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.

Natto, a fermented soybean food made in Japan, is spoiled occasionally by Bacillus subtilis (natto) bacteriophages. Twenty phages, primarily isolated from abnormally fermented natto, were classified into two groups based on host ranges and comparative whole-genome hybridization. JNDMP (group Ⅰ) had a hexagonal head (diameter, 60 nm), a flexible tail (length, 200 nm) and required a magnesium ion for amplification. ONPA (group Ⅱ) had a hexagonal head (diameter, 89 nm) and a sheathed tail (length, 200 nm). Genome sizes of JNDMP and ONPA were estimated to be 42 kb and 91 kb, respectively. Previously reported phages from three serologically different groups of B. subtilis (natto) were also classified into group Ⅰ or group Ⅱ based on the results of Southern hybridization using JNDMP and ONPA genomic DNA as probes. These results suggest that there are at least two groups of B. subtilis (natto) phages in Japan.

Background Understanding the history of anthropogenic vegetation is often difficult due to the lack of tangible historical evidence. In this study, we examined chronological changes of farmland demarcation trees planted on alluvial plains along the Hijikawa River in southwestern Japan based on species distribution patterns, folk nomenclature, and multiple usage of the trees. Methods The species composition of demarcation trees was investigated at 47 sites in 13 villages. We performed hierarchical clustering using Bray–Curtis measures to detect groups of similar tree composition and permutational multivariate analysis of variance to test whether differences in species composition correspond to village units. To better understand the traditional knowledge of demarcation trees, we conducted interviews with 53 farmers, most of whom were over 60 years old. Results Clustering resulted in six tree composition groups. The group characterized by the most frequently planted species, Chaenomeles speciosa , dominated around lower reach villages. The group characterized by Euonymus japonicus dominated around middle reach villages, and that characterized by Salix pierotii was mainly located around upper reach villages. Chaenomeles speciosa was always identified with the standard Japanese name boke or similar names. Euonymus japonicus and several other species were also called boke by many farmers. Several elderly farmers stated that C. speciosa was pervasive in upper and middle reach villages in their youth, suggesting the prototypical use of C. speciosa in the study area. In addition, some minor species were likely to have been left after commercial crop production or subsistence use between the late nineteenth and mid-twentieth centuries, including Morus sp. and Celtis sinensis for sericulture, Salix koriyanagi for fiber production, and Gardenia jasminoides for food coloration. The name kōshin bana recorded for E. japonicus suggests that the species’ use originated from the folk faiths Kōshin-shinkō and/or Shōmen-Kongō. Conclusions The composition of demarcation trees in the region has not been stable over time, but instead changed to reflect the local livelihood, industry, and faiths. Despite the lack of tangible historical evidence, the spatial distribution patterns, folk nomenclature, and traditional knowledge of plants can provide clues to trace the chronological background of ecotopes in anthropogenic landscapes.

Although there are a number of Vietnamese native pig (VnP) populations, some are on the verge of extinction, and therefore adequate management and conservation are necessary. In this study, we conducted a field survey of VnP populations and analyzed interrelationships among their characteristics. We also established a relational database for management of field data on these populations. For data collection, we conducted interviews with farmers and visual inspection of 32 VnP populations in 22 provinces of Vietnam, as well as taking photographs of individual animals. Data on the characteristics of VnP populations were subjected to multiple correspondence analysis (MCA). For establishment of the database, normalization and table partitioning were performed to eliminate redundancy and ensure consistency of the collected data items. Passport data, characteristics data, and image data were collected from a total of 1,918 VnPs and entered as a normalized table. Upon MCA, most of the populations were not separated from each other, but the Mong Cai, O Lam, and Chu Prong populations were separated from the other populations. Thus, we have constructed a relational database from comprehensive information on the characteristics of VnP populations.