Updated on 2025/11/05

写真a

 
YAMAMOTO Toshio
 
Organization
Scheduled update Professor
Position
Professor
External link

Degree

  • 博士（農学） ( 北海道大学 )

Research Interests

  • Genomics

  • breeding

  • genetic resources

  • rice

Research Areas

  • Environmental Science/Agriculture Science / Science in plant genetics and breeding

Education

  • 北海道大学大学院農学研究科修士課程修了    

    - 1991.3

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Research History

  • Okayama University   資源植物科学研究所   Professor

    2018.7

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  • National Agriculture and Food Research Organization   Institute of Crop Science, NARO

    2016.4 - 2018.6

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  • 東京大学新領域創成科学研究科   客員教授

    2014.4 - 2018.6

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  • 国立研究開発法人農業生物資源研究所   イネゲノム育種研究ユニット長

    2011.4 - 2016.3

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  • National Institute of Agrobiological Sciences   応用遺伝研究チーム

    2006.1 - 2006.3

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  • 株式会社本田技術研究所

    2002.3 - 2003.12

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  • 日本たばこ産業株式会社

    1991.4 - 2002.2

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Professional Memberships

Committee Memberships

  • 日本育種学会   運営委員（シンポジウム、地域）  

    2024.4   

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  •   日本育種学会 代議員  

    2022.4   

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    Committee type：Academic society

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  •   Rice 編集委員  

    2022.4   

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  • Plant Breeding   編集委員  

    2020.1   

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  • 日本育種学会   編集委員  

    2016.4   

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    Committee type：Academic society

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Papers

  • Genetic background influences mineral accumulation in rice straw and grains under different soil pH conditions Reviewed

    Toshio Yamamoto, Kazunari Kashihara, Tomoyuki Furuta, Qian Zhang, En Yu, Jian Feng Ma

    Scientific Reports   14 ( 1 )   2024.7

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    Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    Abstract

    Mineral element accumulation in plants is influenced by soil conditions and varietal factors. We investigated the dynamic accumulation of 12 elements in straw at the flowering stage and in grains at the mature stage in eight rice varieties with different genetic backgrounds (Japonica, Indica, and admixture) and flowering times (early, middle, and late) grown in soil with various pH levels. In straw, Cd, As, Mn, Zn, Ca, Mg, and Cu accumulation was influenced by both soil pH and varietal factors, whereas P, Mo, and K accumulation was influenced by pH, and Fe and Ni accumulation was affected by varietal factors. In grains, Cd, As, Mn, Cu, Ni, Mo, Ca, and Mg accumulation was influenced by both pH and varietal factors, whereas Zn, Fe, and P accumulation was affected by varietal factors, and K accumulation was not altered. Only As, Mn, Ca and Mg showed similar trends in the straw and grains, whereas the pH responses of Zn, P, K, and Ni differed between them. pH and flowering time had synergistic effects on Cd, Zn, and Mn in straw and on Cd, Ni, Mo, and Mn in grains. Soil pH is a major factor influencing mineral uptake in rice straw and grains, and genetic factors, flowering stage factors, and their interaction with soil pH contribute in a combined manner.

    DOI： 10.1038/s41598-024-66036-7

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    Other Link： https://www.nature.com/articles/s41598-024-66036-7

  • MCPtaggR: R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison Reviewed

    Tomoyuki Furuta, Toshio Yamamoto

    DNA Research   31 ( 1 )   2023.12

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    Publishing type：Research paper (scientific journal)   Publisher：Oxford University Press (OUP)  

    Abstract

    Reduced representation sequencing (RRS) offers cost-effective, high-throughput genotyping platforms such as genotyping-by-sequencing (GBS). RRS reads are typically mapped onto a reference genome. However, mapping reads harbouring mismatches against the reference can potentially result in mismapping and biased mapping, leading to the detection of error-prone markers that provide incorrect genotype information. We established a genotype-calling pipeline named mappable collinear polymorphic tag genotyping (MCPtagg) to achieve accurate genotyping by eliminating error-prone markers. MCPtagg was designed for the RRS-based genotyping of a population derived from a biparental cross. The MCPtagg pipeline filters out error-prone markers prior to genotype calling based on marker collinearity information obtained by comparing the genome sequences of the parents of a population to be genotyped. A performance evaluation on real GBS data from a rice F2 population confirmed its effectiveness. Furthermore, our performance test using a genome assembly that was obtained by genome sequence polishing on an available genome assembly suggests that our pipeline performs well with converted genomes, rather than necessitating de novo assembly. This demonstrates its flexibility and scalability. The R package, MCPtaggR, was developed to provide functions for the pipeline and is available at https://github.com/tomoyukif/MCPtaggR.

    DOI： 10.1093/dnares/dsad027

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    Other Link： https://academic.oup.com/dnaresearch/article-pdf/31/1/dsad027/56260214/dsad027.pdf

  • Fluctuation in genetic effects with introduced early- or late-heading-date gene alleles in near-isogenic lines with different genetic backgrounds in rice Reviewed

    Kiyosumi Hori, Mitsuo Takamatsu, Jun Hosoi, Taneaki Tsugane, Reiko Hayashi, Manabu Watanabe, Tatsumi Mizubayashi, Tsuyu Ando, Ayahiko Shomura, Yoshiyuki Mukai, Utako Yamanouchi, Toshio Yamamoto

    Breeding Research   25 ( 2 )   123 - 139   2023.12

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    Authorship：Last author   Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Breeding  

    DOI： 10.1270/jsbbr.22j15

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  • A cell wall–localized cytokinin/purine riboside nucleosidase is involved in apoplastic cytokinin metabolism in Oryza sativa Reviewed

    Mikiko Kojima, Nobue Makita, Kazuki Miyata, Mika Yoshino, Akira Iwase, Miwa Ohashi, Alicia Surjana, Toru Kudo, Noriko Takeda-Kamiya, Kiminori Toyooka, Akio Miyao, Hirohiko Hirochika, Tsuyu Ando, Ayahiko Shomura, Masahiro Yano, Toshio Yamamoto, Tokunori Hobo, Hitoshi Sakakibara

    Proceedings of the National Academy of Sciences   120 ( 36 )   2023.8

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Proceedings of the National Academy of Sciences  

    In the final step of cytokinin biosynthesis, the main pathway is the elimination of a ribose-phosphate moiety from the cytokinin nucleotide precursor by phosphoribohydrolase, an enzyme encoded by a gene named LONELY GUY (LOG). This reaction accounts for most of the cytokinin supply needed for regulating plant growth and development. In contrast, the LOG-independent pathway, in which dephosphorylation and deribosylation sequentially occur, is also thought to play a role in cytokinin biosynthesis, but the gene entity and physiological contribution have been elusive. In this study, we profiled the phytohormone content of chromosome segment substitution lines of Oryza sativa and searched for genes affecting the endogenous levels of cytokinin ribosides by quantitative trait loci analysis. Our approach identified a gene encoding an enzyme that catalyzes the deribosylation of cytokinin nucleoside precursors and other purine nucleosides. The cytokinin/purine riboside nucleosidase 1 (CPN1) we identified is a cell wall–localized protein. Loss-of-function mutations ( cpn1 ) were created by inserting a Tos17 -retrotransposon that altered the cytokinin composition in seedling shoots and leaf apoplastic fluid. The cpn1 mutation also abolished cytokinin riboside nucleosidase activity in leaf extracts and attenuated the trans -zeatin riboside-responsive expression of cytokinin marker genes. Grain yield of the mutants declined due to altered panicle morphology under field-grown conditions. These results suggest that the cell wall–localized LOG-independent cytokinin activating pathway catalyzed by CPN1 plays a role in cytokinin control of rice growth. Our finding broadens our spatial perspective of the cytokinin metabolic system.

    DOI： 10.1073/pnas.2217708120

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  • Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice Reviewed

    Kazufumi Nagata, Yasunori Nonoue, Kazuki Matsubara, Ritsuko Mizobuchi, Nozomi Ono, Taeko Shibaya, Kaworu Ebana, Eri Ogiso-Tanaka, Takanari Tanabata, Kazuhiko Sugimoto, Fumio Taguchi-Shiobara, Jun-ichi Yonemaru, Yusaku Uga, Atsunori Fukuda, Tadamasa Ueda, Shin-ichi Yamamoto, Utako Yamanouchi, Toshiyuki Takai, Takashi Ikka, Katsuhiko Kondo, Tomoki Hoshino, Eiji Yamamoto, Shunsuke Adachi, Jian Sun, Noriyuki Kuya, Yuka Kitomi, Ken Iijima, Hideki Nagasaki, Ayahiko Shomura, Tatsumi Mizubayashi, Noriyuki Kitazawa, Kiyosumi Hori, Tsuyu Ando, Toshio Yamamoto, Shuichi Fukuoka, Masahiro Yano

    Breeding Science   73 ( 3 )   332 - 342   2023.7

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    Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Breeding  

    DOI： 10.1270/jsbbs.23006

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  • GBScleanR: robust genotyping error correction using a hidden Markov model with error pattern recognition. Reviewed International journal

    Tomoyuki Furuta, Toshio Yamamoto, Motoyuki Ashikari

    Genetics   224 ( 2 )   2023.5

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    Language：English   Publishing type：Research paper (scientific journal)  

    Reduced-representation sequencing (RRS) provides cost-effective and time-saving genotyping platforms. Despite the outstanding advantage of RRS in throughput, the obtained genotype data usually contain a large number of errors. Several error correction methods employing the hidden Markov model (HMM) have been developed to overcome these issues. These methods assume that markers have a uniform error rate with no bias in the allele read ratio. However, bias does occur because of uneven amplification of genomic fragments and read mismapping. In this paper, we introduce an error correction tool, GBScleanR, which enables robust and precise error correction for noisy RRS-based genotype data by incorporating marker-specific error rates into the HMM. The results indicate that GBScleanR improves the accuracy by more than 25 percentage points at maximum compared to the existing tools in simulation data sets and achieves the most reliable genotype estimation in real data even with error-prone markers.

    DOI： 10.1093/genetics/iyad055

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  • Alleles of high-yielding indica rice that improve root hydraulic conductance also increase flag leaf photosynthesis, biomass, and grain production of japonica rice in the paddy field Reviewed

    Masahiro Yamashita, Chikako Ootsuka, Hikaru Kubota, Shunsuke Adachi, Takuya Yamaguchi, Kazumasa Murata, Toshio Yamamoto, Tadamasa Ueda, Taiichiro Ookawa, Tadashi Hirasawa

    Field Crops Research   289   108725 - 108725   2022.12

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.fcr.2022.108725

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  • Genetic Background Negates Improvements in Rice Flour Characteristics and Food Processing Properties Caused by a Mutant Allele of the PDIL1-1 Seed Storage Protein Gene. Reviewed International journal

    Kiyosumi Hori, Tomoya Okunishi, Kenji Nakamura, Ken Iijima, Masahiro Hagimoto, Katsuyuki Hayakawa, Koka Shu, Takashi Ikka, Hiroto Yamashita, Masanori Yamasaki, Yoshinobu Takeuchi, Shota Koyama, Yoshimasa Tsujii, Toshiaki Kayano, Takuro Ishii, Toshihiro Kumamaru, Yasushi Kawagoe, Toshio Yamamoto

    Rice (New York, N.Y.)   15 ( 1 )   13 - 13   2022.3

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    Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

    Phenotypic differences among breeding lines that introduce the same superior gene allele can be a barrier to effective development of cultivars with desirable traits in some crop species. For example, a deficient mutation of the Protein Disulfide Isomerase Like 1-1 (PDIL1-1) gene can cause accumulation of glutelin seed storage protein precursors in rice endosperm, and improves rice flour characteristics and food processing properties. However, the gene must be expressed to be useful. A deficient mutant allele of PDIL1-1 was introduced into two rice cultivars with different genetic backgrounds (Koshihikari and Oonari). The grain components, agronomic traits, and rice flour and food processing properties of the resulting lines were evaluated. The two breeding lines had similar seed storage protein accumulation, amylose content, and low-molecular-weight metabolites. However, only the Koshihikari breeding line had high flour quality and was highly suitable for rice bread, noodles, and sponge cake, evidence of the formation of high-molecular-weight protein complexes in the endosperm. Transcriptome analysis revealed that mRNA levels of fourteen PDI, Ero1, and BiP genes were increased in the Koshihikari breeding line, whereas this change was not observed in the Oonari breeding line. We elucidated part of the molecular basis of the phenotypic differences between two breeding lines possessing the same mutant allele in different genetic backgrounds. The results suggest that certain genetic backgrounds can negate the beneficial effect of the PDIL1-1 mutant allele. Better understanding of the molecular basis for such interactions may accelerate future breeding of novel rice cultivars to meet the strong demand for gluten-free foods.

    DOI： 10.1186/s12284-022-00560-w

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  • iTRAQ-Based Proteomics Investigation of Critical Response Proteins in Embryo and Coleoptile During Rice Anaerobic Germination Reviewed International coauthorship

    Zhang Guangchen, Liu Zimeng, Liu Youhong, Kuya Noriyuki, Hua Yuchen, Shi Hongru, Zhao Weilin, Han Yuqing, Yamamoto Toshio, Chen Wenfu, Sun Jian

    Rice Science   28 ( 4 )   391 - 401   2021.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.rsci.2021.05.009

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  • Evaluation of the genetic effect of nine yield-related alleles using near-isogenic lines in the genetic backgrounds of Japanese rice cultivars Reviewed

    Tadamasa Ueda, Ken Ishimaru, Akitoshi Goto, Takashi Ikka, Katsuhiko Kondo, Kazuki Matsubara, Takeshi Hayashi, Toshio Yamamoto, Junichi Tanaka

    Breeding Research   23 ( 1 )   16 - 27   2021.6

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    Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：Japanese Society of Breeding  

    <p>Many papers about rice genes related to yield are published every year, but few of these genes have been used in practical rice breeding. Therefore, we generated or received near-isogenic lines (NILs) of nine alleles related to yield in the genetic backgrounds of Japanese rice cultivars, and performed simultaneous comparative cultivation tests. Significant increases in brown rice yield were detected in the NILs for qCTd11Takanari, SD1DGWG, and a combination of TGW6Kasalath and SD1DGWG in the genetic background of 'Koshihikari' and a NIL for DEP1Ballila in the genetic background of 'Akidawara'. These alleles and QTLs may have the genetic potential to improve rice yield, even in the genetic background of Japanese cultivars. On the other hand, an increase in the brown rice yield of NILs for qLIA3Takanari, GPSTakanari, GS3Oochikara, GW2BG1, and GN1ATakanari was not detected in the 'Koshihikari' genetic background probably due to small direct effects to increase sink size by these alleles and QTLs or a relative reduction of their source abilities to the total sink sizes increased in these NILs. In addition, analysis using multiple NILs in the 'Koshihikari' genetic background showed a negative correlation between panicle weight and panicle number. This indicated that an increase in the number of panicles did not subsequently increase yield because of the tradeoff to reduce the weight of one panicle and the thousand grain weight; this was considered the main reason why GW2BG1, GS3Oochikara, and GN1ATakanari, which were expected to increase sink capacity, did not increase yield. We considered that the alleles increasing sink capacity are not sufficient to increase yield in the genetic background of Japanese cultivars and need to be combined with alleles, such as qCTd11Takanari, expected to improve the source ability by increasing photosynthesis per unit leaf area or alleles to improve canopy structure including SD1DGWG and DEP1Ballila.</p>

    DOI： 10.1270/jsbbr.20j21

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  • Quantitative trait loci for leaf inclination angle in rice detected using reciprocal mapping populations Reviewed International coauthorship

    Nan Su San, Kazuya Soda, Yosuke Ootsuki, Masahiro Yamashita, Ryoji Karimata, Kasumi Suzuki, Shunsuke Adachi, Toshio Yamamoto, Takanari Tanabata, Tadamasa Ueda, Taiichiro Ookawa, Tadashi Hirasawa

    Field Crops Research   266   108128 - 108128   2021.6

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.fcr.2021.108128

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  • Diploid Male Gametes Circumvent Hybrid Sterility Between Asian and African Rice Species Reviewed

    Daichi Kuniyoshi, Itaru Masuda, Yoshitaka Kanaoka, Yuki Shimazaki-Kishi, Yoshihiro Okamoto, Hideshi Yasui, Toshio Yamamoto, Kiyotaka Nagaki, Yoichiro Hoshino, Yohei Koide, Itsuro Takamure, Yuji Kishima

    Frontiers in Plant Science   11   579305   2020.11

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Frontiers Media SA  

    DOI： 10.3389/fpls.2020.579305

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  • Semi-dwarf 1 (sd1) gene enhances light penetration into the canopy through regulating leaf inclination angle in rice Reviewed International coauthorship

    Nan Su San, Kasumi Suzuki, Kazuya Soda, Shunsuke Adachi, Hiroyuki Kasahara, Toshio Yamamoto, Takashi Ikka, Katsuhiko Kondo, Utako Yamanouchi, Kazuhiko Sugimoto, Yoshiaki Nagamura, Tadashi Hirasawa, Taiichiro Ookawa

    Field Crops Research   246   107694 - 107694   2020.2

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.fcr.2019.107694

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  • Genetic determination for source capacity to support breeding of high-yielding rice (Oryza sativa) Reviewed International coauthorship

    Adachi, S., Ohkubo, S., San, N.S., Yamamoto, T.

    Molecular Breeding   40 ( 20 )   2020

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    Authorship：Last author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1007/s11032-020-1101-5

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  • Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game. Reviewed International coauthorship International journal

    Jian Sun, Dianrong Ma, Liang Tang, Minghui Zhao, Guangchen Zhang, Wenjia Wang, Jiayu Song, Xiang Li, Zimeng Liu, Wenxing Zhang, Quan Xu, Yuncheng Zhou, Jianzhong Wu, Toshio Yamamoto, Fei Dai, Yan Lei, Song Li, Gang Zhou, Hongkun Zheng, Zhengjin Xu, Wenfu Chen

    Molecular plant   12 ( 5 )   632 - 647   2019.5

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    Language：English   Publishing type：Research paper (scientific journal)  

    Crop weediness, especially that of weedy rice (Oryza sativa f. spontanea), remains mysterious. Weedy rice possesses robust ecological adaptability; however, how this strain originated and gradually formed proprietary genetic features remains unclear. Here, we demonstrate that weedy rice at Asian high latitudes (WRAH) is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice. We also identified novel quantitative trait loci underlying weedy-specific traits, and revealed that a genome block on the end of chromosome 1 is associated with rice weediness. To identify the genomic modifications underlying weedy rice evolution, we generated the first de novo assembly of a high-quality weedy rice genome (WR04-6), and conducted a comparative genomics study between WR04-6 with other rice reference genomes. Multiple lines of evidence, including the results of demographic scenario comparisons, suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication. A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity.

    DOI： 10.1016/j.molp.2019.01.019

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  • Surveillance of panicle positions by unmanned aerial vehicle to reveal morphological features of rice. Reviewed International journal

    Daisuke Ogawa, Toshihiro Sakamoto, Hiroshi Tsunematsu, Toshio Yamamoto, Noriko Kanno, Yasunori Nonoue, Jun-Ichi Yonemaru

    PLOS ONE   14 ( 10 )   e0224386   2019

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    Language：English   Publishing type：Research paper (scientific journal)  

    Rice plant architecture affects biomass and grain yield. Thus, it is important to select rice genotypes with ideal plant architecture. High-throughput phenotyping by use of an unmanned aerial vehicle (UAV) allows all lines in a field to be observed in less time than with traditional procedures. However, discrimination of plants in dense plantings is difficult, especially during the reproductive stage, because leaves and panicles overlap. Here, we developed an original method that relies on using UAV to identify panicle positions for dissecting plant architecture and to distinguish rice lines by detecting red flags attached to panicle bases. The plant architecture of recombinant inbred lines derived from Japanese cultivars 'Hokuriku 193' and 'Mizuhochikara', which differ in plant architecture, was assessed using a commercial camera-UAV system. Orthomosaics were made from UAV digital images. The center of plants was plotted on the image during the vegetative stage. The horizontal distance from the center to the red flag during the reproductive stage was used as the panicle position (PP). The red flags enabled us to recognize the positions of the panicles at a rate of 92%. The PP phenotype was related to but was not identical with the phenotypes of the panicle base angle, leaf sheath angle, and score of spreading habit. These results indicate that PP on orthomosaics could be used as an index of plant architecture under field conditions.

    DOI： 10.1371/journal.pone.0224386

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  • Novel method for evaluation of anaerobic germination in rice and its application to diverse genetic collections Reviewed International coauthorship

    Kuya, N., Sun, J., Iijima, K., Venuprasad, R., Yamamoto, T.

    Breeding Science   69 ( 4 )   633 - 639   2019

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1270/jsbbs.19003

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  • Genetic architecture of leaf photosynthesis in rice revealed by different types of reciprocal mapping populations Reviewed International coauthorship

    Adachi, S., Yamamoto, T., Nakae, T., Yamashita, M., Uchida, M., Karimata, R., Ichihara, N., Soda, K., Ochiai, T., Ao, R., Otsuka, C., Nakano, R., Takai, T., Ikka, T., Kondo, K., Ueda, T., Ookawa, T., Hirasawa, T., Lawson, T.

    Journal of Experimental Botany   70 ( 19 )   5131 - 5144   2019

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    Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/jxb/erz303

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  • Next generation long-culm rice with superior lodging resistance and high grain yield, Monster Rice 1 Reviewed International coauthorship

    Nomura, T., Arakawa, N., Yamamoto, T., Ueda, T., Adachi, S., Yonemaru, J.-I., Abe, A., Takagi, H., Yokoyama, T., Ookawa, T.

    PLoS ONE   14 ( 8 )   e0221424   2019

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1371/journal.pone.0221424

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  • Identification of quantitative trait loci for breaking and bending types lodging resistance in rice, using recombinant inbred lines derived from Koshihikari and a strong culm variety, Leaf Star Reviewed International coauthorship

    Samadi, A.F., Suzuki, H., Ueda, T., Yamamoto, T., Adachi, S., Ookawa, T.

    Plant Growth Regulation   89 ( 1 )   83 - 98   2019

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1007/s10725-019-00517-y

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  • Mapping of QTLs associated with lodging resistance in rice (Oryza sativa L.) using the recombinant inbred lines derived from two high yielding cultivars, Tachisugata and Hokuriku 193 Reviewed International coauthorship

    Jiang, M., Yamamoto, E., Yamamoto, T., Matsubara, K., Kato, H., Adachi, S., Nomura, T., Kamahora, E., Ma, J., Ookawa, T.

    Plant Growth Regulation   87 ( 2 )   1 - 10   2019

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1007/s10725-018-0468-3

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  • Koshihikari: a premium short-grain rice cultivar – its expansion and breeding in Japan Reviewed

    Asako Kobayashi, Kiyosumi Hori, Toshio Yamamoto, Masahiro Yano

    Rice   11 ( 1 )   15   2018.12

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    Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer New York LLC  

    DOI： 10.1186/s12284-018-0207-4

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  • Discovery of QTL Alleles for Grain Shape in the Japan-MAGIC Rice Population Using Haplotype Information Reviewed

    Ogawa D, Nonoue Y, Tsunematsu H, Kanno N, Yamamoto T, Yonemaru J

    G3   8   3559 - 3565   2018.11

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  • A novel QTL associated with rice canopy temperature difference affects stomatal conductance and leaf photosynthesis. Reviewed

    Atsunori Fukuda, Katsuhiko Kondo, Takashi Ikka, Toshiyuki Takai, Takanari Tanabata, Toshio Yamamoto

    Breeding science   68 ( 3 )   305 - 315   2018.8

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    Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    Canopy temperature can be a good indicator of stomatal conductance. To understand the genetic basis of phenotypic differences in stomatal conductance between average and high-yielding rice (Oryza sativa L.) cultivars, we conducted a quantitative trait locus (QTL) analysis of canopy temperature. We developed reciprocal series of backcross inbred lines (BC1F6) derived from a cross between the average-yielding japonica cultivar 'Koshihikari' and the high-yielding indica cultivar 'Takanari'. A stable QTL, qCTd11 (QTL for canopy temperature difference on chromosome 11) on the short arm of chromosome 11, accounted for 10.4 and 19.8% of the total phenotypic variance in the two lines; the 'Takanari' allele decreased the canopy temperature difference value. A chromosome segment substitution line carrying the Takanari qCTd11 showed a greater reduction in canopy temperature than 'Koshihikari', and had higher stomatal conductance and photosynthetic rate. These results suggest that qCTd11 is not only involved in canopy temperature, but is also involved in both stomatal conductance and photosynthetic rate.

    DOI： 10.1270/jsbbs.17129

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  • A near-isogenic rice line carrying a QTL for larger leaf inclination angle yields heavier biomass and grain Reviewed

    Nan Su San, Yosuke Ootsuki, Shunsuke Adachi, Toshio Yamamoto, Tadamasa Ueda, Takanari Tanabata, Takashi Motobayashi, Taiichiro Ookawa, Tadashi Hirasawa

    Field Crops Research   219   131 - 138   2018.4

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier B.V.  

    DOI： 10.1016/j.fcr.2018.01.025

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  • Finding the superior allele of japonica-type for increasing stem lodging resistance in indica rice varieties using chromosome segment substitution lines Reviewed

    Indria Wahyu Mulsanti, Toshio Yamamoto, Tadamasa Ueda, Ahmad Fahim Samadi, Eri Kamahora, Indrastuti Apri Rumanti, Vo Cong Thanh, Shunsuke Adachi, Sakae Suzuki, Motoki Kanekatsu, Tadashi Hirasawa, Taiichiro Ookawa

    RICE   11 ( 1 )   25   2018.4

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12284-018-0216-3

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  • Haplotype-based allele mining in the Japan-MAGIC rice population. Reviewed International journal

    Daisuke Ogawa, Eiji Yamamoto, Toshikazu Ohtani, Noriko Kanno, Hiroshi Tsunematsu, Yasunori Nonoue, Masahiro Yano, Toshio Yamamoto, Jun-Ichi Yonemaru

    Scientific reports   8 ( 1 )   4379 - 4379   2018.3

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    Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan. To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis. Using haplotype-based GWAS, we clearly detected the loci controlling the glutinous endosperm and culm length traits. Information on the alleles of the eight founders, which was based on the effects of mutations revealed by the analysis of next-generation sequencing data, was used to narrow down the candidate genes and reveal the associations between alleles and phenotypes. The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.

    DOI： 10.1038/s41598-018-22657-3

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  • A follow-up study for biomass yield QTLs in rice. Reviewed International journal

    Kazuki Matsubara, Jun-Ichi Yonemaru, Nobuya Kobayashi, Takuro Ishii, Eiji Yamamoto, Ritsuko Mizobuchi, Hiroshi Tsunematsu, Toshio Yamamoto, Hiroshi Kato, Masahiro Yano

    PloS one   13 ( 10 )   e0206054   2018

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    The biomass yield (plant weight) of rice fluctuates from year to year. In a previous study, we demonstrated that six quantitative trait loci (QTLs) contribute to the variation in the plant weight of recombinant inbred lines (RILs) of high-yielding Japanese rice cultivars. However, it remains unclear whether the effects of those QTLs are stable over multiple years. Therefore, we evaluated the effect of the alleles on the plant weight of RILs over multiple years, including a change of fertilization level (i.e., in different environments). Even though the biomass yields of all RILs fluctuated among environments, RILs that were selected on the basis of the genotypes of the detected QTLs had a stable rank order of plant weight that corresponded to their genotypes. This multiple-environment experiment reveals the highly significant contribution of both genotypic and environmental variances to the observed variance in plant weight. A marginally significant QTL-environment interaction was detected at only one of the six QTLs, with a subtle contribution. These results support the idea that the biomass yield of rice can be improved through QTL-based allele selection.

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  • Quantitative trait loci for large sink capacity enhance rice grain yield under free-air CO2 enrichment conditions Reviewed

    Hiroshi Nakano, Satoshi Yoshinaga, Toshiyuki Takai, Yumiko Arai-Sanoh, Katsuhiko Kondo, Toshio Yamamoto, Hidemitsu Sakai, Takeshi Tokida, Yasuhiro Usui, Hirofumi Nakamura, Toshihiro Hasegawa, Motohiko Kondo

    Scientific Reports   7 ( 1 )   1827   2017.12

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    DOI： 10.1038/s41598-017-01690-8

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  • Characterization of a genomic region that maintains chlorophyll and nitrogen contents during ripening in a high-yielding stay-green rice cultivar Reviewed

    Toshio Yamamoto, Tadafumi Suzuki, Kenji Suzuki, Shunsuke Adachi, Jian Sun, Masahiro Yano, Taiichiro Ookawa, Tadashi Hirasawa

    FIELD CROPS RESEARCH   206   54 - 64   2017.5

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    DOI： 10.1016/j.fcr.2017.03.001

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  • Fine Mapping of Carbon Assimilation Rate 8, a Quantitative Trait Locus for Flag Leaf Nitrogen Content, Stomatal Conductance and Photosynthesis in Rice Reviewed

    Shunsuke Adachi, Kazuaki Yoshikawa, Utako Yamanouchi, Takanari Tanabata, Jian Sun, Taiichiro Ookawa, Toshio Yamamoto, Rowan F. Sage, Tadashi Hirasawa, Junichi Yonemaru

    Frontiers in Plant Science   8   60   2017.1

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    DOI： 10.3389/fpls.2017.00060

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  • Genetic dissection of agronomically important traits in closely related temperate japonica rice cultivars Reviewed

    Kiyosumi Hori, Toshio Yamamoto, Masahiro Yano

    Breeding Science   67 ( 5 )   427 - 434   2017

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    DOI： 10.1270/jsbbs.17053

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  • Precise estimation of genomic regions controlling lodging resistance using a set of reciprocal chromosome segment substitution lines in rice Reviewed

    Taiichiro Ookawa, Ryo Aoba, Toshio Yamamoto, Tadamasa Ueda, Toshiyuki Takai, Shuichi Fukuoka, Tsuyu Ando, Shunsuke Adachi, Makoto Matsuoka, Takeshi Ebitani, Yoichiro Kato, Indria Wahyu Mulsanti, Masahiro Kishii, Matthew Reynolds, Francisco Pinera, Toshihisa Kotake, Shinji Kawasaki, Takashi Motobayashi, Tadashi Hirasawa

    Scientific Reports   6   30572   2016.7

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    DOI： 10.1038/srep30572

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  • Detection of QTLs for cold tolerance of rice cultivar 'Kuchum' and effect of QTL pyramiding Reviewed

    Takashi Endo, Bunya Chiba, Kensuke Wagatsuma, Kenichi Saeki, Tsuyu Ando, Ayahiko Shomura, Tatsumi Mizubayashi, Tadamasa Ueda, Toshio Yamamoto, Takeshi Nishio

    THEORETICAL AND APPLIED GENETICS   129 ( 3 )   631 - 640   2016.3

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    DOI： 10.1007/s00122-015-2654-2

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  • Improvement of Rice Biomass Yield through QTL-Based Selection Reviewed

    Kazuki Matsubara, Eiji Yamamoto, Nobuya Kobayashi, Takuro Ishii, Junichi Tanaka, Hiroshi Tsunematsu, Satoshi Yoshinaga, Osamu Matsumura, Jun-ichi Yonemaru, Ritsuko Mizobuchi, Toshio Yamamoto, Hiroshi Kato, Masahiro Yano

    PLOS ONE   11 ( 3 )   e0151830   2016.3

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  • Genetic factors determining varietal differences in characters affecting yield between two rice (Oryza sativa L.) varieties, Koshihikari and IR64 Reviewed

    Kazuhiro Ujiie, Toshio Yamamoto, Masahiro Yano, Ken Ishimaru

    GENETIC RESOURCES AND CROP EVOLUTION   63 ( 1 )   97 - 123   2016.1

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    DOI： 10.1007/s10722-015-0237-3

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  • Detection of QTL for exudation rate at ripening stage in rice and its contribution to hydraulic conductance Reviewed International coauthorship

    Toshio Yamamoto, Tadafumi Suzuki, Kenji Suzuki, Shunsuke Adachi, Jian Sun, Masahiro Yano, Taiichiro Ookawa, Tadashi Hirasawa

    PLANT SCIENCE   242   270 - 277   2016.1

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    DOI： 10.1016/j.plantsci.2015.08.014

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  • Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping Reviewed

    Hiroshi Shinada, Toshio Yamamoto, Hirokazu Sato, Eiji Yamamoto, Kiyosumi Hori, Junichi Yonemaru, Takashi Sato, Kenji Fujino

    BREEDING SCIENCE   65 ( 5 )   388 - 395   2015.12

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    DOI： 10.1270/jsbbs.65.388

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  • Natural Variation in the Flag Leaf Morphology of Rice Due to a Mutation of the NARROW LEAF 1 Gene in Oryza sativa L. Reviewed

    Fumio Taguchi-Shiobara, Tatsuya Ota, Kaworu Ebana, Taiichiro Ookawa, Masanori Yamasaki, Takanari Tanabata, Utako Yamanouchi, Jianzhong Wu, Nozomi Ono, Yasunori Nonoue, Kazufumi Nagata, Shuichi Fukuoka, Hideyuki Hirabayashi, Toshio Yamamoto, Masahiro Yano

    GENETICS   201 ( 2 )   795 - +   2015.10

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    DOI： 10.1534/genetics.115.181040

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  • Quantitative trait loci for whiteness of cooked rice detected in improved rice cultivars in Hokkaido Reviewed

    Hiroshi Shinada, Toshio Yamamoto, Eiji Yamamoto, Kiyosumi Hori, Yuji Hirayama, Toshihiko Maekawa, Hitoshi Kiuchi, Hirokazu Sato, Takashi Sato

    BREEDING SCIENCE   65 ( 3 )   201 - 207   2015.6

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    DOI： 10.1270/jsbbs.65.201

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  • Detection of QTLs for white-back and basal-white grains caused by high temperature during ripening period in japonica rice Reviewed

    Takuya Wada, Katsunori Miyahara, Jun-Ya Sonoda, Tadashi Tsukaguehi, Masayuki Miyazaki, Masao Tsubone, Tsuyu Ando, Kaworu Ebana, Toshio Yamamoto, Norio Iwasawa, Takayuki Umemoto, Motohiko Kondo, Masahiro Yano

    BREEDING SCIENCE   65 ( 3 )   216 - 225   2015.6

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  • Chromosomal locations of a gene underlying heat-accelerated brown spot formation and its suppressor genes in rice Reviewed

    Atsunori Fukuda, Kazuhiko Sugimoto, Tsuyu Ando, Toshio Yamamoto, Masahiro Yano

    MOLECULAR GENETICS AND GENOMICS   290 ( 3 )   1085 - 1094   2015.6

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    DOI： 10.1007/s00438-014-0975-5

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  • Genetic architecture of variation in heading date among Asian rice accessions Reviewed

    Kiyosumi Hori, Yasunori Nonoue, Nozomi Ono, Taeko Shibaya, Kaworu Ebana, Kazuki Matsubara, Eri Ogiso-Tanaka, Takanari Tanabata, Kazuhiko Sugimoto, Fumio Taguchi-Shiobara, Jun-ichi Yonemaru, Ritsuko Mizobuchi, Yusaku Uga, Atsunori Fukuda, Tadamasa Ueda, Shin-ichi Yamamoto, Utako Yamanouchi, Toshiyuki Takai, Takashi Ikka, Katsuhiko Kondo, Tomoki Hoshino, Eiji Yamamoto, Shunsuke Adachi, Hideki Nagasaki, Ayahiko Shomura, Takehiko Shimizu, Izumi Kono, Sachie Ito, Tatsumi Mizubayashi, Noriyuki Kitazawa, Kazufumi Nagata, Tsuyu Ando, Shuichi Fukuoka, Toshio Yamamoto, Masahiro Yano

    BMC PLANT BIOLOGY   15   115   2015.5

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  • Isolation of a Novel Lodging Resistance QTL Gene Involved in Strigolactone Signaling and Its Pyramiding with a QTL Gene Involved in Another Mechanism Reviewed

    Kenji Yano, Taiichiro Ookawa, Koichiro Aya, Yusuke Ochiai, Tadashi Hirasawa, Takeshi Ebitani, Takeshi Takarada, Masahiro Yano, Toshio Yamamoto, Shuichi Fukuoka, Jianzhong Wu, Tsuyu Ando, Reynante Lacsamana Ordonio, Ko Hirano, Makoto Matsuoka

    MOLECULAR PLANT   8 ( 2 )   303 - 314   2015.2

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    DOI： 10.1016/j.molp.2014.10.009

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  • Hybrid Breakdown Caused by Epistasis-Based Recessive Incompatibility in a Cross of Rice (Oryza sativa L.) Reviewed

    Kazuki Matsubara, Eiji Yamamoto, Ritsuko Mizobuchi, Jun-ichi Yonemaru, Toshio Yamamoto, Hiroshi Kato, Masahiro Yano

    JOURNAL OF HEREDITY   106 ( 1 )   113 - 122   2015.1

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  • Genetic mechanisms underlying yield potential in the rice high-yielding cultivar Takanari, based on reciprocal chromosome segment substitution lines Reviewed

    Toshiyuki Takai, Takashi Ikka, Katsuhiko Kondo, Yasunori Nonoue, Nozomi Ono, Yumiko Arai-Sanoh, Satoshi Yoshinaga, Hiroshi Nakano, Masahiro Yano, Motohiko Kondo, Toshio Yamamoto

    BMC PLANT BIOLOGY   14   295   2014.11

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    DOI： 10.1186/s12870-014-0295-2

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  • Isolation of a novel lodging resistance QTL gene involved in strigolactone signaling and its pyramiding with a QTL gene involved in another mechanism. Reviewed International journal

    Yano K, Ookawa T, Aya K, Ochiai Y, Hirasawa T, Ebitani T, Takarada T, Yano M, Yamamoto T, Fukuoka S, Wu J, Ando T, Ordonio RL, Hirano K, Matsuoka M

    Molecular plant   2014.11

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    Lodging has been a major roadblock to attaining increased crop productivity. In an attempt to understand the mechanism for culm strength in rice, we isolated an effective quantitative trait loci (QTL), STRONG CULM3 (SCM3), the causal gene of which is identical to rice TEOSINTE BRANCHED1 (OsTB1), a gene previously reported to positively control strigolactone (SL) signaling. A near-isogenic line (NIL) carrying SCM3 showed enhanced culm strength and increased spikelet number despite the expected decrease in tiller number, indicating that SL also has a positive role in enhancing culm strength and spikelet number. We produced a pyramiding line carrying SCM3 and SCM2, another QTL encoding APO1 involved in panicle development. The NIL-SCM2+SCM3 showed a much stronger culm than NIL-SCM2 and NIL-SCM3 and an increased spikelet number caused by the additive effect of these QTLs. We discuss the importance of utilizing suitable alleles of these STRONG CULM QTLs without inducing detrimental traits for breeding.

    DOI： 10.1093/mp/ssu131

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  • Increased lodging resistance in long-culm, low-lignin gh2 rice for improved feed and bioenergy production Reviewed

    Taiichiro Ookawa, Kazuya Inoue, Makoto Matsuoka, Takeshi Ebitani, Takeshi Takarada, Toshio Yamamoto, Tadamasa Ueda, Tadashi Yokoyama, Chisato Sugiyama, Satoshi Nakaba, Ryo Funada, Hiroshi Kato, Motoki Kanekatsu, Koki Toyota, Takashi Motobayashi, Mehran Vazirzanjani, Seishu Tojo, Tadashi Hirasawa

    SCIENTIFIC REPORTS   4   6567   2014.10

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    DOI： 10.1038/srep06567

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  • Introgression of two chromosome regions for leaf photosynthesis from an indica rice into the genetic background of a japonica rice Reviewed

    Shunsuke Adachi, Leticia Z. Baptista, Tomohiro Sueyoshi, Kazumasa Murata, Toshio Yamamoto, Takeshi Ebitani, Taiichiro Ookawa, Tadashi Hirasawa

    JOURNAL OF EXPERIMENTAL BOTANY   65 ( 8 )   2049 - 2056   2014.5

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    DOI： 10.1093/jxb/eru047

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  • Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars Reviewed

    Jun-Ichi Yonemaru, Ritsuko Mizobuchi, Hiroshi Kato, Toshio Yamamoto, Eiji Yamamoto, Kazuki Matsubara, Hideyuki Hirabayashi, Yoshinobu Takeuchi, Hiroshi Tsunematsu, Takuro Ishii, Hisatoshi Ohta, Hideo Maeda, Kaworu Ebana, Masahiro Yano

    BMC GENOMICS   15   346   2014.5

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    DOI： 10.1186/1471-2164-15-346

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  • Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation Reviewed

    Hiroshi Shinada, Toshio Yamamoto, Eiji Yamamoto, Kiyosumi Hori, Junichi Yonemaru, Shuichi Matsuba, Kenji Fujino

    THEORETICAL AND APPLIED GENETICS   127 ( 4 )   995 - 1004   2014.4

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  • Effect of advanced intercrossing on genome structure and on the power to detect linked quantitative trait loci in a multi-parent population: a simulation study in rice Reviewed

    Eiji Yamamoto, Hiroyoshi Iwata, Takanari Tanabata, Ritsuko Mizobuchi, Jun-ichi Yonemaru, Toshio Yamamoto, Masahiro Yano

    BMC GENETICS   15   50   2014.4

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    DOI： 10.1186/1471-2156-15-50

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  • The genetic architecture of hybrid breakdown emerged in progeny from a cross between Japanese rice varieties Reviewed

    Matsubara Kazuki, Yamamoto Eiji, Kobayashi Nobuya, Tanaka Jun-ichi, Tsunematsu Hiroshi, Mizobuchi Ritsuko, Yonemaru Jun-ichi, Yamamoto Toshio, Yano Masahiro, Kato Hiroshi

    GENES & GENETIC SYSTEMS   88 ( 6 )   385   2013.12

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  • Detection of QTLs to reduce cadmium content in rice grains using LAC23/Koshihikari chromosome segment substitution lines Reviewed

    Tadashi Abe, Yasunori Nonoue, Nozomi Ono, Motoyasu Omoteno, Masato Kuramata, Shuichi Fukuoka, Toshio Yamamoto, Masahiro Yano, Satoru Ishikawa

    BREEDING SCIENCE   63 ( 3 )   284 - 291   2013.9

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  • A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate Reviewed

    Toshiyuki Takai, Shunsuke Adachi, Fumio Taguchi-Shiobara, Yumiko Sanoh-Arai, Norio Iwasawa, Satoshi Yoshinaga, Sakiko Hirose, Yojiro Taniguchi, Utako Yamanouchi, Jianzhong Wu, Takashi Matsumoto, Kazuhiko Sugimoto, Katsuhiko Kondo, Takashi Ikka, Tsuyu Ando, Izumi Kono, Sachie Ito, Ayahiko Shomura, Taiichiro Ookawa, Tadashi Hirasawa, Masahiro Yano, Motohiko Kondo, Toshio Yamamoto

    SCIENTIFIC REPORTS   3   2149   2013.8

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  • QTL Analysis of Leaf Photosynthesis in Rice

    Toshiyuki Takai, Akihiro Ohsumi, Yumiko Arai, Norio Iwasawa, Masahiro Yano, Toshio Yamamoto, Satoshi Yoshinaga, Motohiko Kondo

    JARQ-JAPAN AGRICULTURAL RESEARCH QUARTERLY   47 ( 3 )   227 - 235   2013.7

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  • "MJ3" and "MA22", new high-cadmium-accumulating practical rice lines with non-shattering derived from gamma ray mutation Reviewed

    ABE Tadashi, KURAMATA Masato, IWASAKI Yukimoto, HONMA Toshimitsu, IBARAKI Toshiyuki, YAMAMOTO Toshio, YANO Masahiro, MURAKAMI Masaharu, ISHIKAWA Satoru

    Breeding Research   15 ( 2 )   17 - 24   2013.6

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    DOI： 10.1270/jsbbr.15.17

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  • The mesophyll anatomy enhancing CO2 diffusion is a key trait for improving rice photosynthesis Reviewed

    Shunsuke Adachi, Toru Nakae, Masaki Uchida, Kazuya Soda, Toshiyuki Takai, Takao Oi, Toshio Yamamoto, Taiichiro Ookawa, Hiroshi Miyake, Masahiro Yano, Tadashi Hirasawa

    JOURNAL OF EXPERIMENTAL BOTANY   64 ( 4 )   1061 - 1072   2013.2

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  • Genome-Wide Haplotype Changes Produced by Artificial Selection during Modern Rice Breeding in Japan Reviewed

    Jun-ichi Yonemaru, Toshio Yamamoto, Kaworu Ebana, Eiji Yamamoto, Hideki Nagasaki, Taeko Shibaya, Masahiro Yano

    PLOS ONE   7 ( 3 )   e32982   2012.3

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  • OGRO: The Overview of functionally characterized Genes in Rice online database Reviewed

    Eiji Yamamoto, Jun-ichi Yonemaru, Toshio Yamamoto, Masahiro Yano

    RICE   5 ( 1 )   26   2012

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    DOI： 10.1186/1939-8433-5-26

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  • Molecular distinction in genetic regulation of nonphotochemical quenching in rice Reviewed

    Ichiro Kasajima, Kaworu Ebana, Toshio Yamamoto, Kentaro Takahara, Masahiro Yano, Maki Kawai-Yamada, Hirofumi Uchimiya

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   108 ( 33 )   13835 - 13840   2011.8

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  • Detection of a QTL for accumulating Cd in rice that enables efficient Cd phytoextraction from soil (vol 61, pg 43, 2011) Reviewed

    Tadashi Abe, Fumio Taguchi-Shiobara, Yoichiro Kojima, Takeshi Ebitani, Masato Kuramata, Toshio Yamamoto, Masahiro Yano, Satoru Ishikawa

    BREEDING SCIENCE   61 ( 2 )   221 - 221   2011.6

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  • Identification of Chromosomal Regions Controlling the Leaf Photosynthetic Rate in Rice by Using a Progeny from Japonica and High-yielding Indica Varieties Reviewed

    Shunsuke Adachi, Naoko Nito, Motohiko Kondo, Toshio Yamamoto, Yumiko Arai-Sanoh, Tsuyu Ando, Taiichiro Ookawa, Masahiro Yano, Tadashi Hirasawa

    PLANT PRODUCTION SCIENCE   14 ( 2 )   118 - 127   2011.4

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  • Identification and characterization of genomic regions on chromosomes 4 and 8 that control the rate of photosynthesis in rice leaves Reviewed

    Shunsuke Adachi, Yukiko Tsuru, Naoko Nito, Kazumasa Murata, Toshio Yamamoto, Takeshi Ebitani, Taiichiro Ookawa, Tadashi Hirasawa

    JOURNAL OF EXPERIMENTAL BOTANY   62 ( 6 )   1927 - 1938   2011.3

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  • Detection of a QTL for accumulating Cd in rice that enables efficient Cd phytoextraction from soil Reviewed

    Tadashi Abe, Fumio Taguchi-Shiobara, Yoichiro Kojima, Takeshi Ebitani, Masato Kuramata, Toshio Yamamoto, Masahiro Yano, Satoru Ishikawa

    BREEDING SCIENCE   61 ( 1 )   43 - 51   2011.3

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  • Evaluation of yield performance in rice near-isogenic lines with increased spikelet number Reviewed

    Akihiro Ohsumi, Toshiyuki Takai, Masashi Ida, Toshio Yamamoto, Yumiko Arai-Sanoh, Masahiro Yano, Tsuyu Ando, Motohiko Kondo

    FIELD CROPS RESEARCH   120 ( 1 )   68 - 75   2011.1

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  • Characterization of a rice variety with high hydraulic conductance and identification of the chromosome region responsible using chromosome segment substitution lines Reviewed

    Shunsuke Adachi, Yukiko Tsuru, Motohiko Kondo, Toshio Yamamoto, Yumiko Arai-Sanoh, Tsuyu Ando, Taiichiro Ookawa, Masahiro Yano, Tadashi Hirasawa

    ANNALS OF BOTANY   106 ( 5 )   803 - 811   2010.11

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    DOI： 10.1093/aob/mcq175

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  • Q-TARO: QTL Annotation Rice Online Database Reviewed

    Jun-ichi Yonemaru, Toshio Yamamoto, Shuichi Fukuoka, Yusaku Uga, Kiyosumi Hori, Masahiro Yano

    RICE   3 ( 2-3 )   194 - 203   2010.9

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  • Integration of Genomics into Rice Breeding Reviewed

    Shuichi Fukuoka, Kaworu Ebana, Toshio Yamamoto, Masahiro Yano

    RICE   3 ( 2-3 )   131 - 137   2010.9

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  • A Quantitative Trait Locus for Chlorophyll Content and its Association with Leaf Photosynthesis in Rice Reviewed

    Toshiyuki Takai, Motohiko Kondo, Masahiro Yano, Toshio Yamamoto

    RICE   3 ( 2-3 )   172 - 180   2010.9

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    DOI： 10.1007/s12284-010-9047-6

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  • Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms Reviewed

    Toshio Yamamoto, Hideki Nagasaki, Jun-ichi Yonemaru, Kaworu Ebana, Maiko Nakajima, Taeko Shibaya, Masahiro Yano

    BMC GENOMICS   11   267   2010.4

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    DOI： 10.1186/1471-2164-11-267

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  • QTL analysis for associated traits of superior strong culm in rice : Using progenies of Leaf Star/Takanari cross

    SAKAI Sachi, YAMAMOTO Toshio, YANO Masahiro, KONO Izumi, HIRASAWA Tadashi, OOKAWA Taiichiro

    Abstracts of Meeting of the CSSJ   79   352 - 353   2010.3

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    DOI： 10.14829/jcsproc.229.0.352.0

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  • Quantitative trait locus (QTL) analysis for rate of photosynthesis using backcross inbred lines (BC_1F_6) derived from two rice cultivars,Koshihikari and Takanari

    UCHIDA Masaki, SODA Kazuya, TAKAI Toshiyuki, YAMAMOTO Toshio, OOKAWA Taiichiro, YANO Masahiro, HIRASAWA Tadashi

    Abstracts of Meeting of the CSSJ   79   96 - 97   2010.3

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    DOI： 10.14829/jcsproc.229.0.96.0

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  • Quantitative trait locus (QTL) analysis for inclination angle of leaf blades in the ripening stage using backcross inbred lines (BC_1F_6) derived from two rice cultivars, Koshihikari and Takanari

    SODA Kazuya, TAKAI Toshiyuki, YAMAMOTO Toshio, OOKAWA Taiichiro, YANO Masahiro, HIRASAWA Tadashi

    Abstracts of Meeting of the CSSJ   79   98 - 99   2010.3

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    DOI： 10.14829/jcsproc.229.0.98.0

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  • A major quantitative trait locus for increasing cadmium-specific concentration in rice grain is located on the short arm of chromosome 7 Reviewed

    Satoru Ishikawa, Tadashi Abe, Masato Kuramata, Masayuki Yamaguchi, Tsuyu Ando, Toshio Yamamoto, Masahiro Yano

    JOURNAL OF EXPERIMENTAL BOTANY   61 ( 3 )   923 - 934   2010.3

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    DOI： 10.1093/jxb/erp360

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  • Canopy temperature on clear and cloudy days can be used to estimate varietal differences in stomatal conductance in rice Reviewed

    Toshiyuki Takai, Masahiro Yano, Toshio Yamamoto

    FIELD CROPS RESEARCH   115 ( 2 )   165 - 170   2010.1

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    DOI： 10.1016/j.fcr.2009.10.019

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  • Isolation and functional analysis of the gene controlling the stub-spreading trait in rice (Oryza sativa L.) Reviewed

    T. Komori, M. Miyata, T. Yamamoto, N. Nitta, Y. Hiei, M. Yano, J. Ueki, T. Komari

    PLANT BREEDING   128 ( 6 )   568 - 575   2009.12

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    DOI： 10.1111/j.1439-0523.2009.01639.x

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  • A novel quantitative trait locus, qCL1, involved in semi-dwarfism derived from Japanese rice cultivar Nipponbare Reviewed

    Kiyosumi Hori, Toshio Yamamoto, Kaworu Ebana, Yoshinobu Takeuchi, Masahiro Yano

    BREEDING SCIENCE   59 ( 3 )   285 - 295   2009.9

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    Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1270/jsbbs.59.285

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  • Towards the Understanding of Complex Traits in Rice: Substantially or Superficially? Reviewed

    Toshio Yamamoto, Junichi Yonemaru, Masahiro Yano

    DNA RESEARCH   16 ( 3 )   141 - 154   2009.6

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    Authorship：Lead author   Language：English  

    DOI： 10.1093/dnares/dsp006

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  • Detection of a quantitative trait locus controlling carbon isotope discrimination and its contribution to stomatal conductance in japonica rice Reviewed

    Toshiyuki Takai, Akihiro Ohsumi, Yumiko San-oh, Ma. Rebecca C. Laza, Motohiko Kondo, Toshio Yamamoto, Masahiro Yano

    THEORETICAL AND APPLIED GENETICS   118 ( 7 )   1401 - 1410   2009.5

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1007/s00122-009-0990-9

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  • Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice Reviewed

    Tsuyu Ando, Toshio Yamamoto, Takehiko Shimizu, Xiu Fang Ma, Ayahiko Shomura, Yoshinobu Takeuchi, Shao Yang Lin, Masahiro Yano

    THEORETICAL AND APPLIED GENETICS   116 ( 6 )   881 - 890   2008.4

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    DOI： 10.1007/s00122-008-0722-6

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  • Detection and molecular cloning of genes underlying quantitative phenotypic variations in rice Reviewed

    Toshio Yamamoto, Masahiro Yano

    Biotechnology in Agriculture and Forestry   62   295 - 308   2008

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    Authorship：Lead author   Language：English   Publishing type：Part of collection (book)   Publisher：Springer International Publishing  

    DOI： 10.1007/978-3-540-74250-0_22

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  • Marker-assisted selection and evaluation of the QTL for stigma exsertion under japonica rice genetic background Reviewed

    Maiko Miyata, Toshio Yamamoto, Toshiyuki Komori, Naoto Nitta

    THEORETICAL AND APPLIED GENETICS   114 ( 3 )   539 - 548   2007.2

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    DOI： 10.1007/s00122-006-0454-4

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  • Mapping QTLs that control the performance of rice tissue culture and evaluation of derived near-isogenic lines Reviewed

    F Taguchi-Shiobara, T Yamamoto, M Yano, S Oka

    THEORETICAL AND APPLIED GENETICS   112 ( 5 )   968 - 976   2006.3

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    DOI： 10.1007/s00122-005-0200-3

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  • Development of isogenic lines of rice cultivar Koshihikari with early and late heading by marker-assisted selection Reviewed

    Yoshinobu Takeuchi, Takeshi Ebitani, Toshio Yamamoto, Hiroyuki Sato, Hisatoshi Ohta, Hideyuki Hirabayashi, Hiroshi Kato, Ikuo Ando, Hiroshi Nemoto, Tokio Imbe, Masahiro Yano

    Breeding Science   56 ( 4 )   405 - 413   2006

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    DOI： 10.1270/jsbbs.56.405

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  • Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems Reviewed

    A Nishimura, M Ashikari, S Lin, T Takashi, ER Angeles, T Yamamoto, M Matsuoka

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   102 ( 33 )   11940 - 11944   2005.8

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    DOI： 10.1073/pnas.0504220102

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  • Cytokinin oxidase regulates rice grain production Reviewed

    M Ashikari, H Sakakibara, SY Lin, T Yamamoto, T Takashi, A Nishimura, ER Angeles, Q Qian, H Kitano, M Matsuoka

    SCIENCE   309 ( 5735 )   741 - 745   2005.7

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    DOI： 10.1126/science.1113373

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  • Fine scale and physical mapping of Spk(t) controlling spreading stub in rice Reviewed

    M Miyata, T Komori, T Yamamoto, T Ueda, M Yano, N Nitta

    BREEDING SCIENCE   55 ( 2 )   237 - 239   2005.6

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    DOI： 10.1270/jsbbs.55.237

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  • Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice cultivar 'Kasalath' in a genetic background of japonica elite cultivar 'Koshihikari' Reviewed

    T Ebitani, Y Takeuchi, Y Nonoue, T Yamamoto, K Takeuchi, M Yano

    BREEDING SCIENCE   55 ( 1 )   65 - 73   2005.3

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    DOI： 10.1270/jsbbs.55.65

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  • Isolation of a rice regeneration QTL gene and its application to new transformation system

    A Nishimura, M Ashikari, SY Lin, T Takashi, ER Angeles, T Yamamoto, M Matsuoka

    PLANT AND CELL PHYSIOLOGY   46   S193 - S193   2005

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  • Fine genetic mapping of the nuclear gene, Rf-1, that restores the BT-type cytoplasmic male sterility in rice (Oryza sativa L.) by PCR-based markers Reviewed

    T Komori, T Yamamoto, N Takemori, M Kashihara, H Matsushima, N Nitta

    EUPHYTICA   129 ( 2 )   241 - 247   2003

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    DOI： 10.1023/A:1021915611210

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  • Mapping quantitative trait loci for days-to-heading, and culm, panicle and internode lengths in a BC1F3 population using an elite rice variety, Koshihikari, as the recurrent parent Reviewed

    T Yamamoto, F Taguchi-Shiobara, Y Ukai, T Sasaki, M Yano

    BREEDING SCIENCE   51 ( 2 )   63 - 71   2001.6

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    DOI： 10.1270/jsbbs.51.63

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  • Characterization and detection of epistatic interactions of 3 QTLs, Hd1, Hd2, and Hd3,controlling heading date in rice using nearly isogenic lines Reviewed

    HX Lin, T Yamamoto, T Sasaki, M Yano

    THEORETICAL AND APPLIED GENETICS   101 ( 7 )   1021 - 1028   2000.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1007/s001220051576

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  • Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny Reviewed

    T Yamamoto, HX Lin, T Sasaki, M Yano

    GENETICS   154 ( 2 )   885 - 891   2000.2

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  • Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors Reviewed

    T Yamamoto, Y Kuboki, SY Lin, T Sasaki, M Yano

    THEORETICAL AND APPLIED GENETICS   97 ( 1-2 )   37 - 44   1998.7

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    DOI： 10.1007/s001220050864

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  • A high-density rice genetic linkage map with 2275 markers using a single F-2 population Reviewed

    Y Harushima, M Yano, P Shomura, M Sato, T Shimano, Y Kuboki, T Yamamoto, SY Lin, BA Antonio, A Parco, H Kajiya, N Huang, K Yamamoto, Y Nagamura, N Kurata, GS Khush, T Sasaki

    GENETICS   148 ( 1 )   479 - 494   1998.1

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  • Genetic analysis of spreading stub using indica/japonica backcrossed progenies in rice Reviewed

    T Yamamoto, T Sasaki, M Yano

    BREEDING SCIENCE   47 ( 2 )   141 - 144   1997.6

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  • Genetic Analysis of Spreading Stub Using indica/japonica Backcrossed Progenies in Rice. Reviewed

    Yamamoto T, Sasaki T, Yano M

    Breeding Science   47 ( 2 )   141 - 144   1997.6

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    Improving plant type is one of the principal objectives of rice breeding programs. However, Iittle information about the genetic basis of plant type is available. For progenies derived from indica/japonica crosses, the variation of plant type is continuous and complex, so genetic analysis of such traits is often difficult. This study was undertaken to clarify the genetic basis of spreading stub, an inferior plant type character for recent Japanese elite rice varieties. Two different plant types, spreading stub and erect, were observed in one population (BC3F2) derived from a selected backcrossed plant, in which a japonica variety, Nippon-bare, was the recurrent parent and an indica variety, Kasalath, was the donor parent. BC3F3 Iines derived from each BC3F2 individual were also classified into 3 distinct types, erect (9 Iines), spreading (12 Iines) and segregating into both types (29 Iines). Spreading type was observed about 3 times more frequently than erect type in each segregated line. These results suggest that spreading stub was controlled by a single dominant gene. Moreover the tentatively designated locus, Spk(t), was mapped, with RFLP markers, on chromosome 9.

    DOI： 10.1270/jsbbs1951.47.141

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Books

  • Revised Consensus Document on the Biology of Rice (Oryza sativa L.) Series on the Harmonisation of Regulatory Oversight in Biotechnology No.70

    （ Role： Contributor ,  SECTION 1. GENERAL DESCRIPTION INCLUDING TAXONOMY AND MORPHOLOGY, 1.2. Description）

    OECD Environment Directorate, Environment, Health and Safety Division  2021.12 

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  • 光合成研究と産業応用最前線

    安達俊輔, 山本敏央（ Role： Contributor ,  作物の光合成速度を向上させる自然変異遺伝子の解明）

    （株）エヌ・ティー・エス  2014 

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  • Genomics of Plant Genetic Resources

    Yamamoto T, Uga Y, Yano M（ Role： Contributor ,  Genomics-assisted allele mining and its integration into rice breeding）

    2014 

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  • Rice Biology in the Genomics Era

    Yamamoto T, Yano M（ Role： Contributor ,  Detection and Molecular cloning of genes underlying quantitative phenotypic variation in rice）

    Springer  2007 

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MISC

  • A Few Selected Approaches to Increase Genetic Diversity in Rice Breeding Invited Reviewed

    Toshio Yamamoto, Tomoyuki Furuta, Daisuke Ogawa, Jun-ichi Yonemaru, Daichi Kuniyoshi, Yuji Kishima

    Journal of Crop Research   65   83 - 87   2020.10

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    Authorship：Lead author,　Corresponding author   Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (scientific journal)  

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  • 水稲の収量および倒伏抵抗性関連形質の量的形質遺伝子座解析―極多着粒・極強稈系統LTAT‐29とタカナリのF2の分離集団を用いて―

    野村知宏, 山本敏央, 上田忠正, 米丸淳一, 阿部陽, 高木宏樹, 安達俊輔, 平沢正, 大川泰一郎

    育種学研究   19   21   2017.10

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  • バイオマス増大に向けたイネ次世代育種法の開発と利用

    山本敏央

    JATAFFジャーナル   45 ( 5 )   65   2016

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  • ブータン品種「Kuchum」由来の穂ばらみ期耐冷性QTLを保有する「ひとめぼれ」準同質遺伝子系統の育成

    遠藤貴司, 佐伯研一, 安藤露, 正村純彦, 水林達実, 山本敏央

    育種学研究   16   72   2014.9

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  • 多収イネの光合成能力に貢献する遺伝子の特定

    山本 敏央, 髙井 俊之

    明日の食品産業 = Food industry for tomorrow   2014 ( 7 )   35 - 39   2014.7

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  • 北海道のイネ品種群の集団構造解析

    池ケ谷智仁, 品田博史, 山本敏央, 山本英司, 堀清純, 米丸淳一, 松葉修一, 藤野賢治

    育種学研究   16   13   2014.3

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  • 多収稲の光合成能力に貢献するGPS遺伝子を発見

    山本 敏央

    ニューカントリー   64 ( 8 )   50 - 51   2014

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  • Map-based cloning of QTL, GPS (GREEN FOR PHOTOSYNTHESIS), controlling leaf photosynthesis in rice high-yielding variety, Takanari

    TAKAI Toshiyuki, ADACHI Shunsuke, TAGUCHI Fumio, ARAI Yumiko, IWASAWA Norio, YOSHINAGA Satoshi, YAMANOUCHI Utako, OOKAWA Taiichiro, HIRASAWA Tadashi, YANO Masahiro, KONDO Motohiko, YAMAMOTO Toshio

    日本作物學會紀事   81   178 - 179   2012.3

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  • 多収性インド型品種タカナリと日本型品種コシヒカリの交雑後代に見出されたタカナリを大きく上回る高い光合成速度を示す系統は高い電子伝達速度と葉内CO2拡散に優れた形態的特徴を示す

    安達俊輔, 中江徹, 高井俊之, 山本敏央, 大川泰一郎, 矢野昌裕, 平沢正

    日本作物学会講演会要旨・資料集   232nd   170 - 171   2011.8

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  • Whole genome sequencing of "Koshihikari", a leading rice variety in Japan

    YAMAMOTO Toshio, NAGASAKI Hideki

    農林水産技術研究ジャーナル   34 ( 4 )   35 - 39   2011.4

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  • Characterization of the leaf photosynthesis with a transgressive high rate found in the progenies of the high yielding indica variety, Takanari, crossed with the japonica variety, Koshihikari

    ADACHI Shunsuke, NAKAE Toru, UCHIDA Masaki, TAKAI Toshiyuki, YAMAMOTO Toshio, OOKAWA Taiichiro, YANO Masahiro, HIRASAWA Tadashi

    日本作物學會紀事   80   148 - 149   2011.3

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  • What we have learned about a marker assisted selection in rice

    YANO Masahiro, YAMAMOTO Toshio

    農林水産技術研究ジャーナル   33 ( 12 )   5 - 11   2010.12

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  • Genomics-assisted breeding in rice

    ( 47 )   1 - 10   2010.5

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  • コシヒカリゲノムの解読とその育種的利用 (基礎研究を生かす種苗産業国際化戦略の最前線--ハイブリットライスの経験に学ぶ)

    山本 敏央, 矢野 昌裕

    Techno innovation   20 ( 2 )   13 - 19   2010

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  • インド型水稲品種の高い個葉光合成能に関与するQTL

    高井俊之, 近藤始彦, 荒井裕見子, 石丸努, 吉永悟志, 矢野昌裕, 山本敏央

    農研機構作物研究所成果情報(Web)   2010   2010

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  • Development and utilization of chromosomal segment substitution lines (CSSLs) in rice

    YAMAMOTO T., YANO M.

    78   453 - 453   2009.3

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  • ゲノミクスを背景とした新たな作物育種

    矢野昌裕, 福岡修一, 江花薫子, 山本敏央

    ブレインテクノニュース   133   1 - 7   2009

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  • ゲノム育種による効率的品種育成技術の開発-QTL遺伝子解析の推進-1 QTL遺伝子解析のための基盤整備(2)QTL遺伝子解析手法の体系化ならびに研究支援

    矢野昌裕, 長村吉晃, 上田忠正, 福岡修一, 宇賀優作, 山本敏央, 安藤露

    農林水産省農林水産技術会議事務局研究成果   ( 473 )   2009

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  • 遺伝子情報にもとづくイネのゲノム育種への展開 (特集 稲と<自然>の再定義)

    山本 敏央, 矢野 昌裕

    科学   77 ( 6 )   607 - 613   2007.6

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    Language：Japanese   Publisher：岩波書店  

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  • Rice genome research as a linker of plant genetics and molecular biology

    T Sasaki, M Yano, K Yamamoto, T Matsumoto

    FASEB JOURNAL   11 ( 9 )   A1004 - A1004   1997.7

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Industrial property rights

  • 品種出願 稲（山形１１９号）

    結城和博, 佐野智義, 中場勝, 後藤元, 森谷真紀子, 齋藤信弥, 阿部洋平, 渡部幸一郎, 齋藤寛, 佐藤久実, 齋藤久美, 本間猛俊, 山本敏央, 矢野昌裕

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    Application no：第30962号  Date applied：2016.6.28

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  • 品種出願 稲（ファイレメCD１号）

    安部匡, 石川覚, 倉俣正人, 矢野昌裕, 山本敏央

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    Application no：第29773 号  Date applied：2015.6.26

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  • 品種出願（命名登録） 稲（関東ＨＤ２号）

    竹内善信, 安東郁男, 井邊時雄, 太田久稔, 佐藤宏之, 平山正賢, 加藤浩, 根本博, 平林秀介, 出田収, 石井卓朗, 前田英郎, 矢野昌裕, 田口文緒, 蛯谷武志, 山本敏央

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    Application no：第21536号  Date applied：2007.9.28

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  • 穀物の収量を増加させる遺伝子、並びにその利用

    芦苅 基行, 松岡 信, 林 少揚, 山本 敏央, 西村 明日香, 高師 知紀

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    Applicant：本田技研工業株式会社

    Application no：特願2006-228763  Date applied：2006.8.25

    Announcement no：特開2007-049994  Date announced：2007.3.1

    Patent/Registration no：特許第4462566号  Date issued：2010.2.26

    J-GLOBAL

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  • 穀物の収量を増加させる遺伝子、並びにその利用

    芦苅 基行, 松岡 信, 林 少揚, 山本 敏央, 西村 明日香, 高師 知紀

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    Applicant：本田技研工業株式会社

    Application no：特願2006-228763  Date applied：2006.8.25

    Announcement no：特開2007-049994  Date announced：2007.3.1

    J-GLOBAL

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  • 品種出願（命名登録） 稲（コシヒカリ関東ＨＤ１号）

    竹内善信, 安東郁男, 井邊時雄, 太田久稔, 佐藤宏之, 平山正賢, 加藤浩, 根本博, 平林秀介, 出田収, 坂井真, 青木法明, 矢野昌裕, 田口文緒, 蛯谷武志, 山本敏央

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    Application no：第20119号  Date applied：2006.8.22

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  • 穀物の収量を増加させる遺伝子、並びにその利用

    芦苅 基行, 松岡 信, 林 少揚, 山本 敏央, 西村 明日香, 高師 知紀

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    Applicant：本田技研工業株式会社

    Application no：JP2003014434  Date applied：2003.11.13

    Announcement no：WO2004-044200  Date announced：2004.5.27

    J-GLOBAL

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  • 穀物の収量を増加させる遺伝子、並びにその利用

    芦苅 基行, 松岡 信, 林 少揚, 山本 敏央, 西村 明日香, 高師 知紀

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    Applicant：本田技研工業株式会社

    Application no：特願2004-551229  Date applied：2003.11.13

    Patent/Registration no：特許第4448031号  Date issued：2010.1.29

    J-GLOBAL

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  • 品種登録 稲（いわた１３号）

    柏原正和, 沼澤広宣, 中村崇, 山本敏央

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    Application no：第10870号  Date applied：2002.12.16

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  • 混入種籾の検出方法

    新田 直人, 山本 敏央

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    Applicant：日本たばこ産業株式会社, シンジェンタ リミテッド

    Application no：特願2001-281109  Date applied：2001.9.17

    Announcement no：特開2002-291488  Date announced：2002.10.8

    J-GLOBAL

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  • イネBT型雄性不稔細胞質に対する稔性回復遺伝子座の遺伝子型を推定する方法

    小森 俊之, 山本 敏央, 新田 直人, 竹森 尚樹

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    Applicant：日本たばこ産業株式会社, シンジェンタ リミテッド

    Application no：特願2001-247600  Date applied：2001.8.17

    Announcement no：特開2002-345485  Date announced：2002.12.3

    J-GLOBAL

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  • 品種登録 稲（いわた１２号）

    柏原正和, 伊藤広昭, 山本敏央, 沼澤広宣, 香村敏郎

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    Application no：第8631号  Date applied：2001.2.9

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  • 品種登録 稲（いわた８号）

    柏原正和, 伊藤広昭, 山本敏央, 沼澤広宣, 香村敏郎

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    Application no：第8630号  Date applied：2001.2.9

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  • 品種登録 稲（いわた１５号）

    柏原正和, 伊藤広昭, 山本敏央, 沼澤広宣, 香村敏郎

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    Application no：第8632号  Date applied：2001.2.9

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  • 品種登録 稲（いわた５号）

    柏原正和, 伊藤広昭, 山本敏央, 沼澤広宣, 長谷川勉, 中村崇, 久保友明, 香村敏郎

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    Application no：第7690号  Date applied：2000.2.22

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  • 品種登録 稲（いわた１１号）

    柏原正和, 伊藤広昭, 山本敏央, 沼澤広宣, 久保友明, 香村敏郎

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    Application no：第7691号  Date applied：2000.2.22

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  • 品種登録 稲（いわた３号）

    柏原正和, 馬場広昭, 山本敏央, 久保友明, 香村俊郎

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    Application no：第5189号  Date applied：1996.10.15

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Awards

  • 論文賞

    2013.3   日本作物学会   Identification of chromosomal regions controlling the leaf photosynthetic rate in rice by using a progeny from Japonica and high-yielding Indica varieties

    Adachi S, Nito N, Kondo M, Yamamoto T, Arai-Sanoh Y, Ando T, Ookawa T, Yano M, Hirasawa T

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  • 論文賞

    2012.3   日本育種学会   Detection of a QTL for accumulating Cd in rice that enables efficient Cd phytoextraction from soil

    Abe T, Taguchi-Shiobara F, Kojima Y, Ebitani T, Kuramata M, Yamamoto T, Yano M, Ishikawa S

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  • 論文賞

    2010.3   日本育種学会   A novel quantitative trait locus, qCL1, involved in semi-dwarfism derived from Japanese rice cultivar Nipponbare

    Hori K, Yamamoto T, Ebana K, Takeuchi Y, Yano M

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  • 論文賞

    2006.3   日本育種学会   Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice cultivar ‘Kasalath’ in a genetic background of Japonica elite cultivar ‘Koshihikari’

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Research Projects

  • 限られた育種母本から高能率に遺伝的多様性を生み出す多系交雑育種システムの開発

    Grant number：20H02958  2020.04 - 2024.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    山本 敏央, 小川 大輔, 米丸 淳一, 古田 智敬

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    Grant amount：\17550000 （ Direct expense: \13500000 、 Indirect expense：\4050000 ）

    品種改良や遺伝実験において、用いる集団の遺伝構成は目標の達成に大きな影響を与える重要な要素である。自殖性作物の育種では2種類の両親に由来する交雑集団から表現型をもとに優良個体の選抜を繰り返す方法が一般的だが，この場合，対立遺伝子の組み合わせが二つの親間のみに限定されることから多様性の拡大という点で必ずしも最適とは言えない。
    課題担当者らは、これまでに複数品種の積み上げ交雑からなる多系交雑集団（Multi-parent Advanced Generation Inter-Cross ; MAGIC集団）の作出を開始し，8種類の国内多収水稲品種の8系交雑F1に由来し、これらゲノムがほぼ均等に存在する恒久的な自殖集団を育成した．これまでの遺伝解析で用いられてきたRecombinant Inbred Lines (RIL)集団，Genome Wide Association Study (GWAS)集団，Nested Association Mapping (NAM)集団等と比較して，本集団は多数のハプロタイプが交雑によって混合された集団という点でユニークなものである。MAGIC集団は由来親を識別する多数のハプロタイプ多型を活用することで，高精度な連関解析やゲノムワイド予測モデルの構築に貢献する。
    今年度は、MAGIC集団がGxEの検出に有効かどうかを評価する実験を出穂期を例に行った。出穂期は日長の影響を強く受けることから、主要な感光性遺伝子の違いが表れにくい2地点として、比較的緯度の近い東日本のつくば市と西日本の倉敷市でMAGIC集団の出穂期を調査し、GWAS解析の結果をもとに地域共通および特有のゲノム領域の検出を試みた。

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  • Biological sustainability of double-cropping supported by seasonal change in root microbiome

    Grant number：19KT0011  2019.07 - 2022.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    谷 明生, 山本 敏央, 山地 直樹, 山下 純, 門田 有希, 中川 智行, 最相 大輔, 持田 恵一

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    Grant amount：\18590000 （ Direct expense: \14300000 、 Indirect expense：\4290000 ）

    植物の生育は植物の遺伝背景や環境要因等の相互作用の結果として捉えることができる。根圏微生物叢は植物の生育に多大な影響を与えており、逆に、植物の遺伝的背景や環境要因にも規定され、相互作用すると考えられる。本研究の目的は、圃場環境において微生物叢を含むあらゆるパラメータをデータ化し、それらの要因間のネットワークを可視化し，農業生態系としての季節変動動態を理解することである。
    研究所実験圃場の慣行区と無施肥区において、アルミニウムに対する感受性の異なるイネとオオムギの品種対を対象に、隔週で各条件3植物個体ずつ（イネは6個体）サンプリングした。環境要因として、フィールドサーバーを用いて日照、降雨、温度、湿度、風向、風速を測定した。土壌環境データとして根圏土壌を採取し、ICP-MSによる水抽出可能な元素の組成を測定し、土壌センサを用いて土壌pHを測定した。さらに土壌の根圏微生物DNAを精製し、16S rRNA遺伝子アンプリコンシーケンスを行った。
    施肥の有無によりイオン等の動態は変化し、pHは慣行区で低く、カリウム、リンは慣行区で高濃度であるが早い時期に消費された。慣行区の硫黄、無施肥区のマグネシウム、マンガン、銅が落水により増加した。同じく落水によると考えられるヒ素の増加、カドミウムの低下が無施肥区で見られた。
    微生物叢は、イネではMassilia属、Pseudomonadaceae、Oxalobacteraceaeがstar1で多い傾向が見られた。オオムギでは根圏土壌と根のサンプルで相違が見られ、根のサンプルにのみJanthinobacterium, Methylibium属細菌が多く存在することが分かった。これらはオオムギ根のエンドファイトであると考えられ、そのオオムギに対する共生機構や成長への影響に興味が持たれる。

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  • イネ小胞子に潜在する個体分化能と倍数化能を活用した育種基盤の新構築

    Grant number：19H00937  2019.04 - 2023.03

    日本学術振興会  科学研究費助成事業 基盤研究(A)  基盤研究(A)

    貴島 祐治, 山本 敏央, 長岐 清孝, 小出 陽平, 金 鍾明

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    Grant amount：\45890000 （ Direct expense: \35300000 、 Indirect expense：\10590000 ）

    本研究はイネの葯培養に関係して大きく２つの内容に大別される。１つ目は、葯の発達初期に内包されている小胞子が高い脱分化能と個体再分化能を有する点に着目した研究。2つ目は、アジアとアフリカに起源を異にする栽培イネの種間雑種の葯培養産物から倍数体（四倍体）植物個体が再生したことに端緒を得て始めた、小胞子の倍数性発生に着目した研究。
    2019年度は本研究を行うために組織した分担者を交えて、7月7日に研究の進め方、それぞれの役割の確認を行う会議を開催した。本研究を構成する5つの問題は、１）小胞子から個体分化を誘導するメカニズム、２）イネ小胞子から効率的に個体を再生するシステムの構築、３）イネ種間雑種の葯培養個体で誘導される倍数性の発生メカニズムの解明、４）イネ種間雑種の葯培養個体によって雑種不稔性を回避する遺伝機構の解析、５）葯培養個体から生じた倍数体種間雑種による新しい育種材料の開発。上記の項目で2019年度において主に進展した研究は、３）および５）であった。
    ３）はO. sativaとO. glaberrimaのF1雑種や得られた四倍体の個体を用いて減数分裂の異常と倍数体形成が密接に関連することを示すデータを得た。減数分裂の第１分裂と第２分裂にそれぞれ非還元が発生することによって、倍数体の原資となる二倍性の配偶体が発生することが判明した。
    ５）はO. sativaとO. glaberrimaのF1雑種から葯培養を経て、多様な植物体を得ることができ、雑種不稔性遺伝子がヘテロ接合の場合（通常、二倍体では花粉が崩壊する）でも、稔性を有する四倍体を得、これらの個体をさらに葯培養によって二倍体に還元した稔性を有する個体を作出できた。さらに、F1雑種からの葯培養でも高い稔性を有する倍加半数体の二倍体個体を育成した。これらを用いて、現在稔性を獲得する原因を調べるため、遺伝的な解析を行なっている。

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  • Identification of QTL promoting hydraulic conductance at ripening stage in high yielding rice variety

    Grant number：17K07614  2017.04 - 2018.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    山本 敏央, 安達 俊輔

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    Grant amount：\4810000 （ Direct expense: \3700000 、 Indirect expense：\1110000 ）

    １． アケノホシとコシヒカリの交雑集団を用いた候補ゲノム領域の特定
    申請時点で4.2Mb となっていた候補領域周辺で組換えを起こした系統の出穂期以降の出液量の推移を調査して遺伝子の遺伝学的な絞り込みを行った。その結果、候補領域は第2染色体長腕のRM5460からRN3535の間の922kb に絞り込むことができた。候補領域周辺におけるアケノホシおよびコシヒカリのゲノム塩基配列情報の配列比較からさらに3個のINDELマーカーを作出し、候補領域内での更なる絞り込みに供試可能な組換え系統を得た。
    ２． 候補ゲノム領域に関するアケノホシ系譜上のハプロタイプの伝達の調査
    候補ゲノム領域について日本晴を参照配列としてアケノホシとコシヒカリを比較した結果、得られた一塩基置換多型の殆どはアケノホシと日本晴が共通で、コシヒカリが異なるパターンを示した。またアケノホシの系譜における候補ゲノム領域は日本品種コチカゼに由来する可能性が高いことが示唆された。
    ３． 候補ゲノム領域をアケノホシ型に置換したコシヒカリ系統の特性評価
    候補遺伝子を含むゲノム断片をアケノホシ型に置換したコシヒカリ準同質遺伝子系統について10 株×3 反復の簡易生検を行い、籾重、わら重、精籾重、精玄米重を評価したが、コシヒカリと比較して明瞭な差は見られなかった。また、ワグネルポットに生育させた登熟期の準同質遺伝子系統は、コシヒカリに比べて根の表面積が大きいことによって根の通水抵抗が小さく、結果として植物体全体の通水抵抗が小さくなることが示された。

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  • Elucidation of the mechanism of plant oxalate accumulation on the basis of wide targeted metabolomics

    Grant number：16K20953  2016.04 - 2019.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)  Grant-in-Aid for Young Scientists (B)

    Atsuko Miyagi, Kawai Maki, Yamaguchi Masatoshi, Ishikawa Toshiki, Nagano Minoru, Oono Yutaka, Hase Yoshihiro, Ookawa Taiichiro, Adachi Shunsuke, Noguchi Ko, Tokida Takeshi, Usui Yasuhiro, Nakamura Hirofumi, Sakai Hidemitsu, Hasegawa Toshihiro, Yamamoto Toshio

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    Grant amount：\4160000 （ Direct expense: \3200000 、 Indirect expense：\960000 ）

    Oxalate is accumulated in leaves of various plant species. Excess uptake of oxalate is harmful for human and livestock. However, the mechanism of oxalate accumulation remains unknown. To elucidate the mechanism of oxalate accumulation in rice, metabolome and molecular genetic analysis were performed. The results showed that isocitrate lyase (ICL) might involve in oxalate synthesis in the submerged leaves. Metabolome analysis of low oxalate-plants obtained from ion beam-irradiated rice revealed that the decrease of other organic acids would lead low oxalate content. Moreover, it was found that oxalate content in Takanari leaves is markedly lower than those in Koshihikari ones, suggesting that the difference of oxalate content between two cultivars is caused by particular chromosomal region.

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  • 実験系統群を用いたフェノーム解析と連鎖遺伝子の同定

    2016.04 - 2018.03

    農林水産省  次世代ゲノム基盤プロジェクト 

    山本 敏央

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    Authorship：Principal investigator  Grant type：Competitive

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  • バイオマスの増大に向けたイネ次世代育種法の開発と利用

    2015.04 - 2016.03

    農林水産省  農林水産業・食品産業科学技術研究推進事業 

    山本 敏央

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    Authorship：Principal investigator  Grant type：Competitive

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  • Rapid Mobilization of Alleles for Rice Cultivar Improvement in Sub-Saharan Africa

    2014.01 - 2018.06

    AficaRice  Bill & Melinda Gates Foundation 

    Yamamoto Toshio

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    Authorship：Principal investigator  Grant type：Competitive

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  • 光合成効率を高めるQTLの単離と集積

    2013.04 - 2018.03

    農林水産省  次世代ゲノム基盤プロジェクト 

    山本 敏央

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    Authorship：Principal investigator  Grant type：Competitive

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  • 系譜ハプロタイプ情報を利用したイネの食味関連領域の推定と検証

    2013.04 - 2015.03

    農林水産省  次世代ゲノム基盤プロジェクト 

    山本 敏央

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    Authorship：Principal investigator  Grant type：Competitive

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  • Development of genetic tools for crop science using genome information -low-temperature germination in rice

    Grant number：13556004  2001 - 2004

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    NEMOTO Keisuke, TSUTSUMI Nobuhiro, KAMOSHITA Akihiko, YAMAMOTO Toshio, JINUSHI Kenji, KOMARI Toshihiko

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    Grant amount：\14100000 （ Direct expense: \14100000 ）

    Although the current rice genome database potentially has great impact on agriculture, its effective application needs more genetic tools that facilitate to understand genetic control of traits of agronomic importance. This project was aimed to develop such tools (mapping populations for studying quantitative trait loci (QTL) for agronomic traits in rice). We developed for mapping populations, viz., Akihikari (lowland japonica) x IRAT 109 recombinant inbred lines, Nekken 2 (lowland japonica) x Gaya (lowland indica) recombinant inbred lines, Kamenoo (lowland japonica) x Dular (rainfed-lowland indica) recombinant inbred lines, and IR36 (lowland indica) x Genjah Wangkal (upland japonica) recombinant inbred lines. Many agronomic traits including germination ability have mapped using these population by researchers in Japan and China. These results were presented in the synpodium 'Why QTL information is needed in agronomy?' hold by us in the 2005 meeting of Japanese Crop Scicene Society. We also assessed the possibility to propagate and distribute these populations in cooperation with commercial company. We have successfully exchanged opinion and information with some leading companies in rice biotechnology.

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Class subject in charge

  • Crop Genomic Breeding （2025academic year） Late  - その他

  • Plant Genome Dynamics （2025academic year） Second semester  - 月5,月6

  • Advanced Study （2025academic year） Other  - その他

  • Integrated Genomic Breeding （2025academic year） Late  - 木5～8

  • Seminar in Integrated Genomic Breeding （2025academic year） Prophase  - その他

  • Seminar in Integrated Genomic Breeding （2025academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2025academic year） Other  - その他

  • Seminar in Integrated Genomic Breeding （2025academic year） Year-round  - その他

  • Crop Genomic Breeding （2024academic year） Late  - その他

  • Plant Genome Dynamics （2024academic year） Second semester  - 月5,月6

  • Advanced Study （2024academic year） Other  - その他

  • Integrated Genomic Breeding （2024academic year） Late  - 木5～8

  • Seminar in Integrated Genomic Breeding （2024academic year） Prophase  - その他

  • Seminar in Integrated Genomic Breeding （2024academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2024academic year） Year-round  - その他

  • Crop Genomic Breeding （2023academic year） Late  - その他

  • Crop Genomic Breeding （2023academic year） Late  - その他

  • Plant Genome Dynamics （2023academic year） Second semester  - 月5,月6

  • Plant Molecular Cytogenetics （2023academic year） Late  - 木5～8

  • Advanced Study （2023academic year） Other  - その他

  • Specific Research of Bioresources Science （2023academic year） Year-round  - その他

  • Integrated Genomic Breeding （2023academic year） Late  - 木5～8

  • Seminar in Integrated Genomic Breeding （2023academic year） Prophase  - その他

  • Seminar in Integrated Genomic Breeding （2023academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2023academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2023academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2023academic year） Prophase  - その他

  • Seminar in Integrated Genomic Breeding （2023academic year） Prophase  - その他

  • Seminar in Integrated Genomic Breeding （2023academic year） Year-round  - その他

  • Crop Genomic Breeding （2022academic year） Late  - その他

  • Plant Genome Dynamics （2022academic year） Second semester  - 月5,月6

  • Plant Molecular Cytogenetics （2022academic year） Late  - 木5～8

  • Specific Research of Bioresources Science （2022academic year） Year-round  - その他

  • Seminar in Integrated Genomic Breeding （2022academic year） Prophase  - その他

  • Seminar in Integrated Genomic Breeding （2022academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2022academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2022academic year） Prophase  - その他

  • Crop Genomic Breeding （2021academic year） Late  - その他

  • Plant Genome Dynamics （2021academic year） Second semester  - 月5,月6

  • Plant Molecular Cytogenetics （2021academic year） Late  - 木5～8

  • Specific Research of Bioresources Science （2021academic year） Year-round  - その他

  • Topics in Bioresources Science 1 （2021academic year） Summer concentration  - その他

  • Seminar in Integrated Genomic Breeding （2021academic year） Prophase  - その他

  • Seminar in Integrated Genomic Breeding （2021academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2021academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2021academic year） Prophase  - その他

  • Crop Genomic Breeding （2020academic year） special  - その他

  • Plant Genome Dynamics （2020academic year） Second semester  - 月5,月6

  • Plant Molecular Cytogenetics （2020academic year） Late  - その他

  • Specific Research of Bioresources Science （2020academic year） Year-round  - その他

  • Seminar in Integrated Genomic Breeding （2020academic year） Prophase  - その他

  • Seminar in Integrated Genomic Breeding （2020academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2020academic year） Late  - その他

  • Seminar in Integrated Genomic Breeding （2020academic year） Prophase  - その他

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Social Activities

  • 農作物の品種改良のいま① ～しくみや技術、めざすもの～

    Role(s)：Lecturer

    倉敷市  倉敷市大学連携講座  2021.10.16

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    Type：Visiting lecture

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  • 農作物の品種改良のいま① ～しくみや技術、めざすもの～

    Role(s)：Lecturer

    倉敷市  倉敷市大学連携講座  2021.10.16