Preserving biodiversity for food security in an era of climate change
Plant Accessions
Plant Diversity Lost
New Resources Annually
Renamed to NARO Genebank
Imagine a library where instead of books, the shelves contain the very building blocks of our food supply—seeds, tissues, and genetic material that have sustained human civilization for millennia. This is not science fiction; it's the reality of the NIAS Genebank Project in Japan, a vital scientific institution working to preserve agricultural biodiversity in the face of mounting challenges. With 75% of plant genetic diversity already lost worldwide due to the spread of industrial mono-cropping, such genebanks have become arks of hope against the twin threats of climate change and food insecurity .
What began decades ago as the NIAS Genebank has evolved since 2016 into the NARO Genebank, operating under Japan's National Agriculture and Food Research Organization 2 . This living library doesn't simply store genetic material—it actively studies, characterizes, and distributes these precious resources to scientists and breeders worldwide.
In an era where developing new crop varieties resistant to pests, diseases, and changing climates is increasingly crucial, the work of the NARO Genebank has never been more relevant to our collective future .
The genebank's journey reflects Japan's long-term commitment to agricultural conservation. Originally established as the NIAS Genebank, it was renamed in 2016 following a reorganization, though it continues its pioneering work under the new designation 2 . Located in Tsukuba, Ibaraki, the facility serves as the central coordinating institute for conserving agricultural genetic resources throughout Japan, working in collaboration with a network of sub-banks across the country 2 .
Originally founded as NIAS Genebank to preserve Japan's agricultural heritage
Renamed to NARO Genebank under National Agriculture and Food Research Organization
Central coordinating institute with network of sub-banks across Japan
The scale of the NARO Genebank's collections is staggering. The plant section alone maintains approximately 240,000 registered accessions as of 2024, organized into 12 distinct crop groups 6 . The genebank adds over 5,000 new plant genetic resources to its collection each year, obtained through both domestic and international exploration missions and exchanges with research institutes worldwide 6 .
| Crop Group | Examples | Significance |
|---|---|---|
| Rice | Nipponbare, Wataribune | Foundation of Japanese cuisine and culture |
| Wheat & Barley | Various landraces | Source of unique brewing characteristics |
| Fruit Trees | Japanese native varieties | Adapted to local growing conditions |
| Legumes | Azuki bean, Black gram | Important traditional protein sources |
| Vegetables | Japanese heirlooms | Unique flavors and nutritional profiles |
| Ornamental Plants | Native flowers and trees | Cultural and ecological value |
Different types of genetic material require different conservation strategies. While seeds of many crops can be preserved through low-temperature and low-moisture storage, some plants produce recalcitrant seeds that cannot withstand drying, and others are propagated vegetatively because their seeds don't remain true to type . The NARO Genebank employs multiple conservation techniques to address this diversity:
Orthodox seeds preserved in controlled low-temperature, low-moisture environment for long-term conservation 6 .
Living plants maintained in field collections for crops that cannot be seed-preserved .
Plant tissues maintained in sterile culture collections for medium-term storage .
Materials stored frozen in liquid nitrogen at ultra-low temperatures for secure long-term conservation .
What transforms a collection of seeds into a powerful scientific resource? The answer lies in the sophisticated database systems developed by the NIAS Genebank. These systems don't merely track what's in the collection—they unlock the potential within each sample by connecting genetic information with practical applications 3 .
The original NIAS Genebank database, known as NIASGBdb, consists of three integrated components: a genetic resources database, a plant diseases database, and a web retrieval database that links them together 3 4 .
The genebank employs an ANSI/SPARC three-level schema architecture, which separates the internal data storage structure from the external applications that researchers use to access information 3 .
One of the genebank's most innovative concepts is the development of NIAS Core Collections—carefully selected sets of accessions that represent the genetic diversity of entire crop species with minimum repetition 3 . These condensed collections make practical research on genetic diversity feasible by providing scientists with manageable numbers of samples that still capture the essential variation within a species.
| Core Collection | Number of Accessions | Genetic Coverage | Research Applications |
|---|---|---|---|
| Global Rice Core | 69 accessions | 90% of RFLP alleles from ~30,000 accessions | Breeding, allele screening |
| Japanese Rice Landraces | 50 accessions | 95% of SSR alleles from ~2,000 accessions | Crop evolution studies |
| Japanese Maize Landraces | 86 accessions | Selected from 1,300 accessions using AFLP data | Linkage disequilibrium studies |
The rice core collections have been particularly impactful. The global collection condenses approximately 30,000 accessions down to just 69 that contain 90% of the RFLP alleles detected in the broader collection, while the Japanese landraces collection represents 95% of the SSR alleles found in about 2,000 accessions with just 50 carefully chosen samples 3 .
Rice has been a central focus of the NIAS Genebank's research efforts, reflecting its cultural, nutritional, and economic importance in Japan and across Asia. The completion of the high-quality map-based genome sequence of rice in 2004 through the International Rice Genome Sequencing Project (IRGSP) marked a turning point in rice research 5 .
Japanese scientists made significant contributions to this international effort, sequencing more than half of the entire genome across six chromosomes 5 . The Rice Annotation Project Database (RAP-DB) was developed to provide comprehensive information on the rice genome, including functional annotation for gene models 5 .
Completion of high-quality rice genome sequence
Launch of Rice Annotation Project Database (RAP-DB)
Functional genomics and gene discovery research
One compelling application of genebank resources involves addressing the devastating problem of rice blast disease, caused by fungal infection and one of the most destructive diseases in Japanese rice production 5 .
Researchers identified a gene called pi21 in the cultivar 'Okabo' that controls strong resistance to rice blast. However, there was a significant challenge: introducing this gene into commercial cultivars also resulted in poor eating quality.
Using genome information from genebank resources, scientists clarified the positional relationship between the pi21 gene and genes affecting eating quality on the chromosome 5 . This precise understanding enabled them to develop a rice strain with both strong blast resistance and good eating quality.
Another notable success story comes from research on root systems. Japanese scientists successfully isolated a gene called DRO1 that controls deep rooting in rice 5 . When this gene was introduced into shallow-rooting rice cultivars, the resulting plants developed extensive root systems that penetrated deeply into the soil.
The implications of this discovery are particularly relevant in the context of climate change. The DRO1 gene offers potential for developing rice cultivars with stronger resistance against drought stress, especially valuable in many Asian and African countries frequently affected by severe dry seasons 5 .
This example illustrates how traits preserved in genetic resources can provide solutions to emerging agricultural challenges.
The NARO Genebank provides researchers with a comprehensive toolkit for agricultural innovation. These resources transform genetic diversity from a concept into practical research materials that drive scientific discovery and crop improvement.
| Resource Type | Examples | Research Applications |
|---|---|---|
| Core Collections | Rice, Maize, Legumes | Genetic diversity studies, breeding programs |
| Molecular Markers | SSR markers for azuki bean, black gram | Genetic mapping, trait association studies |
| Genomic Resources | cDNA clones, BAC/PAC libraries | Gene discovery, functional analysis |
| Microorganism Strains | Fusarium strains with sequence data | Plant-pathogen interaction studies |
| Information Tools | Plant diseases database, evaluation data queries | Research planning, resource selection |
Researchers worldwide can access the genebank's resources through sophisticated online search systems. The plant search system allows queries based on passport data such as cultivar, origin, and JP number (the unique accession numbers assigned to plant genetic resources) 3 .
For more advanced investigations, the evaluation data query system enables searching based on specific characteristics 3 . Particularly innovative is the system's ability to display distribution patterns of evaluation data as circular or bar graphs, helping users understand the diversity within the collection.
A unique feature of the genebank's database system is the integration of plant disease information with genetic resources 3 . Based on the listing of common names of plant diseases compiled by the Phytopathological Society of Japan, this database links disease information with relevant plant and microorganism genetic resources 3 .
This integration creates a powerful research pathway: scientists studying a particular plant disease can quickly identify both host plants and pathogen strains available for their work, significantly accelerating the research process.
While seed banking works well for many crops, significant challenges remain for species with recalcitrant seeds that cannot tolerate drying or freezing, such as cacao, coffee, and avocado . Similarly, crops that don't produce seeds at all (like edible bananas) or that are clonally propagated to maintain specific gene combinations (including potatoes and many fruit trees) require alternative approaches .
Cryopreservation—storing biological materials at ultra-low temperatures in liquid nitrogen (-196°C)—represents the most promising long-term solution for many challenging species . At these temperatures, all metabolic activity effectively stops, allowing theoretically indefinite storage.
The ultimate goal of genetic conservation is not merely storage but utilization. The genebank is increasingly focused on enhancing the bridge between conserved resources and practical applications. This involves not only distributing materials to researchers but also providing comprehensive data that helps identify the most promising resources for specific breeding or research objectives.
Recent enhancements to the genebank's database systems reflect this orientation toward utilization. The addition of plant genome data and improvements to the microorganism search system demonstrate a commitment to providing researchers with the most actionable information possible 1 .
The NARO Genebank operates within a global network of genetic resource conservation, recognizing that food security and agricultural sustainability are universal concerns that transcend national borders 2 . The institution actively participates in collaborative activities with overseas research institutes, following international community norms and national regulations in all its conservation activities 2 .
This global perspective is essential in an era of climate change, population growth, and evolving agricultural challenges. By contributing to international efforts to conserve and utilize agricultural genetic diversity, the NARO Genebank helps ensure that the genetic building blocks needed to adapt our food systems will be available to researchers and breeders worldwide.
The NARO Genebank represents far more than a storage facility for seeds and tissues; it is a dynamic scientific institution dedicated to preserving biological diversity and transforming it into solutions for pressing agricultural challenges. From its comprehensive collections encompassing hundreds of thousands of accessions to its sophisticated database systems that make this diversity accessible to researchers worldwide, the genebank serves as a crucial link between our agricultural heritage and our food future.
As environmental pressures intensify and the global population continues to grow, the work of institutions like the NARO Genebank becomes increasingly vital. The genetic diversity conserved within its collections may hold the key to developing crops resistant to emerging pests, varieties capable of withstanding drought or extreme temperatures, or plants with enhanced nutritional profiles to address malnutrition.
The genebank's ongoing efforts to enhance its conservation methods, expand its collections, improve its information systems, and strengthen its collaborations ensure that this living library will continue to serve as an indispensable resource for building a more secure, sustainable, and resilient global food system.