GRM 2011: Improving cassava to withstand drought and disease in Africa ‒ E Okogbenin
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GRM 2011: Improving cassava to withstand drought and disease in Africa ‒ E Okogbenin
- 2. Cassava CI projects Project 1: Development of a genetic resources base for drought and biotic stress improvement in cassava – M. Ferguson Project 2: Improving and Deploying Markers for Biotic Stresses in Cassava – C. Egesi Project 3: Implement MAS Project for drought tolerance – E. Okogbenin Project 4: Project 4: QTL analysis of drought tolerance in South America – A. Alves Project 5: A Cassava Breeding Community of Practice in Africa for Accelerated Production and Dissemination of Farmer-Preferred Cassava Varieties Resistant to Pests and Diseases – E. Okogbenin
- 3. Overall objective Overall objective: To deliver a set of germplasm to NARS breeders that encompasses diversity per se as well as trait-based diversity to be incorporated into breeding programs to broaden the genetic base for enhanced genetic gain. Observations: 1. Breeders germplasm in many NARS breeding programs in SEC Africa had a narrow genetic base 2. Breeders found it difficult to acquire new germplasm. What germplasm to request? 0 0.5 DRC Kenya Madagascar Rwanda Tanzania Mozambique Uganda Project1: Development of a genetic resources base for drought and biotic stress improvement in cassava Morag
- 4. • 250 accessions • The number of accessions selected per cluster was proportional to the log of the number of accessions in that cluster. The methodology used was thought to represent diversity yet minimise population structure. • Of 250, 102 from IITA, 144 from CIAT and 4 from EMBRAPA • Represents 82.5% of alleles of composite set • 29 of 46 countries represented (63%) • The reference sets have been placed in vitro GCP Phase 1: (2) Selection of CIAT/IITA/EMBRAPA Reference Set 2306 accessions, 48 countries Americas 1273 (1139 from S. America) Asia 36 SEC Africa 61 West Africa 884 Unknown 24 Wild 28 <2% germplasm in IITA genebank from SEC.
- 5. GCP Phase II: Definition of trait-based global reference set Southern eastern and central Africa (100) IITA breeders germplasm (100) IITA genebank (102) CIAT breeders germplasm (100) CIAT genebank (148)
- 6. GCP Phase II: (1) Definition of SEC Africa Reference Set 100 Genotypes Methodology Breeders in seven countries selected 10 varieties with traits of specific interest, all with SSR genotyping data (70 accessions) 30 accessions selected, in relation to the 70, to maximise diversity Characteristics: 1401 Varieties 100 Reference set Total number of alleles 192 157 Average gene diversity 0.6439 0.6556 Effective number of alleles (Ae) 3.2613 3.2788
- 7. GCP Phase II: (2) Definition of 100 IITA breeders lines Trait Number of genotypes Multiple pest resistance 51 CMD Resistance 39 Stay green 32 High yield 31 High dry matter 25 High β-carotene 24
- 8. Future AA AB BB Genotyped using 1,536 SNPs on Illumina’s GoldenGate platform Selection of ~ 250 genotypes to make up GCP Reference Set ?
- 9. Project 2: Biotic stresses Hybridizations of parents in a bi-parental crossing design for the development of two CMD mapping populations for 2 putative resistance genes Resistant (♀) x Susceptible (♂) 1. 97/2205 x 30555 (CMD3) 2. 96/1089A x 30555 (CMD4) Egesi
- 10. Preliminary Phenotype Data: CMD 0 10 20 30 40 50 60 70 80 1 2 3 4 5 CMD 3 MAP: 97/2205 x 30555 0 10 20 30 40 50 60 70 80 1 2 3 4 5 CMD 4 MAP: 97/2205 x 30555 0 20 40 60 80 100 1 2 3 4 5 CMD 3 MAP: 96/1089A x 30555 0 10 20 30 40 50 60 70 80 1 2 3 4 5 CMD 4 MAP: 96/1089A x 30555 Disease scores of 1 – 5 where 1: no symptoms; 5: severe symptoms #Diseasedplants
- 11. S/No Parent Resistance Status # SNP Polymorphic markers 1 97/2205 Resistant 619 2 96/1089A Resistant 623 3 30555 Susceptible 636 SNP Polymorphisms S/No Mother Father # SNP Polymorphic markers 1 97/2205 30555 984 3 96/1089A 30555 927
- 12. SUMMARY OF SEEDS GENERATED FOR CBSD Parents Number of F1 Seeds Established mapping population Resistant Susceptible Namikonga AR37-80 5551 Kiroba 3C83-13 926 Muzege Cheupe 657 B2C20-65 AR37-80 302
- 13. Project 3: MARS IAR – Kano, Nigeria SARI, Tamale, Ghana Trial sites:
- 14. 0 10 20 30 40 50 60 TMS 419 TMS 92/0326 TMS 95/0289 TMS 98/0505 TMS 98/0510 TMS 98/0581 DMC (%) Tolerant SusceptibleCheck
- 16. Established progenies on the field Pedigree Progeny size in field Polymorphic markers TMS 98/0505 X TMS 98/0510 192 856 TMS 98/0505 X TMS 98/0581 278 871 TMS 98/0505 X TMS 91/02324 162 960
- 17. Phenotyping site Improvement Pump house and deep well system currently under construction Irrigation system Trial sites at advanced stages in development Weather station provided by GCP
- 18. Project 4: QTL mapping for drought tolerance
- 19. Physiological traits • Partial closure/ less stomatal openings • Less stomatal conductance • More chlorophyll content during drought • Decline of photosynthetic efficiency
- 20. Stomatal conductivity in cassava genotypes MCOL 1468 76% reduction STC susceptible V3 CM4403 68% reduction STC susceptible V1 CG 1141-1 46% reduction STC tolerant V2
- 21. Effect of drought on biomass production in cassava 30-40% biomass reduction due to drought in cassava
- 22. http://www.cassavacop.org/cbcopa/ Sharing knowledge and technology among research partners Project 5 : Cassava breeeding CoP
- 23. MAB based programmes Validation of stability of CMD resistance in CMD2 genotypes MAS developed CMD resistant variety released in Nigeria Genotypes combining CBSD and CMD resistance developed in Tanzania Genetic stock fixed for CMD2 and CGM alleles developed Genetic diversity of breeding lines analyzed Genetic mapping for early bulking and high protein conducted Breeding populations for key traits developed Introgression of novel traits into CMD resistance genetic background achieved – Protein, delayed PPD, drought tolerance.
- 25. Response profile of CMD2 genotypes 0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 1 MAP 3 MAP 6 MAP 9 MAP 12 MAP Months After Planting CMDseverityScore(1-5) AR1-82 CR14A-1 CR52A-41 CR36-2CR36-5 0 0.5 1 1.5 2 2.5 YEAR1 YEAR2 YEAR3 YEAR4 Years CMDseverityScore(1-5) AR9-5 AR14-10 AR15-5 CR100-15 CR100-215
- 26. MAS Scheme to Improve Cassava Germplasm Seedling trial Crossing block Polycross design (MAS) Combining ability studies Farmer participatory trial Field trials Local varieties (selected by farmers) Improved introductions
- 27. Variety release:MAS develop Latin American genotype
- 28. New generation of cassava breeders Country - Uganda Nigeria Ghana Ghana Ghana Tanzania Name - Mr. Esuma Dr. Olasanmi Mr. Peprah Ms. Prempeh Mr. Danquah Ms. Kimata Degree - M.Sc. Ph.D. M. Phil Ph.D. Ph.D. M.Sc. Status On-going Completed On-going On-going On-going Ongoing
- 30. Inbred line development (six families) Root Weight(kg) 0 2 4 6 8 10 12 14 NoofGenotypes 0 20 40 60 80 100 120 Harvest Index 0.0 0.2 0.4 0.6 0.8 NoofGenotypes 0 20 40 60 80 Plant Height(cm) 50 100 150 200 250 300 350 400 NoofGenotypes 0 10 20 30 40 Vigour 1 2 3 4 5 NoofGenotypes 0 20 40 60 80 100 120
- 31. Selection index based on two year data for for Latin America germplasm 0 5 10 15 20 25 30 35 40 45 50 CW525-1 spplot AR9-5 TMS91/02324 CW450-75 CW451-80 TMS98/0581 CR14B-180 NR87/184 TME419 TMS30572 TMS95/0289 CR14B-218 CR20A-2 CW450-106 TMS92/0067 AR14-4 AR9-45 CW451-13 TMS98/0510 CW450-46 CW450-36 CR15B-9 CR52A-1 AR9-19 CR100-15 CR15B-7 CW482-16 CW482-3 TMS97/0057 Dakata FRY(ton/ha) Potentials Localcheck
- 32. Tanzania
- 33. Cont’d Screen shot captures the implementation of cassava trait ontology with 125 traits defined. www.cropontology-curationtool.org
- 35. FOCUS FOR 2012 • Upload datasets into ICASS • Curate cassava pedigrees • Collaborate with partners to continuously add new traits to ontology • Annotation cassava datasets using ontology-based tool • Harmonize cassava ontologies with other ontologies – Submit cassava specific terms to Gramene trait ontology (TO) – Begin cassava plant ontology to describe plant structure, anatomy and growth stages
- 36. Finger printing project There are 270 genotypes fingerprinted with 1740 SNPs Finger printing project is a new opportunity to finger print more accessions Is this a project targeting CI countries or open to others Considerations for countries like Mozambique, Liberia and Sierra Leone were suggested for inclusion in the project We have a broader list of accession earlier submitted by breeders in Africa (six countries) and Brazil. A possible list from which accesssions could be chosen from List to be compiled by Oct 15.
- 37. CoP DM WUR led CoP for DM and technical trainers Identification of appropriate candidates and minimum eligibility criteria for particpants Structured over three years to handle germplasm mgt and evaluation, field trial mgt system, update on tools, molecular analysis, genotyping data mgt system, data analysis, analytical pipeline, breeding decision, and decision support system Resource persons with experience in cassava canvassed – tailored to meet crop needs and NOT generalized applications
- 38. CoPs after GCP IBP sustainability crucial to CoP Relevant to regional development CoP to transform to self-sustainable entities: functionality critical for attracting funding support from donor bodies Seek institutional and public funding support Must be willing to pay for services
- 39. Cassava Information Resources Germplasm and its documentation – ICASS (DMS, GMS, GeMS) Molecular resources and sequence information – cassava genome sequence, transcriptome datasets, MOLCAS, PlanTFDB, PlnTFD
- 40. Four main areas for consideration • (1) Information related to accessions stored in genebanks • (2) Information relating to breeding material • (3) Information related to genetic markers, genetic linkage maps, QTLs, expression data and transformation • (4) Geographic information. Ideally information from these broad areas should be interconnected. In addition: • supplementary sites and tools are proposed such as decision-making tools and a cassava community site.
- 41. To enable the cassava community to work efficiently, a means of connecting researchers to relevant data is essential. Communities for other species have developed integrated data sites to combat this problem, notably SOLgenomics, TAIR and SoyBase. One advantage of this approach is the ability to integrate publicly available data with private data through the use of user accounts, which also allows sharing of pre- published data between users.
- 42. Acknowledgement Y. Baguma A. Pariyo B. Kimata C. Sichalwe C. Egesi E. Parkes B. Peprah G. Mkamilo J. Onyeka M. Fregene S. Rounsley E. Lotsu M.D. Quain P. Rabinowicz Z. Myburg P. Kulakow H. Murtah X. Delannay Ndeye Ndack Diop Luis Augusto BecerraLopez lavalle Hernan ceballos K. Ogundapo F. Ewa B. Olasanmi E. Okogbenin H. Gomez C. de Vicente M. Gedil A. Dixon H. Kulembeka A. Mbanaso R. Thompson P. Boateng O. Akinbo M. Reynolds A. Okono N.C. Ezebuiro Larry Butler Ismail Rabbi Dominique Dumet Franco Jorge