Masaru Takeya

NIASGBdb: NIAS Genebank databases for genetic resources and plant disease information

The National Institute of Agrobiological Sciences (NIAS) is implementing the NIAS Genebank Project for conservation and promotion of agrobiological genetic resources to contribute to the development and utilization of agriculture and agricultural products. The project’s databases (NIASGBdb; http://www.gene.affrc.go.jp/databases_en.php) consist of a genetic resource database and a plant diseases database, linked by a web retrieval database. The genetic resources database has plant and microorganism search systems to provide information on research materials, including passport and evaluation data for genetic resources with the desired properties. To facilitate genetic diversity research, several NIAS Core Collections have been developed. The NIAS Rice (Oryza sativa) Core Collection of Japanese Landraces contains information on simple sequence repeat (SSR) polymorphisms. SSR marker information for azuki bean (Vigna angularis) and black gram (V. mungo) and DNA sequence data from some selected Japanese strains of the genus Fusarium are also available. A database of plant diseases in Japan has been developed based on the listing of common names of plant diseases compiled by the Phytopathological Society of Japan. Relevant plant and microorganism genetic resources are associated with the plant disease names by the web retrieval database and can be obtained from the NIAS Genebank for research or educational purposes.

Principal components analysis - K-means transposon element based foxtail millet core collection selection method

BackgroundCore collections are important tools in genetic resources research and administration. At present, most core collection selection criteria are based on one of the following item characteristics: passport data, genetic markers, or morphological traits, which may lead to inadequate representations of variability in the complete collection. The development of a comprehensive methodology that includes as much element data as possible has been explored poorly. Using a collection of (Setaria italica sbsp. italica (L.) P. Beauv.) as a model, we developed a method for core collection construction based on genotype data and numerical representations of agromorphological traits, thereby improving the selection process.ResultsPrincipal component analysis allows the selection of the most informative discriminators among the various elements evaluated, regardless of whether they are genetic or morphological, thereby providing an adequate criterion for further K-mean clustering. Overall, the core collections of S. italica constructed using only genotype data demonstrated overall better validation scores than other core collections that we generated. However, core collection based on both genotype and agromorphological characteristics represented the overall diversity adequately.ConclusionsThe inclusion of both genotype and agromorphological characteristics as a comprehensive dataset in this methodology ensures that agricultural traits are considered in the core collection construction. This approach will be beneficial for genetic resources management and research activities for S. italica as well as other genetic resources.

Genebank data-management software incorporating seed-viability test results

The National Institute of Agrobiological Sciences’ (NIAS) Genebank is the coordinating institute in Japan for the conservation of plant, microorganism and animal genetic resources related to food and agriculture. The NIAS Genebank manages this activity in collaboration with subbanks located across Japan and acts as the central bank. It is important for genebanks to maintain the viability of genetic resources during conservation. Generally, seeds are stored at low temperature and low humidity. Germination percentage is used to monitor seed viability. We have developed data-management software to manage germination testing data in the NIAS Genebank. The software can monitor the pattern of the loss of seed viability of each accession and also support the selection of accessions that need regeneration of seeds. Web-based plant accessions search software displays the latest data on the availability and germination percentages of accessions.

Collecting the Wild Relatives of Crops in the Tropics

There remains much that is not known about wild relatives of major crops. Hence the need for further collecting and study of these wild genetic resources is warranted. In recent years international and legal aspects of collecting and using germplasm have changed and need to be considered carefully in the preparatory phase of collecting. In addition, improved ability of collectors to document, map and sample plant populations (i.e. taking DNA samples) has added new dimensions to collecting. A wealth of information on the wild relatives of crops can be found from web-based databases that can help guide in planning collecting missions. To the extent possible collectors of plant germplasm need to promote the characterization and evaluation of collected materials.

Systems for making NIAS Core Collections, single-seed-derived germplasm, and plant photo images available to the research community

The National Institute of Agrobiological Sciences (NIAS) Genebank coordinates the conservation of plant, microorganism, and animal genetic resources related to food and agriculture in Japan. It also coordinates the distribution of genetic resources in the public domain for research, breeding, and educational purposes. To operate the NIAS Genebank efficiently, we have developed a genetic resources database, data management software, and web-based data retrieval systems to make the data available worldwide. This article describes the NIAS Genebank’s Core Collections of global and Japanese soybean (Glycine max (L.) Merr.), Japanese azuki bean (Vigna angularis (Willd.) Ohwi et Ohashi), and Japanese wheat (Triticum aestivum L. s. l.), all of which are available through the Genebank website. This article also describes new features of the NIAS Genebank database, such as the ability to select single-seed-derived germplasm of soybean in the plant search system and to download photographic data on accessions. By using the downloaded plant image PDF files, users can obtain detailed passport and agronomic information by clicking on the image of an accession of interest.