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Joe Tohme

CIAT Agrobiodiversity Teams Driving discovery, development and delivery for an Eco-Efficient Agriculture Annual Program Review 2011 Nairobi, Kenya 10 May 2011. Joe Tohme. Agrobiodiversity Teams. Research Advances on genetic resources GRiSP : a successful start

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Joe Tohme

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  1. CIAT Agrobiodiversity Teams Driving discovery, development and delivery for an Eco-Efficient Agriculture Annual Program Review 2011 Nairobi, Kenya10 May2011 Joe Tohme

  2. Agrobiodiversity Teams • Research Advances on genetic resources • GRiSP: a successful start • Research Areas of Emphasis in rice and biotechnology • Challenges and outlook for 2012

  3. Putative common bean domestication (2000 ybp) Putative lima bean domestication, gene pool MI (1300 ybp) Putative lima bean domestication, gene pool AI (5600 ybp) Common bean domestication (4000 ybp) cpDNA gene pools Wild MI Domesticated MI Wild AI Domesticated AI Research Highlight: Genetic Resources New Insights on Origins of Lima bean Towards a better definition of the conservation targets Crop Science 50 (5): 1773-1787 [2010]

  4. Acquisition of relevant bean germplasm by comparing potential distribution as revealed by herbarium studies with accessions existing ex situ Explorations in western Mexico are likely to be relevant and rewarding Collaboration between GRU, DAPA and the Global Crop Trust Gap analysis published in PLoSONE 5 (10): 1-18 [2010]

  5. Continuous improvement of seed production, distribution and conservation:Flowering and seed setting of Phaseoluscostaricensis Flowering and seed setting of Phaseoluscostaricensisin Tenerife, at 2400 masl, high up above Palmira in the Central Cordillera All attempts to multiply this species before, in Palmira or in Popayan, have failed, while the GRU got success from the first planting

  6. GRU Continuous improvement of seed production, distribution and conservation:Diseasesindexingstatus theManihotcollectionat CIAT Outcome: Different materials of Manihot distributed to date: 6,110 (or 91%)

  7. GRiSP: A Successful Start • Well integrated workplan between IRRI, AfricaRice, CIAT, IRD, CIRAD and JIRCAS • WebEx PMT conference call every 3 weeks • A major collaboration with the Beijing Genomics Institute (BGI) established • Workshops and Grants initiated

  8. GRiSP New Initiatives • GRiSP • New Partnerships for Global Networking • New Frontiers Research 2011 for discovery/basic research • PhD Scholarships

  9. IRG Traditional Germplasm 100,000 cultivated accessions GRiSP-Beijing Genomics Institute (BGI) Collaboration Unique major sequencing effort in plants Sequencing 10,000 accessions fully funded by BGI BGI de novo sequencing 200 @ 50X depth 1000 @ 10-20X depth rest @ 5-10X depth Iterative sampling Start @ 5X depth 10,000 GeneBank accessions1 Cultivated + close wild relatives 1Include publicly accessible germplasmfrom IRRI, AfricaRice, CIAT and regional collections 10,000 genomes April 2011 Sept 2012 May 2011 >3000 DNA to BGI Sept 2011 Sequence data from BGI Nov 2011 Bioinformatics(prelimin analysis) March 2012? Sequence data July 2012 Bioinformatic Second batch of DNA (>5,000) to BGI

  10. GRiSP evaluation decision tree Is the activity research or delivery? Regular reviews No Yes Impact pathway analysis Is the theory of change clear? No Yes Yes Are the milestones being met? Has the research been reoriented? Targeted review No No Yes Progress monitoring Is the research product yet trialable? No Yes Is it established that the product meets user demands? Product evaluation No Yes Average treatment effect assessment Is the contribution to on farm performance known? No Yes Is the research product widely/rapidly adopted? Adoption constraint analysis No Yes Aggregate adoption analysis Is the adoption documented? No Yes Ex post impact assessment

  11. GRiSP: Towards a global phenotypingstrategy • Association genetics using common core collections and special genetic stocks • Phenotype a common set of 2000 lines that are finely genotyped (1 SNP/500bp) • Functional inference with specialized genetic populations • Use breeding materials and transgenes to validate gene function prediction • Validate relationship between phenotypes determined by HTP and conventional methods • Identify HTP phenotyping applicable to breeding; establish genetic correlation, proxy for agronomic traits • Genetic stocks to determine the “ground truth” of HTP phenotyping • 3. Establish phenotyping hubs with general and specialized phenotyping capabilities and functions • Hubs for a broad set of phenotypes • Hubs for transgenic materials (could be 2-3 sites) • Centers and labs for evaluating conditional traits (e.g. stress tolerance) that require specialised methods

  12. GRiSP 2011 Calendar • May: allocate GRiSP scholarships; call for new frontiers research proposals • June: final budget allocation for 2011 • June 6-9: Africa mechanization workshop, Senegal (AfricaRice) • Aug 15-18: W-C Asia workshop, Iran (IRRI) • Aug 22-26: Yield potential workshop and annual review LA, Cali (CIAT) • Sep 12-15: Annual review Africa, Cotonou (AfricaRice) • Sep 19-23: Annual review Asia & GRiSP Annual Science Forum, Los Baños (IRRI) • Oct 10: GRiSP annual report and business plan for next year completed for approval by BOT & OC (virtual) • Oct 15: submit GRiSP annual report and budget proposal to Consortium • Nov 15: Expected FC approval of 2012 budget proposal • Dec 15: annual staff evaluation finished, budget for next year allocated to research teams

  13. Latin America research for different rice systems relevant globally

  14. CIAT strength Product development High productivity rice genotypes for irrigated and upland systems 1998 CIAT rice program contributed at least 60% of the 400 varieties released by national programs in Latin America The Rice team is currently working on a second genetics revolution using biotechnology

  15. Phenotyping Genetics CIAT/IRD Bioinformatics Molecular biology The team Germplasm Physiology Pathology Quality Genetic transformation J. Rane WUE,NUE, drought tolerance G. Mosquera Pyricularia, Burkholderia Katherine Loaiza Amylose, Milling quality, Nutrient content Breeding CIAT/FLAR Breeding –CIAT/Cirad M. Lorieux iBridges, NAMs, CSSLs,T-DNA/Tos17 mutants M. Lorieux Drought tolerance Panicle architecture Yield components M. Lorieux RHBV, RSNV, M. Lorieux Grain aroma S Ayling Sequence analysis, SNP identification M. Ishitani Abiotic stresses G. Mosquera Identification of pathogen population B. Dedicova New Transgenic Events Abiotic stresses; C. Martinez E. Torres Inter-generic crosses Inter-specifics E. Torres Yield potential Stay green C. Martinez E. Torres VHB C. Martinez E. Torres Zn and Fe enrichment Milling and cooking quality C. Grenier Synthetic populations with large genetic base C. Grenier WUE, NUE, tolerance to drought, acid soils and Al toxicity

  16. Where yield increase will come from in Latin America? CIAT Strategies • An agronomical revolution • Define breeding objectives in the context of Eco-Efficient Agriculture and climate changes • Target specific traits breeding • Quality- nutrition / biofortification • Blast, sheath blight, virus resistance • Cold tolerance, stay green, large panicle … • Exploring natural genetic variation from wild species • Marker assisted selection for accelerating breeding (SNP) • Transgenics for water and nitrogen use efficiency • Hybrids (initiated in 2010)

  17. Rice Priority Traits Multi-institutional Approaches Abiotic, Biotic, Quality and Yield

  18. The O. sativa x O. glaberrima sterility barrierhampers the use of interspecific lines in breeding Sterility loci • O. sativa x O. glaberrimaBC3 lines are fertile, but produce sterile hybrids with O.sativa • Phenomenon also found in NERICAs • Hampers full use of CSSLs for breeding

  19. Opening the African rice diversity to breeders • Africa rice (O. glaberrima) has many useful genes (Nematodes, Striga, blast, viruses, drought, NUE, etc.) • The Asian x African rice reproductive barrier hampers full use of Africa rice diversity in breeding programs •  Need for interspecific bridges = iBridges • We mapped the main sterility gene, S1 • We use the S1 markers to derive iBridges • iBridges = lines with 20-25% of O. glaberrima genes • iBridges x O. sativa hybrids are fertile  direct use in breeding schemes • From 25 donor accessions  broad access to the diversity available in the African species RM190 0,9 RM19349 0,8 RM19350 0,8 RM19353 3,5 RM19357 0,9 RM19361 0,0 RM5199 0,0 RM19363 0,8 RM19367 0,8 RM19369 0,0 Os05260Int 0,8 RM19377 5,1 RM_S1_34 0,9 CG14 38E01 2,0 RM19391 0,9 0,0 RM19398 0,8 RM3805 RM19414 0,8 RM19420 0,8 RM204 A CIAT – IRD project supported by Generation, with many partners (AfricaRice – PhilRice - NARs from Asia, Africa and Latin America)

  20. Confined field available for two different ecological sites Santa Rosa Palmira - CIAT HQ

  21. Upland Drought Evaluation at CIAT Palmira (Rainout shelter) and Santa Rosa (natural condition)Transgenic and Non transgenic Transgenic CIAT-JIRCAS • Promoter-gene combination • 4 promoters + 13 genes • Transgenic events • Curinga, Japonica upland • NERICA, Upland from JIRCAS • IR64, Indica lowland from IRRI • Growth stages • Reproductive, Vegetative, Seedling • Automation/IR & Visible Images • 500 images/40 minutes At Palmira Non transgenic CIAT-CIRAD Transgenic CIAT-JIRCAS Non transgenic CIAT-CIRAD • 400 lines(4 population of 100 S1 lines) + 6 checks At Santa Rosa (Dry season) Abiotic, Biotic, Quality and Yield

  22. CIAT Research on Nitrogen Use Efficiency (NUE) • Genetic Improvement for NUE • Transgenic approach • Non-transgenic approach • Precise phenotyping for trait discovery Unique position for transgenic research • Water Management • Reduce production cost • Improve fertilizer use • Reduce CH4 emission • Gas Emission Analysis • Impact assessment • Translation to CO2 credit A new research model for eco-efficient agriculture Ample experience in farmer’s field in Latin America

  23. NUE Field Preparation over 3 years Creation of N use efficiency platform • N omission plots • By growing successive crops of Maize without N fertilizer over 2 years • N level brought down by 50% • 50% reduction in grain yield of popular variety Fedearroz-50 • Evaluation of candidate genotypes • Local check and transgenic events that were proved to be superior in pot experiment • CSSL lines available at CIAT

  24. Lowland Rice NUE evaluation 1.5 ha of area- expandable based on necessity N-omission plots (> 200 lines, 4 Reps) 50% and 100%N Treatments Screening protocols to differentiate tolerant and intolerant lines Nitrogen Use Efficiency testing at CIAT • Traits • N uptake • N utilization • Leaf chlorosis • Biomass • Yield and yield components Abiotic, Biotic, Quality and Yield

  25. NUE Field Testing Methods • Field design • Randomized block design for each of the 3 treatments • No N; 50% N(75kg/ha) 100%N(150Kg/ha) • Each N treatment as a separate growth environment for GXE interaction • Fertilizer application • 3 splits • At the time of transplanting(40%) along with P2O5 and K2O, Zn • 30 days after sowing/ 2 days after transplanting • 54 days after sowing • 64 days after sowing • Dry surface of the soil after regulating irrigation and draining down excess surface water • Known amount of Urea was dissolved in measured quantity of water and spread in between rows by using spray pump without nozzle

  26. JICA/JSPS Program Posting of S & T Researchers (2011-2012) “Development of NUE technology to reduce greenhouse gas effect in agriculture system” Impact Assessment Precise Phenotyping Gas emission analysis Imaging analysis Dr. Takahiro Koide Drs. Kenji Omasa, Yutaka Urano, Fumiki Hosoi N20, CO2, methane to measure Automatic measurement of fluorescence, environmental impact canopy team to select best performer

  27. Gas Emission Analysis for Impact Assessment • Participated Institutes in Colombia • Fedearroz • Cenicaña • Local University • Dr. Takahiro Koide, JICA Expert • Measurement of N20, CO2, methane in paddy fields at CIAT

  28. Gas emission chamber in the field at CIAT in 2011 Whole plants covered Able to catch ebullition • CO2 budget • GHG emission via vascular system

  29. Rice Hybrid Breeding at CIAT Hybrid rice technology is a new approach to contribute to increase rice productivity in Latin America Currently the CIAT Rice Program is working in hybrid rice using two strategies: Conventional trough the Hybrid Rice Development Consortium (HRDC) with IRRI and GRiSP. to produce highly heterotic hybrids. new parental lines CMS and TGMS and transferring alogamy traits from wild species New male sterility system working with Yale University and University of Rhode Island to understand and monoecius traits present in a rice related genus

  30. Conventional Hybrid Breeding Objectives To develop experimental hybrids with high heterosis resistance to diseases and good grain quality for the tropical conditions in LAC; To develop new CMS pairs using the system WA (wild abortive) with good combinatory ability and adaptation to the tropics in LAC; To develop new TGMS (Termosensitive male sterility) lines with good combinatory ability and adaptation to the tropics in LAC; To develop new restores for the CMS system; To establish pilot test of seed production under field conditions using direct seeding

  31. Conventional Hybrid Breeding Some results A CMS pairs with excellent outcrossing capacity, high milling yield (total and whole grain), high amilose content, tolerance to the RHBV and tolerance to Tagosodeoryzicoulous have been identified 19 hybrids were identified in preliminary testing with good potential to be tested in advanced yield trials A total of 16 lines are under conversion to produce new AB pairs with CIAT material In 2010, a total of 384 new testcrosses in field conditions were produced, these are under preliminary testing now Currently three CMS pairs are under multiplication with the objective of increasing the amount of seed to establish experimental plots of seed production

  32. A new system for rice hybrid?Hybrid Technologies for Cosexual Cereals Strategies Breeding → mapping & wide crosses Genetic → SD orthologs Molecular → synthetic lethality Yale, U. Rhode Island, CIAT. BREAD-NSF

  33. A new system for rice hybrid?Hybrid Technologies for Cosexual Cereals Results from the inter genus crosses The Luziola genus and the Zizaniaare the two monoecius genus in the Oryzaetribe. Our objective was to produce a mapping populations between Oryzaand Luziola Using conventional hand pollination procedures and embryo rescue, we were able obtain F1 hybrids. These produced panicles with perfect florets and secondary panicles with female florets Because of complete sterility, a procedure to produce callus and plantlets was establish Currently we are working to produce allopolyoid plants

  34. Operational Challenges • Staffing • Virology position advertised • Programs leaderships over stretched due to the CRP • Staff retention of newly recruited staff a major concern (Issues: spouse employment and offers from top institutions in the US and UK) • Mega Programs (CRP) • Big transaction cost – affecting fund raising • Legumes CRP requires further work

  35. Research Challenges • How the new sequencing tools will change breeding/transgenicstrategies to develop better – superior genotypes? • How can we bridge the gap between sequences data generation and analysis? • What kind of phenotyping platforms we need to put in place? • How will information be managed and distributed?

  36. Areas for Emphasis in 2012 • Calibration of the breeding objectives in context of climate change • Evaluate how the sequencing data will change breeding – transgenicsstrategies • Biotechnology- Genetic Resources Platforms: Completion of Phase I (Strengthening CIAT internal capacities) and starting Phase II of linking with LAC institutions

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