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

  1. 1. Cassava ChallengeInitiativeARI
  2. 2. Cassava CI projectsProject 1: Development of a genetic resources basefor drought and biotic stress improvement in cassava– M. FergusonProject 2: Improving and Deploying Markers forBiotic Stresses in Cassava – C. EgesiProject 3: Implement MAS Project for droughttolerance – E. OkogbeninProject 4: Project 4: QTL analysis of droughttolerance in South America – A. AlvesProject 5: A Cassava Breeding Community of Practicein Africa for Accelerated Production andDissemination of Farmer-Preferred Cassava VarietiesResistant to Pests and Diseases – E. Okogbenin
  3. 3. Overall objectiveOverall objective:To deliver a set of germplasm to NARSbreeders that encompasses diversity perse as well as trait-based diversity to beincorporated into breeding programs tobroaden the genetic base for enhancedgenetic gain.Observations:1. Breeders germplasm in many NARSbreeding programs in SEC Africa had anarrow genetic base2. Breeders found it difficult to acquirenew germplasm. What germplasm torequest?0 0.5DRCKenyaMadagascarRwandaTanzaniaMozambiqueUgandaProject1: Development of a genetic resources base for drought andbiotic stress improvement in cassavaMorag
  4. 4. • 250 accessions• The number of accessions selected percluster was proportional to the log of thenumber of accessions in that cluster. Themethodology used was thought to representdiversity yet minimise population structure.• Of 250, 102 from IITA, 144 from CIAT and 4from EMBRAPA• Represents 82.5% of alleles of composite set• 29 of 46 countries represented (63%)• The reference sets have been placed in vitroGCP Phase 1: (2) Selection of CIAT/IITA/EMBRAPAReference Set 2306 accessions, 48 countriesAmericas 1273 (1139 from S.America)Asia 36SEC Africa 61West Africa 884Unknown 24Wild 28<2% germplasm in IITA genebankfrom SEC.
  5. 5. GCP Phase II: Definition of trait-based globalreference setSouthern easternand central Africa(100)IITA breedersgermplasm (100)IITA genebank(102)CIAT breedersgermplasm (100)CIAT genebank(148)
  6. 6. GCP Phase II:(1) Definition of SEC Africa Reference Set100 GenotypesMethodology Breeders in seven countries selected 10 varietieswith traits of specific interest, all with SSRgenotyping data (70 accessions) 30 accessions selected, in relation to the 70, tomaximise diversityCharacteristics:1401 Varieties 100 Reference setTotal number of alleles 192 157Average gene diversity 0.6439 0.6556Effective number ofalleles (Ae)3.2613 3.2788
  7. 7. GCP Phase II:(2) Definition of 100 IITA breeders linesTrait Number of genotypesMultiple pestresistance51CMD Resistance 39Stay green 32High yield 31High dry matter 25High β-carotene 24
  8. 8. FutureAA AB BBGenotyped using 1,536SNPs on Illumina’sGoldenGate platformSelection of ~ 250genotypes to make upGCP Reference Set?
  9. 9. Project 2: Biotic stressesHybridizations of parents in a bi-parental crossing designfor the development of two CMD mapping populations for2 putative resistance genesResistant (♀) x Susceptible (♂)1. 97/2205 x 30555 (CMD3)2. 96/1089A x 30555 (CMD4)Egesi
  10. 10. Preliminary Phenotype Data: CMD010203040506070801 2 3 4 5CMD 3 MAP: 97/2205 x 30555010203040506070801 2 3 4 5CMD 4 MAP: 97/2205 x 305550204060801001 2 3 4 5CMD 3 MAP: 96/1089A x 30555010203040506070801 2 3 4 5CMD 4 MAP: 96/1089A x 30555Disease scores of 1 – 5 where 1: no symptoms; 5: severe symptoms#Diseasedplants
  11. 11. S/No ParentResistanceStatus# SNP Polymorphicmarkers1 97/2205 Resistant 6192 96/1089A Resistant 6233 30555 Susceptible 636SNP PolymorphismsS/No Mother Father# SNP Polymorphicmarkers1 97/2205 30555 9843 96/1089A 30555 927
  12. 12. SUMMARY OF SEEDS GENERATED FOR CBSDParentsNumberof F1SeedsEstablishedmappingpopulationResistant SusceptibleNamikonga AR37-80 5551Kiroba 3C83-13 926Muzege Cheupe 657B2C20-65 AR37-80 302
  13. 13. Project 3: MARSIAR – Kano, Nigeria SARI, Tamale, GhanaTrial sites:
  14. 14. 0102030405060TMS 419 TMS92/0326TMS95/0289TMS98/0505TMS98/0510TMS98/0581DMC (%)TolerantSusceptibleCheck
  15. 15. Established progenies on the fieldPedigreeProgeny size infieldPolymorphicmarkersTMS 98/0505 X TMS 98/0510 192 856TMS 98/0505 X TMS 98/0581 278 871TMS 98/0505 X TMS 91/02324 162 960
  16. 16. Phenotyping site ImprovementPump house and deepwell system currentlyunder constructionIrrigation systemTrial sites at advancedstages in developmentWeather station provided by GCP
  17. 17. Project 4: QTL mapping for droughttolerance
  18. 18. Physiological traits• Partial closure/ less stomatalopenings• Less stomatal conductance• More chlorophyll content duringdrought• Decline of photosynthetic efficiency
  19. 19. Stomatal conductivity in cassava genotypesMCOL 1468 76% reduction STC susceptible V3CM4403 68% reduction STC susceptible V1CG 1141-1 46% reduction STC tolerant V2
  20. 20. Effect of drought on biomassproduction in cassava30-40% biomass reduction due to drought in cassava
  21. 21. knowledgeand technology amongresearch partnersProject 5 :Cassavabreeeding CoP
  22. 22. MAB based programmes Validation of stability of CMD resistance in CMD2genotypes MAS developed CMD resistant variety released inNigeria Genotypes combining CBSD and CMD resistancedeveloped in Tanzania Genetic stock fixed for CMD2 and CGM allelesdeveloped Genetic diversity of breeding lines analyzed Genetic mapping for early bulking and high proteinconducted Breeding populations for key traits developed Introgression of novel traits into CMD resistancegenetic background achieved – Protein, delayed PPD,drought tolerance.
  23. 23. Genetic diversityEsuma, 2011Co002/COL1734ARC028/AR12.37Co017/COL22Ug027/AnditekuGh023/BankyeBotanUg086/Unknown/TororoNi038/TMS98/0505Ni043/TMS4/21425Gh030/AW36Kz037/Type3.3ARC014/MSAF1Kz035/Type3.1ARC012/SM707.17Co023/CM2177/CM2177-2Kz017/Clone5.3Kz025/Clone7.3Br013/BGM0063Br060/BGM0890Co001/VEN77Ug088/Unknown2/KakumiroUg090/Alado-AladoUg013/LugwaraUg089/Unknown1/MasindiUg022/ObudugavuUg026/NamunyuraUg007/KakwaleUg021/KajaliUg019/LyahoroleGh022/UCCGh006/EssiabayaGh015/TuakaARC018/MOZKz011/Clone7.1Kz014/Clone7.4Kz039/Clone6.1Kz041/Clone6.3Ug018/NjuleRedUg025/NjuleWhiteUg003/BaoUg001/NyarabokeUg002/EgabuARC019/Hombolo954Ug036/MM96/4271Ug039/52/TME14ARC001/01/1649Ni069/TMS01/1442Br061/Col2215ARC013/SM1053.23Ni006/TMS94/0330Gh058/KwaseabediawuNi058/NR01/0161Ni064/NR8082Ug087/Unknown2/HoimaBr050/BGM0260Ug067/YellowRKz002/FemaleCKz027/TypeC1Kz030/TypeC4Kz031/TypeA1Ni015/TMS87/0052ARC022/AR40.17ARC030/AR37.99ARC025/AR42.3ARC026/CR25.4Ug020/MaganaGh017/AgbelifiaARC011/AR23.1Ug085/Unknown/LuweroNi008/CR41-10Ug074/CR36-2/1ARC020/Mkondezi21Kz006/FemaleDGh020/EssamBankyeNi025/TMS99/2123Ni040/TMS96/1089ANi010/Z97/0474Gh031/K25Co024/NGA2Gh016/AfisiafiGh057/Sisipe166Ni013/TMS30572Co018/Mex17ARC015/97/4763Ni051/TMS96/1431Ni052/TMS01/1413Ni044/TMS97/2205Ni050/TMS97/2205ARC023/AR9.18Ni003/NR87/184Ug047/AR9-24Ug076/CR97x-1Ni034/MM96/JW1Ni042/MH94/4041Ug030/Nase12Gh029/AW3Ni056/NR8212Kz007/FemaleEKz019/TypeB1ARC002/92B/00061Ni028/TMS01/1412Br008/BGM0924Ni045/TME1Gh007/Nyamebekyere2Ni032/TME9Br003/BGM0001Ni048/TMS01/0040ARC005/I92/0057Ni068/TMS98/0002ARC029/AR17.2Ni047/TMS98/2132Ni017/TMS00/0355Ni062/TMS99/0558Gh019/DokuDuadeARC007/MM96/1751Ug043/TME204Co016/TME-3Gh021/NkabomARC006/TME7Gh012/Sisipe290Ni027/M98/0115Ug065/MM96/0469Co015/Mven30qARC010/L9/304/1616Kz009/Clone9Br026/BGM0931Br012/BGM0456Br054/SM1438-2Ug097/MH04/3123Br035/BGM0211Co009/MCol1468Gh028/NK26Kz001/FemaleFARC003/94/0026ARC021/Maunjili6Ni067/TMS92/0325Ni024/TMS94/0561Ni035/TMS01/1371Ug082/95/SE-00036ARC027/AR42.4ARC004/98/0581ARC016/14/48Br055/TAI16Kz003/Male1Br021/BGM1269Co019/GUA76Br025/BGM1318Br045/BGM2017Br036/BGM0249Br049/BGM1696Br051/BGM0384Br029/BGM0070Br046/BGM2019Br056/TAI8Br031/BGM2018Br034/BGM1810ARC008/MM96/5280Br042/BGM0120Br037/BGM1694Br038/BGM0867Br048/BGM0876Gh001/DagartiGh005/AgricBankyeBr001/BGM1148Br018/BGM1693Br023/BGM1811Br005/BGM0549Co008/BRA255Br041/BGM0600Br016/BGM0255Br052/BGM0195Br059/BGM0086Br040/BRA997ARC024/SM1433.4Br024/BGM1153Br014/BGM0021Br043/BGM1672Br011/BGM1627ARC009/P1/16Br028/BGM1697ARC017/B847Br019/BGM0537Gh014/TME11Co020/BRA12Ni016/TMS96/14320.05MelissaBased on 48 SNPsSSR markers
  24. 24. Response profile of CMD2 genotypes00.511.522.533.544.51 MAP 3 MAP 6 MAP 9 MAP 12 MAPMonths After PlantingCMDseverityScore(1-5)AR1-82CR14A-1CR52A-41CR36-2CR36-500.511.522.5YEAR1 YEAR2 YEAR3 YEAR4YearsCMDseverityScore(1-5)AR9-5AR14-10AR15-5CR100-15CR100-215
  25. 25. MAS Scheme to Improve CassavaGermplasmSeedling trialCrossing blockPolycross design(MAS)Combiningability studiesFarmer participatory trialField trialsLocal varieties(selected by farmers)Improvedintroductions
  26. 26. Variety release:MAS develop Latin Americangenotype
  27. 27. New generation of cassavabreedersCountry - Uganda Nigeria Ghana Ghana Ghana TanzaniaName - Mr. Esuma Dr. Olasanmi Mr. Peprah Ms. Prempeh Mr. Danquah Ms. KimataDegree - M.Sc. Ph.D. M. Phil Ph.D. Ph.D. M.Sc.Status On-going Completed On-going On-going On-going Ongoing
  28. 28. Gene pool development
  29. 29. Inbred line development (six families)Root Weight(kg)0 2 4 6 8 10 12 14NoofGenotypes020406080100120Harvest Index0.0 0.2 0.4 0.6 0.8NoofGenotypes020406080Plant Height(cm)50 100 150 200 250 300 350 400NoofGenotypes010203040Vigour1 2 3 4 5NoofGenotypes020406080100120
  30. 30. Selection index based on two year data for for Latin America germplasm05101520253035404550CW525-1spplotAR9-5TMS91/02324CW450-75CW451-80TMS98/0581CR14B-180NR87/184TME419TMS30572TMS95/0289CR14B-218CR20A-2CW450-106TMS92/0067AR14-4AR9-45CW451-13TMS98/0510CW450-46CW450-36CR15B-9CR52A-1AR9-19CR100-15CR15B-7CW482-16CW482-3TMS97/0057DakataFRY(ton/ha)PotentialsLocalcheck
  31. 31. Tanzania
  32. 32. Cont’dScreen shot captures the implementation of cassava trait ontology with 125traits defined.
  33. 33. Trait Ontology Tree
  34. 34. FOCUS FOR 2012• Upload datasets into ICASS• Curate cassava pedigrees• Collaborate with partners to continuously add newtraits to ontology• Annotation cassava datasets using ontology-based tool• Harmonize cassava ontologies with other ontologies– Submit cassava specific terms to Gramene traitontology (TO)– Begin cassava plant ontology to describe plantstructure, anatomy and growth stages
  35. 35. Finger printing projectThere are 270 genotypes fingerprinted with1740 SNPsFinger printing project is a new opportunity tofinger print more accessionsIs this a project targeting CI countries or open toothersConsiderations for countries like Mozambique,Liberia and Sierra Leone were suggested forinclusion in the projectWe have a broader list of accession earliersubmitted by breeders in Africa (six countries)and Brazil. A possible list from whichaccesssions could be chosen fromList to be compiled by Oct 15.
  36. 36. CoP DMWUR led CoP for DM and technical trainersIdentification of appropriate candidates andminimum eligibility criteria for particpantsStructured over three years to handlegermplasm mgt and evaluation, field trialmgt system, update on tools, molecularanalysis, genotyping data mgt system, dataanalysis, analytical pipeline, breedingdecision, and decision support systemResource persons with experience in cassavacanvassed – tailored to meet crop needs andNOT generalized applications
  37. 37. CoPs after GCPIBP sustainability crucial to CoPRelevant to regional developmentCoP to transform to self-sustainableentities: functionality critical forattracting funding support fromdonor bodiesSeek institutional and publicfunding supportMust be willing to pay for services
  38. 38. Cassava Information ResourcesGermplasm and its documentation – ICASS(DMS, GMS, GeMS)Molecular resources and sequenceinformation – cassava genome sequence,transcriptome datasets, MOLCAS, PlanTFDB,PlnTFD
  39. 39. 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 linkagemaps, QTLs, expression data and transformation• (4) Geographic information.Ideally information from these broad areas should beinterconnected.In addition:• supplementary sites and tools are proposed such asdecision-making tools and a cassava community site.
  40. 40. To enable the cassava community to work efficiently, ameans of connecting researchers to relevant data isessential. Communities for other species have developedintegrated data sites to combat this problem, notablySOLgenomics, TAIR and SoyBase.One advantage of this approach is the ability to integratepublicly available data with private data through the useof user accounts, which also allows sharing of pre-published data between users.
  41. 41. 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