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

Abstract

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.

Reciprocal translocation identified in Vigna angularis dominates the wild population in East Japan

“…Detailed information of these accessions is available in NIAS Genebank-Databases https://www.gene.affrc.go.jp/databases_en.php (Takeya et al 2011). F 1 hybrids from 14 cross combinations between the three cultivated and the five wild accessions were used to evaluate seed fertility and to develop F 2 mapping populations for linkage analysis, respectively (Table 2).…”

Development of a National Center of Genetic Resources Passport Database: Managing Agriculture, Forestry, Livestock, Microbial, and Aquatic Genetic Resources with an Integrated Schema

“…For example, GRIN-Global provides a plant genetic resource information management system as open source software (Postman et al 2010). The National Institute of Agrobiological Sciences (NIAS) Genebank in Japan has a well-developed schema for the management of plant, microbial, and animal genetic resources, as well as their interactions and plant disease information (Takeya et al 2011). However, these systems are not suitable for the CNRG's multi-type particularity; therefore, a new schema was developed to facilitate the development of a five-subsystem germplasm inclusive passport database.…”

“…Although several database systems have been developed and implemented by gene banks worldwide (Postman et al 2010, Oppermann et al 2015, Agrawal et al 2007, Blackburn 2009), as well as portal sites that facilitate searches for genetic resources across such databases (Telenius 2011), only a few have addressed the management of multiple genetic resource subsystems (Takeya et al 2011).…”

Genebank data-management software incorporating seed-viability test results

“…Part of the genetic resources database for Web-accessible programs is transferred into the Web retrieval database on a daily update basis by a program written in Perl (Takeya et al, 2011). Web-accessible programs, such as the plant accessions search software, have been developed in the PHP and JavaScript scripting languages.…”