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Aims Longer root hair length (RHL) increases root surface area, thereby contributing to increased phosphorous uptake. This study aimed to identify useful germplasms and quantitative trait loci (QTL) for RHL improvement in wheat. Methods The genetic variation in RHL was examined using hydroponic culture in 117 hexaploid wheat strains. Rhizosheath size and phosphorous uptake ability were also examined using high P-fixing soils with extremely low phosphorous availability (Andisols). QTL analysis was performed using backcross inbred lines from a cross between a Spanish spelt strain and a bread wheat variety. Results A wide range in genetic variation was found, especially in spelt wheat and landraces of bread wheat, whereas modern bread wheat varieties tended to show shorter RHL. Interestingly, remarkably longer RHL were observed in Spanish spelt strains than in strains from other countries. RHL exhibited a significant positive correlation with rhizosheath size and phosphorous uptake in soils. A QTL on chromosome 2A (QRhl.obu-2A) conferring longer RHL by the allele of a Spanish spelt strain was identified. It was co-located with TaRSL4-2AS, a key regulator of root hair elongation. Conclusions Spanish spelt wheat strains could be unique germplasms that provide a useful allele for increasing RHL to enhance phosphorous uptake ability.

DOI： 10.1007/s11104-020-04555-8

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Agronomically important traits often develop during the later stages of crop growth as consequences of various plant-environment interactions. Therefore, the temporal physiological states that change and accumulate during the crop's life course can significantly affect the eventual phenotypic differences in agronomic traits among crop varieties. Thus, to improve productivity, it is important to elucidate the associations between temporal physiological responses during the growth of different crop varieties and their agronomic traits. However, data representing the dynamics and diversity of physiological states in plants grown under field conditions is sparse. In this study, we quantified the endogenous levels of five phytohormones-auxin, cytokinins, abscisic acid, jasmonate, and salicylic acid-in the leaves of eight diverse barley (Hordeum vulgare) accessions grown under field conditions sampled weekly over their life course to assess the ongoing fluctuations in hormone levels in the different accessions under field growth conditions. Notably, we observed enormous changes over time in the development-related plant hormones, such as auxin and cytokinins. Using 3' RNA-seq-based transcriptome data from the same samples, we investigated the expression of barley genes orthologous to known hormone-related genes of Arabidopsis throughout the life course. These data illustrated the dynamics and diversity of the physiological states of these field-grown barley accessions. Together our findings provide new insights into plant-environment interaction, highlighting that there is cultivar diversity in physiological responses during growth under field conditions.

DOI： 10.1093/pcp/pcaa046

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In order to train the neural network for plant phenotyping, a sufficient amount of training data must be prepared, which requires time-consuming manual data annotation process that often becomes the limiting step. Here, we show that an instance segmentation neural network aimed to phenotype the barley seed morphology of various cultivars, can be sufficiently trained purely by a synthetically generated dataset. Our attempt is based on the concept of domain randomization, where a large amount of image is generated by randomly orienting the seed object to a virtual canvas. The trained model showed 96% recall and 95% average Precision against the real-world test dataset. We show that our approach is effective also for various crops including rice, lettuce, oat, and wheat. Constructing and utilizing such synthetic data can be a powerful method to alleviate human labor costs for deploying deep learning-based analysis in the agricultural domain.

DOI： 10.1038/s42003-020-0905-5

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Aluminum (Al) toxicity is a major stress factor limiting crop productivity in acid soil. Although there is great genotypic variation in tolerance to Al toxicity, the underlying molecular mechanisms are poorly understood. Here, we report that, in barley (Hordeum vulgare), the fourth largest cereal crop produced in the world, both retrotransposon insertion and DNA methylation are involved in regulating differential Al tolerance. HvAACT1 is a major gene responsible for citrate secretion from the roots for external detoxification of Al. A multiretrotransposon-like (MRL) sequence insertion at least 15.3 kb in length was detected in the upstream genomic region of HvAACT1 that displayed promoter activity and significantly enhanced HvAACT1 expression, especially in the root tips of Al-tolerant accessions. Furthermore, in a number of accessions with low levels of HvAACT1 expression, this MRL insertion was present but highly methylated. Geographical analysis showed that accessions with this MRL insertion are distributed mainly in European areas with acid soils. Two wild barley accessions were found to possess this MRL insertion, but with a high degree of methylation. These results indicate that the MRL insertion and its degree of DNA methylation influence HvAACT1 expression and that demethylation of this MRL insertion, which facilitates adaptation to acid soils, occurred following barley domestication. Moreover, our results indicate that barley accessions in East Asia and Europe have developed independent but equivalent strategies to withstand Al toxicity in acid soils.

DOI： 10.1104/pp.18.00651

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Crops are exposed to various environmental stresses in the field throughout their life cycle. Modern plant science has provided remarkable insights into the molecular networks of plant stress responses in laboratory conditions, but the responses of different crops to environmental stresses in the field need to be elucidated. Recent advances in omics analytical techniques and information technology have enabled us to integrate data from a spectrum of physiological metrics of field crops. The interdisciplinary efforts of plant science and data science enable us to explore factors that affect crop productivity and identify stress tolerance-related genes and alleles. Here, we describe recent advances in technologies that are key components for data driven crop design, such as population genomics, chronological omics analyses, and computer-aided molecular network prediction. Integration of the outcomes from these technologies will accelerate our understanding of crop phenology under practical field situations and identify key characteristics to represent crop stress status. These elements would help us to genetically engineer “designed crops” to prevent yield shortfalls because of environmental fluctuations due to future climate change.

DOI： 10.3389/fpls.2015.00740

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DOI： 10.1270/jsbbr.17.71

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<p>Brachypodium distachyon, which belongs to the subfamily Pooideae, has recently been studied extensively as a model temperate grass. Since Brachypodium possesses type II cell wall, which is a structural characteristic of Poaceae plants, and is also found in energy crops, such as switchgrass and Miscanthus, as cellulose biomass resources, it has been proposed as a model plant in grass biomass research. In addition, Brachypodium is included in the Pooideae subfamily together with wheat and barley, and therefore, it could be promising to study biological functions related to agronomically important traits, such as seed development and flowering, in Triticeae crops. Brachypodium represents tractable features as a model plant ; small plant size, healthy growth inside laboratory conditions, without any requirement of any specific instruments, short life cycle, small genome size (272 Mb), and availability of transformation. Following the completion of whole-genome sequencing in 2010, various resources for Brachypodium research have been developed world wide. In this review, we introduce the current trends in Brachypodium research as well as provide prospects and expected functionalities of the model grass.</p>

DOI： 10.18978/jscrp.50.2_103

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The spring-type near isogenic line (NIL) of the winter-type barley (Hordeum vulgare ssp. vulgare) var. Hayakiso 2 (HK2) was developed by introducing VERNALIZATION-H1 (Vrn-H1) for spring growth habit from the spring-type var. Indo Omugi. Contrary to expectations, the spring-type NIL flowered later than winter-type HK2. This phenotypic difference was controlled by a single gene, which cosegregated only with phytochrome C (HvPhyC) among three candidates around the Vrn-H1 region (Vrn-H1, HvPhyC, and CASEIN KINASE IIα), indicating that HvPhyC was the most likely candidate gene. Compared with the late-flowering allele HvPhyC-l from the NIL, the early-flowering allele HvPhyC-e from HK2 had a single nucleotide polymorphism T1139C in exon 1, which caused a nonsynonymous amino acid substitution of phenylalanine at position 380 by serine in the functionally essential GAF (39, 59-cyclic-GMP phosphodiesterase, adenylate cyclase, formate hydrogen lyase activator protein) domain. Functional assay using a rice (Oryza sativa) phyA phyC double mutant line showed that both of the HvPhyC alleles are functional, but HvPhyC-e may have a hyperfunction. Expression analysis using NILs carrying HvPhyC-e and HvPhyC-l (NIL [HvPhyC-e] and NIL [HvPhyC-l], respectively) showed that HvPhyC-e up-regulated only the flowering promoter FLOWERING LOCUS T1 by bypassing the circadian clock genes and flowering integrator CONSTANS1 under a long photoperiod. Consistent with the up-regulation, NIL (HvPhyC-e) flowered earlier than NIL (HvPhyC-l) under long photoperiods. These results implied that HvPhyC is a key factor to control long-day flowering directly. © 2013 American Society of Plant Biologists. All Rights Reserved.

DOI： 10.1104/pp.113.222570

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Polyphenol oxidases (PPOs) are copper-containing metalloenzymes encoded in the nucleus and transported into the plastids. Reportedly, PPOs cause time-dependent discoloration (browning) of end-products of wheat and barley, which impairs their appearance quality. For this study, two barley PPO homologues were amplified using PCR with a primer pair designed in the copper binding domains of the wheat PPO genes. The full-lengths of the respective PPO genes were cloned using a BAC library, inverse-PCR, and 3′-RACE. Linkage analysis showed that the polymorphisms in PPO1 and PPO2 co-segregated with the phenol reaction phenotype of awns. Subsequent RT-PCR experiments showed that PPO1 was expressed in hulls and awns, and that PPO2 was expressed in the caryopses. Allelic variation of PPO1 and PPO2 was analysed in 51 barley accessions with the negative phenol reaction of awns. In PPO1, amino acid substitutions of five types affecting functionally important motif(s) or C-terminal region(s) were identified in 40 of the 51 accessions tested. In PPO2, only one mutant allele with a precocious stop codon resulting from an 8 bp insertion in the first exon was found in three of the 51 accessions tested. These observations demonstrate that PPO1 is the major determinant controlling the phenol reaction of awns. Comparisons of PPO1 single mutants and the PPO1PPO2 double mutant indicate that PPO2 controls the phenol reaction in the crease on the ventral side of caryopses. An insertion of a hAT-family transposon in the promoter region of PPO2 may be responsible for different expression patterns of the duplicate PPO genes in barley. © 2010 The Author(s).

DOI： 10.1093/jxb/erq211

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Domesticated barleys produce either two- or six- rowed spikes, whereas their immediate wild ancestor, wild barley, is monomorphic for the two-rowed type. The six-rowed spike is a recessive character, conditioned by a major gene at the vrs1 locus. The wild-type (two-rowed) gene includes a homeodomain-leucine zipper I (HD-Zip 1) sequence (HvHox1). The correspondence between peptide sequence and some spike variants was studied by re-sequencing the HvHox1 sequence across a large sample of both wild and domesticated accessions.

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Adaptation to edaphic stress may have a key role in plant species range expansion. Aegilops tauschii Coss., the common wheat's D-genome progenitor native to the Transcaucasus-Middle East region, is a good model to study the relationships between soil salinity and plant distributions: one of its intraspecific sublineages, TauL1b, drove the long-distance eastward expansion of this species range reaching semi-arid-central Asia. Salt tolerance during germination and seedling growth was evaluated in 206 Ae. tauschii accessions by treating seeds with NaCl solutions differing in concentrations. Differences in natural variation patterns were analyzed between sublineages and associated with natural edaphic condition variables, and then compared with reproductive trait variation patterns. The natural variations observed in NaCl-induced-stress tolerance had clear geographic and genetic structure. Seedling growth significantly increased in the TauL1b accessions that were collected from salt-affected soil habitats, whereas germinability did not. Principal component analysis suggested that the NaCl-induced-stress tolerances and reproductive traits might have had a similar degree of influence on Ae. tauschii's eastward range expansion. Adaptation to salt-affected soils through increased seedling growth was an important factor for the species' successful colonization of the semi-arid central Asian habitats. TauL1b accessions might provide useful genetic resources for salt-tolerant wheat breeds.

DOI： 10.1038/srep38554

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Barley is one of the founder crops of Old world agriculture and has become the fourth most important cereal worldwide. Information on genome-scale DNA polymorphisms allows elucidating the evolutionary history behind domestication, as well as discovering and isolating useful genes for molecular breeding. Deep transcriptome sequencing enables the exploration of sequence variations in transcribed sequences; such analysis is particularly useful for species with large and complex genomes, such as barley. In this study, we performed RNA sequencing of 20 barley accessions, comprising representatives of several biogeographic regions and a wild ancestor. We identified 38,729 to 79,949 SNPs in the 19 domesticated accessions and 55,403 SNPs in the wild barley and revealed their genome-wide distribution using a reference genome. Genome-scale comparisons among accessions showed a clear differentiation between oriental and occidental barley populations. The results based on population structure analyses provide genome-scale properties of sub-populations grouped to oriental, occidental and marginal groups in barley. Our findings suggest that the oriental population of domesticated barley has genomic variations distinct from those in occidental groups, which might have contributed to barley's domestication.

DOI： 10.1038/srep33199

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Originating from the Fertile Crescent in the Middle East, barley has now been cultivated widely on different soil types including acid soils, where aluminium toxicity is a major limiting factor. Here we show that the adaptation of barley to acid soils is achieved by the modification of a single gene (HvAACT1) encoding a citrate transporter. We find that the primary function of this protein is to release citrate from the root pericycle cells to the xylem to facilitate the translocation of iron from roots to shoots. However, a 1-kb insertion in the upstream of the HvAACT1 coding region occurring only in the Al-tolerant accessions, enhances its expression and alters the location of expression to the root tips. The altered HvAACT1 has an important role in detoxifying aluminium by secreting citrate to the rhizosphere. Thus, the insertion of a 1-kb sequence in the HvAACT1 upstream enables barley to adapt to acidic soils.

DOI： 10.1038/ncomms1726

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Language：Japanese   Publisher：一般社団法人 日本土壌肥料学会  

DOI： 10.20710/dohikouen.58.0_76_2

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Non-retroviral RNA virus sequences (NRVSs) have been found in the chromosomes of vertebrates and fungi, but not plants. Here we report similarly endogenized NRVSs derived from plus-, negative-, and double-stranded RNA viruses in plant chromosomes. These sequences were found by searching public genomic sequence databases, and, importantly, most NRVSs were subsequently detected by direct molecular analyses of plant DNAs. The most widespread NRVSs were related to the coat protein (CP) genes of the family Partitiviridae which have bisegmented dsRNA genomes, and included plant-and fungus-infecting members. The CP of a novel fungal virus (Rosellinia necatrix partitivirus 2, RnPV2) had the greatest sequence similarity to Arabidopsis thaliana ILR2, which is thought to regulate the activities of the phytohormone auxin, indole-3-acetic acid (IAA). Furthermore, partitivirus CP-like sequences much more closely related to plant partitiviruses than to RnPV2 were identified in a wide range of plant species. In addition, the nucleocapsid protein genes of cytorhabdoviruses and varicosaviruses were found in species of over 9 plant families, including Brassicaceae and Solanaceae. A replicase-like sequence of a betaflexivirus was identified in the cucumber genome. The pattern of occurrence of NRVSs and the phylogenetic analyses of NRVSs and related viruses indicate that multiple independent integrations into many plant lineages may have occurred. For example, one of the NRVSs was retained in Ar. thaliana but not in Ar. lyrata or other related Camelina species, whereas another NRVS displayed the reverse pattern. Our study has shown that single-and double-stranded RNA viral sequences are widespread in plant genomes, and shows the potential of genome integrated NRVSs to contribute to resolve unclear phylogenetic relationships of plant species.

DOI： 10.1371/journal.ppat.1002146

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In many temperate plant species, prolonged cold treatment, known as vernalization, is one of the most critical steps in the transition from the vegetative to the reproductive stage. In contrast to recent advances in understanding the molecular basis of vernalization in Arabidopsis non-vernalization mutants or the spring growth habits of cereal crops such as wheat and barley, natural variations in winter growth habits and their geographic distribution are poorly understood. We analyzed varietal variation and the geographic distribution of the degree of vernalization requirements in germplasms of domesticated barley and wild barley collections. We found a biased geographic distribution of vernalization requirements in domesticated barley: Western regions were strongly associated with a higher degree of spring growth habits, and the extreme winter growth habits were localized to Far Eastern regions including China, Korea and Japan. Both wild accessions and domesticated landraces, the regions of distribution of which overlapped each other, mainly belonged to the moderate class of winter growth habit. As a result of quantitative evaluations performed in this study, we provide evidence that the variation in the degree of winter growth habit in recombinant inbred lines was controlled by quantitative trait loci including three vernalization genes (VRN1, VRN2 and VRN3) that account for 37.9% of the variation in vernalization requirements, with unknown gene(s) explaining the remaining two-thirds of the variation. This evidence implied that the Far Eastern accessions might be a genetically differentiated group derived for an evolutionary reason, resulting in their greater tendency towards a winter growth habit.

DOI： 10.1093/pcp/pcr046

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Language：English   Publisher：OXFORD UNIV PRESS  

DOI： 10.1093/pcp/pcr049

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Background: The recent rapid accumulation of sequence resources of various crop species ensures an improvement in the genetics approach, including quantitative trait loci (QTL) analysis as well as the holistic population analysis and association mapping of natural variations. Because the tribe Triticeae includes important cereals such as wheat and barley, integration of information on the genetic markers in these crops should effectively accelerate map-based genetic studies on Triticeae species and lead to the discovery of key loci involved in plant productivity, which can contribute to sustainable food production. Therefore, informatics applications and a semantic knowledgebase of genome-wide markers are required for the integration of information on and further development of genetic markers in wheat and barley in order to advance conventional marker-assisted genetic analyses and population genomics of Triticeae species.
Description: The Triticeae mapped expressed sequence tag (EST) database (TriMEDB) provides information, along with various annotations, regarding mapped cDNA markers that are related to barley and their homologues in wheat. The current version of TriMEDB provides map-location data for barley and wheat ESTs that were retrieved from 3 published barley linkage maps (the barley single nucleotide polymorphism database of the Scottish Crop Research Institute, the barley transcript map of Leibniz Institute of Plant Genetics and Crop Plant Research, and HarvEST barley ver. 1.63) and 1 diploid wheat map. These data were imported to CMap to allow the visualization of the map positions of the ESTs and interrelationships of these ESTs with public gene models and representative cDNA sequences. The retrieved cDNA sequences corresponding to each EST marker were assigned to the rice genome to predict an exon-intron structure. Furthermore, to generate a unique set of EST markers in Triticeae plants among the public domain, 3472 markers were assembled to form 2737 unique marker groups as contigs. These contigs were applied for pairwise comparison among linkage maps obtained from different EST map resources.
Conclusion: TriMEDB provides information regarding transcribed genetic markers and functions as a semantic knowledgebase offering an informatics facility for the acceleration of QTL analysis and for population genetics studies of Triticeae.

DOI： 10.1186/1471-2229-8-72

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Barley includes semi-dwarf varieties, called uzu, which are localized in parts of southwestern Japan, the Southern Korea peninsula, and coastal areas of China. The uzu phenotype possesses dark green leaves and short coleoptiles, awns, and panicles. It is controlled by a single recessive gene: uzu. Uzu results from a mutation in the brassinosteroid receptor kinase gene (HvBR11). Brassinosteroid synergistically acts with auxin on plant morphology, which is an important plant hormone for tissue culture. For this study, tissue Culture traits, including callus growth and shoot regeneration capability, were examined in F-2 populations derived from crosses between normal and uzu lines, and in isogenic lines for the uzu gene. The uzu genotype shows a lower percentage of shoot regeneration than the normal genotype in F, populations and isogenic lines. The uzu gene negatively affects shoot regeneration. No significant differences were Found In callus growth capability between uzu and normal genotypes. Uzu isogenic lines show higher sensitivity to exogenous auxin for callus initiation than normal lines, when immature embryos were incubated on media supplemented with several concentrations of 2,4-D under culture at higher temperature (25 degrees C). Tissue Culture traits of uzu might be regulated through cross-talk between brassinosteroid and auxin.

DOI： 10.1270/jsbbs.58.149

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In contrast to other cereals, typical barley cultivars have caryopses with adhering hulls at maturity, known as covered (hulled) barley. However, a few barley cultivars are a free-threshing variant called naked (hulless) barley. The covered/naked caryopsis is controlled by a single locus (nud) on chromosome arm 7HL. On the basis of positional cloning, we concluded that an ethylene response factor (ERF) family transcription factor gene controls the covered/naked caryopsis phenotype. This conclusion was validated by (i) fixation of the 17-kb deletion harboring the ERF gene among all 100 naked cultivars studied; (ii) two x-ray-induced nud alleles with a DNA lesion at a different site, each affecting the putative functional motif; and (iii) gene expression strictly localized to the testa. Available results indicate the monophyletic origin of naked barley. The Nud gene has homology to the Arabidopsis WIN1/SHN1 transcription factor gene, whose deduced function is control of a lipid biosynthesis pathway. Staining with a lipophilic dye (Sudan black B) detected a lipid layer on the pericarp epidermis only in covered barley. We infer that, in covered barley, the contact of the caryopsis surface, overlaid with lipids to the inner side of the hull, generates organ adhesion.

DOI： 10.1073/pnas.0711034105

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Barley (Hordeum vulgare ssp. vulgare) was first cultivated 10,500 years ago in the Fertile Crescent and is one of the founder crops of Eurasian agriculture. Phylogeographic analysis of five nuclear loci and morphological assessment of two traits in &gt;250 domesticated barley accessions reveal that landraces found in South and East Asia are genetically distinct from those in Europe and North Africa. A Bayesian population structure assessment method indicates that barley accessions are subdivided into six clusters and that barley landraces from 10 different geographical regions of Eurasia and North Africa show distinct patterns of distribution across these clusters. Using haplotype frequency data, it appears that the Europe/North Africa landraces are most similar to the Near East population (F-ST = 0.15) as well as to wild barley (F-ST = 0.11) and are strongly differentiated from all other Asian populations (F-ST = 0.34-0.74). A neighbor-joining analysis using these F-ST estimates also supports a division between European, North African, and Near East barley types from more easterly Asian accessions. There is also differentiation in the presence of a naked caryopsis and spikelet row number between eastern and western barley accessions. The data support the differential migration of barley from two domestication events that led to the origin of barley - one in the Fertile Crescent and another farther east, possibly at the eastern edge of the Iranian Plateau - with European and North African barley largely originating from the former and much of Asian barley arising from the latter. This suggests that cultural diffusion or independent innovation is responsible for the expansion of agriculture to areas of South and East Asia during the Neolithic revolution.

DOI： 10.1534/genetics.107.079491

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Cultivated barley (Hordeum vulgare L.) is well known as one of the most widely cultivated crops in the world and as an extensively studied plant species in the field of genetics. In recent years, despite its very large genome size (ca. 5,000 Mb), the research resources needed for barley genomic studies have become available, including a large number of expressed sequence tags (ESTs). These have been widely used for barley genome analyses, such as DNA marker-generation and the construction of microarrays. However, the availability of a large-insert genomic library, which is also essential for genomic studies, has been relatively limited in the barley research community. We described here the construction and characterization of a barley bacterial artificial chromosome (BAC) library, using the Japanese malting barley variety 'Haruna Nijo'. The BAC library consisted of 294,912 clones arrayed in 768 384-well microtiter plates. The average size of each cloned insert was estimated to be 115.2 kb, with approximately 0.5% of the clones lacking inserts. Chroloplast DNAs were present in about 1.7% of the library. Thus, the genomic coverage of the 'Haruna Nijo' BAC library was estimated to be about 6.6 genome-equivalents. In order to rapidly identify specific BAC clones, we developed a screening strategy that combined PCR analysis of pooled BAC DNAs with colony hybridization. Using this screening scheme, we investigated the genomic coverage of this BAC library, using 13 locus-specific ESTs and a sequence-tagged site marker. By screening the whole library with individual markers, we identified an average of 5.1 clones per marker. This screening scheme also enabled us to rapidly construct a physical contig spanning a region of approx. 190 kb around the HvBRII locus, where the mutation responsible for the semi-dwarf plant type 'uzu' is located. These results indicate that the 'Haruna Nijo' BAC library will be useful for barley genomic studies.

DOI： 10.1270/jsbbs.57.29

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The uzu gene shows typical semi-dwarf plant type and has resulted in lodging resistance and improved canopy structure in barley (Hordeum vulgare L.). The geographic distribution of 'uzu' lines is limited in East Asia including Japan, Korean peninsula and China. For many years, majority of cultivated six-rowed barley varieties in southern Japan were 'uzu' type. Inheritance of the uzu gene, located on chromosome 3H, is monogenic recessive and the expression is pleiotropic during developmental process. In cereal crop plants, several semi-dwarf genes have been widely used in breeding programs to increase productivity and it is known that several of these semi-dwarf genes were derived from gibberellin (GA)-related mutations. The barley dwarfing gene uzu is independent to GA. This characteristics are known earlier. In this study, we characterized uzu gene in molecular aspects. As the result of comprehensive study using several pairs of isogenic lines, we found the morphological and physiological similarities of barley uzu gene to rice dwarf mutant, d61. D61 encodes OsBRI1, which is homologous gene for Brassinosteroid insensitive 1 in Arabidopsis. We also found that 'uzu' lines specific single nucleotide polymorphism (SNP) contributed for amino acid substitution in barley homologous sequence of OsBR-I1, HvBRI1. Linkage analysis using a segregating population for uzu showed the co-segregation between uzu and HvBRI1. Furthermore, as the results of derived cleaved amplified polymorphic sequences (dCAPS) marker analysis using more than 260 'uzu' landraces and the genomic sequencing analysis of HvBRII gene derived from 19 barley accessions, all the 'uzu' lines investigated in this study had the same SNP in putative kinase domain of HvBRIL On the basis of these findings, we discussed the phylogeny of 'uzu' landraces in East Asia.

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Brassinosteroids (BRs) play important roles throughout plant growth and development. Despite the importance of clarifying the mechanism of BR-related growth regulation in cereal crops, BR-related cereal mutants have been identified only in rice (Oryza sativa). We previously found that semidwarf barley (Hordeum vulgare) accessions carrying the "uzu" gene, called "uzu" barley in Japan, are non-responding for brassinolide (BL). We then performed chemical and molecular analyses to clarify the mechanisms of uzu dwarfism using isogenic line pairs of uzu gene. The response of the uzu line to BL was significantly lower than that of its corresponding normal line. Measurement of BRs showed that the uzu line accumulates BRs, similar to known BR-insensitive mutants. The marker synteny of rice and barley chromosomes suggests that the uzu gene may be homologous to rice D61, a rice homolog of Arabidopsis BR-insensitive 1 (BRI1), encoding a BR-receptor protein. A barley homolog of BRI1, HvBRI1, was isolated by using degenerate primers. A comparison of HvBRI1 sequences in uzu and normal barley varieties showed that the uzu phenotype is correlated with a single nucleotide substitution. This substitution results in an amino acid change at a highly conserved residue in the kinase domain of the BR-receptor protein. These results may indicate that uzu dwarfism is caused by the missense mutation in HvBRI1. The uzu gene is being introduced into all hull-less barley cultivars in Japan as an effective dwarf gene for practical use, and this is the first report about an agronomically important mutation related to BRs.

DOI： 10.1104/pp.103.026195

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Language：Japanese   Publisher：The Japanese Society for Chemical Regulation of Plants  

Brassinosterois (BRs) play important roles throughout plant growth and development. Despite the importance of clarifying the mechanism of BR-related growth regulation in cereal crops, BR-related cereal mutants have been identified only in rice. We previously found that semi-dwarf barley accessions carrying the "uzu" gene, called "uzu" barley in Japan, are non-responding for brassinolide (BL). We then performed chemical and molecular analyses to clarify the mechanisms of uzu dwarfism using isogenic line pairs of uzu gene. The response of the uzu line to BL was significantly lower than that of its corresponding normal line. Measurement of BRs showed that the uzu line accumulates BRs, similar to known BR-insensitive mutants. The marker synteny of rice and barley chromosomes suggests that the uzu gene may be homologous to rice D61,a rice homolog of Arabidopsis BR-insensitive 1 (BRI1), encoding a BR-receptor protein. A barley homolog of BRI1,HvBRI1,was isolated by using degenerate primers. A comparison of HvBRI1 sequences in uzu and normal barley varieties showed that the uzu phenotype is correlated with a single nucleotide substitution. This substitution results in an amino acid change at a highly conserved residue in the kinase domain of the BR-receptor protein. These results may indicate that uzu dwarfism is caused by the missense mutation in HvBRI1. The uzu gene is being introduced into all hull-less barley cultivars in Japan as an effective dwarf gene for practical use, and this is the first report about an agronomically important mutation related to BRs.

DOI： 10.18978/jscrpanb.38.0_31

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：OXFORD UNIV PRESS  

In barley, there is a single recessive semi-dwarf gene, uzu, which shows a plant type similar to green revolution genes of rice and wheat. The green revolution caused by gibberellin-related mutations, but the uzu gene was known to be independent to GA. In this study, we comprehensively analyzed the uzu gene from both morphological and physiological aspects using uzu isogenic lines. We found that the uzu line showed the similar phenotype to rice brassinosteroid receptor gene mutant, d61: inhibited elongation of the second internode from top, insensitive to exogenous brassinolide and over-accumulation of endogenous brassinosteroids. We examined rice D61 homologous gene in barley and found a single nucleotide substitution in the kinase domain of the gene which led to an amino acid substitution. The mutation was mapped on the same position with uzu, then, we concluded that uzu caused by the mutation in barley brassinosteroid receptor gene.

DOI： 10.14841/jspp.2003.0.185.0

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Language：English   Publisher：GENETICS SOC JAPAN  

We investigated the expressions of genes for alternative oxidase (AOX1a, AOX1b, AOX1c and AOX2) and genes for cytochrome c oxidase (COX5b and COX6b) during germination of Arabidopsis thaliana, and examined oxygen uptakes of the alternative respiration and the cytochrome respiration in imbibed Arabidopsis seeds. A Northern blot analysis showed that AOX2 mRNA has already accumulated in dry seeds and subsequently decreased, whereas accumulation of AOX1a mRNA was less abundant from 0 hours to 48 hours after imbibition and then increased. The increase of the capacity of the alternative pathway appeared to be dependent on the expressions of both AOX2 and AOX1a. On the other hand, steady-state mRNA levels of COX5b and COX6b were gradually increased during germination, and the capacity of the cytochrome pathway was correlated with the increase of expressions of the COX genes. Antimycin A, the respiratory inhibitor, strongly increased the expression of AOX1a but had no effect on the expression of AOX2. A 5'RACE analysis showed that AOX2 consists of five exons, which is different from the case of most AOX genes identified so far. Analysis of subcellular localization of AOX2 using green fluorescent protein indicated that the AOX2 protein is imported into the mitochondria.

DOI： 10.1266/ggs.76.89

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Language：English   Publisher：URBAN & FISCHER VERLAG  

The oxygen uptake in mitochondria can be uncoupled from ATP synthesis by the product of a single gene, the alternative oxidase (AOX) gene, which may be involved in signal transduction from mitochondria to the nucleus. To better understand induction of this gene in higher plants, we investigated the effects of the cytochrome respiratory inhibitors and ATP synthesis inhibitors on the expression of the AOXs of Arabidopsis thaliana. A Northern blot analysis showed the AOX1a transcripts were increased by treatment of antimycin A and myxothiazol, which act on complex III of the respiratory chain, and by NaN3, which acts on complex IV. AOX1a mRNA was also strongly induced by oligomycin (F1F0-ATP synthase inhibitor) and weakly induced by 2,4-DNP (ATP synthesis uncoupler) at the maximum dose. These results indicate that not only inhibition of electron transfer but also inhibition of ATP synthesis in mitochondria induces the transcription of AOX1a.

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Language：English   Publisher：AMER SOC PLANT PHYSIOLOGISTS  

It is known that alcoholic fermentation is important for survival of plants under anaerobic conditions. Acetaldehyde, one of the intermediates of alcoholic fermentation, is not only reduced by alcohol dehydrogenase but also can be oxidized by aldehyde dehydrogenase (ALDH). To determine whether ALDH plays a role in anaerobic metabolism in rice (Oryza sativa L. cv Nipponbare), we characterized a cDNA clone encoding mitochondrial ALDH from rice (Aldh2a). Analysis of sub-cellular localization of ALDH2a protein using green fluorescent protein and an in vitro ALDH assay using protein extracts from Escherichia coli cells that overexpressed ALDH2a indicated that ALDH2a functions in the oxidation of acetaldehyde in mitochondria. A Southern-blot analysis indicated that mitochondrial ALDH is encoded by at least two genes in rice. We found that the Aldh2a mRNA was present at high levels in leaves of dark-grown seedlings, mature leaf sheaths, and panicles. It is interesting that expression of the rice Aldh2a gene, unlike the expression of the tobacco (Nicotiana tabacum) Aldh2a gene, was induced in rice seedlings by submergence. Experiments with ruthenium red, which is a blocker of Ca2+ fluxes in rice as well as maize (Zea mays), suggest that the induction of expression of Adh1 and Pdc1 by low oxygen stress is regulated by elevation of the cytosolic Ca2+ level. However, the induction of Aldh2a gene expression may not be controlled by the cytosolic Ca2+ level elevation. A possible involvement of ALDH2a in the submergence tolerance of rice is discussed.

DOI： 10.1104/pp.124.2.587

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We investigated the effect of oxygen on the expressions of respiratory genes encoded in the nuclear and mitochondrial genomes of rice (Oryza sativa L.). Hypoxic treatment decreased the transcript levels of nuclear-encoded, but not mitochondrial-encoded respiratory genes. The effects of ruthenium red (an inhibitor of Ca2+ fluxes from organelles) and/or CaCl2 on plants under hypoxic conditions suggested that Ca2+ is a physiological transducer of a low-oxygen signaling pathway for expression of the alternative oxidase 1a gene (AOX1a), but not for expressions of genes involved in the cytochrome respiratory pathway, in rice. Copyright (C) 2000 Federation of European Biochemical Societies.

DOI： 10.1016/S0014-5793(00)01411-3

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We investigated the effect of oxygen on the expressions of respiratory genes encoded in the nuclear and mitochondrial genomes of rice (Oryza sativa L.). Hypoxic treatment decreased the transcript levels of nuclear-encoded, but not mitochondrial-encoded respiratory genes. The effects of ruthenium red (an inhibitor of Ca2+ fluxes from organelles) and/or CaCl2 on plants under hypoxic conditions suggested that Ca2+ is a physiological transducer of a low-oxygen signaling pathway for expression of the alternative oxidase 1a gene (AOX1a), but not for expressions of genes involved in the cytochrome respiratory pathway, in rice. Copyright (C) 2000 Federation of European Biochemical Societies.

DOI： 10.1016/S0014-5793(00)01411-3

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Language：English   Publisher：ELSEVIER SCIENCE BV  

We investigated the effect of oxygen on the expressionse of respiratory genes encoded in the nuclear and mitochondrial genomes of rice (Oryza sativa L.). Hypoxic treatment decreased the transcript levels of nuclear-encoded, but not mitochondrial-encoded respiratory gents. The effects of ruthenium red (an inhibitor of Ca2+ fluxes from organelles) and/or CaCl2 on plants under hypoxic conditions suggested that Ca2+ is a physiological transducer of a low-oxygen signaling pathway for expression of the alternative oxidase 1a gene (AOX1a), but not for expressions of genes involved in the cytochrome respiratory pathway, in rice. (C) 2000 Federation of European Biochemical Societies.

DOI： 10.1016/S0014-5793(00)01411-3

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Language：English   Publisher：American Society of Plant Biologists  

It is known that alcoholic fermentation is important for survival of plants under anaerobic conditions. Acetaldehyde, one of the intermediates of alcoholic fermentation, is not only reduced by alcohol dehydrogenase but also can be oxidized by aldehyde dehydrogenase (ALDH). To determine whether ALDH plays a role in anaerobic metabolism in rice (Oryza sativa L. cv Nipponbare), we characterized a cDNA clone encoding mitochondrial ALDH from rice (Aldh2a). Analysis of sub-cellular localization of ALDH2a protein using green fluorescent protein and an in vitro ALDH assay using protein extracts from Escherichia coli cells that overexpressed ALDH2a indicated that ALDH2a functions in the oxidation of acetaldehyde in mitochondria. A Southern-blot analysis indicated that mitochondrial ALDH is encoded by at least two genes in rice. We found that the Aldh2a mRNA was present at high levels in leaves of dark-grown seedlings, mature leaf sheaths, and panicles. It is interesting that expression of the rice Aldh2a gene, unlike the expression of the tobacco (Nicotiana tabacum) Aldh2a gene, was induced in rice seedlings by submergence. Experiments with ruthenium red, which is a blocker of Ca2+ fluxes in rice as well as maize (Zea mays), suggest that the induction of expression of Adh1 and Pdc1 by low oxygen stress is regulated by elevation of the cytosolic Ca2+ level. However, the induction of Aldh2a gene expression may not be controlled by the cytosolic Ca2+ level elevation. A possible involvement of ALDH2a in the submergence tolerance of rice is discussed.

DOI： 10.1104/pp.124.2.587

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Language：English   Publisher：American Society of Plant Biologists  

It is known that alcoholic fermentation is important for survival of plants under anaerobic conditions. Acetaldehyde, one of the intermediates of alcoholic fermentation, is not only reduced by alcohol dehydrogenase but also can be oxidized by aldehyde dehydrogenase (ALDH). To determine whether ALDH plays a role in anaerobic metabolism in rice (Oryza sativa L. cv Nipponbare), we characterized a cDNA clone encoding mitochondrial ALDH from rice (Aldh2a). Analysis of sub-cellular localization of ALDH2a protein using green fluorescent protein and an in vitro ALDH assay using protein extracts from Escherichia coli cells that overexpressed ALDH2a indicated that ALDH2a functions in the oxidation of acetaldehyde in mitochondria. A Southern-blot analysis indicated that mitochondrial ALDH is encoded by at least two genes in rice. We found that the Aldh2a mRNA was present at high levels in leaves of dark-grown seedlings, mature leaf sheaths, and panicles. It is interesting that expression of the rice Aldh2a gene, unlike the expression of the tobacco (Nicotiana tabacum) Aldh2a gene, was induced in rice seedlings by submergence. Experiments with ruthenium red, which is a blocker of Ca2+ fluxes in rice as well as maize (Zea mays), suggest that the induction of expression of Adh1 and Pdc1 by low oxygen stress is regulated by elevation of the cytosolic Ca2+ level. However, the induction of Aldh2a gene expression may not be controlled by the cytosolic Ca2+ level elevation. A possible involvement of ALDH2a in the submergence tolerance of rice is discussed.

DOI： 10.1104/pp.124.2.587

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We identified two genes for alternative oxidase (AOX) from rice. One AOX gene (designated AOX1a) is located approx. 1.9 kb downstream of another AOX gene (designated AOX1b). Comparison of the genomic and cDNA sequences of the two AOX genes showed that the AOX1a gene is interrupted by three introns, as are AOX genes of other plants. On the other hand, two introns are inserted in the AOX1b gene. The predicted AOX1a and AOX1b precursor proteins consist of 332 and 335 amino acid residues, respectively. A genomic Southern hybridization analysis indicated that rice has several AOX genes other than the two tandem-arranged AOX genes. Steady-state mRNA levels of both of the genes for AOX1a and AOX1b were increased under low temperature (4°C). However, no difference in the pattern of induction of transcription between the genes for AOX1a and AOX1b was observed.

DOI： 10.1016/S0378-1119(97)00502-7

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We identified two genes for alternative oxidase (AOX) from rice. One AOX gene (designated AOX1a) is located approx. 1.9 kb downstream of another AOX gene (designated AOX1b). Comparison of the genomic and cDNA sequences of the two AOX genes showed that the AOX1a gene is interrupted by three introns, as are AOX genes of other plants. On the other hand, two introns are inserted in the AOX1b gene. The predicted AOX1a and AOX1b precursor proteins consist of 332 and 335 amino acid residues, respectively. A genomic Southern hybridization analysis indicated that rice has several AOX genes other than the two tandem-arranged AOX genes. Steady-state mRNA levels of both of the genes for AOX1a and AOX1b were increased under low temperature (4°C). However, no difference in the pattern of induction of transcription between the genes for AOX1a and AOX1b was observed.

DOI： 10.1016/S0378-1119(97)00502-7

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Language：English  

We identified two genes for alternative oxidase (AOX) from rice. One AOX gene (designated AOX1a) is located approx. 1.9 kb downstream of another AOX gene (designated AOX1b). Comparison of the genomic and cDNA sequences of the two AOX genes showed that the AOX1a gene is interrupted by three introns, as are AOX genes of other plants. On the other hand, two introns are inserted in the AOX1b gene. The predicted AOX1a and AOX1b precursor proteins consist of 332 and 335 amino acid residues, respectively. A genomic Southern hybridization analysis indicated that rice has several AOX genes other than the two tandem-arranged AOX genes. Steady-state mRNA levels of both of the genes for AOX1a and AOX1b were increased under low temperature (4°C). However, no difference in the pattern of induction of transcription between the genes for AOX1a and AOX1b was observed.

DOI： 10.1016/S0378-1119(97)00502-7

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We investigated the copy number of the gene for alternative oxidase (AOX) of Arabidopsis thaliana by amplification by PCR and Southern hybridization. These studies indicated that there are at least four copies of the AOX gene in Arabidopsis. We isolated genomic clones containing individual copies (designated as AOX1a, AOX1b, AOX1c and AOX2) of the AOX genes. Interestingly, two of the AOX genes (AOX1a and AOX1b) were located in tandem in a ca. 5 kb region on one of the chromosomes of Arabidopsis. Comparison between genomic and cDNA sequences of the four AOX genes showed that all AOX genes are divided by three introns and the positions of the introns in AOX1a, AOX1b, AOX1c and AOX2 are the same. We examined whether expression of Arabidopsis AOX genes, like the tobacco AOX1a gene, is enhanced by treatment with antimycin A, an inhibitor of complex III in the mitochondrial respiratory chain. We found that, in young plants, the amount of Arabidopsis AOX1a mRNA was dramatically increased by addition of antimycin A, while the transcription of the other three genes (AOX1b, AOX1c and AOX2) did not respond to antimycin A. Amplification by RT-PCR showed that AOX1a and AOX1c were expressed in all organs examined (flowers and buds, stems, rosette, and roots of 8-week old plants). In contrast, transcripts of AOX1b were detected only in the flowers and buds, and transcripts of AOX2 were detected mainly in stems, rosette and roots. These results suggested that transcriptions of the four genes for alternative oxidase of Arabidopsis are differentially regulated.

DOI： 10.1023/A:1005818507743

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Language：English  

We investigated the copy number of the gene for alternative oxidase (AOX) of Arabidopsis thaliana by amplification by PCR and Southern hybridization. These studies indicated that there are at least four copies of the AOX gene in Arabidopsis. We isolated genomic clones containing individual copies (designated as AOX1a, AOX1b, AOX1c and AOX2) of the AOX genes. Interestingly, two of the AOX genes (AOX1a and AOX1b) were located in tandem in a ca. 5 kb region on one of the chromosomes of Arabidopsis. Comparison between genomic and cDNA sequences of the four AOX genes showed that all AOX genes are divided by three introns and the positions of the introns in AOX1a, AOX1b, AOX1c and AOX2 are the same. We examined whether expression of Arabidopsis AOX genes, like the tobacco AOX1a gene, is enhanced by treatment with antimycin A, an inhibitor of complex III in the mitochondrial respiratory chain. We found that, in young plants, the amount of Arabidopsis AOX1a mRNA was dramatically increased by addition of antimycin A, while the transcription of the other three genes (AOX1b, AOX1c and AOX2) did not respond to antimycin A. Amplification by RT-PCR showed that AOX1a and AOX1c were expressed in all organs examined (flowers and buds, stems, rosette, and roots of 8-week old plants). In contrast, transcripts of AOX1b were detected only in the flowers and buds, and transcripts of AOX2 were detected mainly in stems, rosette and roots. These results suggested that transcriptions of the four genes for alternative oxidase of Arabidopsis are differentially regulated.

DOI： 10.1023/A:1005818507743

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Language：English  

We investigated the copy number of the gene for alternative oxidase (AOX) of Arabidopsis thaliana by amplification by PCR and Southern hybridization. These studies indicated that there are at least four copies of the AOX gene in Arabidopsis. We isolated genomic clones containing individual copies (designated as AOX1a, AOX1b, AOX1c and AOX2) of the AOX genes. Interestingly, two of the AOX genes (AOX1a and AOX1b) were located in tandem in a ca. 5 kb region on one of the chromosomes of Arabidopsis. Comparison between genomic and cDNA sequences of the four AOX genes showed that all AOX genes are divided by three introns and the positions of the introns in AOX1a, AOX1b, AOX1c and AOX2 are the same. We examined whether expression of Arabidopsis AOX genes, like the tobacco AOX1a gene, is enhanced by treatment with antimycin A, an inhibitor of complex III in the mitochondrial respiratory chain. We found that, in young plants, the amount of Arabidopsis AOX1a mRNA was dramatically increased by addition of antimycin A, while the transcription of the other three genes (AOX1b, AOX1c and AOX2) did not respond to antimycin A. Amplification by RT-PCR showed that AOX1a and AOX1c were expressed in all organs examined (flowers and buds, stems, rosette, and roots of 8-week old plants). In contrast, transcripts of AOX1b were detected only in the flowers and buds, and transcripts of AOX2 were detected mainly in stems, rosette and roots. These results suggested that transcriptions of the four genes for alternative oxidase of Arabidopsis are differentially regulated.

DOI： 10.1023/A:1005818507743

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Language：English   Publishing type：Research paper, summary (international conference)   Publisher：AMER SOC PLANT PHYSIOLOGISTS  

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Event date： 2022.10.24 - 2022.10.25

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：オンライン開催  

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Venue：東京  

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Venue：大阪  

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Venue：大阪  

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Event date： 2019.9.6 - 2019.9.7

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Venue：Tucson,AZ,U.S.A.  

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Venue：University of Dundee,Dundee,Scotland  

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Venue：九州大学  

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Venue：岩手大学  

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Event date： 2017.10.7 - 2017.10.8

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Venue：岩手大学  

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Venue：名古屋大学  

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