CGIAR Initiative on Genebanks

Permanent URI for this collectionhttps://hdl.handle.net/10568/117886

Part of the CGIAR Action Area on Genetic Innovation

Primary CGIAR impact area: Environmental health and biodiversity

https://www.cgiar.org/initiative/03-conservation-and-use-of-genetic-resources-genebanks

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Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.)
(Journal Article, 2024-06-13) Vetriventhan, Mani; Upadhyaya, Hari D.; Deshpande, Santosh; Johnson, Matthew S.; Wallace, Jason G.; Victor, Allan; Naresh, D.; Rayaprolu, Laavanya; Singh, Kuldeep; Mayes, Sean
Proso millet is an important but under-researched and underutilized crop with the potential to become a future smart crop because of its climate-resilient features and high nutrient content. Assessing diversity and marker-trait associations are essential to support the genomics-assisted improvement of proso millet. This study aimed to assess the population structure and diversity of a proso millet diversity panel and identify marker-trait associations for agronomic and grain nutrient traits. In this study, genome-wide single nucleotide polymorphisms (SNPs) were identified by mapping raw genotyping-by-sequencing (GBS) data onto the proso millet genome, resulting in 5621 quality-filtered SNPs in 160 diverse accessions. The modified Roger's Distance assessment indicated an average distance of 0.268 among accessions, with the race miliaceum exhibiting the highest diversity and ovatum the lowest. Proso millet germplasm diversity was structured according to geographic centers of origin and domestication. Genome-wide association mapping identified 40 marker-trait associations (MTAs), including 34 MTAs for agronomic traits and 6 for grain nutrients; 20 of these MTAs were located within genes. Favourable alleles and phenotypic values were estimated for all MTAs. This study provides valuable insights into the population structure and diversity of proso millet, identified marker-trait associations, and reported favourable alleles and their phenotypic values for supporting genomics-assisted improvement efforts in proso millet.
The importance of genotyping within the climate-smart plant breeding value chain – integrative tools for genetic enhancement programs
(Journal Article, 2025-02-06) Garcia-Oliveira, Ana Luisa; Ortiz, Rodomiro; Sarsu, Fatma; Rasmussen, Søren K.; Agre, Paterne; Asfaw, Asrat; Kante, Moctar; Chander, Subhash
The challenges faced by today’s agronomists, plant breeders, and their managers encompass adapting sustainably to climate variability while working with limited budgets. Besides, managers are dealing with a multitude of issues with different organizations working on similar initiatives and projects, leading to a lack of a sustainable impact on smallholder farmers. To transform the current food systems as a more sustainable and resilient model efficient solutions are needed to deliver and convey results. Challenges such as logistics, labour, infrastructure, and equity, must be addressed alongside adapting to increasingly unstable climate conditions which affect the life cycle of transboundary pathogens and pests. In this context, transforming food systems go far beyond just farmers and plant breeders and it requires substantial contributions from industry, global finances, transportation, energy, education, and country developmental sectors including legislators. As a result, a holistic approach is essential for achieving sustainable and resilient food systems to sustain a global population anticipated to reach 9.7 billion by 2050 and 11.2 billion by 2100. As of 2021, nearly 193 million individuals were affected by food insecurity, 40 million more than in 2020. Meanwhile, the digital world is rapidly advancing with the digital economy estimated at about 20% of the global gross domestic product, suggesting that digital technologies are increasingly accessible even in areas affected by food insecurity. Leveraging these technologies can facilitate the development of climate-smart cultivars that adapt effectively to climate variation, meet consumer preferences, and address human and livestock nutritional needs. Most economically important traits in crops are controlled by multiple loci often with recessive alleles. Considering particularly Africa, this continent has several agro-climatic zones, hence crops need to be adapted to these. Therefore, targeting specific loci using modern tools offers a precise and efficient approach. This review article aims to address how these new technologies can provide a better support to smallholder farmers.
CGIAR Report to the Twentieth Regular Session of the Commission on Genetic Resources for Food and Agriculture
(Report, 2025-02-03) CGIAR
This report was prepared by CGIAR in response to an invitation from the Secretariat of the FAO Commission on Genetic Resources for Food and Agriculture. It is structured to correspond, in general, to agenda items 2-10 of the Twentieth Regular Session of the Commission on Genetic Resources for Food and Agriculture (CGRFA-20). Some sections of this report were previously included in the CGIAR submission to the Twelfth Session of the Intergovernmental Technical Working Group on Plant Genetic Resources (ITWG-PGRFA-12), in December 2024.
Stacking beneficial haplotypes from the Vavilov wheat collection to accelerate breeding for multiple disease resistance
(Journal Article, 2024) Jingyang Tong; Tarekegn, Zerihun T.; Jambuthenne, Dilani; Alahmad, Samir; Periyannan, Sambasivam; Lee T. Hickey; Dinglasan, Eric; Hayes, Ben
Wheat production is threatened by numerous fungal diseases, but the potential to breed for multiple disease resistance (MDR) mechanisms is yet to be explored. Here, significant global genetic correlations and underlying local genomic regions were identified in the Vavilov wheat diversity panel for six major fungal diseases, including biotrophic leaf rust (LR), yellow rust (YR), stem rust (SR), hemibiotrophic crown rot (CR), and necrotrophic tan spot (TS) and Septoria nodorum blotch (SNB). By adopting haplotype-based local genomic estimated breeding values, derived from an integrated set of 34,899 SNP and DArT markers, we established a novel haplotype catalogue for resistance to the six diseases in over 20 field experiments across Australia and Ethiopia. Haploblocks with high variances of haplotype effects in all environments were identified for three rusts, and pleiotropic haploblocks were identified for at least two diseases, with four haploblocks affecting all six diseases. Through simulation, we demonstrated that stacking optimal haplotypes for one disease could improve resistance substantially, but indirectly affected resistance for other five diseases, which varied depending on the genetic correlation with the non-target disease trait. On the other hand, our simulation results combining beneficial haplotypes for all diseases increased resistance to LR, YR, SR, CR, TS, and SNB, by up to 48.1%, 35.2%, 29.1%, 12.8%, 18.8%, and 32.8%, respectively. Overall, our results highlight the genetic potential to improve MDR in wheat. The haploblock-based catalogue with novel forms of resistance provides a useful resource to guide desirable haplotype stacking for breeding future wheat cultivars with MDR.
Realizing the potential of plant genetic resources: the use of phenomics for genebanks
(Journal Article, 2025-01-01) Ghamkhar, Kioumars; Hay, Fiona; Engbers, Marleen; Dempewolf, Hannes; Schurr, Ulrich
Societal Impact Statement Genebanks contribute to global food security, directly influencing societal well-being, by providing access to seed or genetic material that is more resilient to pests, diseases, and environmental stresses. The ability to develop crops adapted to changing environmental conditions and with high nutritional value means societies can better cope with the adverse effects of climate change, safeguarding food production and rural livelihoods. Enhancing sustainable crop traits, such as improved water-use efficiency and nutrient utilization, supports the transition toward more sustainable agricultural practices. New technologically advanced phenotyping tools are required to optimally realize the potential of these genetic resources, to identify plant genetic resources that will best enable us to address current global challenges. Summary Plant genebanks have a crucial role as specialized repositories, preserving diverse plant genetic resources and providing essential access to researchers, breeders, and farmers for developing resilient crops. With over 7 million global accessions, these genebanks significantly contribute to global food security, climate change mitigation, and sustainable agriculture. This opinion paper, inspired by an international workshop in 2022 in Wageningen (Netherlands), focuses on the transformative impact of phenomics technology within genebanks, offering a view on its potential applications and implications for preserving and utilizing plant genetic resources. Discussions from the 2022 workshop organized by the International Plant Phenotyping Network are integrated, emphasizing the potential of phenomics for global collaboration without requiring major policy developments. The workshop prioritized traits like disease resistance and drought tolerance, highlighting roots as a critical organ for phenotyping. Participants expressed a keen interest in global collaboration, emphasizing the need for partnerships between genebanks and advanced phenotyping facilities. The workshop's outcomes underscore the transformative impact of phenomics on genebanks, promoting innovation, collaboration, and sustainable agricultural practices. These results will guide future pilot studies, marking a significant step toward integrating phenomics into genebank practices and ensuring the continued prosperity of plant genetic heritage.
Unravelling genomic drivers of speciation in musa through genome assemblies of wild banana ancestors
(Journal Article, 2025-01-23) Martin, Guillaume; Istace, Benjamin; Baurens, Franc-Christophe; Belser, Caroline; Hervouet, Catherine; Labadie, Karine; Cruaud, Corinne; Noel, Benjamin; Guiougou, Chantal; Salmon, Frederic; Mahadeo, Joël; Ahmad, Fajarudin; Volkaert, Hugo A.; Droc, Gaëtan; Rouard, Mathieu; Sardos, Julie; Wincker, Patrick; Yahiaoui, Nabila; Aury, Jean-Marc; D’Hont, Angélique
Hybridization between wild Musa species and subspecies from Southeast Asia is at the origin of cultivated bananas. The genomes of these cultivars are complex mosaics involving nine genetic groups, including two previously unknown contributors. This study provides continuous genome assemblies for six wild genetic groups, one of which represents one of the unknown ancestor, identified as M. acuminata ssp. halabanensis . The second unknown ancestor partially present in a seventh assembly appears related to M. a . ssp. zebrina . These assemblies provide key resources for banana genetics and for improving cultivar assemblies, including that of the emblematic triploid Cavendish. Comparative and phylogenetic analyses reveal an ongoing speciation process within Musa , characterised by large chromosome rearrangements and centromere differentiation through the integration of different types of repeated sequences, including rDNA tandem repeats. This speciation process may have been favoured by reproductive isolation related to the particular context of climate and land connectivity fluctuations in the Southeast Asian region.
Standard Operating Proceedure: Regeneration and characterization of bean genetic resources - CIAT Genebank
(Manual, 2019) Gereda, Javier Mauricio; Sabogal Carvajal, Ramiro; Debouck, Daniel; Wenzl, Peter
Effects of covering structures and gibberellic acid in promoting seed germination of Urochloa
(Journal Article, 2025-01-17) Salazar, Daniel E.; Santos-M, Luis Guillermo; Guzzon, Filippo; Wenzl, Peter
Forage grass species of the genus Urochloa play a crucial role in tropical and subtropical ecosystems, particularly in Latin America, where they are important for livestock production due to their adaptability and productivity. Despite their economic importance, there are no definitive conclusions about dormancy-breaking methods in this genus. This study examined 34 seed lots of U. brizantha, U. ruziziensis, U. decumbens, and U. humidicola, conserved at the International Center for Tropical Agriculture (CIAT) genebank for different periods (from one to 22 years in storage). Seeds of all four species showed high viability for up to 21–22 years of long-term storage, estimated by tetrazolium tests. Additionally, removal of seed covering structures significantly promoted final germination, highlighting the efficacy of this simple method to break seed dormancy in U. brizantha, U. ruziziensis, and U. decumbens, with germination results not statistically different from tetrazolium tests for these three species. However, this method was less efficient in achieving high germination percentages for seeds of U. humidicola, and further research is needed to identify efficient dormancy breaking methods for this species. Finally, this study found that gibberellic acid treatments did not promote seed germination in any of the four evaluated species.
Procedimientos para el manejo de la calidad fitosanitaria en las colecciones internacionales de germoplasma
(Poster, 2024-11-13) Cuervo, Maritza; Ramirez, Julio Cesar; Niño Jimenez, Diana Patricia; Gutierrez, Alejandro; Gonzalez, Laura; Muñoz, Christian
Los bancos de germoplasma desempeñan un papel clave en la conservación, la disponibilidad y el uso de la diversidad fitogenética para la mejora de los cultivos agrícolas para la seguridad alimentaria y nutricional; asegurando la disponibilidad de los recursos genéticos para el presente y las futuras generaciones. Los 11 bancos de germoplasma del CGIAR (Grupo Consultivo sobre Investigación Agrícola Internacional) conservan más de 760.000 accesiones de cereales, leguminosas forrajeras, especies arbóreas, cultivos de raíces y tubérculos y plátanos, representadas en 35 colecciones alrededor el mundo, conservadas en forma de: semilla, material in vitro y plantas vivas en campo o invernadero. En los últimos 10 años se han distribuido más de 864.000 accesiones a 160 países. Este movimiento global de germoplasma se debe realizar con total responsabilidad y sin correr el riesgo de diseminar enfermedades y plagas de importancia cuarentenaria. Para este fin, se han establecido en los centros internacionales, Unidades de Sanidad de Germoplasma (GHU) las cuales dentro de sus objetivos está el evitar la propagación de plagas cuarentenarias en la transferencia de germoplasma, prevenir brotes de plagas, salvaguardar la biodiversidad y fortalecer el desarrollo de las capacidades fitosanitarias. Las GHU realizan de forma rutinaria la evaluación de aproximadamente 340 plagas que son endémicas en los sitios de producción en África, Asia, Europa y Latinoamérica, incluidas bacterias, hongos, insectos, nematodos, oomicetos, fitoplasmas, virus y viroides. Estas evaluaciones de realizan mediante metodologías biológicas, morfológicas, taxonómicas, serológicas, bioquímicas y moleculares.
Advances in sorghum improvement for climate resilience in the global arid and semi-arid tropics: A Review
(Journal Article, 2024-12) Mwamahonje, Andekelile; Mdindikasi, Zamu; Mchau, Devotha; Mwenda. Emmanuel; Sanga, Daines; Garcia Oliveira, Ana Luísa; Ojiewo, Chris O.
Sorghum is a climate-resilient crop which has been cultivated as a staple food in the semi-arid areas of Africa and Asia for food and nutrition security. However, the current climate change is increasingly affecting sorghum performance, especially at the flowering stage when water availability is critical for grain filling, thus lowering the sorghum grain yield. The development of climate-resilient, biotic and abiotic stress-tolerant, market-preferred, and nutrient-dense sorghum varieties offers a potentially cost-effective and environmentally sustainable strategy for adapting to climate change. Some of the common technologies for sorghum improvement include mass selection, single seed descent, pure line selection, and marker-assisted selection, facilitated by backcrossing and genotyping using molecular markers. In addition, recent advancements including new machine learning algorithms, gene editing, genomic selection, rapid generation advancement, and recycling of elite material, along with high-throughput phenotyping tools such as drone- and satellite-based images and other speed-breeding techniques, have increased the precision, speed, and accuracy of new crop variety development. In addition to these modern breeding tools and technologies, enhancing genetic diversity to incorporate various climate resilience traits, including against heat and drought stress, into the current sorghum breeding pools is critical. This review covers the potential of sorghum as a staple food crop, explores the genetic diversity of sorghum, discusses the challenges facing sorghum breeding, highlights the recent advancements in technologies for sorghum breeding, and addresses the perceptions of farmers on sorghum production under the current climate change conditions.
Aplicación de la tecnología de secuenciación Oxford Nanopore Technologies para la confirmación de materiales de referencia bacterianos
(Poster, 2024-11-13) Niño Jimenez, Diana Patricia; Gonzalez, Laura Juliana; Gutierrez, Alejandro; Muñoz, Christian; Ramirez, Julio Cesar; Cuervo, Maritza
El banco de germoplasma de la Alianza Bioversity International y CIAT, conserva tres colecciones de importancia económica: frijol, forrajes tropicales y yuca. El banco conserva y distribuye el germoplasma, asegurando su calidad fitosanitaria con las pruebas de diagnóstico realizadas por la Unidad de Sanidad de Germoplasma (GHU), para detección de patógenos cuarentenarios como hongos, virus, bacterias y fitoplasmas. Los procesos de indexación son realizados siguiendo protocolos de diagnóstico previamente estandarizados y validados. En el caso específico de bacterias, el GHU cuenta con un conjunto de controles positivos (ácidos nucleicos y cepas) para diagnóstico que provienen de aislados propios y material de intercambio con laboratorios asociados. Corroborar la idoneidad de los controles positivos empleados en las pruebas moleculares es fundamental para confirmar la especificidad del diagnóstico. Por esta razón, se identificaron a nivel molecular aplicando la tecnología de secuenciación de Oxford Nanopore Technologies (ONT) para la obtención del genoma completo. Posteriormente se realizó el análisis bioinformático para el ensamblaje y anotación de las secuencias obtenidas. Para la identificación del género de las bacterias fitopatógenas, como referencia se utilizaron las secuencias del gen 16S rRNA desde las bases de datos del NCBI (National Center for Biotechnology Information). La secuenciación con ONT permitió la identificación molecular y, por lo tanto, la confirmación de las cepas conservadas por el GHU, mostrando cepas de especies pertenecientes a géneros tales como Xanthomonas, Curtobacterium, Burkholderia y Acidovorax, los cuales serán aplicados como controles internos para el diagnóstico de rutina aplicando metodologías moleculares como PCR o qPCR, además de contribuir este resultado con los requisitos de la norma en la documentación del material de referencia. Palabras clave: Indexación, material de referencia, ONT, PCR, qPCR.
More fruit diversity for food security
(Website, 2024) Sekandi, Eddie; Machida, Lewis; Carpentier, Sebastien
The overarching goal of the project is (i) to foster food and nutrient security especially in view of climate change, and (ii) to mitigate biodiversity loss and conserve the local diversity by filling the gaps in the local gene bank and the ITC collection in Leuven.
More fruit diversity for fod security
(Poster, 2024-07-26) Carpentier, Sebastien; Machida, Lewis; Tazuba, Anthony Fredrick; Van Gils, Daan
Banana (Matooke) is a staple crop in Uganda and the east and central African region (Tanzania, Rwanda, Burundi, Kenya, and Democratic Republic of Congo). Climate change is expected to increase the growing area of bananas in general but for Matooke this is expected to decrease due to the increased evaporative demand. To avert climate change and drought-induced food shortages and hunger in the Matooke growing areas, mapping the current banana diversity in function of the environment is, therefore, urgently needed to give matooke farmers more cultivar options for improved on farm diversity and resilience to climate change. More than 1600 germplasm accessions kept at the International Transit Centre are currently available for this mapping exercise. Strengthening of collaboration with partners is currently going on, with NARO, TARI and IITA endorsing the need for the mapping exercise for the benefit of breeding programs. A proof of principle of diversity funded by the Belgian Development Cooperation has been delivered but we need more resources to scale up jointly with NARO, TARI and IITA for the benefit of farmers in different agro-eco zones of the East African Great Lakes region
Application of Genomics in Supporting Efficient Conservation and Utilization of Plant Genetic Resources
(Book Chapter, 2024-05-29) Wambugu, P.W.; Ndjiondjop, M.N.; Rangan, P.; Henry, R. J.
Many gene banks have adopted various genomic tools and have integrated them into their routine genebank operations. In this chapter, we review the actual and potential applications of genomics in advancing seed bank-based ex situ conservation and utilization of plant genetic resources. Genomic tools are supporting germplasm acquisition efforts through conservation gap analysis and enabling the identification of rare, threatened, and novel genetic resources that need to be prioritized for conservation. Analysis of germplasm from different environments using transcriptomic approaches assists in identifying the candidate genes associated with desirable traits and biologically important pathways. Identification of genetic redundancy is enabling collection rationalization thus enhancing cost efficiency in plant genetic resources conservation. Genomics is providing greater capacity on developing core collections and trait-specific subsets thus promoting utilization of plant genetic resource collections. Emerging genomic technologies are providing capacity to support in situ conservation and biodiversity restoration using ex situ conserved diversity. Analysis of genome environment associations is enabling the identification of germplasm that potentially possesses the necessary adaptive capacity and desired traits. The lack of a standardized approach on documenting and sharing big genomic data being generated from ex situ collections however remains a major challenge in enhancing genomics-assisted conservation.
Genetic variation and population structure of the rice accessions maintained in the AfricaRice genebank using DArTseq
(Journal Article, 2025-02-01) Gouda, A.C.; Sangare, J.R.; Gnikoua, K.; Wambugu, P.; Huggins, T.D.; Ndjiondjop, Marie-Noelle
Utilizing the full potential of rice collections mainly depends on an in-depth exploration and understanding of the vast diversity in its germplasm. The AfricaRice genebank holds the largest collection of rice germplasm originating from the African continent. In the present study, we comprehensively characterized a collection of 9013 accessions, including Oryza barthii A. Chev., Oryza glaberrima Steud., Oryza longistaminata A. Chev. & Roehr., Oryza sativa L. ssp. indica, and Oryza sativa L. ssp. japonica, for genetic diversity and population structure using genotyping-by-sequencing through DArTseq analysis. We identified 27,718 high-quality single nucleotide polymorphism markers after the genotypic data were filtered. Based on the analyses, the collection has extensive genetic diversity, and the average genetic distance of the entire set was 0.267 (range 0.001–0.469), with 45.1% of pairs of accessions being highly distant and 40.1% moderately distant from each other. Neighbor-joining tree, principal component, and Bayesian population structure analyses clustered the 9013 accessions into six groups, based roughly on their taxonomic and biological status. The first, second, and third groups consisted of accessions belonging to O. glaberrima, O. barthii, and O. longistaminata, respectively. The fourth, fifth, and sixth groups were improved-indica, japonica, and traditional-indica accessions, respectively. The highest value of genetic variance proportion (PhiPT) was found in the species group followed by groups based on cluster analysis and on Bayesian population structure at K = 6. These results allow us to better understand the genetic diversity present in 9013 rice accessions maintained in the AfricaRice genebank and offer a valuable tool for pre breeding, breeding, and further genetic applications.
Mecaxochitl: lo fuerte, lo dulce, y la bandera
(Presentation, 2024-10-26) Debouck, Daniel
Breaking dormancy in Macroptillium and Clitoria species for routine viability monitoring of genebank collections
(Report, 2024-12-15) Olbana, Tamiru; Muchugi, Alice; Hay, F.R.; Negawo, Alemayehu T.; Jones, Christopher S.
Comparative seed longevity study to customize monitoring intervals for seed viability test in Megathyrsus maximus
(Report, 2024-12-15) Olbana, Tamiru; Negawo, Alemayehu T.; Muchugi, Alice; Hay, F.R.; Jones, Christopher S.
Forage productivity of buffel grass (Cenchrus ciliaris) accessions grown in different environments in Ethiopia
(Report, 2024-11-30) Habte, Ermias; Negawo, Alemayehu T.; Muchugi, Alice; Jones, Christopher S.
CBD COP16's decision re digital sequence information & benefit-sharing: A primer for CGIAR scientists
(Video, 2024-12-04) Halewood, Michael; Chiarolla, Claudio; Lopez Noriega, Isabel; Rouard, Mathieu
After years of negotiations, in the early hours of November 2, 2024, the 16th Conference of Parties to the Convention on Biological Diversity (CBD COP 16) adopted a decision to make the so-called ‘multilateral mechanism for benefit-sharing from DSI’ a reality. The decision sets out formulae for payments to the newly established ‘Cali fund’ for benefit sharing, and for disbursements from that fund. It also addresses the management of databases that make DSI publicly available. This webinar for CGIAR staff unpacked the COP decision, and considered its relevance to CGIAR. The webinar was led by CGIAR Genebank Initiative scientists who were engaged in the negotiations.

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