • 54. Nigerian 32 Nigerian Landraces 10 NRCRI Breeding Accessions 12 IITA Breeding Accessions Latin American 16 CIAT Breeding Accessions 10 Wild Manihot derivatives Total: 80 Accessions Plant Materials
  • 55. The Molecular Genetic Diversity of Cassava Network (MOLCAS) SSR diversity of Cassava Land Races -20 -15 -10 -5 0 5 10 15 20 -20 -15 -10 -5 0 5 10 15 20 25 30 PC1 (36%) PC2 (28%) Tanzania Mtwara Tanz. Kibaha Tanz. Naliendele Argentina Brazil Colombia Mexico Peru Venezuela Nigeria Thailand Guatemala Differentiation of Genotypes From Latin America and Africa Automated and Silver-stained SSR analysis of Cassava Diversity http://www.ciat.cgiar.org/molcas Supported by IPICs/SAREC amd CIAT
  • 56. MAB Evaluation of MAS genotypes in Nigeria, Ghana, Tanzania and Uganda
  • 57. MAS bred varietiesMAS bred varieties Three genotypes at farmers level, four additional selected for national wide testing in Nigeria Yield 57.5 t/ha in Uganda; 58 t/ha in Ghana; 48t/ha Nigeria Multiplication of best CMD resistant and CGM tolerant CR 37-108 CR 36-2 CR 14A-1 CR 36-5
  • 58. RELEASE OF VARIETIES AND DISTRIBUTION
  • 59. MAB varieties UMUCASS33 released in Nigeria in 2010 Another variety is under process for release in Nigeria Tanzania released two varieties in 2012 Ghana has four entries in pre-release trials
  • 60. CONCLUSION
  • 61. Bringing the Benefits of Modern Science to Farmer’s Fields Demonstrate superior yield and quality to farmers and processors for accelerated adoption of new pest and disease resistant cassava varieties Disseminate farmer-preferred varieties by integrating formal (scientist-led) and farmer- driven multiplication of improved materials
  • 62. Cassava Value Chains 7 8 HQCF High Quality Cassava Flour (HQCF) Principal market –replacement of up to 10% wheat flour in bread; others – food industry, adhesive industry, dextrins. Demand is over 400,000 tons per year. Starch Native and modified starches We have two functional starch mills in Nigeria with a combined capacity of 27,000 tons (although they currently operate below capacity). Demand is 230,000 tons per year currently met by corn starch imports. Chips Dried Chips Principal market – to meet internal and external demand of cassava for industrial use. China’s demand is expected to exceed 12 mill tons by 2015/16 due to their large ethanol production. Demand is 520,000 tons per year from China and 400,000 tons HFCS Sweeteners - High Fructose Cassava Syrup (HFCS) The total sugar requirement for soft drink bottlers and juice manufacturers in Nigeria is estimated at 200,000 tons of sugar p/a. A replacement of half of this by HFCS from cassava, would create a 100,000 ton demand. Ethanol Fuel Ethanol (E10) Nigeria has adopted the policy of blending gasoline with 10% ethanol, the E-10 policy. This represents a potential one billion liter per year market of fuel ethanol and 3.75billion for cooking fuel, assuming 50% of feedstock comes from cassava, a raw material requirement of over 3 million tons of dried chips is required.
  • 63. Commercial planting Industrial cassava Fundamental for income generation & rural development
  • 64. Acknowledgement Generation Challenge Programme CIAT IITA NRCRI NAQS
  • 65. 81 Do reo THANK YOU FOR LISTENING!

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