Crops In Japan Research Articles

The development of Spodoptera frugiperda (Lepidoptera: Noctuidae) on 8 major crops in Japan and its oviposition preference for maize and soybean.

The fall armyworm, Spodoptera frugiperda (J.E. Smith), is a polyphagous pest native to the Americas. It first invaded Japan in July 2019, and the most damaged crop in this region to date has been maize. To determine pest control strategies, the range of crops potentially damaged by S. frugiperda in Japan should be identified. In this study, the effects of 8 major crops in Japan-forage maize Zea mays subsp. mays, sugarcane Saccharum officinarum, forage and edible rice Oryza sativa subsp. japonica, soybean Glycine max, eggplant Solanum melongena, green bell pepper Capsicum annuum var. grossum, sweet potato Ipomoea batatas, and taro Colocasia esculenta-on the development of S. frugiperda were analyzed by feeding leaves of domestic cultivars during larval stage. Spodoptera frugiperda developed from hatching to adulthood and laid eggs in all 7 treatments, except for taro. However, among them, only soybean showed comparable developmental suitability to maize. Therefore, its oviposition preference for maize and soybean was examined using further nonchoice and choice tests. In the nonchoice test, the number of egg masses oviposited for 3 days on soybean plants was significantly less than that on test containers, while that on maize was comparable to that on containers. These findings can explain partly why major damage has been limited to maize in Japan.

RAD-Seq analysis of wild Japanese garlic (Allium macrostemon Bunge) growing in Japan revealed that this neglected crop was previously actively utilized

Allium macrostemon Bunge, commonly referred to as "no-biru" in Japan, is a widespread wild onion species found across the country. Despite being deeply entwined in ancient Japanese culture, it remains an underutilized crop in Japan. Determining the origins of its domestic populations and understanding their genetic composition is crucial to highlighting the plant's historical significance in Japan. This study aims to bridge this knowledge gap by examining the genetic diversity of 47 A. macrostemon samples from various regions in Japan using RAD-Seq. Our analyses distinguished unique population structures, dividing the samples into three distinct groups: A, B, and C. Notably, groups A and B showed clear evidence of bulb propagation, while group C did not. Group C formed four subgroups: C1, C2, C3, and C4. Hybridization between subgroup C1 and either group A, B, or both, resulted in the emergence of subgroups C2, C3, and C4. Thus, groups A, B, and C1 are posited as the ancestral populations. Additionally, our morphological observations indicated distinct differences among these three groups. Our findings also suggest that human migration may have influenced the plant's distribution, hinting at active usage in the past that later waned, causing its current underutilized status.

Characteristic features of statistical models and machine learning methods derived from pest and disease monitoring datasets.

While many studies have used traditional statistical methods when analysing monitoring data to predict future population dynamics of crop pests and diseases, increasing studies have used machine learning methods. The characteristic features of these methods have not been fully elucidated and arranged. We compared the prediction performance between two statistical and seven machine learning methods using 203 monitoring datasets recorded over several decades on four major crops in Japan and meteorological and geographical information as the explanatory variables. The decision tree and random forest of machine learning were found to be most efficient, while regression models of statistical and machine learning methods were relatively inferior. The best two methods were better for biased and scarce data, while the statistical Bayesian model was better for larger dataset sizes. Therefore, researchers should consider data characteristics when selecting the most appropriate method.

A target cultivar-specific identification system based on the chromatographic printed array strip method for eight prominent Japanese citrus cultivars.

Citrus is a major cultivated crop in Japan, and new cultivars are of great interest in the Japanese and global market. Recently, the infringement of breeders' rights to citrus cultivars bred in Japan has become a problem related to the agricultural product export strategy promoted by the Japanese government. Cultivar identification systems using DNA markers are an effective tool for protecting breeders' rights. Here, a novel target cultivar-specific identification system using the chromatographic printed array strip method was developed for eight prominent Japanese citrus cultivars. A polymorphic InDel fragment specific to each cultivar was explored through the screening of published citrus InDel markers and next-generation sequencing of retrotransposon libraries. The cultivar-specific DNA marker set for each cultivar comprised 1-3 polymorphic InDel fragments in combination with a PCR-positive DNA marker for the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit gene. The DNA markers were detected within 3 hours from DNA extraction to the detection by the C-PAS4 membrane stick following multiplex PCR. The developed system is superior as a convenient, rapid, and cost-effective DNA diagnostic method during inspection. The proposed target cultivar-specific identification system is expected to serve as an efficient tool for the injunction of suspicious registered cultivars, contributing to the protection of breeders' rights.

Characterization of Penicillium Species Isolated from Dioscorea polystachya in Hokkaido, Japan.

Chinese yam (Dioscorea polystachya) has been cultivated as a food crop in Japan. The blue mold disease of Chinese yam during the storage and treatment of forced sprouting is one of the hindrances in attaining productivity that can lead to food security in tropical countries and steady farming that will eventually lead to farmers' profitability. In this study, three species of the genus Penicillium related to the blue mold of yam were isolated from two locations in Hokkaido, Japan. From the morphology and phylogeny, these were Penicillium albocoremium, P. polonicum, and P. sclerotigenum. Pathogenicity was confirmed in all Penicillium-like isolates, and sensitivity against benomyl was evaluated based on MIC. The first two species were newly recorded as the causal fungi of the blue mold of yam in Japan, and the pathogenicity of P. albocoremium is first confirmed in yam seed tuber. Moreover, some isolates showed possible resistance to benomyl.

Developing core marker sets for effective genomic-assisted selection in wheat and barley breeding programs.

Wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) are widely cultivated temperate crops. In breeding programs with these crops in Japan, effective genomic-assisted selection was performed by selecting core marker sets from thousands of genome-wide amplicon sequencing markers. The core sets consist of 768 and 960 markers for barley and wheat, respectively. These markers are distributed evenly across the genomes and effectively detect widely distributed polymorphisms in the chromosomes. The core set utility was assessed using 1,032 barley and 1,798 wheat accessions across the country. Minor allele frequency and chromosomal distributions showed that the core sets could effectively capture polymorphisms across the entire genome, indicating that the core sets are applicable to highly-related advanced breeding materials. Using the core sets, we also assessed the trait value predictability. As observed via fivefold cross-validation, the prediction accuracies of six barley traits ranged from 0.56-0.74 and 0.62 on average, and the corresponding values for eight wheat traits ranged from 0.44-0.83 and 0.65 on average. These data indicate that the established core marker sets enable breeding processes to be accelerated in a cost-effective manner and provide a strong foundation for further research on genomic selection in crops.

Streamlining data requirements based on a problem formulation approach and a concept of data transportability for the environmental risk assessment of genetically modified crops in Japan

Streamlining data requirements based on a problem formulation approach and a concept of data transportability for the environmental risk assessment of genetically modified crops in Japan

Function and Characterization of Fungal Communities in Chestnut Soils (Castanea crenata) of Kansai Region, Japan

Chestnut (Castanea crenata) is an important fruit crop in Japan, grown under three cultivation systems in Kansai region, which succumb to fungal root disease pathogens. The fungal community in soils of chestnut in these cultivation systems were characterized along with the potential of soil bacterial species as biological control agent against these root-invading fungi. Bacteria from the chestnut soil rhizosphere were identified and their ability to suppress diseases in vitro was evaluated. Bacteria DAC17225011 and DAC17225014 showed 99% similarity to Bacillus aryabhattai and Pseudomonas frederiksbergensis, respectively, which could suppress the growth of Armilaria mellea and Phytophtora cambivora, respectively, in in vitro conditions. The assay in vivo indicated the positive effect of these bacteria on the reduction of disease infection spots in chestnut roots; however, no visible symptoms were detected aboveground. For microbial community analysis, chestnut soil was sampled from four locations (Wachi, Ayabe, Fukuchiyama and Sasayama) considering three management systems, conventional, organic and wild. The amplicon from the ITS region (The genomic library of the fungal detection in soils) was sequenced by Illumina MiSeq 250bp and used to analyze the fungal community in the sampled soil. Nectriaceae, which contains pathogenic fungi, was very common in all samples, but lower in wild areas. Ceratobasidiacea was also higher in conventional areas. For the symbiotic families, Hypocraceae and Russulaceae were typical in wild soils, whereas Amanitaceae was found in organic soils. The fungal community was clearly distinct in the wild system, differing from conventional and organic systems.

Evaluation of the Enzymatic Saccharification Efficiency of an Energy Crop, Erianthus arundinaceus, Pretreated with Ca(OH)2 Using both Countercurrent Washing System and pH Adjustment by Nonpressurized CO2.

Erianthus arundinaceus (ER) is greatly appreciated among domestic energy crops in Japan for the production of fermentable sugars from lignocellulosic polysaccharides. In this study, we developed an efficient Ca(OH)2-based pretreatment of both stems and leaves of ER at ambient temperature with the addition of a washing step for enzymatic saccharification. The recoveries of glucans and xylans in the pretreated ER after four countercurrent washing cycles were 91 and 76 %, respectively, the former being considerably higher than that of rice straw (RS) (72 %). Their saccharification ratios in the washed sample under the pressure of 1 atm CO2 were 80 and 92.5 %, respectively. The application of this simple sugar production process from ER would further support the domestic bioprocess development. ER is also foreseen to provide the additional feedstock favorable for harvesting from winter to spring in Japan, preventing a risk for feedstock shortage generated by single harvesting such as RS.

Citizen science and social movements: A case of participatory monitoring of genetically modified crops in Japan

Agrifood related social controversies tend to involve scientific issues and advocacy groups increasingly turn to citizen science (CS), participatory data taking by regular people, to produce health and environmental data. A common assumption is that CS’s value lies in the data produced, and its volume and quality decide its persuasive power. This article describes participatory monitoring of genetically engineered rapeseed (canola) in Japan to suggest that social movements can leverage CS not only for the production of scientific data but also as occasions for recruitment, political awareness-raising, and collaboration with other civic organizations. The article proposes a new framework for understanding CS–social movement relations that is multi-actor (vs. expert–laypeople dyad); process-oriented (vs. product/data-oriented); and long-term (vs. one-shot and isolated data taking). There is an increasing awareness of the diversity of CS. Even those that are led by grassroots organizations have multiple and shifting uses of data and foster varying political subjectivity among participants. The proposed framework helps to understand the dynamics that shape such heterogeneous pathways of CS.

Revision of estimates of climate change impacts on rice yield and quality in Japan by considering the combined effects of temperature and CO<SUB>2</SUB> concentration

Rice is the most important cereal crop in Japan, and therefore the impact of projected climate change on its production and quality has been assessed using rice growth models accounting for the effects of rising temperature and atmospheric CO2 concentration ([CO2]) on important growth processes. Recent experimental studies, however, have shown some negative effects of interactions between [CO2] and temperature on yield and quality of rice which were not accounted for by previous impact assessments. This study examined the importance of [CO2]×temperature interactions in the nationwide impacts of climate change on grain yield and quality of rice in Japan by 2100. We introduced new functions accounting for the effects of interactions on yield. Then we adopted the acceleration by elevated [CO2] in the estimation of the occurrence of chalky grains, an indicator of appearance quality of rice. We applied the modified model to Japan at a spatial resolution of 1 km using 10 climate scenarios (5 Global Circulation Models×2 representative concentration pathways [RCPs]) from 1981 to 2100. The effects of the newly introduced negative effects of [CO2]×temperature were evaluated by comparing simulations with and without the interaction in each scenario. Nationwide production was estimated to decrease by up to 28% and the percentage of white chalky grains to increase up to 16% relative to the previous assessment results, especially in RCP8.5, in which larger increases were projected in both temperature and [CO2]. The result suggests that the positive effect of elevated [CO2], which had been expected to offset the negative effect of increased temperature on rice productivity, may be limited in the future, and rice quality degradation may be more severe than predicted previously.

The effect of zebularine on the heat-activated retrotransposon ONSEN in Arabidopsis thaliana and Vigna angularis.

The Ty1/copia-like retrotransposon ONSEN is conserved among Brassica species, as well as in beans, including adzuki bean (Vigna angularis (Willd.) Ohwi & Ohashi), which is one of the economically important crops in Japan. ONSEN has acquired a heat-responsive element that is recognized by plant heat stress defense factors, resulting in its transcription and the production of full-length extrachromosomal DNA under conditions with elevated temperatures. DNA methylation plays an important role in regulating the activation of this transposon in plants. Therefore, chemical inhibition of DNA methyltransferases has been utilized to study the effect of DNA methylation on transposon activation. To understand the effect of DNA methylation on ONSEN activation, Arabidopsis thaliana and adzuki bean seedlings were treated with zebularine, which is known to be an effective chemical demethylation agent. The results showed that ONSEN transcription levels were upregulated in zebularine-treated plants. Extrachromosomal DNA of ONSEN also accumulated in the treated plants.

Perilla Mosaic Virus Is a Highly Divergent Emaravirus Transmitted by Shevtchenkella sp. (Acari: Eriophyidae).

Shiso (Perilla frutescens var. crispa) is widely grown as an important vegetable or herb crop in Japan. Beginning around the year 2000, occurrences of severe mosaic symptoms on shiso were documented and gradually spread across Kochi Prefecture, one of four major shiso production areas in Japan. Next generation sequencing and cloning indicated the presence of a previously unknown virus related to the members of the genus Emaravirus, for which we proposed the name Perilla mosaic virus (PerMV). The genome of PerMV consists of 10 RNA segments, each encoding a single protein in the negative-sense orientation. Of these proteins, P1, P2, P3a, P3b, P4, and P5 show amino acid sequence similarities with those of known emaraviruses, whereas no similarities were found in P6a, P6b, P6c, and P7. Characteristics of the RNA segments as well as phylogenetic analysis of P1 to P4 indicate that PerMV is a distinct and highly divergent emaravirus. Electron microscopy observations and protein analyses corresponded to presence of an emaravirus. Transmission experiments demonstrated that an eriophyid mite, Shevtchenkella sp. (family Eriophyidae), transmits PerMV with a minimum 30-min acquisition access period. Only plants belonging to the genus Perilla tested positive for PerMV, and the plant-virus-vector interactions were evaluated. The nucleotide sequences reported here are available in the DDBJ/ENA/GenBank databases under accession numbers LC496090 to LC496099.

Screening of Nematicides against the Lotus Root Nematode, Hirschmanniella diversa Sher (Tylenchida: Pratylenchidae) and the Efficacy of a Selected Nematicide under Lotus Micro-Field Conditions

In Japan, Hirschmanniella diversa is an important pest in lotus cultivation in paddy fields and only lime nitrogen is registered for its control. Therefore, additional nematicides are required to control the nematode. The objective of this study was to screen for an effective nematicide. Fourth-stage juveniles and adults of H. diversa sampled from a lotus field were tested in in vitro solution experiments against 37 pesticides that are registered for the pest control of crops in Japan. Carbamate-based benfuracarb, organophosphate-based fenthion, nereistoxin-based cartap hydrochloride and cyanamide showed nematicidal effects against H. diversa. Benfuracarb at 1 μg/mL showed a nematostatic effect on H. diversa in an agar plate assay. Further, H. diversa treated with benfuracarb did not resume activity 7 days post nematicide treatment when transferred to distilled water. Benfuracarb was tested in micro-field experiments, in which H. diversa density and lotus tuber damage levels were monitored. Results showed that benfuracarb reduced H. diversa densities in the roots during the cultivation period in 2012 and consistently reduced damage levels during a five year study period. Thus, benfuracarb is recommended as an effective nematicide to be used for H. diversa control in lotus cultivation.

Consideration of familiarity accumulated in the confined field trials for environmental risk assessment of genetically modified soybean (Glycine max) in Japan

To date, there have been 160 regulatory approvals for environmental safety in Japan for the major genetically modified (GM) crops, including corn, soybean, canola and cotton. Confined field trials (CFTs) have been conducted in Japan for all single events, which contain various traits. The accumulated information from these previously conducted CFTs, as well as the agronomic field study data from other countries, provides a rich source of information to establish “familiarity” with the crops. This familiarity can be defined as the knowledge gained through experience over time, and used to inform the environmental risk assessments (ERA) of new GM crops in Japan. In this paper, we compiled agronomic data from the CFTs performed in Japan for 11 GM soybean events which obtained food, feed and environmental safety approvals from regulatory agencies in Japan. These CFTs were conducted by multiple developers according to Japan regulations to support the ERA of these GM soybean, covering standard measurement endpoints evaluated across developers in Japan. With this dataset, we demonstrate how familiarity gained from the CFTs of GM soybeans in Japan can be used to inform on the ERA of new GM soybean events. By leveraging this concept of familiarity, we discuss potential enhancements to the ERA process for GM soybean events in Japan.

Studies on the identification and diagnosis of pathogenic fungi inhabiting forage crops in Japan

Studies on the identification and diagnosis of pathogenic fungi inhabiting forage crops in Japan

Studies on the identification and diagnosis of pathogenic fungi inhabiting forage crops in Japan

Studies on the identification and diagnosis of pathogenic fungi inhabiting forage crops in Japan

Soil hydro-thermal regimes and water use efficiency of rain-fed soybean (Glycine max) as affected by organic mulches

Soybean (Glycine max) is a commercially important oilseed crop across the world; it is also popularly used as vegetables, cookery and fodder crops in Japan. In areas with limited rainfall and high temperature, mulching can provide greater yield of rain-fed soybean by improving soil hydro-thermal regimes. However, organic mulching like rice straw and shaded newspaper being inexpensive, rapidly degradable, easy to use, and environment friendly may provide more benefits than plastic mulching. Field experiments with rain-fed soybean cultivation were done in 2015 and 2016 at Gifu University farm in Japan. The purposes were to investigate the effects of rice straw and newspaper mulching on moisture and temperature regimes of soil, soil-water consumption (SWC), soil-moisture extraction pattern (SMEP), total readily available moisture (TRAM), water use efficiency (WUE) as well as growth and yield of soybean. Mulching increased seasonal soil-moisture content with lesser fluctuations in the root zone compared to bare soil, and lowered soil temperature by 2 °C at 5 cm and 0.5–1.0 °C at 15–25 cm soil depths. Straw mulch reduced SWC by 41.8 and 13.9% in 2015 and 2016, respectively compared to bare soil; the corresponding reduction in SWC under newspaper mulch was 16.6 and 20.6%. Consequently, mulching improved WUE by 25–47% compared to bare soil. Mulching significantly (p ≤ 0.05) improved plant height, leaf chlorophyll content, nodulations, grain (pod) and seed numbers, biomass, and grain and seed yields of soybean compared to bare soil. Grain yield increased by 12–13% under straw mulching and 6.6–37.2% under newspaper mulching compared to bare soil. Newspaper mulch provided higher yield and WUE by maintaining lower soil temperature and SWC, and greater soil moisture compared to straw mulch. Thus, newspaper can be an alternative option to rice straw mulch for improving soil hydro-thermal regimes for rain-fed soybean cultivation.

Evaluation of Competitiveness, one of assessment endpoints in environmental risk assessment of genetically modified crops in Japan

Evaluation of Competitiveness, one of assessment endpoints in environmental risk assessment of genetically modified crops in Japan

Importance of national or regional specificity in the relationship between pollinator dependence and production stability

Stable production of crops depends on pollination services provided by animals. Although crop production is more stable in pollinator-independent crops than in pollinator-dependent crops at the global scale, the situation at the local scale is unknown. Here, we investigated the relationship between pollinator dependence and production stability of 40 crops in Japan and show that the global relationship does not apply at the local scale, i.e., most pollinator-dependent crops showed stable production and most pollinator-independent showed instable production possibly because of local policies and agricultural practices. Examining relationships at the local scale will help establish effective local management of pollination services and crop production.