2018 ANNUAL REPORT CGIAR Genebank Platform Table of Contents 1. Key Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.1 Highlight Platform achievements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 1.2 Platform progress towards outputs and outcomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1.3 Cross-Cutting Dimensions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2. Effectiveness and Efficiency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2.1 Management and governance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2.2 Partnerships . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2.3 Intellectual assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 2.4 Monitoring, Evaluation, Impact Assessment and Learning (MELIA). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 2.5 Efficiency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 2.6 Management of Risks to Your Platform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 2.7 Use of W1-2 funding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 3. Financial Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 Annex 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Acronyms GOAL Genebank Operations and Advance Learning 3K 3,000 Rice Genomes Project GPA Global Plan of Action ACIAR Australian Center for International Agricultural GRIN Germplasm Resources Information Network Research ICARDA International Center for Agricultural Research in AFS CRP Agri-food System CGIAR Research Program the Dry Areas AGM Annual Genebanks Meeting ICRAF World Agroforestry Center (International Council AOCC African Orphan Crop Consortium for Research in Agroforestry) ARI Advanced Research Institute ICRISAT International Crops Research Institute for the B4R Breeding for Rice Semi-Arid Tropics BBTV Banana Bunchy Top Virus IEA Independent Evaluation Agreement BLE Federal Office for Agriculture and Food, Germa- IITA International Institute for Tropical Agriculture ny ILRI International Livestock Research Institute BMGF Bill & Melinda Gates Foundation IPPC International Plant Protection Convention BrAPI Breeding Application Programming Interface IRRI International Rice Research Institute INIA Agricultural Research Institute, Chile ISI Institute of Scientific Information CATIE Tropical Agricultural Research and Higher Educa- ISPM International Standards for Phytosanitary Mea- tion Center sures CBD Convention on Biological Diversity ITPGRFA International Treaty on Plant Genetic Resources CGRFA Commission on Genetic Resources for Food and for Food and Agriculture Agriculture LPA Long-Term Partnership Agreement CIAT International Center for Tropical Agriculture, MELIA Monitoring, Evaluation, Impact Assessment and Colombia Learning CIMMYT International Maize and Wheat Improvement NARES National Agricultural Research Extension and Center Education System CIP International Potato Center NARS National Agricultural Research System(s) Crop Trust Global Crop Diversity Trust NGS Next Generation Sequencing CRP CGIAR Research Program ODAP Oxalyldiaminopropionic acid DArTSeq Diversity Arrays Technology Sequencing ORT On-line Reporting Tool DG Director General PATSPO Provision of Adequate Tree Seeds Portfolio DGDC Directorate-General for Development Coopera- PDCI Passport Data Completeness Index tion, Belgium PGRFA Plant Genetic Resources for Food and Agriculture DOI Digital Object Identifier POWB Plan of Work and Budget DSI Digital Sequencing Information QMS Quality Management System EiB Excellence in Breeding RTB CGIAR Research Program on Roots, Tubers and ELISA Enzyme-Linked Immunosorbent Assay Bananas EMBRAPA Brazilian Agricultural Research Corporation SGSV Svalbard Global Seed Vault FAO Food and Agriculture Organization of the United SMB System Management Board Nations SMO System Management Office FIGS Focused Identification of Germplasm Strategy SMTA Standard Material Transfer Agreement FTA CGIAR Research Program on Forests, Trees and SNP Single Nucleotide Polymorphism Agroforestry SOP Standard Operating Procedures GHU Germplasm Health Unit SPC-CePaCT Secretariat of Pacific Community-Center for GIGWA Genotype Investigator for Genome-Wide Analy- Pacific Crops and Trees ses USDA United States Department of Agriculture GLDC CGIAR Research Program on Grain Legumes and WG-EFMLS Open-Ended Working Group to Enhance the Dryland Cereals Functioning of the Multilateral System of Access GLIS Global Information System and Benefit-Sharing 2 | 2018 CGIAR Genebank Platform Annual Report ca Rice Cen d Afr caR ce u r A i ’ z pour l Within CGIAR Outside CGIAR 1. Key Results 120.000 100.000 1.1 Highlight Platform achievements 80.000 CGIAR Germplasm distribution 60.000 The activities of the Genebank Platform are tar- 40.000 geted specifically to bring about increased con- 20.000 servation and use of genetic resources with the aim of achieving CGIAR System Level Outcomes 0 2012 2013 2014 2015 2016 2017 2018 (Sub-IDO 1.4) and UN Sustainable Development Goals (Target 2.5). The annual distribution of Figure 1. Annual total samples distributed by CGIAR genebanks from 2012 to 2018 genetic resources from CGIAR genebanks pro- vides a rough indicator for their use, although it should be recognized that numbers distributed row, germplasm distribution outside the CGIAR only correspond to the level of demand in any has exceeded that inside the CGIAR. Develop- one year rather than the general scale of use ing countries also received a larger proportion of these resources. In 2018, a total of 96,566 of germplasm in 2018 (77%) compared to 2017 germplasm samples (66,930 accessions) were (67%). distributed by the CGIAR genebanks to users (Figure 1). Of these, 40,173 samples (42%) were Of the external distributions in 2018, most sam- provided to CGIAR Research Programs (CRPs) ples were sent to universities or research insti- and 56,393 (58%) were distributed to recipients tutes (Figure 4). 61% of the samples distributed outside the CGIAR in 87 countries; the majority represented traditional cultivars and crop wild of samples being distributed to developing coun- relatives (Figure 5). Table 1 lists the top country tries (Figures 2 and 3). For the second year in a recipients of germplasm from CGIAR genebanks Figure 2. Map of countries receiving CGIAR germplasm in 2018 2018 CGIAR Genebank Platform Annual Report | 3 Afri frique Number of samples distributed ter Centr e (not including materials transferred within or go to developing countries outside the top 10, between CGIAR Centers). Most of these coun- suggesting that there is substantial scope for tries (14) featured also in 2017 2017 2018 O athse r recipients of the the CGIAR toOt hsecr ale up external distributions in highest number of samples of 1g1e%rmplasm from the developin9%g world. Annex 1 provides more the CGIAR. Of the top 10 developing countries, details of the disWtirldi b10u%tionAd ovafn cgede/rmplasm to eight host CGIART rCadeitinontael rs. Only 16W%ild o12f% samples countries from individualIm Cpreovnedte rs and by crop. cultivar/Landrace cultivar Advanced/ Traditional 42% 6% Improved cultivar/Landrace cultivar 51% Breeding/Research AfricaRice 7% Bioversity Material 25% Breeding/Research CIAT Material 28% Africa 12,531 (22%) CIMMYT Americas 11,690 (21%) CIP ICARDA Others Others 4% 2017 2% 2018 ICRAF Asia ICRISAT Research Direct use Direct use 25,267 (45%) 29% 36% Research 31% 39% IITA Australia, NZ, & Pacific ILRI Education 168 (0.3%) Breeding Education 16% Europe 4% 19% 6,737 (12%) IRRI Evaluation Breeding 6% Characterization 4% Evaluation Characterization Figure 3. Samples distributed2% by each Center to users outside the CGIAR and geographical r2e%6% gion of recipient in 2018 Individuals/unknown/ Individuals/unknown/ other users Farmers/farmer other users Farmers/farmer 8% 2017 organizations 2% organizations 6% 2018 6% Commercial Commercial sector sector 5% 4% NARS or national genebanks NARS or national 31% genebanks ARIs or 50% Universities ARIs or 32% Universities 56% Figure 4. Recipients of germplasm distributed by CGIAR genebanks in 2017 and 2018 2017 2018 Other Other 11% 9% Wild 10% Advanced/ Traditional Wild 12% Improved cultivar/Landrace cultivar Advanced/ Traditional 42% 6% Improved cultivar/Landrace cultivar 51% Breeding/Research 7% Material 25% Breeding/Research Material 28% Figure 5. Types of materials distributed by CGIAR genebanks in 2017 and 2018 Others Others 4 | 2018 CGIAR Geneba4n%k Platform Annual Report 2017 2% 2018 Research Direct use Direct use 29% 36% Research 31% 39% Education Breeding Education 16% 4% 19% Evaluation Breeding 6% Characterization 4% Evaluation Characterization 2% 2% 6% Individuals/unknown/ Individuals/unknown/ other users Farmers/farmer other users Farmers/farmer 8% 2017 organizations 2% organizations 6% 2018 6% Commercial Commercial sector sector 5% 4% NARS or national genebanks NARS or national 31% genebanks ARIs or 50% Universities ARIs or 32% Universities 56% Developing Developed 43,399 12,994 (77%) (23%) Progress on key performance indicators clonal crop collections is safety duplicated in the By the end of 2018, CGIAR genebanks were form of cryopreserved or in vitro cultures. managing 773,112 accessions, including 25,576 in vitro accessions and 32,212 accessions held as An update of the current accession numbers of plants or trees in screenhouses or fields. Approx- the aggregate collection under CGIAR manage- imately 80% of total accessions are immediately ment is provided in Table 2. Five seed genebanks available for international distribution (Figure 6). have reached 90% targets for availability and one Of the seed accessions, 57% is secured in safety clonal collection is approaching the target. The duplication at two levels and 78% is duplicated individual status of the genebanks is provided in at the Svalbard Global Seed Vault (SGSV). 72% of Figure 7 and Table 3. Table 1. Top 10 developing and developed countries receiving germplasm from CGIAR Centers in 2018 Developing Developed Rank* Country Number of Number of Samples Country Number of Number of Accessions Accessions Samples 1 India 8,009 15,154 United States 3,654 3,727 2 China 4,002 4,311 Belgium 2,722 2,742 3 Morocco 3,780 3,780 Japan 1,874 1,874 4 Mexico 3,701 3,701 United Kingdom 1,695 1,839 5 Nigeria 1,650 2,471 Germany 1,011 1,011 6 Lebanon 2,071 2,071 Italy 424 424 7 Mali 356 1,679 Canada 322 322 8 Ethiopia 778 1,134 Sweden 178 178 9 Colombia 879 1,117 Spain 169 169 10 Kenya 328 984 Australia 152 168 Sub-total 25,554 36,402 Sub-total 12,201 12,454 (% from total) (81%) (84%) (% from total) (96%) (96%) Other countries 6,082 6,997 Other countries 528 540 (% from total) (19%) (16%) (% from total) (4%) (4%) Total 31,636 43,399 Total 12,729 12,994 Notes: *Ranking by number of samples. Excludes distributions to CGIAR programs. Countries in bold were not in Top 10 in 2017. Table 2. Key statistics of the aggregate CGIAR collection between 2012 and 2018 Indicator Description 2012 2013 2014 2015 2016 2017 2018 Base number of accessions in the collections (excluding barley at 1. Total number of CIMMYT, rice at CIAT, Rhizobium accessions and mycorrhiza at CIAT and 710,001 725,244 738,215 750,604 757,767 768,576 773,112 ICARDA, and regional collections of ICRISAT). 2. Total number of Numbers of accessions that are accessions that are viability tested, disease-free and currently available with sufficient seed number for 465,358 492,654 525,410 559,053 580,706 608,751 621,915 immediate distribution. 3. Number of seed accessions Numbers of accessions in seed held in long-term collections held in long-term storage and safety storage and safety duplicated in 386,037 375,271 413,448 381,932 404,074 408,323 420,164 duplicated at 2 levels a major genebank and in SGSV. 4. Number of Number of vegetative- RTB accessions in propagated accessions in cryopreservation or cryopreservation or safety 15,643 16,141 15,554 19,356 19,803 18,144 18,427 safety duplicated duplicated as in vitro samples. 2018 CGIAR Genebank Platform Annual Report | 5 2012 2013 2014 2015 2016 2017 2018 100 90% target 80 60 40 20 0 Availability Safety duplication - seed Safety duplication - clonal Figure 6. Status (%) of availability and safety duplication of CGIAR genebanks between 2012 and 2018 2012 2013 2014 2015 2016 2017 2018 100 90% target 80 60 40 20 0 AfricaRice CIAT CIMMYT CIMMYT ICARDA ICRAF ICRISAT IITA ILRI IRRI maize wheat seed 2012 2013 2014 2015 2016 2017 2018 100 80 60 40 20 0 Bioversity CIAT cassava CIP IITA clonal Figure 7. Status (%) of availability of seed collections between 2012 and 2018 (top) and clonal collections (bottom) between 2012 and 2018 6 | 2018 CGIAR Genebank Platform Annual Report Table 3. Status of CGIAR genebanks with respect to performance targets in 2018 % % % % Center Availability Increase Safety Increase 2018 from duplication from Comments 2017 2018 2017 AfricaRice succeeded in bringing the collection together at AfricaRice 91 3 62 0 one location in Cote d’Ivoire for the first time in 15 years in their newly constructed genebank. Expect to reach targets in 2021. Efforts are underway to address the presence of Banana Bioversity 63 0 69 17 Streak Virus, which is main constraint to availability. Expect to reach targets after 2022. Continued increases in availability and safety duplication. CIAT seed 80 7 84 3 Rationalization of the forages collection has started. Expect to reach targets in 2021. CIAT New methods are being explored for safety duplication cassava 78 50 59 -9 including using bonsai plants and nano-propagation. Expect to reach targets in 2020. CIMMYT Seeds are being bulked up for final safety duplication. wheat 91 0 80 -1 Rationalization also under way in 2019. Expect to reach targets in 2020. Gradual improvement in regeneration success rates are CIMMYT maize 64 3 76 0 helping to improve availability. Seeds are being bulked up for safety duplication in 2019 and 2021. Expect to reach targets after 2022. CIP 37 21 88 13 Important progress made on both health testing and verifying identity. Expect to reach targets after 2022. These figures still include the collection in Syria. Wheat, ICARDA 64 8 35 21 barley, lentil and chickpea are due to reach targets in 2021. Expect to reach targets in other crops after 2022. Field accessions (not included here) are available only locally ICRAF seed 75 36 17 40 and are not sufficiently safety duplicated. However, field collections are in the process of being rationalized. Expect to reach targets after 2022. ICRISAT continues to negotiate with the Indian Government ICRISAT 95 0 15 0 in order to release shipments for first level duplication. Expect to reach targets in 2022. Phyosanitary issues are resolved with Colombia and IITA IITA seed 94 5 48 3 is expected to be able to safety duplicate at CIAT in 2019 which will allow it to reach targets in 2020. Yam meristem culture continues to be the main constraint IITA clonal 39 11 33 -21 to conservation activities. Levels of safety duplication decreased because of renovation works in Benin laboratory. Expect to reach targets after 2022. Alignment of operations with CIAT has required the retesting of all accessions for specific seed-borne diseases. ILRI 0 -100 21 11 There is a current moratorium on distribution until the testing is complete. The Ethiopian Government is also imposing additional conditions on the distribution of non- Annex 1 material. Expect to reach targets after 2022. Safety duplication due to take place as soon as legal IRRI 93 1 89 0 agreements are signed with partners in the USA. Long-term partnership agreement awarded in 2019. 2018 CGIAR Genebank Platform Annual Report | 7 1.2 Platform progress towards outputs ber of genebanks in achieving safety duplication and outcomes targets. This has been due to three reasons: two Centers are currently constrained from allowing 1.2.1 Overall Platform progress certain parts of the collection outside of the host The activities of the Genebank Platform are closely country while negotiations are ongoing (see 2.6 following those of the 2016 proposal and the 2018 Management of Risks), a number of Centers have Plan of Work and Budget (POWB), with steady delayed the shipment of safety duplicates to CIAT improvement overall in the status of the collections because of new national phytosanitary regulations and the operations of the genebanks and germ- in Colombia, and ICARDA has been using safety plasm health units (GHUs). Table 4 presents the duplicates from SGSV to reconstitute active col- achievement of milestones. Progress in the avail- lections of wheat, barley, lentil and chickpea in ability of accessions is proceeding as expected Morocco and crop wild relatives, forages and food but there is a noted delay in progress for a num- legumes in Lebanon. Center management and Table 4. Progress against 2018 milestones Module Platform outcome POWB 2018 Progress an (2022) milestone milestone status Evidence Output 1.1 80% accessions available Achieved Online reporting, Disease-free, Genesys viable documented germplasm made 60% seed accessions safety 57% seed accessions safety Safety duplication is available duplicated duplication currently hampered by various factors 75% clonal accessions 72% clonal accessions safety Safety duplication safety duplicated duplicated of clonal collections is repeated annually and is influenced by multiple factors. 80% relevant requests met 90% requests met Online reporting Output 1.2 40 SOPs in place 156 SOPs in place Drafted SOPs are Conservation Crop diversity compiled but not yet conserved in publicly available a rational and effective global 500 accessions successfully 702 accessions introduced into cryo: Cryotanks at system introduced into cryobanks 55 banana at Bioversity, 563 potato Bioversity, CIP and at CIP, 60 sweetpotato at CIP, 24 IITA cassava at IITA Diversity trees developed Achieved Online reporting representing 14 crop genepools 20 NARS staff involved in 186 NARS staff involved capacity- Online reporting capacity building events building events at Platform level and >2,000 NARS staff involved in Center-organized capacity building events and >5,000 participated in genebank visits Output 2 100% accessions with DOIs 97% accessions with DOIs Genesys More effective Use access and use One new subset for a Achieved Report available. of germplasm defined user developed in Subsets will be made enabled each genebank available through Genesys in 2019. Output 3 CGIAR contributions to CGIAR representation at 6 Reports available at Supportive policy four intergovernmental international meetings CGIAR Sharepoint environment meetings under rubric of upon request developed the CBD/Nagoya Protocol and the ITPGRFA Policy CGIAR guidance document Guidance provided in 2 documents: Documents available on transferring PGRFA i) Guidelines on the Nagoya Protocol for at CGSpace: under development CGIAR Research Centers https://hdl.handle.net/10568/96240 ii) Guidance Note on CGIAR Research https://hdl.handle.net/10568/93396 Center Public Disclosures related to the Management of Intellectual Assets 8 | 2018 CGIAR Genebank Platform Annual Report staff are actively pursuing resolution of the for- clonal crop collections in the long term, with less mer issues. The plans of the GHU Community of threat from contamination and somaclonal vari- Practice to develop a “GreenPass” system to rec- ation than field or tissue culture collections, but ognize and facilitate the movement of germplasm the technique demands a tremendous amount from CGIAR Centers represents a longer-term of team discipline and skill to ensure accessions effort to address the possibility of national phy- are disease-free, true-to-type and able to be tosanitary agencies imposing unwarranted reg- successfully regenerated after cryopreservation, ulations. In general, however, these issues do which sometimes requires optimized protocols not appear to be preventing the distribution of for individual genotypes. Cryopreserved samples germplasm to requesters with an overall 90% of can be safety duplicated, precluding the need requests being met. for the annual multiplication and shipment of in vitro duplicates to multiple locations, and cryopre- Important progress is being made in strengthen- served collections also pave the way for rational- ing quality management systems (QMS) of both ization of field and in vitro collections. The CGIAR, genebanks and GHUs with staff in key positions having achieved this scale of implementation in continuing to draft and improve standard operat- cryopreservation, is in a unique position to build ing procedures (SOPs) and all genebanks under- on this capacity and to provide support to cryo- going documentation audits for key procedures. preserve other clonal crop collections on a large Expected milestones for drafted SOPs have been scale elsewhere. significantly exceeded due to the rapid progress made by the GHUs in developing their SOPs. The Efforts to promote the use of diversity in the audits ensure that the written SOPs are follow- collections are focusing on the association of ing expected standards. Planned in situ expert existing or new data with genebank accessions, reviews in 2019 and 2020 will use the audits and including characterization and evaluation data genebank annual reports to validate the reported and published or available trait data. The Gen- status of the collections and the implementation ebank Platform has also spearheaded a global of the SOPs. effort, instigated by the International Treaty on Plant Genetic Resources for Food and Agriculture CIP have succeeded in cryopreserving more than (ITPGRFA), to enable the traceability of acces- 50% of the clonal potato collection. With nearly sions through the use of Digital Object Identifiers 3,000 accessions established in cryotanks, this (DOIs). Targets for the implementation of DOIs makes the CIP collection one of the largest crop are now effectively met with all genebanks having cryo-collections in the world. Cryopreservation applied DOIs to all collections. The next steps represents the most secure way of conserving are to mainstream the use of DOIs in genebank CIP in Peru is rapidly building one of the largest cryopreserved clonal crop collections in the world. Photo: Luis Salazar/Crop Trust. 2018 CGIAR Genebank Platform Annual Report | 9 processes and to encourage their use once acces- events, sharing practices and expertise, student- sions have left the genebank. All genebanks are ships and Platform-level meetings, and externally also engaging different users, both inside and through workshops, exchange visits, project outside the CGIAR, to develop subsets based collaborations and particularly through ad hoc ad- on desirable traits, environmental parameters vice and support that is provided not just for the or genetic diversity. The subsets developed are selection of germplasm but for a wide range of listed in Table 7 and collaborations are summa- purposes. Figure 13 provides an indication of the rized in Table 11. A major effort will begin in 2019 range of services and advice that genebanks pro- to bring accession-level characterization and vide. According to reported figures, more than evaluation data for all CGIAR collections into one 3,000 NARS scientists and farmers have been in- place in the global online portal, Genesys. volved in capacity building events and more than 5,000 people have participated in tours of CGIAR The Policy Module has played a very active role genebanks in 2018. The work on QMS and staff in 2018 in international negotiations and events succession has been particularly timely given the relating to plant genetic resources for food and retirement of six long-serving genebank man- agriculture (PGRFA) policy and has worked to agers. The dedication of these managers to the ensure CGIAR activities, guidelines, and reporting long-term conservation of plant genetic resources processes comply with legal and other require- was recognized by the Crop Trust with a “Legacy ments. The Policy Module has set up and devel- Award” at the tenth anniversary of the Svalbard oped consultation processes with multiple CGIAR Global Seed Vault. decision-making and implementation bodies, including the System Management Board (SMB), 1.2.2 Progress by Platform Modules System Management Office (SMO), Director Gen- erals of Centers that are signatory to the Article Conservation Module 15 of the ITPGRFA, the newly established CGIAR The progress of individual genebanks in upgrad- Genetic Resources Policy Working Group, and ing collections and reaching performance targets also external stakeholders. Planned participation is described above. Further significant outputs of in international meetings and development of the Conservation Module in 2018 are: publications and guidance documents in 2018 have all been achieved. IRRI and Crop Trust enter into a Long-term Partnership Agreement (LPA) Finally, a large proportion of the activities of the Marking an important milestone in the function- Genebank Platform involve capacity building; ing of the Crop Trust endowment and achieve- internally through strengthening QMS, training ment of the Genebank CRP and Platform, the Recipients of the Crop Trust Legacy Awards during the celebrations of the tenth anniversary of the Svalbard Global Seed Vault. Photo: Neil Palmer/Crop Trust 10 | 2018 CGIAR Genebank Platform Annual Report Ahmed Amri from ICARDA genebank redepositing safety Marie Haga (Crop Trust) and Matthew MoreIl (IRRI) at the duplicates after regeneration at the Svalbard Global Seed Vault signing of the Long-term Partnership Agreement during the fifth in Norway. Photo: Neil Palmer/Crop Trust International Rice Congress in Singapore. Photo: Shawn Landersz Crop Trust and IRRI signed a new and unique ceeded in regenerating 38,073 safety duplicates agreement that guarantees funding for the IRRI over two seasons despite unseasonably dry genebank into the distant future at an event held conditions in Morocco. Exceeding expectations, at the International Rice Congress in October ICARDA had produced enough seed to pop- 2018. The Long-Term Partnership Agreement ulate base and active collections in Lebanon (LPA) was made possible due to IRRI genebank and Morocco and to deposit 43,000 accessions, sustaining performance targets under a fixed including both new and “old” materials, back budget for more than five years. The agreement into SGSV in October 2018 (Figure 8). One of is underpinned by a comprehensive business plan the complementary outputs of this massive which places the genebank at the heart of the regeneration effort has been the newly gathered “Harnessing rice genetic diversity to accelerate characterisation data. The regeneration contin- impact” outcome theme in IRRI’s institutional ues with support from the Genebank Platform. strategy, with the Crop Trust covering all essential At the same time, CIMMYT and ICARDA are operations of the genebank and funding from working together to develop a business plan IRRI to support complementary activities includ- for a single rationalized CGIAR wheat collection ing capacity building, conservation research, and managed under harmonized processes and stan- promotion of the use of diversity in the collection. dards, which will potentially form the core of a new LPA with the Crop Trust. An Arte film1 that ICARDA re-deposits seeds at SGSV documents ICARDA’s efforts was broadcast in Since 2016, ICARDA has been regenerating 2018. extraordinary numbers of accessions retrieved from the SGSV. In the past two years, staff suc- 1https://www.arte.tv/en/videos/080754-000-A/seeds-of-war/ 80,000 60,000 40,000 20,000 0 2015 2017 2019 2021 2023 2025 2027 2029 Self-pollinated cultivated cereals (Morocco) Self-pollinated wild cereals (Lebanon) Self-pollinated food legumes (Lebanon & Morocco) Cross-pollinated food legumes (Lebanon) Cross-pollinated forages (Morocco) Figure 8. Reconstitution of ICARDA’s active and base collections in Lebanon and Morocco 2018 CGIAR Genebank Platform Annual Report | 11 Number of accessions Measuring diversity and gap analysis and breeding lines to 132 countries. AFS CRPs ICARDA, CIAT, and the Crop Trust have teamed account for 66% of the distribution events but a together to develop methods and metrics to total of 71% of the samples health-tested were measure the level of representation of crop diver- for conservation in the genebanks (Table 5 and sity in CGIAR genebanks and to identify gaps for Figure 10). targeted collecting. The Crop Trust has devel- oped 14 crop genepool “diversity trees” based GHU activities under the Genebank Platform aim on consultations with 43 experts and more than to develop improved processes to remove bottle- 200 scientific papers. Genebank accessions are necks in health testing. A significant achievement mapped onto the trees and visualizations devel- is the adoption of Next Generation Sequencing oped to help assess where genetic groups are (NGS)-based indexing in a cross-Center initiative well represented or not at all in CGIAR collections for clonal crop collections. Other developments (Figure 9).2 Diversity trees have been developed have led to significant results, including: for more than 14 crops and a further 8 are under • Molecular tools for detecting and eliminating cassava development. frogskin-associated viruses have increased the availabil- ity of the CIAT cassava collection from 9% in 2017 to % Germplasm Health Units (GHUs) by the end of 2018. In 2018, the GHUs health-tested a total of • CIMMYT developed a new protocol for testing maize 245,369 samples, including samples for import lethal necrosis for bulk sample analysis. (10,236) and export (61,236) from Agrifood Sys- • IITA developed a polyclonal antibody-based ELISA assay tem CRPs (AFS CRPs) as well as those for gene- for testing cassava bacterial blight in stems and plants. banks. GHUs facilitated distribution of germplasm • ICARDA developed an improved seed management package that contributed to the decrease of wheat 2 Diversity trees are based on a concept first published in van Treuren, accessions infected with common bunt from 1.7% in R., et al. 2009. Optimization of the composition of crop collections for ex situ conservation. Plant Genetic Resources: Characterization and 2014 to 0.06% in 2018. Utilization 7(2); 185-193 doi:10.1017/S1479262108197477. M. beccarii M. borneensis Callimusa cluster M. campestris Fe'i PNG E. gilleti M. coccinea Fe'i FSM E. glaucum M. monticola Fe'i FJI Ensete E. ventricosum M. violascens Fe'i PYF Others Ensete M. viridis Fe'i USA Fe'i MHL Fe'i Fe'i NRU Section Callimusa Fe'i NCL Fe'i PLW The thickness of branches is proportional to the Fe'i SLB Fe'i TON number of accessions conserved. Fe'i TUV Australimusa cluster Fe'i VUT M. boman M. jackeyi M. lolodensis Wild M. acuminata subsp. banksii M. textilis M. acuminata subsp. malaccensis M. maclayi Autonomus region of Bouganville M. acuminata subsp. zebrina M. peekelii East New Britain M. acuminata subsp. siamea East Sepik M. ornata M. acuminata subsp. burmannica M. acuminata Eastern highlands M. laterita M. acuminata subsp. microcarpa Hela M. velutina M. acuminata subsp. truncata Madang Musa M. mannii M. acuminata subsp. errans Manus M. rosea M. acuminata subsp. truncata Milne bay M. rubra Others M. acuminata New Ireland Rhodochlamys genetic cluster M. sanguinea Oro M. mannii M. balbisiana PHL AA PNG Southern highlands M. balbisiana VNM AA IDN M. rosea West New Britain M. chunii M. balbisiana CHN AA PHL West Sepik M. kattuvazhana M. balbisiana IND AA MYS Western Highlands M. balbisiana M. balbisiana MMR AA VNM M. rubinea Western province M. schizocarpa M. balbisiana LAO AA THA M. zaifui AA origin not known AA TZA M. aurantiaca M. itinerans M. balbisiana LKA Simbu M. cheesmani AA other origin M. balbisiana THA Enga Eumusa cluster-Wild M. basjoo AA TLS M. balbisiana other or unknown origin Gulf M. griersonii AA IND Jiwaka M. insularimontanDai AA SLB Section Musa M. lanceolata AA MDG Diploids M. nagensium M. ochracea Kunnan M. shankarii AB Ney Poovan M. siamensis AS Others AB M. sikkimensis M. thomsonii mutika/lujugira M. yamiensis Cavendish M. yunnanensis red M. celebica Gros Michel Eumusa genetic cluster M. flaviflora AAA Ibota M. tomentosa Orotava M. tonkinensis Rio Ambon Ambon Others AAA Plantain Silk Mysore Laknao Eumusa cluster-Domesticated Cultivars Triploids AAB Maia maoli/Popoulu Pisang Kelat Pisang Raja Iholena Pome hybrid Others AAB Pisang Awak Bluggoe Monthan Saba ABB Pelipita AAT Kalapua other triploids Teparod Others ABB AAAA AAAB AABB Tetraploids ABBB ABBT Figure 9. Banana cultivated and wild genepool illustrated in a “diversity tree” 12 | 2018 CGIAR Genebank Platform Annual Report Table 5. Germplasm samples processed for conservation and distribution by GHUs in 2018 Center Total accessions Total samples Total samples Total diagnostic analyzed analyzed rejected reactions AfricaRice - - - - Bioversity 192 374 92 1,104 CIAT 10,520 12,145 1,348 61,255 CIMMYT 8,194 1,489 151 22,778 CIP 1,175 4,576 4,756 56,057 ICARDA 30,178 24,328 446 309,472 ICRAF 531 531 0 531 ICRISAT 6,778 6,792 842 13,584 IITA 7,846 118,614 7,074 138,505 ILRI 1,204 1,739 256 6,922 IRRI 12,185 - 643 - Total 78,803 170,588 15,608 610,208 180,000 160,000 140.000 120,000 100,000 80,000 60,000 40,000 20,000 0 Import Export Conservation Import Export Genebanks AFS CRPs Figure 10. Numbers of health tests carried out by GHUs for genebanks and AFS CRPs in 2018 CIAT and ILRI have made major progress towards aligning Efforts to improve germination testing are underway at tropical forages collection, including exchange visits of key ILRI. Photo: Shawn Landersz staff such as Arsenio Ciprián (CIAT). Photo: Shawn Landersz 2018 CGIAR Genebank Platform Annual Report | 13 Number of health tests Use Module accessions. In addition, Australia, Brazil, and Digital Object Identifiers (DOIs) Kenya national genebanks added data on more CGIAR Centers are among the first institutes than 200,000 accessions to Genesys. Passport worldwide to implement DOIs for genebank Data Completeness Index (PDCI) also continued accession identification under the Global Infor- to improve (Table 6). mation System (GLIS) of the ITPGRFA. DOIs pro- vide a global standard by which germplasm may Subsetting be traced as it moves from collections to release All genebanks are actively developing user-fo- as improved varieties or to research leading to cused subsets of genebank accessions to pro- publications. In 2018, 97% of CGIAR genebank mote the use of new diversity in research and accessions were assigned a DOI (Table 6). The breeding. In 2018, subsets were made available focus is now on mainstreaming the use of DOIs in online or elsewhere (Table 7). genebank operations and beyond the genebanks for research and breeding. Training events and presentations have been made to national gene- banks in Lebanon and Indonesia, and breeders at AfricaRice, CIP, ICARDA, IITA, and IRRI. Genesys (www.genesys-pgr.org) Genesys is a recognized pillar of GLIS. In 2018, with co-funding from Germany’s Federal Office for Agriculture and Food (BLE), the Crop Trust worked with national partners, the WorldVeg, CATIE, and the CGIAR genebanks to incorporate phenotypic datasets into the online portal. Rather than attempting to standardize formats for trait data, the new application allows different file formats to be uploaded and searched using stan- dardized meta-data. Images and maps are also being incorporated into the portal. In 2018, trait Genesys portal -- the global gateway to genetic resources. data were published involving more than 230,000 www.genesys-pgr.org Table 6. Status of CGIAR germplasm data in 2018 in Genesys Number of Number of % target Passport data completeness index (PDCI)* Center accessions accessions accessions uploaded with DOI with DOI 2015 2016 2017 2018 AfricaRice 21,300 18,934 89% 5.62 5.62 5.60 5.89 Bioversity 1,566 1,566 100% 5.27 5.77 5.57 5.94 CIAT 66,787 66,787 100% 4.51 4.51 6.70 6.94 CIMMYT 209,216 204,415 98% 5.3 5.31 5.65 6.22 CIP 17,901 17,883 100% 5.38 5.43 5.61 7.53 ICARDA 155,414 153,256 99% 5.83 5.75 6.76 6.65 ICRAF 5,391 5,391 100% 5.34 5.34 6.69 6.68 ICRISAT 126,830 120,431 95% 6.05 6.05 6.89 6.95 IITA 33,713 33,713 100% 4.66 4.69 4.69 5.12 ILRI 18,643 18,638 100% 6.46 6.56 6.88 6.80 IRRI 130,154 124,489 96% 5.22 5.50 5.45 5.40 All 786,915 765,503 97% 5.42 5.50 6.04 6.34 *Van Hintum, T., Menting, F., & Van Strien, E. (2011). Quality indicators for passport data in ex situ genebanks. Plant Genetic Resources, 9(3), 478-485. doi:10.1017/S1479262111000682. 14 | 2018 CGIAR Genebank Platform Annual Report Table 7. Subsets made publicly available from genebanks in 2018 Genebank Subsets AfricaRice Minicore of Oryza glaberrima developed from DArTSeq data Bioversity Banana reference set Cassava subsets with phenotypic extremes in selected traits: Dry matter content (%) HCN content (ppm) CIAT Total sugars (%) Amylose (%) Paste clarity (%) Pulp color Wheat: over 300 subsets developed • Milling, baking, nutritional quality, and tasty flours • Heritage, hallmark and high impact wheat varieties • Heat or drought tolerance, and high grain yield with broad adaptation • Tolerance to diseases, insects, viruses, nematodes CIMMYT • Physiological traits, tolerance to abiotic stresses, and promiscuous wheat Available by choosing “wheat” at: http://wgb.cimmyt.org/gringlobal/descriptors.aspx? Maize: • Jala, Tripsacum, Teosinte subsets • Morelos 1966-67 Collection • CIMMYT maize lines: Popping and nutritional set • Potato artisanal colored set (2017) CIP • Potato mini core (2017) • SWP artisanal colored set (2018) • SWP mini core (2018) New FIGS subsets: • Wheat Septoria (115 accessions) ICARDA • Lentil frost-resistance (115 accessions) • Lentil Ascochyta Blight-resistance (87 accessions) • Barley Leaf Blight (110 accessions) • Barley Spot Blotch-resistance (52 accessions) • Faidherbia albida by molecular characterization (data to be linked with the reverse phenology ICRAF phenotypes) • Allablackia spp by molecular characterization (data to be linked with oil content phenotypes) • Adansonia digitata accessions by nutritional characteristic • Core collections: chickpea (1,956 accessions), groundnut (1,702 accessions), sorghum (2,246 accessions), pearl millet (2,094 accessions), pigeonpea (1,290 accessions), finger millet (622 accessions), foxtail millet (155 accessions), proso millet (106 accessions), barnyard millet (89 accessions), kodo millet (75 accessions) and little millet (56 accessions) ICRISAT • Mini-core collections: sorghum (242 accessions), pearl millet (238 accessions), chickpea (211 accessions), groundnut (184 accessions), pigeonpea (146 accessions), finger millet (80 accessions), foxtail millet (35 accessions). • Reference sets: sorghum (375 accessions), pearl millet, chickpea, pigeonpea, groundnut finger millet and foxtail millet (300 accessions each). • Cassava, cowpea, yam core collections IITA • Cowpea mini core • Cowpea FIGS-drought and heat subsets (with assistance from ICARDA) • Lablab core ILRI • Highland core • Dryland core • False smut panel (60 accessions) IRRI • New subsets for drought plus disease screening (2 panels of 100 accessions) • New subset for salinity (200 accessions from Indonesia) • Breeder selected subset from 3K accessions for India 2018 CGIAR Genebank Platform Annual Report | 15 Policy Module Policy Module’s recommendations, calling for Enhancing Centers’ contributions to international systemwide efforts to generate and share infor- PGRFA policy fora mation in the Annual Intellectual Assets Manage- The Policy Module coordinated CGIAR’s engage- ment Reports and Centers’ public disclosures. ment in the ongoing negotiations of the ITPGR- The Policy Module is working with the SMO and FA’s multilateral system of access and benefit Centers to improve reporting and to develop a sharing. In 2018 in consultation with the CGIAR submission in response to Resolution 4/2017 in Genetic Resources Policy Working Group, the the first half of 2019. Policy Module developed and subsequently promoted agreed CGIAR policy positions at Promoting compliance of CGIAR Centers with meetings of key negotiators convened by the PGRFA policies and laws ITPGRFA Secretariat and the Open-Ended Work- The Policy Module organized its second in a ing Group to Enhance the Functioning of the series of annual, regionally-focused capacity Multilateral System of Access and Benefit-Sharing building workshops for CGIAR scientists and key (WG-EFMLS). Reception to CGIAR positions, so national partners, as well as training workshop far, has been positive. The Policy Module also and webinars for genebank staff and Intellec- coordinated CGIAR participation in multiple tual Property (IP) focal points. It set up a CGIAR meetings under the aegis of the Convention on Genetic Resources Policy Helpdesk for use by Biological Diversity (CBD) and Nagoya Protocol CGIAR scientists and responded to numerous to provide technical guidance and inputs in dis- requests for assistance.3 Policy statements on cussions on the use of digital sequencing infor- biotechnology and gene editing were drafted mation (DSI). One CGIAR submission to the CBD with inputs from approximately 20 scientists from concerning DSI was substantially reproduced in a across the CGIAR and will be considered and peer reviewed journal article in 2018. adopted in 2019. The SMB also adopted the Guidelines on the Nagoya Protocol for CGIAR In 2017, the Governing Body of the ITPGRFA Research Centers developed by the Policy Mod- adopted Resolution 4/2017 inviting CGIAR to ule in 2018. submit annual reports concerning the use of restrictive licenses and intellectual property appli- In addition, the Policy Module convened a mul- cations over Centers’ improved plant genetic tistakeholder consultation to get feedback from resources. In 2018, the SMB recognized possible civil society organizations, negotiators in the ITP- reputation risks for the CGIAR and adopted the 3Requests can be sent to: GRPolicy-Helpdesk@groups.cgiar.org Wheat accessions from CIMMYT being prepared for distribution. In 2018, CIMMYT distributed more than 5,000 samples of wheat to users outside the CGIAR from its headquarters in Mexico. Photo: Luis Salazar/Crop Trust 16 | 2018 CGIAR Genebank Platform Annual Report GRFA process, and the seed industry on CGIAR in order to inform both managers and users on positioning in the Treaty negotiations, in response patterns of diversity within collections, poten- to resolution 4/2017 and on internal policies and tially having implications for the sampling and best practices. management of conserved materials. The project succeeded in sending 14,000 DNA samples from Capacity building for national programs to 865 accessions to Diversity Arrays. The resulting implement international genetic resources data will be analyzed in 2019 and plans are being agreements made to ensure that the initiative is associated Two decision-making tools for national policy with capacity building efforts to ensure that NARS makers were finalized and published in 2018 partners benefit from any new information and involving members of the Policy Module as lead approaches. authors: • Decision-making tool for national implemen- 1.2.4 Publications tation of the ITPGRFA’s multilateral system of The Center genebanks’ management of genetic access and benefit-sharing; resources and associated data complies with the • Mutually supportive implementation of the CGIAR Principles on the Management of Intel- Nagoya Protocol and the ITPGRFA: Scenarios lectual Assets and Open Access Policy. Genesys for consideration by national focal points and publishes data supplied by CGIAR and gene- other interested stakeholders. banks worldwide in accordance with data sharing agreements between the Crop Trust and the The Policy Module coordinated, together with individual data providers. In total, more than 1.9 CIP, Bioversity, and partners, a workshop in Peru million records were updated in Genesys in 2018. for the National Focal Points for the ITPGRFA and Genesys now contains records on 4 million acces- the Nagoya Protocol involving 13 countries in the sions from 461 institutes. region. The focus of the workshop was the mutu- ally supportive implementation of the ITPGRFA The Genebank Platform website (www.gene- and the Nagoya Protocol. banks.org) provides links to research papers, pol- icy briefs, conservation protocols, training mate- rials, and submissions to international policy fora 1.2.3 Variance from Planned Program for in conformance with the CGIAR Open Access and this year Data Management Policy. In 2018, the genebanks Under the Use Module, an opportunity was taken reported a total of 150 publications by genebank to pool resources between seven genebanks and staff in journals, conference proceedings, books to send samples from multiple crops to Diversity and book chapters, covering a wide range of top- Arrays in Australia for DArTseq genotyping. The ics (Figure 11). Out of 79 peer-reviewed journal project focused on assessing the genetic het- articles, 80% are publicly available in open-access erozygosity within and between seed accessions publications and 73% are published in ISI journals. General in formation on plant genetic resources Agronomy General in formation on collections Morphological and genotypic characterization Nutrition value Seed physiology & longevity Stress & disease tolerance 0 5 10 15 20 25 30 35 40 45 50 AfricaRice Bioversity CIAT CIMMYT CIP ICARDA ICRAF ICRISAT IITA ILRI IRRI Figure 11. Publications authored by genebank staff in 2018 by topic (excluding publications from the Policy Module) 2018 CGIAR Genebank Platform Annual Report | 17 1.3 Cross-Cutting Dimensions 1.3.1 Capacity Development While the Genebank Platform primarily carries The Genebank Platform undertakes numerous out services to CRPs and national partners to con- capacity building activities to the benefit of both serve, test, clean and distribute germplasm, the CGIAR staff and national partners at the level of genebanks also serve as the primary knowledge the Platform, Modules and individual Center gen- hub in their respective regions for the crops they ebanks, many are supported by bilateral fund- conserve. In 2018, more than 800 capacity build- ing sources. At the Platform level, 18 capacity ing events took place across the Center gene- building events took place in 2018 involving 436 banks (Table 9). The activities involved more than participants from 11 CGIAR Centers plus national 8,000 participants in 85 countries. This includes partners (Table 8). The participants of the listed 660 tours of genebanks provided to visitors to capacity building events gained knowledge and promote the importance of crop diversity and the skills that allowed them to adhere to international work of CGIAR. Outreach to NARS and national standards and policy in genebank management genebanks has contributed to increased learning and the distribution of germplasm and related within the global system for PGRFA conservation information. and use. Table 8. Platform and Module level capacity building events in 2018 Date Event Location Number of % % participants CGIAR Female 10–12 Apr Expert consultation workshop to facilitate adoption and application of the FAO Genebank Standards Bonn, Germany 25 12% 68% 16–20 Apr ILRI-CIAT forage collections harmonization meeting ILRI, Ethiopia 6 100% 50% 4–8 Jun Genesys and GRIN-Global workshop Porto, Portugal 47 57% 19% 8–15 Oct LRI-CIAT forage collections harmonization meeting ILRI, Ethiopia 22 62% 38% 1–6 Nov Annual Genebank Meeting Fortaleza, Brazil 45 100% 45% Policy module workshops 18–19 Jun Multi-stakeholder Consultation Meeting Paris, France 13 46% 8% Capacity building workshop on genetic resource 1–20 Sep policies for CGIAR scientists and partners from Near Beirut, Lebanon 34 59% 38% East and neighboring countries Workshop for Nagoya Protocol and Plant Treaty 25–28 Sep National Focal Points in Latin America and the Lima, Peru 64 22% 39% Caribbean 31 Oct–1 Nov Pre-AGM special session on Genetic Resources Policy Fortaleza, Brazil 19 79% 37% GHU workshops CGIAR GreenPass Phytosanitary Protocol for 18–19 Apr Germplasm Exchange: Expert Consultation Rome, Italy 6 33% 50% Workshop 23–27 Apr 3rd working group meeting of the CGIAR GHUs IRRI, Philippines 28 100% 57% 27 Apr–2 May Seed Health Testing Procedures IRRI, Philippines 7 100% 57% 25–29 Jun Library Preparation and Bioinformatics for Virus Indexing by sRSA ICRAF, Kenya 18 67% 22% QMS workshops 2–7 Apr QMS intensive ICARDA, Lebanon 15 100% 40% 30 Apr-4 May QMS intensive IRRI, Philippines 8 100% 63% 14–18 May GOAL workshop IICA, Costa Rica 31 10% 52% 3-7 Sep Crawford GOAL Kuala Lumpur, Malaysia 32 9% 44% 8–19 Sep QMS intensive SPC-CePaCT, Fiji 16 0% 69% Total 436 50% 42% 18 | 2018 CGIAR Genebank Platform Annual Report Table 9. Capacity building events in 2018 Event category Number of Number of % % Number of events participants non-CGIAR female countries involved Genebank visits and tours 660 5,574 90% 39% 71 Genebank-organized training/workshop 17 521 77% 50% 30 Genebank staff as resource person in a capacity development event 47 550 52% 45% 20 Visit from partners for research/scientific work 60 309 92% 19% 21 Hosting a scholar/student in the genebank for educational purpose 62 168 57% 39% 19 Farmers' open day 3 1,041 100% 34% 2 Total 849 8,163 87% 39% 85 1.3.2 Climate Change 2. Effectiveness and The most relevant aspect of the work to address Efficiency climate change under the Genebank Platform is the development of subsets to promote the 2.1 Management and governance evaluation and use of diversity in the collections. There have been no major changes to gover- Table 7 presents the subsets available from each nance arrangements. A Memorandum of Under- genebank, including more than 300 wheat sub- standing was signed between the Crop Trust and sets from CIMMYT, many of which contain acces- CGIAR reinforcing the partnership in overseeing sions that have the potential to address abiotic and sustaining funding to the CGIAR genebanks. or biotic stresses in multiple environments. in the context of climate change The FIGS (Focused 2.2 Partnerships Identification of Germplasm Strategy) approach developed by ICARDA associates specific traits 2.2.1 External partnerships with environmental conditions and allows users The key external partnerships are presented in to screen collections to identify those accessions Table 10. The primary partners of the genebanks from target environments that are likely to harbor and GHUs are the wide-ranging users from the desired traits. Through the Genebank Platform, many countries who requested germplasm, ICARDA is also consulting users to identify where advice and information in 2018. The exchange gaps may exist in collections for priority traits. of germplasm takes place within a policy frame- work that demands close partnership with the Table 10. Key external partnerships of the Genebank Platform in 2018 Module Description Name of partner Main area of partnership Ultimate safety duplication of CGIAR germplasm. SGSV Risk management Research collaboration, partnership for germplasm distribution, safeguarding of genetic resources, recipient of capacity building and other genebank National genebanks Capacity building and Risk management services Conservation Collaboration in the delivery of the Global Plan of Action CGRFA International policy Collaboration in safe exchange of germplasm IPPC & national plant Phytosanitary and international protection agencies policy Provision of germplasm, clean planting materials, information and advice. >130 countries Delivery Use Global information system (GLIS) on PGRFA ITPGRFA Delivery and Policy International PGRFA policy development Policy and compliance, capacity building for policy ITPGRFA & CBD ational policy implementation at national level Secretariats Intern 2018 CGIAR Genebank Platform Annual Report | 19 ITPGRFA, the Commission on Genetic Resources for Food and Agriculture (CGRFA), and the Inter- national Plant Protection Convention (IPPC). The SGSV is an essential partner in long-term conser- vation, as well as in communicating to the wider world the importance of crop diversity and the organizations that conserve it. CGIAR genebanks provide more than germplasm to users. Individual genebanks provide a range of services, capacity building and support to national partners (Figure 13). The services rendered involved working with 80 institutes in 39 countries. 2.2.1 Cross-CGIAR Partnerships (CRPs and other Platforms) The most significant cross-CGIAR exchange occurring within the framework of the Genebank Platform concerns the movement of germplasm and associated data: the acquisition of materials from CGIAR breeding programs by genebanks and the health-testing and distribution of germ- plasm from genebanks to research and breeding programs. In 2018, 1,592 samples were acquired from CGIAR breeding programs and 40,173 sam- ples were sent to breeding programs. In addition, many exchanges occurred between genebanks, GHUs and other Platforms or CRPs, some of which are captured in Table 11. Rice accessions sorted by country of origin at IRRI. IRGC 611 is from Indonesia (DOI: 10.18730/1Q2XS). Photo: Shawn Landersz Conservation or distribution of breeders’ and AfricaRice researchers’ materials, e.g., genetic stocks Conservation or distribution of DNA Bioversity Conservation or distribution of microbial materials CIAT Hosting safety duplicates on behalf of partners or co lleagues CIMMYT In-depth advice on genebank operations or establishment CIP In-depth advice on selection or use of germplasm ICARDA Inputs or advice on plant genetic resources policy development or implementation ICRAF Multiplicat ion, cleaning, processing o f materials other than genebank accessions ICRISAT Provision of germplasm data IITA Provision of planting material for specific accessions on a large scale (outside o f normal germplasm distr ibution) ILR I Taxonomy verification IRRI Other services 0 10 20 30 40 50 60 Figure 13. Number of genebank services provided to partners by category in 2018 20 | 2018 CGIAR Genebank Platform Annual Report Table 11. Internal Cross-CGIAR Collaborations Brief description of the collaboration Name of collaborator • Participated in BrAPI hackathon in Paris to develop the compliance of MGIS with BrAPI and link breeding EiB and genebank data. (Bioversity) • Presentation of the banana phenotyping module was presented at the PhenoHarmonis workshop. (Bioversity) • Participation in Expert Advisory Groups for all EiB Modules (multiple Centers) • Coordination with Module 5 to design an enterprise system for data management including BMS, genotypic data management system and genebank documentation systems. (ICARDA) • Adopted GIGWA for genotypic data management and will start uploading genebank accessions data mid 2019. (ICARDA) • Interaction on germplasm genotyping and data analysis (ICRISAT) • Development of genotyping services in cowpea and use of genetic resources in pre-breeding in Module 1 (IITA) • Testing of low-cost low-density SNP chips for identity verification as a quality control tool to guard against labelling errors during regeneration and characterization. The 10 SNP chip is adequate for breeders but not for genebanks. The 24 SNP chip is better but still not sufficiently informative. (IRRI) • Collaborating on B4R (“Breeding for Rice”, the breeders’ workflow management system) to include SMTA processing, DOI assignment, and workflow management. (IRRI) • Selection and development of new forage options, including subjecting 105 Napier grass accessions to Livestock Genotyping-by-Sequencing to demonstrate the variation in the collection and identify unique materials received from EMBRAPA. The diversity analysis has helped determine the suitability of the population for genome-wide association studies (poster presented at the “Global Nutrition Symposium”, Jan. 2018, Ethiopia). (ILRI) • Identification of a “core” subset of 12 accessions that best represents the diversity held in the entire collection for further characterisation and evaluation. (ILRI) • 84 accessions are currently being evaluated in the field for nutritional value, agronomic performance and water use efficiency and 14 accessions, representing the phenotypic and genetic diversity, have been identified for future research on performance under well-watered and water-deficit conditions. (ILRI) • Development and evaluation of FIGS subsets for diseases resistance in barley and use of wild relatives in interspecific crosses. Also 421 accessions of Lathyrus were evaluated for low ODAP content and resistance to Orobanche. Interspecific crosses with grass pea were initiated. (ICARDA) • Promotion of use of genebank collection under FTA projects and the following bilateral projects: Fruit FTA Africa, PATSPO-Ethiopia, ACIAR-Rwanda, Re-greening Africa (Sahel); Tree for Food Security project-Eastern Africa. Generation of evaluation data from FTA projects and other bilateral such as the African Orphan Crop Consortium (AOCC) genome sequencing and FruitAfrica (ICRAF) • Development of FIGS subsets and other sets for evaluation for Fusarium wilt in wild lentil. Selection for GLDC resistance to Ascochyta blight and for mechanization of harvest among chickpea and lentil accessions regenerated in Morocco. (ICARDA) • In collaboration with Grain Quality and Postharvest Unit at AfricaRice, evaluation of the 350 minicore African Rice rice accessions for various grain physicochemical properties. Additional grain physicochemical data will be collected in 2019 before final analyses to detect genes and quantitative trait loci associated with each trait using genome-wide association analysis. (AfricaRice) • The new multi-disciplinary Outcome Theme “Harnessing Genetic Diversity to Accelerate Impact” embeds the Business Plan of the IRRI-Crop Trust LPA. This draws in other expertise on policy, gender, breeding, sustainable systems and economics, with the aim of ensuring a complete integrated pathway to impact from genebank to consumer. All subsets developed by the genebank were designed and used as an integral component of the Rice CRP, Flagship Project 5. The genebank has been able not only to define and manage the subsets, but to participate in their evaluation and subsequent data analysis, in collaborative trials funded mainly by the users. (IRRI) • Development of FIGS subsets for wheat and their evaluation by students, use of wild relatives in pre- Wheat breeding activities, participation in the global wheat breeding training course. (ICARDA) • Extensive definition and description of wheat germplasm subsets was undertaken. To date, more than 80 wheat subsets have been defined using data from more than 120 publications, and from nearly a dozen CIMMYT research programs. (CIMMYT) • Publication citations of more than 1,300 scientific articles describing 4,139 accessions held in the Wheat Germplasm Collection have been uploaded into GRIN Global. (CIMMYT) • Support for open access publication (AfricaRice) Big Data • Data Sprint award for the largest number of datasets with quality metadata for the Bioversity institutional repository (Bioversity) • Storage and curation of genotyping data (ICRISAT) 2018 CGIAR Genebank Platform Annual Report | 21 Brief description of the collaboration Name of collaborator • Research to develop seed cryopreservation and conventional low temperature conservation protocols. RTB Project funded by the Directorate-General for Development Cooperation (DGDC), Belgium to focus on developing and optimizing cryopreservation protocols for plant species that have the potential to be cryopreserved, and training of technicians and researchers mainly from developing countries. Also seed conservation research and collecting of Musa accessions in target regions (Bioversity) • BBTV mitigation and management in Nigeria and screening wild banana progenitors for resistance. (Bioversity) • Within the scope of the DGDC, Belgium, “More fruit for food security: developing climate smart bananas for the Great Lakes region” project, high throughput phenotyping of the Bioversity genebank for drought tolerance identified 32 drought tolerant accessions. (Bioversity) • Descriptors of Banana have been included in the ontology. A variable submission tool has been developed in collaboration with BTI, to easily submit new terms to the Crop Ontology. (Bioversity) • A large historical dataset comprising evaluation data for approximately 70% of CIAT’s cassava collection, obtained across seven agroecological environments in Colombia, was obtained from CIAT’s Cassava Program, curated and standardized for future integration with CIAT’s online database and Genesys. (CIAT) • Collaborative collection missions were designed and executed as part of the Crop Wild Relative Project with INIA-Peru. Eleven collecting missions were made in 2018 with a combined collection for the project of 337 new accessions from 46 taxa according to Hawkes. (CIP) • Collaboration with Cluster D1.4 include mapping of diversity hotspots for yam species in Benin carried out with the University of Abomey-Calavi, which is connected to genotyping work undertaken under the Genebank Platform and the BMGF funded project on improved detection and cleaning of viruses in clonal crops. (IITA) • CGIAR Genetic Resources Policy Working Group (Policy Module) EiB, Big Data, SMO, Science Leaders Group, CLIPNet, CGIAR Centers 2.3 Intellectual assets 2.4 Monitoring, Evaluation, Impact (a) How have intellectual assets been strategically managed Assessment and Learning (MELIA) by the Platform in order to maximize their global accessibility and/or impact in line with the CGIAR Principles on the Man- Evaluations, reviews, and audits are important agement of Intellectual Assets? activities in monitoring the performance of each All CGIAR genebanks have agreements with the genebank. Table 12 summarizes key evaluation ITPGRFA, placing their germplasm collections exercises. under the Multilateral System of Access and Ben- efit Sharing. In 2018, 95% of samples externally Quality management systems (QMS) distributed by the Centers where transferred Documentation audits on standard operating under Standard Material Transfer Agreements procedures (SOPs) for individual genebank oper- (SMTA). ations are under way. In 2018, SOPs for conser- vation, regeneration and characterization were (b) Indicate any published patents and/or plant variety right audited to verify CGIAR genebank compliance applications (or equivalent) associated with intellectual assets with FAO genebank standards, International developed in the Platform and filed by Centers and/or part- Treaty on Plant Genetic Resources for Food and ners involved in the Platform Agriculture (ITPGRFA) policy and International The collections and germplasm contained within Standards for Phytosanitary Measures (ISPMs), them remain publicly available and no patents or as well as other relevant international standards. plant variety protection rights are sought on the In total, 160 findings were made and addressed. germplasm. Additional documentation audits will be per- formed on remaining SOPs in 2019-2020. So far, (c) List any critical issues or challenges encountered in the 156 SOPs have been drafted by genebanks and management of intellectual assets in the context of the Plat- GHUs under the Genebank Platform (Figure 12). form Critical issues and challenges involving the CGIAR genebanks are addressed and reported under the Policy Module. 22 | 2018 CGIAR Genebank Platform Annual Report Table 12. Monitoring, Evaluation, Learning and Impact Assessment (MELIA) Studies/learning Type of exercises planned Status study or Comments for this year activity CGIAR IEA On-going Program An Independent Evaluation Arrangement (IEA) commissioned study on evaluation evaluation the “Evaluation of the CGIAR research support program for Managing and Sustaining Crop Collections: Genebanks CRP” was published in April 2017. The report listed several recommendations with implications to the activities of the Genebank Platform in 2018, particularly the costing reviews and QMS audits. Costing reviews On-going Program A costing review started in late 2017 with a visit to IRRI to collate data evaluation on routine costs for genebank operation. In 2018, reviewers visited CIAT, CIMMYT, CIP and ICARDA to gather new data on operational costs. The results of the analysis will feed into a systematic review of the financial allocations to individual genebanks for essential operations. Document audits On-going Audit Two documentation audits were conducted during 2018. 7 genebanks for Regeneration, participated in the Regeneration and Characterization Audit. 58 findings Characterization, and were found and all were closed by November 2018. 9 genebanks Conservation participated in the Conservation audit. 102 findings were found and all were closed by November 2018. Genebank Impacts Extended Outcome The workplan supported 6 fellows to work on documenting the impact of Fellowship study the CGIAR genebanks. The following research papers are expected to be completed in 2019: • Impact of IRRI genebank on rice productivity on farms in Eastern India • Contribution of CIAT genebank in the development of high-iron bean varieties and farm-level impacts in Rwanda • Role of the CIMMYT and ICARDA genebanks in the development, use, and impact of wheat synthetic hexaploids • Use and impact of ICRAF tree germplasm distributions: Calliandra calothyrsus and Gliricidia sepium in E. Africa • Use and impact of ILRI forage germplasm: Pennisetum purpureum, Sesbania sesban, and Medicago sativa • Assessing the economic impacts of CIP genebank • Impacts of Jala maize rematriation by CIMMYT genebank to farm communities • Use and impact of Musa ITC germplasm in Asia and Africa External technical On-going Program The first meeting of the technical reviewers was held in December 2018 in reviews and evaluation Bonn, Germany. In 2019, review visits are scheduled for five genebanks. validation of quality management systems (QMS) work of defined routine operations. The costing 160 Mapped; 139 reviews will be complemented by expert external 140 technical reviews, which will take place in 2019 120 and 2020. The technical reviews will validate 100 Drafted; 93 Mapped; 100 genebank SOPs, the status of collections, and 80 Drafted; 63 the efficiency of operations. Findings from both 60 financial and technical reviews will be assessed at 40 a system level by a High-Level Panel with the aim 20 Audited; 16 of determining new genebank budgets for 2022. Audited; 0 0 GHUs Genebanks ILRI’s reported zero availability this year does Figure 12. SOPs mapped, drafted and audited in 2018 have a silver lining. The change represents a major alignment between CIAT and ILRI in the 2.5 Efficiency management of tropical and sub-tropical forages collections. Key staff from both institutes met In 2018, a second systemwide costing study of together for the first time in Ethiopia and com- the genebanks was initiated. The previous study pared processes in depth with the facilitation of took place in 2009 and has provided the basis an expert consultant. As a result, 15 recommen- for the individual budgets for the CGIAR gen- dations were formulated and both Centers are ebank’s routine operations under the CRP and working towards strengthened operations, devel- the Platform. Detailed costs and transactions oping more complementary roles, aligning data are reviewed for each genebank within a frame- and data resources and rationalized collections. 2018 CGIAR Genebank Platform Annual Report | 23 Simon Kang’ethe (ICRAF) conducts seed characterization Raja Srinvias and Naga Jyothi from ICRISAT analyzing seed of ‘Annona squamosa’ using the Marvin5 seed analyser. moisture. Photo: Michael Major/Crop Trust Photo: Michael Major/Crop Trust Meanwhile, each genebank continues to address seed health testing (all centers) ongoing recommendations from previous • Increased rate of germplasm health testing reviews, QMS audits and from expert visits (e.g. (CIAT, ICARDA, ICRISAT, IITA) on seed quality management). Under the QMS framework, genebanks submit annual improve- 2.6 Management of Risks to Your ment plans. In total, 158 improvements have Platform been fully or partly addressed in 2018. Notable improvements and gains in efficiency include: Programmatic risks • Reduced seed processing time (e.g. pneumatic The Crop Trust works assiduously to raise funds seed counting trays at CIMMYT, high volume to support both the Genebank Platform and its thresher at IITA, automated seed sorter at IRRI) endowment fund for the long-term support of the • Improved seed monitoring and storage pro- CGIAR genebanks. The investment policies of the cesses for seed longevity (CIP, ICARDA, IITA, Crop Trust permit the annual withdrawal of up to ILRI) 4% of the average market value of the endow- • Improved screenhouses and regeneration tech- ment fund over the previous 12 quarters. In 2018, niques (CIAT, ICARDA, IITA) 2.5% (USD 5 million) was withdrawn from the • Barcoding of laboratory and field operations endowment fund of which 92% was provided to (AfricaRice, CIAT, CIP, ICARDA, IITA, ILRI) the international genebanks of CGIAR. In 2018, • Use of mobile devices and apps to capture the Crop Trust raised more than USD 5 million in data (Bioversity, CIAT, IITA, ILRI) bilateral funds to support the Genebank Platform. • Improved lighting and conditions of in vitro Thanks to contributions from the European Union, conservation to extend subculture period and the Governments of Germany, Switzerland and reduce contamination (CIAT, CIP, CIP/ and Finland, the Crop Trust was able to reach its EMBRAPA, IITA) commitment of USD 9 million to the Genebank • Improved indexing and regeneration success Platform. In 2019, the commitment from the Crop rate through modified facilities or procedures Trust rises to USD 11.5 million, and increases in the field (CIAT beans and forages, CIMMYT ultimately to USD 15 million in 2021, which pres- maize, IITA) ents a very considerable fund-raising challenge • Testing of trueness-to-type and removal of off- to the Crop Trust. While the Genebank Platform types (Bioversity, CIP, IITA) Management Team is putting contingency plans • Improvements in in vitro and cryopreservation in place, a shortfall of more than 4% in funding protocols (CIP, CIAT, IITA) would have grave consequences to the function- • Elimination of duplicate samples or duplicate ing of the genebanks, GHUs and Policy Module. accessions (CIMMYT, CIP, IITA, ILRI) • Improved capacity for phytosanitation and 24 | 2018 CGIAR Genebank Platform Annual Report Contextual risks A number of CGIAR host countries are con- straining the safety duplication of genebank accessions from CGIAR Centers, which poses a major risk to the security of the collections. In two cases, political measures are preventing the distribution of materials that should be available in accordance with those Centers’ ITPGRFA Arti- cle 15 Agreements. The Centers involved are in active discussions with the countries in question. The situation is preventing the genebanks from reaching performance targets and thus securing funding through the Crop Trust endowment. It may become necessary to reconsider longer term funding commitments for, and management of, those collections. Extracting the banana meristem for cryopreservation at Institutional risks Bioversity in Leuven. Photo: Michael Major/Crop Trust Institutional financial management practices con- tinue to constrain the management of genebank budgets and the pursuit of cost efficiencies. Gen- ebank budget holders appear to have access only to limited up-to-date information on expenditures and have only minor inputs into the attribution and reporting of expenditures. Constraining issues arise from general financial management practices, attribution of full-cost recoveries, effec- tiveness of data management tools, procurement practices and the effects of unexpected and last-minute changes in institutional income. Charlotte Lusty (Crop Trust/Genebank Platform Coordinator) presenting on genebank costs. Photo: Michael Major/Crop Trust AfricaRice genebank is now re-established in one location in Côte d’Ivoire. Photo: Neil Palmer/Crop Trust 2018 CGIAR Genebank Platform Annual Report | 25 Wheat regeneration plots at the American University of Beirut’s AREC station near ICARDA’s Terbol station in Lebanon’s Beqaa Valley. Photo: Michael Major/Crop Trust 2.7 Use of W1-2 funding In 2018, 30% of the Genebank Platform cost was funded by the Crop Trust and the rest was funded by W1-2 funding. The Crop Trust funding covers a significant part of the essential operations of nine of the 11 genebanks. The W1-2 funding covers the remaining costs in all 11 genebanks. The W1-2 funding also supports other activities of the Genebank Platform including upgrading of the genebanks and GHUs, and activities of the Conservation, Use and Policy Modules. All of the achievements described in the report have been either fully or partly funded by W1-2 funding. 3. Financial Summary Table 13. Platform financial report for 2018 Planned budget 2018 Actual expenditure 2018 Difference (USD millions) (USD millions) (USD millions) W1-2 W3/ bilateral Total W1-2 W3/ bilateral Total W1-2 W3/ bilateral Total Module 1 16.63 9.06 25.69 16.84 8.98 25.83 (0.21) 0.08 (0.13) Module 2 1.19 0 1.19 1.13 - 1.13 0.05 - 0.05 Module 3 0.81 0 0.81 0.81 - 0.81 - - - Management & Support Costs 0.69 0 0.69 0.69 - 0.69 - - - Genebank Platform costs 1.75 0 1.75 1.70 - 1.70 0.05 - 0.05 Other Commissioned Expenses (0.02) 0 (0.02) - - - (0.02) - (0.02) Platform Total 21.06 9.06 30.12 21.18 8.98 30.16 (0.12) 0.08 (0.05) 26 | 2018 CGIAR Genebank Platform Annual Report Annex 1 Figure 1. External distributions by CGIAR Center genebanks in 2018 2018 CGIAR Genebank Platform Annual Report | 27 Developed Developing 0% 20% 40% 60% 80% 100% Andean roots & tubers banana barley beans cassava chickpea cowpea faba bean forages fruit trees groundnut lentil maize misc. legumes multp. trees pearl millet pigeonpea potato rice small millets sorghum sweet potato wheat yam Figure 2. Distribution by crop to developed and developing countries in 2018 Others Others 6% 2017 4% 2018 Direct use 11% Direct use 16% Education 6% Education Characterization 7% 6% Research Characterization Research 42% 4% 49% Evaluation 20% Evaluation 13% Breeding 9% Breeding 7% Figure 3. Types of request for stated purposes in 2017 and 2018 28 | 2018 CGIAR Genebank Platform Annual Report Table 1. List of policy contributions Name and description of policy, legal instrument, investment or curriculum to Level of Link to CGIAR cross-cutting marker score Link to evidence Maturity sub-IDOs which CGIAR contributed (max. 2) gender youth capdev climate change International Treaty on Plant Genetic 1= Increased 0 – Not 0 – Not 1 – 0 – Not Published Resources for Food and Agriculture Research conser- targeted targeted Significant targeted guidelines, (ITPGRFA) http://www.fao.org/plant-treaty/en/ taken up vation and objective reports, - provided guidance to the CGIAR SMB in its by next use of journal responses to the Governing Body Resolution user genetic articles, 4/2017. (decision resources and maker workshop Nagoya Protocol or inter- reports https://www.cbd.int/abs/ mediary) available - finalized the text of the draft Guidelines on the Nagoya Protocol for CGIAR Research Centers at . CGSpace The guidelines were adopted by the CGIAR SMB in and March 2018. CGIAR Sharepoint Convention on Biological Diversity (CBD) https://www.cbd.int/intro/default.shtml - participated in discussions on access and benefit- sharing issues related to the generation and use of digital sequence information under the CBD. Global Plan of Action (GPA) for Plant Genetic Resources for Food and Agriculture http://www.fao.org/agriculture/crops/ thematic-sitemap/theme/seeds-pgr/gpa/en/ - currently revising the 2009 Guide to the Centers’ use of the SMTA, taking into account intervening developments since 2009. These plans were shared with the genebank managers at the Annual genebank meeting (AGM) 2018 in Brazil. Once the draft revision is completed, it will be submitted for consideration and approval by the Article 15 DGs and the CGIAR SMB. International Plant Protection Convention (IPPC) https://www.ippc.int/en/ - GHUs are working towards developing an accredited system for GHU procedures, termed as “GreenPass Protocol”, which will facilitate the exchange of phytosanitary clean germplasm from CGIAR centers. Implementation of GreenPass will require IPPC accreditation. Table 2. Number of peer-reviewed publications from current reporting period Number Percent Peer-reviewed publications 79 100 Open-access 63 80 ISI 58 73 2018 CGIAR Genebank Platform Annual Report | 29 Table 3. Update on Actions Taken in Response to Relevant Evaluations Status of Concrete actions Recommen- response Name of the Text of recommen- taken for this dation to this By whom When Comments evaluation dation recommen- number recommen- dation dation Evaluation of the CGIAR IEA Revisit the Parity On-going Costing reviews Platform Visits per 2017 – IRRI CGIAR research evaluation Study to establish manage- Center 2018 – CIAT, support program realistic and ment planned in CIMMYT, CIP, for Managing transparent budget 2018-2020 ICARDA and Sustaining for each Center 2019 – ICRISAT, Crop Collections: genebank IITA, ILRI, ICRAF, Genebanks CRP Bioversity 2020 – AfricaRice Promote the On-going Genebank Science Website received Genebank Platform Platform communi- 9,491 users during communications website actively cations 2018 who accounted maintained specialist for 24,884 page and promoted. views. Facebook Facebook and page has more than Flickr pages were 500 followers and launched in mid- monthly reaches 2018 nearly 7,000 people. Flickr page offers 618 images. Two email newsletters were sent out in 2018. External validation On-going Technical reviews External Visits per of QMS reviewers Center planned in 2019-2020 Enhance linkages On-going Minting of DOIs Use module 97% of accessions between genebank Enriching data with DOIs characterization and on collections Genesys has 2,187 breeders’ evaluation through focal subsets published and pedigree data subsets Debre Zeit Research Center of the Ethiopian Institute of Agricultural Research. Photo: Shawn Landersz 30 | 2018 CGIAR Genebank Platform Annual Report qwerty. Photo: Mic2h0a1e8l MCGajAIo f ArricaRice genebank. PhRo tGoe: nNeebial nPka lPmlaetfro/Crmro Apn Tnruaslt Report | 31