By successfully sequencing the entire genome of common wheat (Triticum aestivum L.) in 2018, the International Wheat Genome Sequencing Consortium (IWGSC) achieved its goal of publishing the first reference genome sequence of this important crop. During this period, various technological innovations have dramatically evolved genome sequencing technology; these advances have made it possible to rapidly decode large and complex genomes, including that of polyploid wheat. IWGSC completed reference genome sequence by exploiting these latest technologies via two primary approaches, “whole-genome sequencing” and “sequencing by chromosome.” As collaborators in the IWGSC project, a Japanese research team led by the National Agriculture and Food Research Organization was responsible for sequencing chromosome 6B, one of the 21 wheat chromosomes, and contributed to constructing the reference genome sequence. This article presents an outline of reference genome sequence construction and provides an overview of the common wheat genome information obtained. Moreover, it describes the methods used to sequence chromosome 6B, together with the associated analytical data and novel knowledge, including the structural analyses of Nor-B2 and Gli-B2 obtained during this work. Furthermore, it describes the recently undertaken sequencing of the genomes of diploid and tetraploid wheat and reviews the overall development of wheat genomic resources.

The second of the United Nations’ 17 Sustainable Development Goals aims to end hunger, achieve food security and improve nutrition, and promote sustainable agriculture. However, it is well known that the agricultural potential in developing regions including Africa has not been fully realized because adverse environments and changing climate conditions impose abiotic (e.g., low soil fertility, droughts) and biotic (e.g., pests, diseases) stresses on plant growth and development. To ensure food and nutrition security in such regions, the Environmental Stress-tolerant Crops project, the Highyielding Biomass Crops project and the Pest and Disease Control project in the Program for Stable Agricultural Production at the Japan International Research Center for Agricultural Sciences aimed to develop technologies and crops with high productivity and adaptability to adverse environments and changing climate conditions. In order to develop crops with environmental stress tolerance and disease resistance, we have clarified and used the genes and loci involved in these traits toward the development of breeding materials. And in order to develop technology for effectively controlling transboundary pests, we have elucidated the ecology of their occurrence and developed pest management technology based on that information. We hope that these materials and technologies will contribute to achieving food and nutrition security in developing regions.

Norin-PL3 and Norin-PL4 are rice (Oryza sativa L.) breeding lines that carry a brown planthopper (BPH) resistance gene. Norin-PL3 was bred by introgressing BPH1 derived from the Indica Group variety Mudgo into Japonica Group rice, whereas Norin-PL4 was bred by introgressing BPH2 derived from the Indica Group variety IR 1154-243 into Japonica Group rice. To detect the alleles derived from resistance donor varieties in these lines, we developed a simple method to create graphical genotypes using a part of the InDel information obtained by a short-read next-generation sequencing system. In Norin-PL3, chromosomal regions derived from Mudgo were found on chromosome 12 and two other locations on the short arm of chromosome 1. In Norin-PL4, the chromosomal regions derived from IR 1145-243 were found on chromosomes 5 and 12, the short arm of chromosome 4, and chromosome 8. Among these regions derived from resistant donors, chromosomal regions contributing to resistance were identified. This method could also assist in creating graphical genotypes of the other rice lines with both Japonica Group and Indica Group varieties as parents. Moreover, the results of the graphical genotype and DNA marker information of Norin-PL3 and Norin-PL4 will be useful for rice breeding research on BPH resistance.

To determine whether visits by wild pollinators correspond well with the physiological patterns of animal-pollinated crops, we investigated the diurnal dynamics of nectar secretion in the male and female flowers of cultivated kabocha squash Cucurbita maxima Duch, and its effect on the temporal visitation pattern by bumblebees, their Japanese wild pollinators, relative to visits by introduced honeybees Apis mellifera L. in Hokkaido, Japan. The amount of nectar secreted and the frequency of pollinator visits were monitored from floral opening at dawn until wilting in the early afternoon. Flowers of both sexes secreted nectar in a unimodal diurnal pattern, with secretion peaking during the middle stage of anthesis. The total production of nectar in female flowers was twice that in male flowers. Although the availability of pollinators varied between days, the frequency of visits by bumblebees corresponded well with the dynamics of nectar secretion by the flowers. The diurnal dynamics of nectar secretion and the large availability of nectar reward in female flowers would increase the probability of transferring viable pollen to female flowers and contributing to fruit production of this crop. Bumblebee visits were negatively correlated with honeybee visits. Although this negative correlation could be explained by the complementary effects of pollinators or competitive exclusion, the effects of introducing honeybees on wild pollinators cannot be easily evaluated and thus should be carefully examined by considering the local environmental context in future studies.

General Utilities for Genotyping Study (GUGS) is a toolbox for aiding the analysis of DNA marker data and its design in Microsoft Excel (MS Excel). GUGS provides more than 100 flexible functions for the manipulation, evaluation, and conversion of genotype data. It also provides functionalities for genotype format conversion to support linkage analysis using JoinMap software, frequency analysis for population genetics, parentage analysis, and statistical genetic analysis. Its functionality for the manipulation of nucleotide or amino acid sequences also assists DNA marker design. These GUGS features enable users to conduct all steps from DNA marker design to preliminary evaluation, data analysis, and format conversion for advanced study in a single environment without having to export/import data. GUGS is freely available at https://github.com/tokurou/GUGS under the GPL v3 license.

Seed tubers of potato (Solanum tuberosum) plants were grown in five locations in Japan: Hokkaido, Yamagata, Ibaraki, Hiroshima, and Nagasaki. One hundred colonies of pink-pigmented facultative methylotrophs (PPFMs) were isolated from potato leaves at flowering time. The 16S rRNA gene sequences of isolates were determined, and clustering analysis (≥ 99% identity) identified 11 operational taxonomic units (OTUs). Phylogenetic analysis revealed that all OTUs were grouped in genus Methylobacterium. The OTU M9 was distributed among all five collection sites, and other OTUs were distributed among several collection sites. These data indicated that the distribution of PPFMs in the potato phyllosphere differed according to the plant’s geographical location.

Yacon, an Andean crop, was historically introduced into Japan for local consumption of its tuberous roots as a sweet vegetable. We recently examined the multi-functional effects of yacon herbal tea to establish the aerial part as a health food material. The current study aimed to investigate whether any functional differences exist among the yacon leaves from four domestic cultivars—‘Sarada otome’ (SY201), ‘Andesu no yuki’ (SY206), ‘Sarada okame’ (SY217), and ‘Andesu no otome’ (SY237)—and a Peru A line (SY11) maintained for several years in the Aso area of Kyushu. The total polyphenol content (TPC) and antioxidant activity of cultivar SY237 exceeded those of SY11, but the values for individual cultivars were inconsistent over the tested years. In carbohydrate-hydrolyzing enzyme inhibition assays, there was a large variation in all cultivars among the tested years, with three cultivars including SY237 partially demonstrating α-glucosidase inhibition comparable to or stronger than that of SY11. Based on multivariate analysis with functional data from over four years, the characteristic positioning of these yacon cultivars was systematically visualized. As a result, we found that SY237 could be a candidate cultivar that is partially superior to SY11, although the yearly variance should be considered.

Carotenoid mutants are useful for elucidating carotenoid metabolism. ‘Kusaie’ is a yellow-fruited form of ‘Rangpur’ (Citrus limonia Osbeck). Hyuganatsu (C. tamurana hort. ex Tanaka) is a mediumsized, light yellow fruit. Its bud mutation, wherein the fruit rind color becomes orange, is named ‘Orange-hyuga.’ To elucidate the mechanism underlying this alteration, their carotenoid composition and abscisic acid content were analyzed. In the flavedo of ‘Kusaie,’ significant phytoene accumulation, decreased xanthophyll, and ABA contents were observed, suggesting that phytoene desaturase was suppressed. Moreover, the total carotenoids in the juice sac of ‘Kusaie’ was significantly lesser than those in that of ‘Rangpur,’ suggesting that the production of carotenoids is suppressed in ‘Kusaie.’ In ‘Orange-hyuga,’ the total carotenoids was approximately 6-fold that of Hyuganatsu, and a significant xanthophyll accumulation, especially violaxanthin, was observed. Furthermore, ABA content was significantly lower. Accordingly, those might be associated with an altered gene expression balance upstream and downstream of biosynthesis. Difference in biosynthesis regulation in these color-altered cultivars might cause a change in the carotenoid contents and composition in fruits, which seemed to result in color changes from reddish-orange in ‘Rangpur’ to yellow in ‘Kusaie’ and from a light yellow color in Hyuganatsu to an orange color in ‘Orange-hyuga.’ In this study, these color-changing citrus mutants were observed to accumulate carotenoids differently from the original type, and we speculated that different changes occurred in carotenoid biosynthesis regulation.

In northern Ethiopia, considerable enrichment planting is essential to enhance the regeneration of dry forests. However, planted seedlings suffer high levels of mortality in arid climates. Biochar can enhance seedling survival and growth. Therefore, this study aimed to determine the effect of biochar (derived from Vachellia etbaica) on the survival of V. etbaica and Faidherbia albida seedlings. We planted V. etbaica and F. albida into soil treated with 1 kg of biochar per seedling and into soil without biochar (control) using a randomized complete block design. We analyzed the soil nutrients, plant growth, and plant elements. The application of biochar did not increase the nutrient levels in the soil. However, the total dry mass of V. etbaica and F. albida increased following biochar application. Moreover, the total contents of several nutrients were higher in the leaves of biochar-treated V. etbaica and leaves and roots of biochar-treated F. albida than in the controls. These results suggest that biochar can alter the chemical properties of soil, resulting in the accelerated uptake of nutrients. In conclusion, the application of biochar enhances the uptake of nutrients, thereby enhancing the growth of V. etbaica and F. albida.

Information about site conditions is essential to select teak (Tectona grandis) plantation sites in Northeast Thailand. We examined the effects of topography (slope steepness, elevation, and slope aspect), soil organic matter, and chemical factors on tree growth (site index) in 7- to 30-year-old teak plantations (n = 87) in Northeast Thailand. Soil organic matter and chemistry data were collected from the topsoil (0 cm-20 cm) and subsoil (40 cm-60 cm). The linear mixed model indicated that teak growth was positively affected by slope steepness (P < 0.05) and Ca content and negatively by Na content. Mg showed a weak correlation (P < 0.1) due to its association with Ca. We suggest that slope steepness alters the balance of exchangeable cations, and that accumulation of soil organic matter due to surface drainage plays an important role. In conclusion, suitable sites for growing teak in the study area in Northeast Thailand are those on slopes with topsoil rich in Ca.