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Analytical algorithms based on Raman spectroscopy are proposed for the determination of amylopectin and amylose concentrations in polished white rice, and applied to characterize and compare linear and branched polysaccharide structures in nine different types of Japanese rice. A selected algorithm used symmetric bending vibrations of the C O C glycosidic linkage from a relatively narrow spectral zone between 830 and 895 cm−1. It specifically compared the intensity of Raman signals from two types of bending common to both starch components (C1-O-C5 and C1-O-C4 at 868 and 855 cm−1, respectively) and that at the branch point peculiar to amylopectin (C1-O-C6 at 844 cm−1). Raman data were confronted with data collected by conventional amylose-iodine colorimetry method. Consistency was found between Raman and colorimetric methods over the entire series of tested rice cultivars, thus validating the newly proposed spectroscopic algorithm. The amylose content of the tested rice species broadly varied between 1.2 and 20.4%. The proposed Raman algorithm allows fast and nondestructive determination of amylose content in rice with minimal sample preparation. These characteristics might be key in the development of portable Raman devices capable to promptly screen polysaccharides in different rice cultivars with respect to their interannual and plantation-related fluctuations.

This study aimed to determine the appropriate steam treatment conditions, using a steam nursery cabinet, to break the dormancy of Japanese rice cultivar seeds exhibiting various dormancy levels. The influence of the temperature and duration of the steam treatments on the germination percentage and germination rate was investigated. In highly dormant ‘Takanari’ seeds, the steam treatment at 40 °C for 7 d increased the germination percentage and decreased the 50% germination time (T50S; based on seed number); this treatment was as effective as the dry heat treatment at 50 °C for 7 d. For the medium dormant ‘Moeminori’ and ‘Hitomebore’ seeds, the steam treatment at 40 °C for 5 d decreased T50S sufficiently and more effectively than did the dry heat treatment at 50 °C for 7 d. For the slightly dormant ‘Moeminori’ seeds, the steam treatment at temperatures ranging from 24 °C to 40 °C for 7 d decreased T50S without a corresponding decrease in germination percentage to

Phosphorus (P) acquisition through extensive root growth and P allocation to different plant organs through efficient remobilization are important for acclimation of crop plants to P-limited environments. This study elucidated changes in rice root growth and leaf P-remobilization and their influence on grain yield under P deficiency. Two pot experiments were conducted with (P100) and without (P0) inorganic P supply using two Japanese rice cultivars: Akamai (Yamagata) and Koshihikari. Multiple harvests were made until the panicle initiation stage. Root and shoot growth response, P acquisition, and temporal leaf P-remobilization efficiency were measured. A separate experiment ascertained the final yield and grain P status. The Akamai rice cultivar showed enhanced root growth and more acquired soil P. The Akamai root dry weight was 66% greater than that of Koshihikari under P0. Confronting P deficiency, Akamai remobilized some P from its lower mature leaves to upper younger leaves starting from early growth. The remobilized P fraction increased to 72% at panicle initiation under P0. Under P0, Akamai exhibited two-fold higher leaf P-remobilization efficiency than under P100. Enhanced root growth that facilitates acquisition of more soil P through better soil exploration coupled with efficient leaf P remobilization from the early growth stage improves adaptation of Akamai rice cultivar to P-limited environments. Nevertheless, P-starvation responses did not facilitate higher grain yields in P-limited conditions.

Two pyroglutamyl peptides with anti-colitic activity were identified in Japanese rice wine, sake, by oral administration of a small dose (0.1–1.0 mg/kg body weight) and in vivo activity-guided fractionation. Compounds in sake were fractionated by preparative isoelectric focusing followed by preparative reversed phase-liquid chromatography. Anti-colitic activity was evaluated using a dextran sulphate sodium (DSS)-induced colitis mouse model. The final active fraction contained three pyroglutamyl peptides: pyroglutamyl-tyrosine (pyroGlu-Tyr), pyroglutamyl-asparaginyl-isoleucine (pyroGlu-Asn-Ile) and pyroglutamyl-asparaginyl-isoleucyl-asparagyl-asparaginyl-proline (pyroGlu-Asn-Ile-Asp-Asn-Pro). Orally administrating artificially synthesized pyroGlu-Tyr (1.0 mg/kg body weight) and pyroGlu-Asn-Ile (0.1 and 1.0 mg/kg body weight) exhibited a significant protective effect against colitis in mice, whereas pyroGlu-Asn-Ile-Asp-Pro showed no significant effect. Additionally, administrating pyroGlu-Asn-Ile normalized colitis-induced colonic dysbiosis, whereas pyroGlu-Tyr did not. These results suggest that identified pyroglutamyl peptides exhibited an anti-colitic activity via different mechanisms.

Reported risk factors for food/foreign body asphyxia include old age, poor dentition, and certain types of foods. The present report describes a rare autopsy case of a Japanese patient who ate mochi, a traditional rice cake, and died of asphyxiation. Multislice computed tomography (MSCT) as part of the pre-autopsy screening showed an impacted mochi cake in the lower tracheal space, facilitating forensic autopsy planning. In this report, we discuss the role of MSCT in cases of fatal food choking.

Flowering time is one of the most important agronomic traits in rice (Oryza sativa L.), because it defines harvest seasons and cultivation areas, and affects yields. We used a map-based strategy to clone Heading date 18 (Hd18). The difference in flowering time between the Japanese rice cultivars Koshihikari and Hayamasari was due to a single nucleotide polymorphism within the Hd18 gene, which encodes an amine oxidase domain-containing protein and is homologous to Arabidopsis FLOWERING LOCUS D (FLD). The Hayamasari Hd18 allele and knockdown of Hd18 gene expression delayed the flowering time of rice plants regardless of the day-length condition. Structural modeling of the Hd18 protein suggested that the non-synonymous substitution changed protein stability and function due to differences in interdomain hydrogen bond formation. Compared with those in Koshihikari, the expression levels of the flowering-time genes Early heading date 1 (Ehd1), Heading date 3a (Hd3a) and Rice flowering locus T1 (RFT1) were lower in a near-isogenic line with the Hayamasari Hd18 allele in a Koshihikari genetic background. We revealed that Hd18 acts as an accelerator in the rice flowering pathway under both short- and long-day conditions by elevating transcription levels of Ehd1 Gene expression analysis also suggested the involvement of MADS-box genes such as OsMADS50, OsMADS51 and OsMADS56 in the Hd18-associated regulation of Ehd1 These results suggest that, like FLD, its rice homolog accelerates flowering time but is involved in rice flowering pathways that differ from the autonomous pathways in Arabidopsis.

The objective of this study was to discrimination the cultivar, growing region, and geographical origin of rice (Oryza sativa) using a mass spectrometry-based electronic nose (MSE-nose). The inside-needle dynamic extraction (INDEX) system was used to concentrate the samples for MSEnose, following which the ion fragment data obtained were used to perform discriminant function analysis. Discriminant functions 1 and 2 readily separated all 16 cultivars of rice sampled. It was also confirmed that MSE-nose could distinguish the region in which rice cv. Chucheong and Koshihikari were grown, likely due to variation in environmental factors, such as soil and climate. Finally, it was confirmed that MSE-nose could be used to detect the geographical origin of rice, discrimination Korea rice from Japanese rice. Therefore, this simple and rapid technique is of value for discriminating the cultivar, growing region, and geographical origin of rice.

Sake, a traditional Japanese rice wine, contains various oligosaccharides (Sake oligosaccharides; SAOs) derived from rice starch. We previously found that SAOs reach a high degree of polymerization (DP). In this study, we developed a hydrophilic interaction liquid chromatography-time-of-flight/mass spectrometry (HILIC-TOF/MS) based analytical method to separate isomeric SAOs. Isomers of SAOs with DP = 6, 7, and 8, which were named DP6-1, DP7-1, DP8-1 and DP8-2, respectively, were purified from sake and their structures were determined by two-dimensional NMR spectroscopy. These were novel oligosaccharides containing two α-1, 6 bonded branches on an α-1, 4-linked glucose main chain. Interestingly, adjacent double α-1, 6 branches that have not been identified in starch, were found in DP6-1, DP7-1, and DP8-1, suggesting the presence of the branching pattern in starch. DP6-1 was poorly digested by fungal glucoamylase, and this may be attributed to its adjacent double branches at the non-reducing end.

We have succeeded in selecting four higher yield mutants from five gamma-ray irradiated high-yielding Japanese rice varieties using a novel approach. A total of 464 M2 plants which had heavier total panicle weights per plant were first selected from 9801 irradiated M2 plants. Their higher yields were confirmed by yield trials conducted for three years with a six to ten-pairwise replicated plot design. FukuhibikiH6 and FukuhibikiH8 were selected from an irradiated high-yielding variety Fukuhibiki and showed 1.2% to 22.5% higher yield than their original significantly. YamadawaraH3 was selected from an irradiated high-yielding variety Yamadawara and its yield advantages were 2.7% to 3.9%. However, there was no difference in the genotypes of the 96 SNP (single nucleotide polymorphism) markers between the higher yield mutants and their respective original varieties. The differences in the measured phenotypical traits between each mutant and its original variety were not constant and the actual differences were marginal. Therefore, the higher yields of the selected mutants were likely to have been caused by physiological traits rather than phenotypical traits. The selection method used in this study is an application of the directed evolution method which has long been commonly used in the substantial improvements of microorganisms and their proteins.

In Japan, rice seedlings grown in nurseries and used for transplanting are subject to a damping-off disease caused by Pythium spp. In this study, 148 isolates of Pythium spp. were obtained from rice seedlings in 39 locations of northern Japan. Among the isolates, 137 were identified as Pythium arrhenomanes using polymerase chain reaction (PCR) with species-specific primers, DNA sequencing analyses of the internal transcribed regions of ribosomal DNA, and the morphologies of oogonia, antheridia, oospores, and zoosporangia. Inoculation tests showed that the isolates identified as P. arrhenomanes were pathogenic to rice seedlings and parasitic to southern crabgrass with only minor damage. P. arrhenomanes was reisolated from the roots of both rice seedlings and southern crabgrass. Poaceae weeds, hosts of Pythium spp., grow in and around nurseries and in ridges surrounding rice fields. To detect Pythium spp., 188 Poaceae weeds were collected from 37 locations in Akita Prefecture. P. arrhenomanes was frequently detected in 164 weed roots from all locations by PCR using species-specific primers. Thus, we determined that P. arrhenomanes exists in and around rice seedling nurseries and rice fields, and that it is much more widely distributed than previously recognized in northern Japan.

The genotype of the Pi-cd locus found in blast-resistant rice variety Kitakurin, which is a cultivated rice from Japan belonging to Oryza sativa japonica, is identical to that of its wild relative O. meridionalis. Crop domestication from wild relatives to cultivated species has encompassed significant phenotypic changes. However, little is known about the genetic changes involved in domestication. Here, we surveyed the origin of the Pi-cd locus across Oryza species with AA genomes by comparison with the genome sequences of Hoshinoyume (HS), which does not carry the Pi-cd blast resistance gene, and Kitakurin (KK), which carries the Pi-cd blast resistance gene. We found that variety-specific transposons were enriched at the Pi-cd locus. The genotype of the Pi-cd locus characterized by transposons in HS and KK was specific to each Oryza species with the AA genome. The Kitaake (KT) genotype at the Pi-cd locus found in KK was identical only to that of O. meridionalis and distributed only in subgroups of japonica in the World Rice Collection and tropical japonica in the Japanese Rice Collection, whereas it was not present in O. rufipogon accessions. The distinct distributions of genotypes of the Pi-cd locus clearly demonstrated that the Pi-cd locus was introgressed from O. meridionalis into O. sativa, specific to tropical japonica.

In Japan, farming companies, particularly those that grow rice, have recently been promoted to supersede conventional small farms under increasing competitive pressure. Modernization of farm management is a key concept that measures the extent to which modern enterprise management has evolved from the family farms. We conducted unique benchmarking surveys to compare the degrees of modernization between Japanese rice-farming companies and their major international competitor, Californian rice farmers. It was found that Californian producers outperform those in Japan not only in terms of farm scale and rice yield but also in terms of farmers’ capabilities and economic modernization metrics. It was revealed that entrepreneurial advancement, information gathering, and risk-accepting behavior were influential capabilities of Japanese rice farmers with regard to their business innovations. From the perspective of global competitiveness, Japanese rice farmers need to enhance their managerial abilities to further progress in the modernization of their farm business and to get further involved in effective marketing management. Also, our analysis suggests that the research methodologies designed to explore farm management modernization originating from studies in Japan would be worth applying as an international benchmark.

Environmental stresses are the major factors that limit the geographical distribution of plants. As a consequence, plants have developed different strategies to adapt to these environmental changes among which can be outlined the maintenance of membranes' integrity and fluidity. Lipids are key molecules for this environmental adaptation and a comprehensive understand of the molecular mechanisms underlying is still required. Here, lipidome changes in Japanese rice (Oryza sativa var. Japonica) upon heat and hydric stresses are assessed using an untargeted approach based on liquid chromatography coupled with mass spectrometry (LC-MS). The obtained data were analyzed using different multivariate data analysis tools. A total number of 298 lipids responded to these abiotic stresses, and 128 of them were tentatively identified. Diacylglycerols (DG), triacylglycerols (TG), phosphatidylcholines (PC) and phosphatidylethanolamines (PE) were the most altered lipid families heat and hydric stress. Interpretation of the obtained results showed relevant changes related to the unsaturation degree in the identified lipids. In the case of heat stress, a decrease in the unsaturation degree of lipids can be linked to an increase in the cell membranes' rigidity. In contrast, the hydric stress produced an increase in the lipids unsaturation degree causing an increase in the cell membranes' fluidity, in an attempt to adapt to these non-optimal conditions. © 2018, The research leading to these results has received funding from the European Research Council under the European Union Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement n. 320737 . Also, the authors acknowledge support from both the Ministry of Economy, Industry and Competitiveness (Grant CTQ2017-82598-P ) and the Catalan Agency for Management of University and Research Grants (AGAUR) ( 2017SGR753 ). The authors would like to thank CRAG for kindly supplying Japanese rice seeds.

Rice blast caused by Pyricularia oryzae (syn. Magnaporthe oryzae) is a destructive disease of rice worldwide that poses a serious threat to rice production. Strengthening blast resistance is an important objective in rice breeding programs. Race-specific resistance genes (R-genes) confer complete resistance to blast, but new races of blast pathogen can overcome it. After the first report of breakdown of resistance conferred by the R-gene Pik in 1963, this type of resistance has frequently been broken 1–7 years after the release of resistant varieties to farmers in Japan and other countries. To overcome this genetic vulnerability, Japanese rice breeders have focused on the use of race-nonspecific resistance in Japanese upland rice varieties whose resistance has been maintained for a long time. However, linkage drag between genes controlling this type of blast resistance and undesired traits has hindered its use. Therefore, researchers genetically dissected race-nonspecific resistance to rice blast. Among detected QTLs, a single recessive resistance gene, pi21, was identified by map-based cloning. The use of pi21 has improved durable resistance in rice breeding programs.

There is an increasing demand for special types of rice that have black or red pericarp, low amylose (subspecie japonica) or aromatic. However, intense breeding process for obtaining and indicating genetically promising new cultivars and adapted to cultivation environments are demanded. In this sense, for evaluating the special types of irrigated rice genotypes, and determining the adaptability and stability of these using mixed models. First, a preliminary agronomic evaluation of genotypes for special types of irrigated rice was performed, and later, the agronomically promising genotypes were evaluated in multi-site trials, aiming at verifying the interactions with the environment. Statistical analyzes were performed considering mixed models, using the SELEGEN-REML/BLUP software. High genotypic variability among genotypes for special types of irrigated rice was observed, obtaining some agronomically promising and with good adaptability and stability, with high accuracy and selection efficiency using mixed models. The observed wide diversity and rice genetic variability presented new prospects and opportunities for producers for acquiring food of higher added value to consumer market.

Eating quality of cooked rice grains is an important determinant of its market price and consumer acceptance. To comprehensively assess the variation of eating-quality traits in 152 Japanese rice cultivars, we evaluated activities of eight endosperm enzymes related to degradation of starch and cell-wall polysaccharides. Endosperm enzyme activities showed a wide range of variations and were lower in recently developed cultivars than in landraces and old improved cultivars. Activities of most endosperm enzymes correlated significantly with the eating-quality score and surface texture of cooked rice grains. Principal component analysis revealed that rice cultivars with high eating-quality scores had high stickiness of the grain surface and low levels of endosperm enzyme activities. These results suggest that endosperm enzyme activities control texture and eating quality of cooked rice grains in Japanese rice cultivars.

Engagement with the notions of “traditional” related to the narrative of rice and its place in Japanese culture is presented with a discussion regarding the relationship of rice and the traditional Japanese diet or washoku to ideas about Japanese identities. The research methodology, theoretical focus, and overview of current research in the field will be included as well. This book uses a qualitative methodology with in-depth interviews, which provides rich in-depth information that will examine sites and interviewees across Japan. A literature review is also presented which provides a context for the book and situates it within the disciplines of political science, history, and social science.

The fungal pathogen Pyricularia oryzae causes blast, a severe disease of rice (Oryza sativa L.). Improving blast resistance is important in rice breeding programs. Inoculation tests have been used to select for resistance genotypes, with DNA marker-based selection becoming an efficient alternative. No comprehensive DNA marker system for race-specific resistance alleles in the Japanese rice breeding program has been developed because some loci contain multiple resistance alleles. Here, we used the Fluidigm SNP genotyping platform to determine a set of 96 single nucleotide polymorphism (SNP) markers for 10 loci with race-specific resistance. The markers were then used to evaluate the presence or absence of 24 resistance alleles in 369 cultivars; results were 93.5% consistent with reported inoculation test-based genotypes in japonica varieties. The evaluation system was successfully applied to high-yield varieties with indica genetic backgrounds. The system includes polymorphisms that distinguish the resistant alleles at the tightly linked Pita and Pita-2 loci, thereby confirming that all the tested cultivars with Pita-2 allele carry Pita allele. We also developed and validated insertion/deletion (InDel) markers for ten resistance loci. Combining SNP and InDel markers is an accurate and efficient strategy for selection for race-specific resistance to blast in breeding programs.

This paper proposes a temperature monitoring system as an application of IoT. The system is designed for mash temperature monitoring during sake, Japanese rice wine, brewing. The system has been installed in a brewery and is being used to monitor temperature of sake-mash fermentation process. We demonstrate that sake-mash temperature transition can be observed in real time and logged by the system.

Dinotefuran is an insecticide belonging to the neonicotinoid class, which is frequently used to control pests in paddy rice owing to its permeability and effectiveness against sucking insects. Since 2002, this insecticide has been commercially available in Japan, and has become controversial due to its high detection frequency in brown rice for primary consumption. In this study, the effects of processing and cooking on the reduction of dinotefuran residues in commercially available brown rice were investigated. Boiled rice is difficult to homogenise and extract with acetonitrile. Using pre-freezing and cryogenic milling with powdered dry ice, dinotefuran in boiled rice was extracted well. A measurement method comprising sample preparation (acetonitrile extraction, gel permeation chromatography, and SPE) and detection with anLC-MS/MS system was used. In 10 out of 25 commercial brown rice samples, dinotefuran was detected at a concentration of 0.04 μg/g (mean), which was more than the limit of quantitation of 0.01 μg/g. The dinotefuran levels were significantly less than the MRL of 2 μg/g in Japan. Even after polishing, washing, and boiling, dinotefuran was detected in 10 brown rice samples, with mean residue levels of 74.7%, 60.8%, and 39.6%, respectively, of the original concentration in brown rice. Based on these data, the processing factor of dinotefuran in boiled rice has been estimated to be approximately 0.4. Dinotefuran residues were reduced in the boiled rice, but less so than other pesticides. Although the maximum daily intake of dinotefuran in boiled rice was 0.0065 mg/person/day, its percent ratio to the ADI of dinotefuran in Japan was less than 0.05%. These results suggest that the daily intake of dinotefuran from rice might not be a critical problem at present, in spite of its relatively high detection frequency in boiled rice.

Defensins are a group of plant antimicrobial peptides. In a previous study, it was reported that two recombinant rice (Oryza sativa L.) defensin (OsDEF) genes (OsDEF7 and OsDEF8) produced heterologously by bacteria inhibited the growth of several phytopathogen. Here, we analyzed gene expression patterns in Thai jasmine rice (O. sativa L. ssp. indica 'KDML 105') using quantitative reverse transcription-polymerase chain reaction and compared them with those in Japanese rice (O. sativa L. ssp. japonica 'Nipponbare'). Although the cultivars exhibited similar gene expression patterns at the developmental stages examined, the expression levels differed between organs. Upon Xanthomonas oryzae pv. oryzae infection in the leaves, both OsDEFs were highly upregulated at 8 days post-infection, suggesting that they play a role in pathogen defense. Moreover, in silico analyses revealed that OsDEF expression levels were affected by drought, cold, imbibition, anoxia, and dehydration stress. Using green fluorescent protein (GFP) fusions, we found that both OsDEFs were in the extracellular compartment, confirming their functions against pathogen infection. However, when recombinant OsDEFs (without GFP) were produced in tobacco BY-2 cells or Nicotiana benthamiana leaves, they could not be detected in either the culture medium or the cells. Yet, N. benthamiana leaves infiltrated with OsDEF7 or OsDEF8 constructs exhibited in planta inhibitory activity against the phytopathogen Xanthomonas campestris pv. glycines, suggesting that recombinant OsDEFs were present. Additionally, when targeting them to the ER compartment, recombinant OsDEFs could be detected. Lower inhibitory activity was observed when recombinant OsDEFs were targeted to the ER. These results suggest that OsDEFs play a role in controlling plant diseases.

Japanese policies leave its retail market closed to U.S. rice. This study examined prospects of U.S. rice if these markets opened, with required country-of-origin labeling (COOL). Data were from auction experiments examining preferences for U.S. and Japanese rice under two scenarios (COOL with observation and COOL with tasting) using Japanese female primary shoppers. Two segments were identified: those open to U.S. rice at prices equal or above domestic, as likely due to tariffs, and those closed to U.S. rice at any price. About 7% of subjects were in the first segment, while nearly 26% fell in the latter. Tasting failed to generate large changes. Frequent COOL readers were especially closed even after tasting. Tasting did change the profile of open consumers, with demographics mattering less afterward. Under any policy change, U.S. rice would need a discounted price relative to domestic rice; even then, a substantial market segment appears closed.

The eating quality of cooked rice is important and determines its market price and consumer acceptance. To comprehensively describe the variation of eating quality in 183 rice germplasm accessions, we evaluated 33 eating-quality traits including amylose and protein contents, pasting properties of rice flour, and texture of cooked rice grains. All eating-quality traits varied widely in the germplasm accessions. Principal-components analysis (PCA) revealed that allelic differences in the Wx gene explained the largest proportion of phenotypic variation of the eating-quality traits. In 146 accessions of non-glutinous temperate japonica rice, PCA revealed that protein content and surface texture of the cooked rice grains significantly explained phenotypic variations of the eating-quality traits. An allelic difference based on simple sequence repeats, which was located near a quantitative trait locus (QTL) on the short arm of chromosome 3, was associated with differences in the eating quality of non-glutinous temperate japonica rice. These results suggest that eating quality is controlled by genetic factors, including the Wx gene and the QTL on chromosome 3, in Japanese rice accessions. These genetic factors have been consciously selected for eating quality during rice breeding programs in Japan.

A pair of complementary genes, Hwc1-1 at HWC1 locus and Hwc2-1 at HWC2 locus, cause a weakness phenomenon in rice. For this study, we performed haplotype analysis around the HWC2 locus in two core collections comprising 119 accessions. We also examined reactions to phenol and Xanthomonas oryzae pv. oryzae (Xoo) Japanese race I. To elucidate the genetic relations among all accessions, we analyzed their banding patterns of 40 Indel markers covering the rice genome. The classification by Indel markers was almost consistent with that using 4,357 SNPs. The testcross with Hwc1-1 carrier indicated that 37 accessions carried Hwc2-1 allele, whereas 82 carried hwc2-2 allele. Strong association between HWC2 and Ph genes was observed. Based on 14 DNA markers around HWC2 locus and Ph genotype, the 119 accessions were divided into 50 haplotypes. To examine the HWC2 candidate chromosomal region specifically, the ‘haplotype group’ characterized by the six DNA markers closely linked with HWC2 were analyzed. Hwc2-1 carriers had the same haplotype group. Some hwc2-2 haplotype groups were associated with resistance against the Xoo race. The relation between varietal differentiation and haplotypes around the HWC2 locus was discussed, along with its breeding significance.

Yayoi-murasaki is a traditional black sticky rice cultivar, which has long been grown locally in Tokushima prefecture in Japan for celebratory or religious occasions. This cultivar is characterized by late heading and easy seed shattering habits compared with modern Japanese rice cultivars, resulting in low yield performance. Severe seed shattering has been the major concern, especially under typhoon attacks. Therefore, mutant breeding using γ-ray was undertaken to mitigate seed shattering trait. Several lines selected for reduced seed shattering exhibited various phenotypes for seed shattering, fertility, and panicle morphology. These lines are a good resource for the improvement of Yayoi-murasaki and can be useful to understand the molecular mechanism of seed shattering trait in rice.

There are many rice paddy fields with relatively high arsenic (As) concentrations in areas that have not been subjected to countermeasures because the As level was below the criterion value established by the Agricultural Land Soil Contamination Prevention Law in Japan. To reduce the risk of excessive As in rice paddy fields using agronomic methods applicable to common farming practices, we examined the effect of the application of iron (Fe) and silicate materials on As uptake by rice plants in bottomless concrete frames filled with soil collected from an area surrounding a former As-polluted region. Following the application of calcium silicate slag at a rate of 0.5 kg m − 2 , no significant effect was observed on the As concentration in rice grain or straw, but the available silicate in the soil was increased. The application of Fe materials at a rate of 0.5 kg m − 2 resulted in a significant reduction of the As concentration in grain and straw, as shown by an analysis of variance. The lowest concentrations of As in both grain and straw were obtained with the application of a metal Fe powder (EM), followed by that with an Fe oxide material (FB), a converter furnace slag (FM), and the control. The EM and FB applications both significantly reduced the 1 M HCl-soluble As concentration in soil compared to the control. The levels of both acid ammonium oxalate extractable Fe (Fe- ox ) and citrate–bicarbonate–dithionite extractable Fe (Fe- CDB ) in the soil were significantly increased by the application of EM and that of FB compared to the FM and the control. A negative significant correlation was obtained between the amount of 1 M HCl-soluble As and two types of free Fe oxide. These results suggest that the available As in soil was strongly fixed with the Fe oxides that were increased by the application of Fe materials, and that the decrease of available As in the soil induced a decrease in the As uptake by rice plants. The application of Fe materials will thus be effective to lower or prevent the risk of the rice cultivation in paddy fields with relatively high levels of As.

Rice was introduced to northern Japan in the prehistoric era, when the local climate was relatively cool for rice cultivation. Ancient strains of rice could potentially be productive in unfavorable conditions for cultivation; modern strains sharing genetic traits with ancient rice may contribute useful genetic diversity. To understand the variation in Japanese rice, a comparison of seed sizes and chloroplast and nuclear DNA sequences was conducted, on modern rice accessions from diverse geographical areas, and eleven populations with seven reference populations of rice seed remains from 800 BC to 1500 AD. The populations of rice seed remains shared short grain shape and a specific chloroplast genotype with modern Japanese and worldwide rice accessions. This morphology and genotype may have been introduced to Japan along with farming techniques. Variability of seed shape and diversity of the nuclear genome both reduced through time, indicating genetic erosion in Japanese rice. Greater diversity in the populations of rice seed remains, taken together with archaeological and historical evidence, suggests that older rice populations had genetic traits that could adapt to unfavorable conditions of cultivation, such as flooding and low temperatures. Modern landraces share a genome structure with rice seed remains populations, which suggests that the modern landraces may have useful breeding traits such as tolerance of flooding and low temperatures.

Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar 'Koshihikari' was performed to extract regions containing large indels (10-51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between 'Koshihikari' and other diverse cultivars, we subtracted the indel regions detected in 'Koshihikari' from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including 'Khao Nam Jen' as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.

This chapter provides results of the simultaneous measurements of emission, production, and oxidation of methane (CH4) in a Japanese rice paddy field during an entire cultivation period. It focuses on seasonal changes of CH4 production and oxidation in different depths of paddy soil, and their relationship to CH4 emission, in order to understand factors controlling this process in paddy fields. A field study was carried out in an experimental paddy field of the Ryugasaki Branch of the Ibaraki Agricultural Experiment Station during the 1991 growing season. The soil of the paddy field is classified as Gley soil. The closed chamber method was used for the measurements of the CH4 emissions from paddy fields into the atmosphere. Temperature of air and paddy soil at the depths of 0, 2, 5, and 10 cm was continuously recorded during the cultivation periods by using Pt-resistance thermometers and a data logger.

Grain-filling ability is one of the factors that controls grain yield in rice (Oryza sativa L.). We developed a method for describing grain weight distribution, which is the probability density function of single grain weight in a panicle, using 128 Japanese rice varieties. With this method, we quantitively analyzed genotypic differences in grain-filling ability and used the grain weight distribution parameters for genomic prediction subject to genetic improvement in grain yield in rice. The novel description method could represent the observed grain weight distribution with five genotype-specific parameters of a mixture of two gamma distributions. The estimated genotype-specific parameters representing the proportion of filled grains had applicability to explain the grain filling ability of genotypes comparable to that of sink-filling rate and the conventionally measured proportion of filled grains, which suggested the efficiency and flexibility of grain weight distribution parameters to handle several genotypes. We revealed that perfectly filled grains have to be prioritized over partially filled grains for the optimum allocation of the source of yield in a panicle, from the analysis for obtaining an ideal shape of grain weight distribution. We conducted genomic prediction of grain weight distribution considering five genotype-specific parameters of the distribution as phenotypes relating to grain filling ability. The proportion of filled grains, average weight of filled grains, and variance of filled grain weight, which were considered to control grain yield to a certain degree, were predicted with accuracies of 0.30, 0.28, and 0.53, respectively. The proposed description method of grain weight distribution facilitated not only the investigation of the optimum allocation of nutrients in a panicle for realizing high grain-filling ability, but also allowed genomic selection of grain weight distribution.

The incidence of extreme rain is expected to increase with climate change and affect rice productivity in Japan. This study aims to evaluate the impacts of long and heavy rain on Japanese rice total-factor productivity (TFP) by estimating causality functions. We measured rice TFP by using the TornqvistTheil and Malmquist indexes for dependent variables and predicted, the influences of future temperature and rain on rice TFP by the causality function associated with crop models and a hydrological model based on climate projections from the global-climate model (GCM). The results initially showed no significant differences between Tornqvist-Theil and Malmquist indices in the effects of climate factors, although some differences emerged in the causality of socioeconomic factors. Second, the effects of rain were always negative, and absolute TFP elasticity against rain was lower than temperature via yield and quality, but poorly drained surface water as well as flooding reduced rice TFP by 2.5 to 4.5%. Third, changes in predicted rainfall under future climate change caused annual rice TFP to fluctuate, and an impact of rain on TFP fluctuations exceeded that of temperature via yield and quality. This is due to significant variations in annual rainfall, even though the measured elasticity against rain was low. Based on these findings, the implications for research and policy-making are discussed.

To evaluate the effects of O3 on the net photosynthetic rate in flag leaves of rice (Oryza sativa L.) based on stomatal O3 flux and reactive oxygen species (ROS) scavenging enzyme activities, the Japanese rice cultivar Koshihikari was exposed to O3 for 1 month after heading in O3-exposure chambers. During the exposure period, rice plants were exposed to charcoal-filtered air or O3 at 60 or 100 nl l(ppb) daily (10:00–17:00). Light-saturated net photosynthetic rate (Asat) and ROS scavenging enzyme activities in the flag leaves were periodically measured during the exposure period. The O3 exposure significantly reduced Asat on the 20th and 31st days after the beginning of O3 exposure (DAE). The degree of O3-induced reduction in Asat was explained by the cumulative flux of O3 compared with concentration-based O3 indices. The activities of ROS scavenging enzymes such as ascorbate peroxidase and catalase at 32 DAE were lower than at 1 DAE. During the latter half of the O3 exposure period (21–31 DAE), the daily average stomatal O3 flux was also lower than that during the first half of the period (1–20 DAE), which was mainly caused by lower photosynthetic photon flux density, lower air temperature and leaf senescence. These results suggest that the balance between stomatal O3 flux and leaf cellular detoxification capacity in the flag leaves of rice, which determines the degree of O3 damage, might have been similar between the first half and latter half of the O3 exposure period.

The effect of rice bran on dry matter production of different rice cultivars, namely the Chinese panicle weight types and Japanese panicle number types, was evaluated in field conditions, with growth, canopy production structure and the root system determined over a period of 60 days. The treatments consisted of rice cultivars with 1000 kg ha1 rice bran without agrochemicals (RB), cultivars with chemical fertilizer and cultivars with herbicide, with the latter serving as a control. The crop growth rate (CGR) and mean leaf area index (mLAI) in RB treatment were lower than that of the control; however, the net assimilation rate (NAR) was higher for all growth stages in this treatment. It was noted that CGR in RB and the control treatment depended greatly on mLAI during the early and middle growth stages, whereas CGR was more dependent on NAR in the late growth stage. Correlation between CGR in middle stage and the extinction coefficient of the canopy (k) at heading was apparent (p < 0.05). NAR in middle stage was positively correlated with mean leaf color and specific leaf weight (SLW). The correlations between NAR in the late stage and bleeding rate per number of primary roots, and per leaf area at maturity was apparent (p < 0.01). Root vitality and NAR were higher in RB treatment. The photosynthesis-related traits after heading in RB treatment were better than the control. Reduction of ∆W in RB treatment as well as the spikelets number (SN) was unapparent. The panicle number type cultivars did not inhibit growth during the early and middle growth stages with the presence of rice bran. The difference between growth, panicle number and weight cultivars was insignificant in the late stage. Discipline: Crop production Additional key words: bleeding rate, growth analysis, light extinction coefficient, the panicle number type cultivars, root system. This research was supported in part by Tianjin natural science fund for Scientific Research (No.11JCYBJC27100) from the Tianjin Municipal Science and Technology Commission, China. The Project Sponsored by the Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry (No.46). This research was supported in part by the ScienceT accepted 2 March 2015 Introduction The use of nitrogen in paddy cultivation in China is three times higher than in Japan. In this context, excess application of chemical fertilizer in paddy cultivation pollutes the environment and has adverse effects on both aquatic and terrestrial organisms. The use of chemical fertilizers increases operation costs, resulting in higher rice and rice product prices. It is, therefore, important to find new alternatives as substitutes for chemical fertilizer in paddy farming to alleviate environmental issues arising from their use. Rice bran is often used in the organic paddy farming in Japan because of its efficacy as a fertilizer and herbicide. This cultivation technique fulfills the growing demand for agriculture products with fewer or no agrochemicals to

Future climate change will affect rice production, but whether these changes will be beneficial or detrimental is unclear. The present study evaluates the effect of climate change on Japanese rice production, rice price, agricultural income, and regional economies by using a recursive-dynamic regional computable general equilibrium (CGE) model, which is associated with crop-growth and crop-quality models. Simulation results demonstrate that future climate change will increase overall Japanese rice production nationwide, but that the price of rice will decrease. As a result, agricultural income will decrease, despite increased production in northern and eastern Japan, such as Hokkaido, Tohoku, and Kanto (including Niigata prefecture). Climate change will not benefit rice farmers in these regions. However, the western region will benefit, despite the decrease in production, and the consumer surplus in most regions will increase. This happens because rice demand is inelastic and an increase in production results in a serious decline in price, which more than offsets the effects of climate change on production. As such, the impacts of climate change are complicated and differ by region, so a CGE model can provide useful information to consider policy countermeasures.

This article examines the largely unexplored topic of Japan’s foreign trade in rice during the Meiji period. In the middle decades of that era, japonica -type rice became a major Japanese export, highly esteemed in Western countries. In the 1890s, however, Western markets for Japanese rice shrank as the price of the grain rose; meanwhile, crop failures in Japan, combined with the ready availability of cheaper, long-grain indica varieties from Southeast Asia, prompted huge imports of rice; and the steady increase in per capita consumption drove Japan to become a chronic net importer of the commodity after the turn of the century.

Clostridium oryzae was originally isolated from the soil of a Japanese rice field. C. oryzae represents a novel species within the genus Clostridium and is associated with anaerobic rice straw degradation. Here, we present the draft genome sequence of C. oryzae DSM 28571 (5.076 Mbp), containing 4,590 predicted protein-coding genes.

O presente estudo tem como objetivo realizar a análise térmica do amido de arroz japônica submetido a diferentes processos de moagem (bolas, discos e facas). O amido foi extraído com a solução de metabissulfito de sódio (0,2%), triturado, decantado e seco a (50 ºC) até peso constate. As propriedades térmicas foram analisada através das técnicas de termogravimetria e calorimetria exploratória diferencial. Pode-se afirmar que os grânulos do amido nativo de arroz japônica são pouco resistentes e a trituração com moinho de facas os deixou mais susceptíveis à quebra com o aquecimento prolongado. As diferentes técnicas de moagem modificaram significativamente as propriedades térmicas do amido de arroz japônica, visto que na análise termogravimetria a formulação obtida através do moinho de discos apresentou distinção em relação a perda de massa, enquanto que para a calorimetria exploratória diferencial o amido obtido no processo de moagem com o moinho de bolas apresentou menor temperatura inicial de gelatinização e maior entalpia de gelatinização.

Fejervarya kawamurai (Dicroglossidae) is an invasive species occurring in several populations in the Kanto region, including Fujisawa City, Kanagawa Prefecture, Japan. To estimate the ecological impacts of this frog, we investigated the food habits of invasive populations. We collected 119 individuals of F. kawamurai. Of these, 108 (90.8%) had stomach contents that included various small animals. Therefore, this invasive frog might influence the ecosystem via predation pressure on small native animals.

A total of 324 Japanese rice accessions, including landrace, improved, and weedy types were used to 1) investigate genetic variations in blast resistance to standard differential isolates, and 2) across the genome using polymorphism data on 64 SSR markers. From the polymorphism data, the accessions were classified into two clusters,. Accessions from irrigated lowland areas were included mainly in cluster I, and upland and Indica types were mainly in cluster II. The accessions were classified into three resistance subgroups, A2, B1 and B2, based on the reaction patterns to blast isolates. The accessions in A2 were postulated to have at least two resistance genes Pish and Pik-s, whereas those in B1 had various combinations of the resistance genes Pish, Pia, Pii, Pi3, Pi5(t), and Pik alleles. The B2 accessions were resistant to almost all isolates, and many accessions of cluster II were included, and had Pish, Pia, Pii, Pi3, Pi5(t), certain Pik, Piz and Pita alleles, and unknown genes. The frequencies of accessions of B1 originating in Hokkaido, and those of B2 originating in the Kanto and Tohoku regions were remarkably higher than in the other regions.

Ferulic and p-coumaric acids were analyzed in 50 rice (Oryza sativa L.) samples from 32 cultivars harvested in Japan. In brown rice, ferulic and p-coumaric acid levels ranged from 309 to 607 mg/kg and from 49 to 100 mg/kg, respectively. In 70% polished rice, ferulic and p-coumaric acid levels ranged from 27 to 103 mg/kg and from 0.4 to 3.5 mg/kg, respectively. Ratios of average phenolic acid levels in the 70% polished rice to the brown rice were 13.9% for ferulic acid and 1.9% for p-coumaric acid. The ferulic acid level was highly correlated between brown and 70% polished rice (R = 0.815; P < 0.01), but there was no clear correlation for p-coumaric acid. Phenolic acid levels in the 70% polished rice did not show any clear correlations between the analytical index measurements for sake brewing suitability (weight of 1,000 grains, water absorption, digestibility, crude protein, and potassium content). Phenolic acid levels in the 70% polished rice directly affected levels in the rice koji enzyme dig...

Instantaneous growth related changes of leaves of Radish, Soybean and rice plants were investigated with a highspeed and ultra-high accuracy optical interferometer. The interferometer, called statistical interferometer, SIT (Statistical Interferometric Technique) is a real-time, non-contact, and robust one and has a subnanometric accuracy and can measure leaf elongation changes every 500 ms. SIT revealed the existence of nanometric fluctuations in the elongation of leaves. Control experiments with dead and mature leaves did indeed establish the existence of null or smaller standard deviations in the fluctuations in contrast to the large deviations obtained for young and healthier leaves. Moreover, the standard deviations of the fluctuations were found to be sensitive to environment of ozone(O3), a secondary atmospheric pollutant. Long term O3 exposure with Radish and Soybean leaves led to a decrease in the standard deviations of nanometric fluctuations with increase in O3 concentrations which correlated with a decrease of gas exchange measures. Under short term O3 exposures for 3 h with two Japanese rice cultivars, cv. Koshihikari and cv. Fusaotome that are known to have varying O3 tolerance made the nanometric fluctuations to decrease in comparison to gas exchange measures which showed no variation. The fluctuations could also differentiate the cultivar’s sensitivity to O3 with cv. Koshihikari showing a drastic reduction in comparison to cv. Fusaotome. The results suggest that the nanometric fluctuations may possibly relate to the life maintaining physiological state of the plant and thus may act as an indicator of the vitality of the plant.

The appearance of brown rice grown under high temperature conditions is an important characteristic for improvement in Japanese rice breeding programs. We performed a QTL analysis of the appearance quality of brown rice using chromosome segment substitution lines of the indica cultivar 'Habataki' in the 'Koshihikari' genetic background. A line carrying a 'Habataki' segment on chromosome 7 showed a high percentage of perfect grains produced under high temperature conditions during the ripening period. To verify the role of this segment, and to narrow down the region containing the useful allele, substitution mapping was performed using multiple paired lines. As a result, the chromosomal location of a gene that we named Appearance quality of brown rice 1 (Apq1) was delimited to a 48-kb region. In addition, we developed an Apq1-near isogenic line (NIL) to evaluate the effect of Apq1 on various agronomic traits. Under high temperature conditions during the ripening period, the Apq1-NIL produced significantly higher percentages of perfect grains than 'Koshihikari'. Other agronomic traits, including yield and palatability, were similar between the Apq1-NIL and 'Koshihikari'. Therefore, the 'Habataki' allele of Apq1 will be useful in breeding programs aimed at improving the quality of grains ripened under high temperature conditions.

The main motivation in studying different types of rice was to determine how processing of rice affects its mineral composition, and to compare how it affects rice dietary intake. Specifically the estimated difference in between the brown and white rice produced in Japan and California are studied. These various rice samples were analyzed using neutron activation analysis technique available at the Utah Nuclear Engineering Program (UNEP). Samples were prepared using novel technique developed at UNEP and submitted for short and long irradiation. The detected elements were As, Br, Cl, Cd, Mn, Na, K. The concentrations of Mn, K and Na are significantly higher in the brown then in the white rice, while As, Br and Cl have more homogeneous presence and therefore smaller difference in concentration. Elemental concentration was compared with The Institute of Medicine (IOM) in the United States values of recommended dietary allowance and Food and Drug Administration (FDA) limits for harmful elements. From these measurements, only the concentration of Mn in rice satisfies daily needs in the range set as defined by IOM. The concentrations of potentially harmful elements are lower than FDA limits.