Papers - TANAKA Hidenori
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Pongpiyapaiboon S., Aoki K., Hashiguchi M., Akashi R., Kishima Y., Tanaka H.
Plant Phenome Journal 8 ( 1 ) 2025.12
Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Plant Phenome Journal
High-throughput and noninvasive phenotyping methods are promising technology for improving efficiency in plant research and breeding. In this study, we evaluated the performance of a digital phenotyping system (DPS) based on three-dimensional (3D) model reconstruction for quantifying key growth traits in rice (Oryza sativa). The DPS was used to estimate plant height, biomass, color, leaf morphology, and tiller angle in four rice varieties (Koshihikari, Nipponbare, PL9, and Tachiaoba). The results show high accuracy and correlation between manually measured and DPS-derived traits. Notably, the 3D volume analysis can quantify biomass accumulation and growth dynamics and revealed distinct differences among varieties. The strong correlation between the green-red normalized difference index (a red-green-blue-based index) and soil plant analysis development also demonstrated the viability of the system in monitoring leaf color without using a multispectral instrument. The analysis also captured growth patterns over time, including canopy development and senescence, which are often challenging to quantify through manual measurements alone. Furthermore, the tiller angle estimation derived from DPS provided an alternative method to plant architecture evaluation, demonstrating its potential for use in breeding programs aimed to optimize canopy structure. These findings establish DPS as a reliable and scalable tool for a digital phenotyping platform that enables comprehensive trait analysis with reduced labor and increased precision and the capability to continuously monitor plant growth and biomass accumulation. This study shows the potential of this novel digital tool for automating manual measurements, which can increase efficiency and expedite research and breeding in rice and other crops.
DOI： 10.1002/ppj2.70054
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Umino R., Ng H.M., Tanaka H., Ishigaki G.
Australian Journal of Crop Science 19 ( 10 ) 1035 - 1040 2025.10
Publishing type：Research paper (scientific journal) Publisher：Australian Journal of Crop Science
This study investigated the agronomical traits of three soybean (Glycine max L. Merr) cultivars differing in maturity stages—extremely early-maturing ‘Yukihomare’ (Yu), early-maturing ‘Kitamusume’ (Ki), and late-maturing ‘Fukuyutaka’ (Fu)—intercropped with Rhodes grass (Chloris gayana Kunth.) in the southwest warm region Japan (Experiment I) and their applicability to agricultural machinery system (Experiment II). In Experiment I, soybeans were sown under different seeding rates at 10 seeds/m<sup>2</sup> in 2022 and 20 seeds/m<sup>2</sup> in 2023. As a result, while ‘Fu’ showed the lowest germination rate in 2022, it had the same trend in mean of two years (54%). At 90 days after sowing in 2023, plant height of ‘Fu’ was significantly higher among cultivars and had the highest dry matter yield (DMY) of 448 kg/10a with a soybean mixing rate of 93.1%, indicating improved soybean competitiveness with Rhodes grass under higher seeding rate. In Experiment II, broadcaster seeding trial identified a 10 m operational spacing as optimal for achieving the target seeding rate of 20 seeds/m<sup>2</sup> based on the result of Experiment I. Subsequently, a performance using agricultural machinery for seeding and harvesting showed that DMY of ‘Fu’ (344kg/10a) was significantly higher than that of Rhodes grass (101kg/10a). However, lodging and harvesting inefficiencies resulted in an estimated dry matter loss of 59.4 kg/10a (13.4%), highlighting the need for further refinement of mechanical harvesting. These findings demonstrate the potential of late-maturing soybean cultivar ‘Fu’ for forage production in intercropping systems and suggest the feasibility of mechanized cultivation and harvest at a practical scale.
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Arifin A.G., Shimamoto Y., Tanaka H., Hashiguchi M., Akashi R., Gondo T.
Legume Research 48 ( 1 ) 57 - 63 2025.1
Language：English Publishing type：Research paper (scientific journal) Publisher：Legume Research
Background: Identifying biomass-related genes to meet the increasing demand for food supply is important approach for agricultural and scientific efforts. In this study, we employed the Full-length cDNA Over-eXpressing gene hunting system (FOX hunting system) to identify biomass-related genes through ectopic expression of Arabidopsis thaliana full-length cDNA in bird’s-foot trefoil (Lotus corniculatus). Methods: A total of 66 FOX superroot lines (FSLs) from Lotus corniculatus cv. Viking were transferred in vermiculite after two weeks in half-strength Murashige and Skoog (MS) medium. These FSLs were then grown in a growth chamber for four weeks, during which their plant length and root length were measured. High biomass lines were selected from this group. FSL #83 and #121 were then grown for an additional four months in a greenhouse until they reached maturity, at which point they were evaluated for their agronomic traits. Result: Out of the 66 analyzed FSLs, 15 displayed superior growth characteristics in plant length and total root length. Arabidopsis cDNA, categorized into genes related to various functions such as membrane transport, photosystems, phytohormone synthesis, amino acid synthesis and unknown genes, was introduced into these lines. Two lines were grown to maturity in the greenhouse and their agronomic traits were analyzed in detail. FSL #83 expressed brassinosteroid biosynthetic pathway gene (CPD) led to significant differences in internode length, number of stems, number of flowers and above-ground dry matter weight compared to non-transgenic Super-growing roots (SR). On the other hand, FSL #121 expressed Asparaginyl-tRNA synthetase (SYNC1) gene exhibited increases in plant length and the number of stem nodes.
DOI： 10.18805/LRF-813
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Nakamura K., Gondo T., Chiba S., Akimoto S., Narushima J., Kondo K., Sugano Y., Tanaka H., Hashiguchi M., Shiwa Y., Akashi R.
Agriculture (Switzerland) 14 ( 12 ) 2024.12
Language：English Publishing type：Research paper (scientific journal) Publisher：Agriculture (Switzerland)
Gene expression in individual germinated seeds of four different soybean (Glycine max [L.] Merr.) cultivars, GL3494, OAC Kent, Williams 82, and Jackson, was examined using single seed high-throughput RNA sequencing (ssRNA-seq). The gene expression was similar between two individual seeds of the same cultivar, but different among individual seeds of the four cultivars. Notably, ssRNA-seq identified five genes that were not stably expressed in Williams 82, having either no detectable sequence reads or less than five sequence reads mapped to the exon regions of chromosomes in Williams 82. These findings were validated by reverse transcription polymerase chain reaction analysis. The study’s results demonstrate that gene expression in germinated seeds is unique to an individual seed from each soybean cultivar. This uniqueness may affect composition and content of nutrients in germinated soybeans used as food ingredients.
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Li F., Sayama T., Yokota Y., Hiraga S., Hashiguchi M., Tanaka H., Akashi R., Ishimoto M.
DNA Research 31 ( 2 ) 2024.4
Language：English Publishing type：Research paper (scientific journal) Publisher：DNA Research
Wild soybean (Glycine soja), the ancestor of the cultivated soybean (G. max), is a crucial resource for capturing the genetic diversity of soybean species. In this study, we used a set of 78 genome-wide microsatellite markers to analyse the genetic diversity and geographic differentiation patterns in a global collection of 2,050 G. soja accessions and a mini-core collection of G. max stored in two public seed banks. We observed a notable reduction in the genetic diversity of G. max compared with G. soja and identified a close phylogenetic relationship between G. max and a G. soja subpopulation located in central China. Furthermore, we revealed substantial genetic divergence between northern and southern subpopulations, accompanied by diminished genetic diversity in the northern subpopulations. Two clusters were discovered among the accessions from north-eastern China-one genetically close to those from South Korea and Southern Japan, and another close to those from Amur Oblast, Russia. Finally, 192 accessions were assigned to a mini-core collection of G. soja, retaining 73.8% of the alleles detected in the entire collection. This mini-core collection is accessible to those who need it, facilitating efficient evaluation and utilization of G. soja genetic resources in soybean breeding initiatives.
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Ng H.M., Gondo T., Tanaka H., Akashi R.
Plant Cell Reports 43 ( 2 ) 2024.2
Language：English Publishing type：Research paper (scientific journal) Publisher：Plant Cell Reports
Key Message: Genome editing by CRISPR/Cas9 can be applied to Z. matrella ‘Wakaba’, and knockout mutants of ZmNYC1 gene exhibited stay-green phenotype and reduced tillering. Abstract: Zoysia matrella is a widely used C4 warm-season turfgrass for landscaping, golf courses, and sports fields. Here, we used the CRISPR/Cas9 system to target the Non-Yellow Coloring1 (ZmNYC1) gene in the highly heterozygous allotetraploid Z. matrella ‘Wakaba’, aiming to generate a novel stay-green variety. Of 441 Agrobacterium-infected calli, 22 (5.0%) were transformed, and 14 of these (63.6%) showed targeted mutations through cleaved amplified polymorphic sequences analysis. Sequencing analysis revealed mutations mostly consisting of 1 or 2 bp indels, occurring 2 to 4 bp upstream of the PAM sequence. Regenerated plants exhibited five ZmNYC1 target locus genotypes, including homozygous mutants with a complete knockout of all four alleles in the T0 generation. Under dark treatment, ZmNYC1-mutated plants displayed suppressed chlorophyll b (Chl b) degradation, leading to higher chlorophyll content and Chl b, with a lower chlorophyll a/chlorophyll b ratio compared to the wild type (WT). However, the ZmNYC1 mutation also inhibited plant growth in homozygous mutant genotypes, exhibiting reduced tillering compared to WT. Additionally, during winter simulation, mutant with a complete knockout retained greenness longer than the WT. This is the first successful use of CRISPR/Cas9 genome editing in zoysiagrass. The mutants of the ZmNYC1 gene would serve as valuable breeding material for developing improved zoysiagrass varieties that can maintain their green color for longer periods, even during winter dormancy.
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Bungsrisawat P., Tumwasorn S., Loongyai W., Nakthong S., Nitthaisong P., Tanaka H., Akashi R., Sopannarath P.
Animal Science Journal 95 ( 1 ) 2024.1
Language：English Publishing type：Research paper (scientific journal) Publisher：Animal Science Journal
Betong chicken (KU line) is a slow-growing Thai native chicken used for meat production. The objectives of this study were to identify polymorphisms of the calpain1 (CAPN1) and calpain3 (CAPN3) genes and to investigate their effects on growth, carcass, and meat quality traits in Betong chickens (KU line). A sample of 252 Betong chickens (KU line) was screened for CAPN1 and CAPN3 polymorphisms. The polymorphisms of CAPN1 were detected using gel electrophoresis and DNA sequencing, whereas the polymorphisms of CAPN3 were identified using restriction fragment length polymorphism. Polymorphisms were detected in both CAPN1 (AA, AB, and BB genotypes) and CAPN3 (CC, CT, and TT genotypes). The frequency of the B allele was higher than for the A allele (0.78 and 0.22, respectively) in CAPN1, while the C allelic frequency was higher than for the T allele (0.54 and 0.46, respectively) in CAPN3. The CAPN1 genotype and the combination of the CAPN1 and CAPN3 genotypes could be used as genetic markers for meat lightness. The CAPN3 could be useful for increasing body weight, live weight, and breast meat weight in Betong chickens (KU line).
DOI： 10.1111/asj.13986
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Ng H.M., Gondo T., Yamada T., Tanaka H., Akashi R.
Grassland Science 2024
Language：English Publishing type：Research paper (scientific journal) Publisher：Grassland Science
Bahiagrass (Paspalum notatum Flügge) is a warm-season grass where high lignin content limits its forage quality, negatively affecting animal performance. To create a new breeding method by genome editing, isolation and characterization of lignin biosynthesis genes and identification of their molecular relationships are essential. The caffeic acid O-methyltransferase (COMT) and cinnamyl alcohol dehydrogenase (CAD) cDNA clones were isolated from bahiagrass, and their protein sequences showed high similarity to other C4 monocot species through phylogenetic analysis. Gene expression analysis of phenylalanine ammonia-lyase (PAL), COMT and CAD, involved in crucial stages of lignin biosynthesis and lignin content, was conducted at different plant developmental stages. The highest gene expression levels of these genes were observed in the vegetative (V) and early reproductive stages, while the lignin content increased until the middle reproductive stage and remained constant thereafter. Additionally, to further understand the molecular relationships in lignin biosynthesis, the effect of CAD downregulation was analyzed in transgenic bahiagrass lines introduced with sorghum CAD antisense and RNAi vector obtained from a previous report. This led to a reduced lignin content and affected the expression of PAL and COMT working upstream of CAD. In the V stage, PAL expression was lower in transgenic lines compared to wild type (WT), while COMT expression showed no significant differences. However, PAL and COMT expression of transgenic lines in the middle reproductive stage (R2) was significantly higher than in the WT. These findings suggest that the downregulation of CAD gene expression affects PAL and COMT expression and induces a feedback system in the R2 stage. Lignin content influenced the phenotype of the transgenic plants with significantly reduced lignin, exhibiting a dwarf phenotype with shorter plant heights. The findings of this study can be applied to genome editing for the development of practical new breeding materials with improved digestibility in bahiagrass.
DOI： 10.1111/grs.12419
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Development of a digital phenotyping system using 3D model reconstruction for zoysiagrass Reviewed
Pongpiyapaiboon S., Tanaka H., Hashiguchi M., Hashiguchi T., Hayashi A., Tanabata T., Isobe S., Akashi R.
Plant Phenome Journal 6 ( 1 ) 2023.6
Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Plant Phenome Journal
Digital phenotyping, particularly the use of plant 3D models, is a promising method for high-throughput plant evaluation. Although many recent studies on the topic have been published, further research is needed to apply it to breeding research and other related fields. In this study, using a 3D model phenotyping system we developed, we reconstructed and analyzed 20 accessions of zoysiagrass (Zoysia spp.), including three species and their hybrid, over a period of 1 year. Artificial neural network with three hidden layers was able to effectively remove nonplant parts while retaining plant parts that were incorrectly removed using the cropping method, offering a robust and flexible approach for post-processing of 3D models. The system also demonstrated its ability to accurately evaluate a range of traits, including height, area, and color using red green blue (RGB)-based vegetation indices. The results showed a high correlation between the estimated volume obtained from voxel 3D model and dry weight, enabling its use as a non-destructive method for measuring plant volume. In addition, we found that the green red normalized difference index from RGB-based indices was similar to the commonly used normalized difference vegetation index in controlled illumination conditions. These results demonstrate the potential for three-dimensional model phenotyping to facilitate plant breeding, particularly in the field of turfgrass and feed crops.
DOI： 10.1002/ppj2.20076
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Jiamtae P., Hashiguchi T., Pongpiyapaiboon S., Lelapiyamit I., Tanaka H., Hashiguchi M., Akashi R.
Journal of Crop Science and Biotechnology 26 ( 4 ) 467 - 488 2023
Language：English Publishing type：Research paper (scientific journal) Publisher：Journal of Crop Science and Biotechnology
Soybean is a major crop that is rich in proteins, lipids, and isoflavones. Although the seeds are widely used for food and industrial purposes, soybean is recognized as a crop that does not store well, as storage conditions greatly affect seed quality. In this study, we selected 10 recombinant inbred lines (RILs) of soybean that are either sensitive or tolerant to storage, and examined the biochemical characteristics of the lines and their parents under storage-related stresses. The germination rates of all of the lines in the tolerant group were higher than those of the sensitive group for all storage conditions. Malondialdehyde (MDA) content was higher in the sensitive group than in the tolerant group, with the MDA content typically increasing under long-term storage conditions. Superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities were also more affected by long-term storage, but not by higher temperatures. Isoflavones were also assayed and it was found that the aglycones (except glycitein) increased with an increase of storage temperature. Malonyl isoflavone glucosides tended to decrease under long-term storage and high temperature conditions, suggesting that malonyl glucosides are converted to their aglycones. These results illustrate the mechanisms underlying storage-related stresses and the importance of screening for lines that can tolerate environmental stresses.
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Jiamtae P., Hashiguchi M., Lelapiyamit I., Harada K., Gondo T., Tanaka H., Akashi R.
Euphytica 218 ( 12 ) 2022.12
Language：English Publishing type：Research paper (scientific journal) Publisher：Euphytica
Soybean (Glycine max L. Merr.) seeds are highly sensitive to the environmental conditions experienced in STORAGE. The objectives of this study were to identify QTLs for soybean seed storability by evaluating seed viability and seed vigor and investigating candidate genes for these traits in detected QTL regions. These objectives will aid in developing soybean cultivars with a high capacity for storability. The seeds of 109 and 90 recombinant inbred lines (RILs) derived from a cross between Misuzudaizu and Moshidou Gong 503 in 2010 and 2019, respectively, were used to evaluate seed viability by a germination test and seed vigor by an accelerated aging test, after storage under two temperature conditions (25 °C and 35 °C) for six months. Seed viability and seed vigor of Moshidou Gong 503 were higher than those of Misuzudaizu in both temperature conditions. The average seed viability and seed vigor of RILs decreased when stored at the higher temperature. A total of five QTLs were found for the two traits, seed viability and seed vigor, located in chromosomes 2, 6 and 8. The Misuzudaizu alleles decreased seed viability and seed vigor at all detected QTLs. Most QTLs in this study were found near loci controlling seed viability, maturity, germination, seed hardness, and seed surface micromorphology, indicating that seed storability is related to these traits. In addition, two new QTLs were found that are associated with seed storability.
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Construction of prediction models for growth traits of soybean cultivars based on phenotyping in diverse genotype and environment combinations. Reviewed International journal
Andi Madihah Manggabarani, Takuyu Hashiguchi, Masatsugu Hashiguchi, Atsushi Hayashi, Masataka Kikuchi, Yusdar Mustamin, Masaru Bamba, Kunihiro Kodama, Takanari Tanabata, Sachiko Isobe, Hidenori Tanaka, Ryo Akashi, Akihiro Nakaya, Shusei Sato
DNA research : an international journal for rapid publication of reports on genes and genomes 29 ( 4 ) 2022.8
Language：English Publishing type：Research paper (scientific journal)
As soybean cultivars are adapted to a relatively narrow range of latitude, the effects of climate changes are estimated to be severe. To address this issue, it is important to improve our understanding of the effects of climate change by applying the simulation model including both genetic and environmental factors with their interactions (GxE). To achieve this goal, we conducted the field experiments for soybean core collections using multiple sowing times in multi-latitudinal fields. Sowing time shifts altered the flowering time and growth phenotypes, and resulted in increasing the combinations of genotypes and environments. GWAS for the obtained phenotypes revealed the effects of field and sowing time to significance of detected alleles, indicating the presence of GxE. By using accumulated phenotypic and environmental data in 2018 and 2019, we constructed multiple regression models for flowering time and growth pattern. Applicability of the constructed models were evaluated by the field experiments in 2020 including a novel field, and high correlation between the predicted and measured values was observed, suggesting the robustness of the models. The models presented here would allow us to predict the phenotype of the core collections in a given environment.
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宮崎大学における遠隔授業の教育効果について（２）—2020年度の学生アンケートと教員アンケートの結果から—
田中 秀典, 武方 壮一
宮崎大学教育・学生支援センター紀要 ( 6 ) 2022.3
Authorship：Lead author Language：Japanese Publishing type：Research paper (bulletin of university, research institution)
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Tanabata Takanari, Kodama Kunihiro, Hashiguchi Takuyu, Inomata Daisuke, Tanaka Hidenori, Isobe Sachiko
Breeding Science advpub ( 0 ) 2022
Language：English Publishing type：Research paper (scientific journal) Publisher：日本育種学会
Plant phenotyping technology has been actively developed in recent years, but the introduction of these technologies into the field of agronomic research has not progressed as expected, in part due to the need for flexibility and low cost. “DIY” (Do It Yourself) methodologies are an efficient way to overcome such obstacles. Devices with modular functionality are critical to DIY experimentation, allowing researchers flexibility of design. In this study, we developed a plant conveyance system using a commercial AGV as a case study of DIY plant phenotyping. The convey module consists of two devices, a running device and a plant-handling device. The running device was developed based on a commercial AGV (Automated Guided Vehicle) Kit. The plant-handling device, plant stands, and pot attachments were originally designed and fabricated by us and our associates. Software was also developed for connecting the devices and operating the system. The run route was set with magnetic tape, which can be easily changed or rerouted. Our plant delivery system was developed with low cost and having high flexibility, as a unit that can contribute to others’ DIY’ plant research efforts as well as our own. It is expected that the developed devices will contribute to diverse phenotype observations of plants in the greenhouse as well as to other important functions in plant breeding and agricultural production.
DOI： 10.1270/jsbbs.21070
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Ng H.M., Gondo T., Ushiyama M., Cho S., Maemura S., Hashiguchi M., Tanaka H., Akashi R.
Grassland Science 2022
Language：English Publishing type：Research paper (scientific journal) Publisher：Grassland Science
Zoysia matrella (L.) Merrill is a perennial C4 warm-season turfgrass grown for landscapes, golf courses, sports fields and recreation parks. To create a new breeding method by genome editing, an efficient genetic transformation system is essential. In this study, we report the efficient protocol of Agrobacterium-mediated transformation through the establishment of a stable tissue culture system for Z. matrella ‘Wakaba’. The embryogenic callus was induced from shoot apices of nodal segments incubated in Murashige and Skoog (MS) medium containing 2 mg/l 2,4-dichlorophnoxyacetic acid (2,4-D), 0.1 mg/l 6-benzylaminopurine (BAP) and 5 μM CuSO4 (MS-DBC). Repeated subculture of compact high-quality callus in MS-DBC medium produced a highly regenerative callus with dense pre-embryogenic clusters, and it was used as a transformation target. Agrobacterium strain EHA105 harboring pANIC8B vector containing the β-glucuronidase gene (GUS) and hygromycin B phosphotransferase gene was used. Agrobacterium-infected calli were cocultured for 5 days with 100 μM acetosyringone and then subjected to selection pressure of 50 mg/l hygromycin. This optimized protocol yielded transformation efficiencies of up to 6.6%. Southern blot analysis verified one to three copies of the GUS gene in different independent transgenic plants. All transgenic plants were morphologically normal, and the GUS expressions were stable. Our optimized in vitro and transgenic system will facilitate the new breeding technology of genome editing in zoysiagrass.
DOI： 10.1111/grs.12396
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Evaluation of seed amino acid content and its correlation network analysis in wild soybean (Glycine soja) germplasm in Japan Reviewed International journal
Awatsaya Chotekajorn, Takuyu Hashiguchi, Masatsugu Hashiguchi, Hidenori Tanaka, Ryo Akashi
Plant Genetic Resources: Characterisation and Utilisation 2021.3
Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)
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宮崎大学における遠隔授業の教育効果について—2019年度と2020年度の成績とアンケート結果を比較して（1）—
田中 秀典, 武方 壮一
宮崎大学教育・学生支援センター紀要 ( 5 ) 2021.3
Authorship：Lead author Language：Japanese Publishing type：Research paper (bulletin of university, research institution)
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Quantitative analysis of seven plant hormones in Lotus japonicus using standard addition method Reviewed
Hashiguchi T., Hashiguchi M., Tanaka H., Fukushima K., Gondo T., Akashi R.
PLoS ONE 16 ( 2 February ) 2021.2
Language：English Publishing type：Research paper (scientific journal) Publisher：PLoS ONE
© 2021 Hashiguchi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Plant hormones have been identified to be versatile signaling molecules essential for plant growth, development, and stress response. Their content levels vary depending on the species, and they also change in response to any external stimuli. Thus, simultaneous quantification of multiple plant hormones is required to understand plant physiology. Sensitive and quantitative analysis using liquid chromatography-linked mass spectrometry (LC-MS/MS) has been used in detecting plant hormones; however, quantification without stable isotopes is yet to be established. In this study, we quantified seven representative plant hormones of Lotus japonicus, which is a model legume for standard addition method. Accurate masses for monoisotopic ions of seven phytohormones were determined for high-resolution mass spectrometry (HR-MS). Selected ion monitoring (SIM) mode based on accurate masses was used in detecting phytohormones in the roots, stems, and leaves. Evaluation of matrix effects showed ion suppression ranging from 10.2% to 87.3%. Both stable isotope dilution and standard addition methods were able to detect plant hormones in the roots, stems, and leaves, with no significant differences in using both approaches and thus a standard addition method can be used to quantify phytohormones in L. japonicus. The method will be effective, especially when stable isotopes are not available to correct for matrix effects.
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Kajiya-Kanegae H., Nagasaki H., Kaga A., Hirano K., Ogiso-Tanaka E., Matsuoka M., Ishimori M., Ishimoto M., Hashiguchi M., Tanaka H., Akashi R., Isobe S., Iwata H.
DNA research : an international journal for rapid publication of reports on genes and genomes 28 ( 1 ) 2021.1
Language：English Publishing type：Research paper (scientific journal) Publisher：DNA research : an international journal for rapid publication of reports on genes and genomes
© The Author(s) 2021. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. We performed whole-genome Illumina resequencing of 198 accessions to examine the genetic diversity and facilitate the use of soybean genetic resources and identified 10 million single nucleotide polymorphisms and 2.8 million small indels. Furthermore, PacBio resequencing of 10 accessions was performed, and a total of 2,033 structure variants were identified. Genetic diversity and structure analysis congregated the 198 accessions into three subgroups (Primitive, World, and Japan) and showed the possibility of a long and relatively isolated history of cultivated soybean in Japan. Additionally, the skewed regional distribution of variants in the genome, such as higher structural variations on the R gene clusters in the Japan group, suggested the possibility of selective sweeps during domestication or breeding. A genome-wide association study identified both known and novel causal variants on the genes controlling the flowering period. Novel candidate causal variants were also found on genes related to the seed coat colour by aligning together with Illumina and PacBio reads. The genomic sequences and variants obtained in this study have immense potential to provide information for soybean breeding and genetic studies that may uncover novel alleles or genes involved in agronomically important traits.
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Effects of silicate fertilizer on growth and silicic acid accumulation in turfgrass Reviewed
Inoue T., Hashiguchi M., Koga K., Muguerza M., Tanaka H., Akashi R.
Asian Journal of Plant Sciences 20 ( 2 ) 324 - 331 2021
Language：English Publishing type：Research paper (scientific journal) Publisher：Asian Journal of Plant Sciences
Background and Objective: Silicon is a globally important soil nutrient to crops for productivity and alleviates the effects of environmental stress in higher plants, including turfgrass. Therefore, this study aimed to evaluate the effects of silicate fertilizer in two turfgrass species, Zoysia matrella ‘Wakaba’ and creeping bentgrass, Agrostis stolonifera ‘Nightlife’, in terms of plant growth, coverage rate, silicic acid content in shoots and roots and root elongation and growth in both turfgrasses. Materials and Methods: The Z. matrella and creeping bentgrass were cultured under SiO2 treatments (0, 500 and 1,000 g mG2). Plant height, number of shoots, stolon length and coverage were investigated in Z. matrella. In addition, dry matter weight and silicic acid content of shoots, stolons and roots were analyzed in Z. matrella and the same was done in creeping bentgrass except stolons. Results: Silicate treatments tended to increase plant growth, coverage rate, dry matter weight and shoot silicon content in Z. matrella and increased silicon content of shoots and roots in creeping bentgrass. Conclusion: Higher silicic acid content in the shoots than in roots of Z. matrella and creeping bentgrass confirms that they are both silicon-accumulating species. Moreover, the content of silicic acid in Z. matrella increased in the order of roots, stolons and shoots which suggests the existence of a gradual silicic acid transport mechanism in Zoysia species.