Delgado Munoz, Luis Fernando

Morante, Nelson

Pino Duran, Lizbeth

Salazar, Sandra

Zhang, Xiaofei

CGSpace

Enhancing food security and nutrition in Africa-- NextGen CassavaSalazar, Sandra  Morante, Nelson Pino Duran, LizbethDelgado Munoz, Luis FernandoZhang, Xiaofei Create New Opportunities• High and stable dry matter• CBSD resistance• Whitefly resistance• Drought and heat tolerance• FloweringEnhance Global Impact• Update product profiles• Essential traitsBuild Solid Foundation• Stage&Gate• RACI• Advancement meetings• Training workshopModernize Breeding ProgramKey Elements of Plant BreedingProductWP1, ReFOCUSProduct & Pipeline• Dry matter • Dry matter + CMD + CBSD• Boiled cassava • Boiled cassava + CMD + CBSD• Biofortified cassava• Biofortified cassava + CMD + CBSDUpdate product profiles with the inputs from NARSClarify essential traits and their thresholdWP1, ReFOCUSWP3, TRANSFORMThe Agro-climatic Similarity between Colombia and AfricaSubhumid lowland tropicsSemi-arid lowland tropicsHumid lowland tropicsCreate New Opportunities• High and stable dry matter• CBSD resistance• Whitefly resistance• Drought and heat tolerance• FloweringEnhance Global Impact• Update product profiles• Essential traitsBuild Solid Foundation• Stage&Gate• RACI• Advancement meetings• Training workshopModernize Breeding ProgramKey Elements of Plant BreedingWP2, ReORGANIZEOperational ExcellenceSalazar, Sandra MilenaS.M.Salazar@CGIAR.ORGSenior Coordinator8 years of experience at CIAT• Lead the field management team• Process Steward• Coordinate collaborations in ColombiaTrialing and Nursery Team in Palmira Campus1. Product Development Process - Stage&Gates0Market research, Product design, Product profile, Crop strategy 1Evaluation of germplasm sources, trait validation, inheritance and molecular discovery2Selection to elite adapted background including disease resistance and other required traits3Parent selection and production of new genetic variation for variety development4Clone development, small plot testing5Advanced clones in replicated multi-site6National Performance Trials and On-Farm trials7Official release and product launchStage 0:Product DesignStage 1: Trait DiscoveryStage 2:Trait DevelopmentStage 3: Crossing and ScreeningStage 4: Early TestingStage 5: Late Testing6: Precommercial and Product RegistrationStage 7: Product IntroductionSelect Set 2ClonesSet 4PAMDefine Trait development strategy Crop strategy & Product Profile AgreementDefine combinationsSelect Set 3ClonesSet 5PAM64 2721 unique roles12 disciplinesNext Step is to include the NARES in AsiaStakeholder Landscape for Cassava Advancement Decision Making across CIAT and NARES partnersWe have now 91 people mapped2. Decision Rights Mapping at Discipline level: RACI ModelDisciplinary expertResearch & DevelopmentSeed Supply ChainMarketing, Outreach & Social ImpactResearch & DevelopmentDisciplinary expertSeed Supply ChainCIAT-ColombiaCIAT-AsiaResearch & DevelopmentDisciplinary expertNARS: AgrosaviaStandardized DisciplineDecision Right in Gate 0=>1Crop strategy & Product Profile AgreementDecision Right in Gate 1=>2Define Trait development strategyDecision Right in Gate 2=>3Define combinations for CrossingDecision Right in Gate 3=>4Select Clones for Early ScreeningDecision Right in Gate 4=>5Select Clones for Late Development TestingDecision Right in Gate 5=>6Advance canditates to National Performnace and On-Farm TrialsDecision Right in Gate 6=>7Advance canditates to variety releaseBreeding R A A A A A AData Science C R R R R REntomologist C C CFood Scientist C R R R IVirologist C I C IGeneticist C R R R I I IPlatform C CTissue culture C R I RSeed System specialist C I I I R RBreeding R A A A A A AAgronomist C C C C CVirologist C C C C CPhysiologist C C C ISeed System specialist C I R RMarket-/Socio Economics A C C I C R RBreeding C C C C R RAgronomist C C CGeneticist CPhysiologist CNext Step is to practice advancement meetings3. Process Management Team _Trialing and NurseryPurposeHarmonize Trailing and Nursery Processes across CGIAR/NARES breeding network for efficiency and effectiveness.TeamGustavo Teixeira: Process OwnerTheresa Heitman: Process ConsultantSara Johnson: Process ConsultantAlick Mulenga: Process Steward (IITA)Prasad Peteti: Process Steward (IITA – cassava)Princess Dela Cruz: Process Steward (IRRI)Carolina St. Pierre: Process Steward (CIMMYT – Wheat)Safaa Kumari: Process Steward (ICARDA – Wheat)Marcela Pineda: Process Steward (CIAT - Rice)Sandra Salazar: Process Steward (CIAT – Cassava)Shailesh Yadav: Process Steward (Africa - Rice)Trialing and Nursery Service processes Team• Vision To have a standardized process across the CGIAR centers in the trialing and nursery process that can help maintain a constant flow of information and improve breeding programs.• Objectives1. Establish the breeding operational teams to define and implement T&N processes/services.2. Establish structured ways of working to ensure collaboration across CGIAR/NARS T&N processes.3. Identify and standardize the processes carried out in Trailing & Nursery.4. Establish Key Performance Indicators for T&N.5. Define the capabilities needed and implement the capacity development plan for T&N.6. Improve & standardize CGIAR/NARS phenotyping platform (including data collection).• SIPOC – In process• SOPs – Next stepTrialing and Nursery Service processes TeamIt's still in draftDuration of Selection Cycle• Early flowering• Genomewide Prediction-- Mate and parent selectionAccuracy• CassavaBase for all traits• GBLUP with one rep• Genetic gain-based desire selection Index   • Operational Excellence (SOP)• QC/QA• MAS-- CMD, CBSD, DM, carotenoid, HCN, WAB, sprouting, ID, flowering, mites, thrips, small granule, plant typeGenetic Diversity• Variation profiling• Genome, Pangenome & diversity • Hybrid Breeding-- SelfingIntensity• GeoRadar for yield• QualitySpec for WAB• Hyperspectral imaging• Drone imaging for early vigor• Imaging for whitefly• Imaging for PPDToolsWP4, DISCOVERWP5, ACCELERATECassava Flower-inducing TechnologyMorante, NelsonN.Morante@cgiar.org30 years of experience at CIAT• Lead the cassava pollination team• Manage F1 populations and pedigree database• In charge of germplasm sharingTraditional SystemFlowering Induction                                                                     (Red light + Pruning + Growth regulators)Plant age at first branching 6 Months 4 MonthsBranching level for Start Pollinations 2 - 3 Level 1 LevelPlant age Start Pollinations 7 - 8 Months 5 MonthsCrossing Cycle Duration 6-7 months 1 Monthfruit maturation 3 Months 3 MonthsFlower maturation time per inflorescence 1 Day 20 - 30 DaysNumber of  female flowers per inflorescence 3 - 5 More than 50area per plant 2 M2 1 M2Total cycle duration until obtaining hybrid seed 18 Months 10 MonthsFlowering InductionFlower Inducing TechnologyPhotoperiod Extension induced early flowering by 2-3 months for progenitors with erect plant architecture.Reaction to PruningGood Reaction to Pruning ( 5 )Intermediate Reaction to Pruning ( 3 )Little Reaction to Pruning ( 1 )Reaction to the Application of Growth Regulators - BALittle Reaction to BA Application ( 1 )BA, cytokinin benzyladenineIntermediate Reaction to BA Application  ( 3 )Reaction to the Application of Growth Regulators - BAGood Reaction to BA Application ( 5 )Reaction to the Application of Growth Regulators - BAFlowering Induction - Activity summaryTrial plantingAugust 11 - 2022Start of pruningOctober 18-2022Start of PollinationsNovember 3- 2022  End of PollinationsMarch - 2023Seed harvestJune - 20232 Months3 Months7 Months10 MonthsActivity QuantityCombinations between parents 2273Number pollinated flowers (Feb. 9/23) 34907Expected seeds ~25.000Average pollinated flowers per inflorescence15.26Maximum number of pollinated flowers in 1 inflorescence203Minimum number pollinated flowers in 1 inflorescence1Duration of Selection Cycle• Early flowering• Genomewide Prediction-- Mate and parent selectionAccuracy• CassavaBase for all traits• GBLUP with one rep• Genetic gain-based desire selection Index   • Operational Excellence (SOP)• QC/QA• MAS-- CMD, CBSD, DM, carotenoid, HCN, WAB, sprouting, ID, flowering, mites, thrips, small granule, plant typeGenetic Diversity• Variation profiling• Genome, Pangenome & diversity • Hybrid Breeding-- SelfingIntensity• GeoRadar for yield• QualitySpec for WAB• Hyperspectral imaging• Drone imaging for early vigor• Imaging for whitefly• Imaging for PPDToolsWP4, DISCOVERWP5, ACCELERATEData ManagementPino Duran, Lizbeth l.pino@cgiar.org10 years of experience at CIAT• Lead breeding data management• Monitor trialing statusCassavabase – 2022 as an exampleIn total, 25,391 plots.Cassavabase71 7080 77 818870 6683111871061170204060801001201402010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022No Trials creating# Trials in Cassavabase, 2010-2022Harvest and data collection using Fieldbook• Jorge Iván• Camilo• Sandra• NelsonShare data in Teams App• With LizbethCheck quality upload to CassavaBase• Lizbeth• SandraData analysis using R programing • Xiaofei• Camilo• Luis FernandoSelected clones and send list• Xiaofei• Camilo• Jorge Ivan• Sandra, NelsonLuis F. LondoñoDesign trial using FieldHub and plantingCamilo, Jorge Ivan, Sandra, Nelson Data FlowRow and Col; Consistent checksSame ontology< 1 week after collecting the data< 1 week after receiving the data< 1 week after accessing dataTIME TOPIC and ACTIVITY RESPONSIBLE GOAL8:00 – 9:00 Trial design – Field Hub Sandra Salazar & Camilo VargasAll team members can run FieldHub to design a trial9:00– 10:00 Cassava Ontology – Traits Sandra Salazar All team members agree on the ontology and use the ontology in practice.10:00 – 10:15 Coffee Break10:15 – 11:00 Fieldbook demo and practice Lizbeth Pino All team member know how to import, collect, and export data, and all use the same .trt file.11:00 – 12:00 Data flow demoUse one example to show the data management process, from trial design, receiving data, quality check, uploading to CassavaBase.Lizbeth Pino & Sandra Salazar All team members understand and agree on the data flow and share data on time12:00 – 13:00 Lunch13:00-15:00 Field trip:1) show the trial design of GxE and DVGST trials (30min)2) practice Fieldbook – collecting data (30 min)3) discuss ontology (30 min)4) flower inducing (30 min)Lizbeth Pino, Sandra Salazar, Camilo Vargas & Nelson MoranteHave practice view of trail design, Fieldbook, and ontology. Scaling -- Workshop on Cassava Trial OperationNext Step1. Curate historical data including Genebank accessions.2. Genotypic data management in CassavaBase3. NIRS spectra, wet chemistry data, and prediction data4. Train NARES for using CassavaBase and Fieldbook5. Discuss how can other teams use CassavaBaseDuration of Selection Cycle• Early flowering• Genomewide Prediction-- Mate and parent selectionAccuracy• CassavaBase for all traits• BLUP and GBLUP• Genetic gain-based desire selection Index   • Operational Excellence (SOP)• QC/QA• MAS-- CMD, CBSD, DM, carotenoid, HCN, WAB, sprouting, ID, flowering, mites, thrips, small granule, plant typeGenetic Diversity• Variation profiling• Genome, Pangenome & diversity • Hybrid Breeding-- SelfingIntensity• GeoRadar for yield• QualitySpec for WAB• Hyperspectral imaging• Drone imaging for early vigor• Imaging for whitefly• Imaging for PPDToolsWP4, DISCOVERWP5, ACCELERATEData AnalysisDelgado Munoz, Luis FernandoLuis.Delgado@cgiar.org7 months of experience at CIAT• Lead breeding data analysis and training• Manage GitHub, Cassava2050Data analysis stepsWithin-location design of plant breeding trialsAugmented Trial layout Spatial correction analysisAugmented designs are used in early-generation trialAchievements• Pipeline of augmented trials data analysis (p rep , augmented)• Pipeline of replicated trials data analysis (RCBD, Row col)• Manage all data analysis projects through GitHub platform.https://github.com/Cassava2050Scaling and GAPs• Develop data analysis packages or pipelines for partners in Asia and Africa.• Implement desire gains-based selection indices.• Test mate selectionDuration of Selection Cycle• Early flowering• Genomewide Prediction-- Mate and parent selectionAccuracy• CassavaBase for all traits• GBLUP with one rep• Genetic gain-based desire selection Index   • Operational Excellence (SOP)• QC/QA• MAS-- CMD, CBSD, DM, carotenoid, HCN, WAB, sprouting, ID, flowering, mites, thrips, small granule, plant typeGenetic Diversity• Variation profiling• Genome, Pangenome & diversity • Hybrid Breeding-- SelfingIntensity• GeoRadar for yield• QualitySpec for WAB• Hyperspectral imaging• Drone imaging for early vigor• Imaging for whitefly• Imaging for PPDToolsWP4, DISCOVERWP5, ACCELERATE5 years 3 yearsGenomewide PredictionCeballos, et al, 2021Training populationBreeding populationCycle 1➢ Genomic selection models➢ Improved progenitors with CMD resistance➢ Genetic architecture of traits in product profileGenomewide Prediction123➢ Focused on all traits in product profiles➢ Obtained moderate to high predictive ability➢ Continue accumulating data of training populationsChr Pos P.value MAF Effect1 33,161,201 5.29E-12 0.44 -0.459 6,598,412 7.46E-15 0.15 -0.66Favorable allele is dominantFavorable allele is recessive, but might have high inbreeding depression. By Barrera, Vianey Paola <V.Barrera@cgiar.org>

Enhancing food security and nutrition in Africa: Nextgen cassava

https://cgspace.cgiar.org/bitstream/10568/131653/1/Enhancing%20food%20security%20and%20nutrition%20in%20Africa.pdf

Enhancing food security and nutrition in Africa: Nextgen cassava

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