Updated on 2024/03/23

写真a

 
FURUTA Tomoyuki
 
Organization
Institute of Plant Science and Resources Associate Professor
Position
Associate Professor
External link

Degree

  • Ph.D(Agriculture) ( Nagoya University )

Research Interests

  • イネ遺伝育種、GWAS、NGS解析、ゲノム構築

Research Areas

  • Environmental Science/Agriculture Science / Science in plant genetics and breeding  / Genetics and breeding of rice

Education

  • Nagoya University   生命農学研究科生命技術科学専攻   高次生体分子機能研究分野

    2011.4 - 2014.3

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  • Nagoya University   理学研究科生命理学専攻   分子神経生物学研究室

    2009.4 - 2011.3

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  • Nagoya University   理学部生命理学科   分子神経生物学研究室

    2005.4 - 2009.3

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Research History

  • Okayama University   Institute of Plant Science and Resources   Associate Professor

    2024.3

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    Country:Japan

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  • Okayama University   Insitute of Plant Science and Resources   Assistant Professor

    2019.3 - 2024.2

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  • Nagoya University   Bioscience and biotechnology center   Post doctoral fellow

    2014.4 - 2019.2

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Professional Memberships

 

Papers

  • Genetic variation in heading dates and phenological parameters of Myanmar rice Reviewed

    Moe Moe Hlaing, Yoshiyuki Yamagata, Tomoyuki Furuta, Khin Thanda Win, Ohm Mar Saw, Akinori Ozaki, Hideshi Yasui, Atsushi Yoshimura

    Plant Production Science   2024.2

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

    DOI: 10.1080/1343943X.2024.2308336

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  • 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   2024.2

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    Authorship:Lead author, Corresponding author   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/dnares/dsad027

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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 )   2023.3

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    Authorship:Lead author, Corresponding author   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 datasets and achieves the most reliable genotype estimation in real data even with error-prone markers.

    DOI: 10.1093/genetics/iyad055

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  • Regulator of Awn Elongation 3, an E3 ubiquitin ligase, is responsible for loss of awns during African rice domestication. Reviewed International journal

    Kanako Bessho-Uehara, Kengo Masuda, Diane R Wang, Rosalyn B Angeles-Shim, Keisuke Obara, Keisuke Nagai, Riri Murase, Shin-Ichiro Aoki, Tomoyuki Furuta, Kotaro Miura, Jianzhong Wu, Yoshiyuki Yamagata, Hideshi Yasui, Michael B Kantar, Atsushi Yoshimura, Takumi Kamura, Susan R McCouch, Motoyuki Ashikari

    Proceedings of the National Academy of Sciences of the United States of America   120 ( 4 )   e2207105120   2023.1

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

    Two species of rice have been independently domesticated from different ancestral wild species in Asia and Africa. Comparison of mutations that underlie phenotypic and physiological alterations associated with domestication traits in these species gives insights into the domestication history of rice in both regions. Asian cultivated rice, Oryza sativa, and African cultivated rice, Oryza glaberrima, have been modified and improved for common traits beneficial for humans, including erect plant architecture, nonshattering seeds, nonpigmented pericarp, and lack of awns. Independent mutations in orthologous genes associated with these traits have been documented in the two cultivated species. Contrary to this prevailing model, selection for awnlessness targeted different genes in O. sativa and O. glaberrima. We identify Regulator of Awn Elongation 3 (RAE3) a gene that encodes an E3 ubiquitin ligase and is responsible for the awnless phenotype only in O. glaberrima. A 48-bp deletion may disrupt the substrate recognition domain in RAE3 and diminish awn elongation. Sequencing analysis demonstrated low nucleotide diversity in a ~600-kb region around the derived rae3 allele on chromosome 6 in O. glaberrima compared with its wild progenitor. Identification of RAE3 sheds light on the molecular mechanism underlying awn development and provides an example of how selection on different genes can confer the same domestication phenotype in Asian and African rice.

    DOI: 10.1073/pnas.2207105120

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  • Effectiveness of Create ML in microscopy image classifications: a simple and inexpensive deep learning pipeline for non-data scientists. Reviewed International journal

    Kiyotaka Nagaki, Tomoyuki Furuta, Naoki Yamaji, Daichi Kuniyoshi, Megumi Ishihara, Yuji Kishima, Minoru Murata, Atsushi Hoshino, Hirotomo Takatsuka

    Chromosome research   29 ( 3-4 )   361 - 371   2021.10

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

    Observing chromosomes is a time-consuming and labor-intensive process, and chromosomes have been analyzed manually for many years. In the last decade, automated acquisition systems for microscopic images have advanced dramatically due to advances in their controlling computer systems, and nowadays, it is possible to automatically acquire sets of tiling-images consisting of large number, more than 1000, of images from large areas of specimens. However, there has been no simple and inexpensive system to efficiently select images containing mitotic cells among these images. In this paper, a classification system of chromosomal images by deep learning artificial intelligence (AI) that can be easily handled by non-data scientists was applied. With this system, models suitable for our own samples could be easily built on a Macintosh computer with Create ML. As examples, models constructed by learning using chromosome images derived from various plant species were able to classify images containing mitotic cells among samples from plant species not used for learning in addition to samples from the species used. The system also worked for cells in tissue sections and tetrads. Since this system is inexpensive and can be easily trained via deep learning using scientists' own samples, it can be used not only for chromosomal image analysis but also for analysis of other biology-related images.

    DOI: 10.1007/s10577-021-09676-z

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  • Antagonistic regulation of the gibberellic acid response during stem growth in rice. Reviewed International journal

    Keisuke Nagai, Yoshinao Mori, Shin Ishikawa, Tomoyuki Furuta, Rico Gamuyao, Yoko Niimi, Tokunori Hobo, Moyuri Fukuda, Mikiko Kojima, Yumiko Takebayashi, Atsushi Fukushima, Yasuyo Himuro, Masatomo Kobayashi, Wataru Ackley, Hiroshi Hisano, Kazuhiro Sato, Aya Yoshida, Jianzhong Wu, Hitoshi Sakakibara, Yutaka Sato, Hiroyuki Tsuji, Takashi Akagi, Motoyuki Ashikari

    Nature   584 ( 7819 )   109 - 114   2020.8

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

    The size of plants is largely determined by growth of the stem. Stem elongation is stimulated by gibberellic acid1-3. Here we show that internode stem elongation in rice is regulated antagonistically by an 'accelerator' and a 'decelerator' in concert with gibberellic acid. Expression of a gene we name ACCELERATOR OF INTERNODE ELONGATION 1 (ACE1), which encodes a protein of unknown function, confers cells of the intercalary meristematic region with the competence for cell division, leading to internode elongation in the presence of gibberellic acid. By contrast, upregulation of DECELERATOR OF INTERNODE ELONGATION 1 (DEC1), which encodes a zinc-finger transcription factor, suppresses internode elongation, whereas downregulation of DEC1 allows internode elongation. We also show that the mechanism of internode elongation that is mediated by ACE1 and DEC1 is conserved in the Gramineae family. Furthermore, an analysis of genetic diversity suggests that mutations in ACE1 and DEC1 have historically contributed to the selection of shorter plants in domesticated populations of rice to increase their resistance to lodging, and of taller plants in wild species of rice for adaptation to growth in deep water. Our identification of these antagonistic regulatory factors enhances our understanding of the gibberellic acid response as an additional mechanism that regulates internode elongation and environmental fitness, beyond biosynthesis and gibberellic acid signal transduction.

    DOI: 10.1038/s41586-020-2501-8

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  • Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding Reviewed

    Takeshi Kuroha, Keisuke Nagai, Rico Gamuyao, Diane R. Wang, Tomoyuki Furuta, Masanari Nakamori, Takuya Kitaoka, Keita Adachi, Anzu Minami, Yoshinao Mori, Kiyoshi Mashiguchi, Yoshiya Seto, Shinjiro Yamaguchi, Mikiko Kojima, Hitoshi Sakakibara, Jianzhong Wu, Kaworu Ebana, Nobutaka Mitsuda, Masaru Ohme-Takagi, Shuichi Yanagisawa, Masanori Yamasaki, Ryusuke Yokoyama, Kazuhiko Nishitani, Toshihiro Mochizuki, Gen Tamiya, Susan R. McCouch, Motoyuki Ashikari

    Science   361 ( 6398 )   181 - 186   2018.7

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    Publishing type:Research paper (scientific journal)   Publisher:American Association for the Advancement of Science (AAAS)  

    DOI: 10.1126/science.aat1577

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  • Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species. Reviewed International journal

    Stefan Reuscher, Tomoyuki Furuta, Kanako Bessho-Uehara, Michele Cosi, Kshirod K Jena, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Motoyuki Ashikari

    Communications biology   1   162 - 162   2018

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    The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata. Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species.

    DOI: 10.1038/s42003-018-0171-y

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  • Construction of rice chromosome segment substitution lines harboring Oryza barthii genome and evaluation of yield-related traits Reviewed

    Kanako Bessho-Uehara, Tomoyuki Furuta, Kengo Masuda, Shuto Yamada, Rosalyn B. Angeles-Shim, Motoyuki Ashikari, Tomonori Takashi

    BREEDING SCIENCE   67 ( 4 )   408 - 415   2017.9

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:JAPANESE SOC BREEDING  

    Rice (Oryza sativa L.) is one of the most important staple food in the world. To meet the increasing demand for food, a strategy for improving rice yield is needed. Alleles of wild relatives are useful because they confer adaptation to plants under diverse harsh environments and have the potential to improve rice. O. barthii is a wild rice species endemic to Africa and the known progenitor of the African cultivated rice, O. glaberrima. To explore the genetic potential of the O. barthii as a genetic resource, 40 chromosome segment substitution lines (CSSL) of O. barthii in the background of the elite japonica cultivar Koshihikari were developed and evaluated to identify QTLs associated with 10 traits related to flag leaf morphology, grain yield and other agronomic traits. More than 90% of the entire genome of the donor parent was represented in contiguous or overlapping chromosome segments in the CSSLs. Evaluation of the CSSLs for several agriculturally important traits identified candidate chromosome segments that harbors QTLs associated with yield and yield-related traits. These results suggest that alleles from O. barthii might be used as a novel genetic resource for improving the yield-related traits in cultivars of O. sativa.

    DOI: 10.1270/jsbbs.17022

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    Other Link: http://orcid.org/0000-0002-0869-6626

  • Adapting Genotyping-by-Sequencing for Rice F2 Populations Reviewed

    Tomoyuki Furuta, Motoyuki Ashikari, Kshirod K. Jena, Kazuyuki Doi, Stefan Reuscher

    G3-GENES GENOMES GENETICS   7 ( 3 )   881 - 893   2017.3

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:GENETICS SOCIETY AMERICA  

    Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata. While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories.

    DOI: 10.1534/g3.116.038190

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    Other Link: http://orcid.org/0000-0002-0869-6626

  • Development of chromosome segment substitution lines harboring Oryza nivara genomic segments in Koshihikari and evaluation of yield-related traits Reviewed

    Tomoyuki Furuta, Kanako Uehara, Rosalyn B. Angeles-Shim, Junghyun Shim, Keisuke Nagai, Motoyuki Ashikari, Tomonori Takashi

    BREEDING SCIENCE   66 ( 5 )   845 - 850   2016.12

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    Language:English   Publisher:JAPANESE SOC BREEDING  

    Chromosome segment substitution lines (CSSLs) are rich genetic resources that can be mined for novel, agriculturally useful loci or that can be used directly as materials for breeding. To date, a number of rice CSSLs have been developed by crossing rice cultivars with its wild relatives as a means to tap into the potential of wild alleles in rice improvement. Oryza nivara is a wild relative of rice that is thought to be a progenitor of O. sativa spp. indica. In the present study, 26 CSSLs that covers the entire genome of O. nivara as contiguous, overlapping segments in the genomic background of a japonica cultivar, O. sativa cv. Koshihikari were developed. Evaluation of the CSSLs for several agriculturally important traits identified candidate chromosome segments that harbors QTLs associated with yield and yield-related traits. The results of the study revealed the potential of O. nivara as a source of novel alleles that can be used to improve the existing japonica cultivar.

    DOI: 10.1270/jsbbs.16131

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    Other Link: http://orcid.org/0000-0002-0869-6626

  • Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice Reviewed

    Kanako Bessho-Uehara, Diane R. Wang, Tomoyuki Furuta, Anzu Minami, Keisuke Nagai, Rico Gamuyao, Kenji Asano, Rosalyn B. Angeles-Shim, Yoshihiro Shimizu, Madoka Ayano, Norio Komeda, Kazuyuki Doi, Kotaro Miura, Yosuke Toda, Toshinori Kinoshita, Satohiro Okuda, Tetsuya Higashiyama, Mika Nomoto, Yasuomi Tada, Hidefumi Shinohara, Yoshikatsu Matsubayashi, Anthony Greenberg, Jianzhong Wu, Hideshi Yasui, Atsushi Yoshimura, Hitoshi Mori, Susan R. McCouch, Motoyuki Ashikari

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   113 ( 32 )   8969 - 8974   2016.8

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATL ACAD SCIENCES  

    Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown. Herewe isolate and characterize a previously unidentified EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family member named REGULATOR OF AWN ELONGATION 2 (RAE2) and identify one of its requisite processing enzymes, SUBTILISIN-LIKE PROTEASE 1 (SLP1). The RAE2 precursor is specifically cleaved by SLP1 in the rice spikelet, where the mature RAE2 peptide subsequently induces awn elongation. Analysis of RAE2 sequence diversity identified a highly variable GC-rich region harboring multiple independent mutations underlying protein-length variation that disrupt the function of the RAE2 protein and condition the awnless phenotype in Asian rice. Cultivated African rice, on the other hand, retained the functional RAE2 allele despite its awnless phenotype. Our findings illuminate the molecular function of RAE2 in awn development and shed light on the independent domestication histories of Asian and African cultivated rice.

    DOI: 10.1073/pnas.1604849113

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    Other Link: http://orcid.org/0000-0002-0869-6626

  • Development of chromosome segment substitution lines (CSSLs) of Oryza longistaminata A. Chev. & Rohr in the background of the elite japonica rice cultivar, Taichung 65 and their evaluation for yield traits Reviewed

    Joie M. Ramos, Tomoyuki Furuta, Kanako Uehara, Niwa Chihiro, Rosalyn B. Angeles-Shim, Junghyun Shim, Darshan S. Brar, Motoyuki Ashikari, Kshirod K. Jena

    EUPHYTICA   210 ( 2 )   151 - 163   2016.7

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

    Oryza longistaminata (AA genome) is a wild rice species that is phenotypically inferior to cultivated rice but possesses useful alleles that can be used to improve agronomically important traits. Interspecific hybrids that are derived from cultivated rice and wild rice species with AA genome are important contributors of genetic diversity in rice. To illustrate the potential of wild rice relatives as a source of novel alleles for rice improvement, a total of 40 chromosome segment substitution lines (CSSLs) of O. longistaminata in the background of the elite japonica cultivar Taichung 65 were developed and evaluated for yield and various yield-related traits. A number of CSSLs carrying putative quantitative trait loci (QTLs) controlling different yield-related traits were identified during both dry and wet seasons. In particular, 10 major putative QTLs controlling early heading date, plant height, tiller number, panicle length, number of primary branches per panicle, grain number per panicle, grain width, and grain thickness were identified. Interestingly, one of the CSSL lines, LTSL26, with major putative QTLs on chromosomes 1 and 8 that increase grain number per panicle, showed pleiotropic effects on other traits such as plant height, days to flowering, tiller number, number of branches per panicle, and grain length. These results suggest that O. longistaminata is a good source of new alleles that can be used to improve yield-related traits in cultivated rice varieties.

    DOI: 10.1007/s10681-016-1685-3

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    Other Link: http://orcid.org/0000-0002-0869-6626

  • Construction of a versatile SNP array for pyramiding useful genes of rice Reviewed

    Yusuke Kurokawa, Tomonori Noda, Yoshiyuki Yamagata, Rosalyn Angeles-Shim, Hidehiko Sunohara, Kanako Uehara, Tomoyuki Furuta, Keisuke Nagai, Kshirod Kumar Jena, Hideshi Yasui, Atsushi Yoshimura, Motoyuki Ashikari, Kazuyuki Doi

    PLANT SCIENCE   242   131 - 139   2016.1

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:ELSEVIER IRELAND LTD  

    DNA marker-assisted selection (MAS) has become an indispensable component of breeding. Single nucleotide polymorphisms (SNP) are the most frequent polymorphism in the rice genome. However, SNP markers are not readily employed in MAS because of limitations in genotyping platforms. Here the authors report a Golden Gate SNP array that targets specific genes controlling yield-related traits and biotic stress resistance in rice. As a first step, the SNP genotypes were surveyed in 31 parental varieties using the Affymetrix Rice 44K SNP microarray. The haplotype information for 16 target genes was then converted to the Golden Gate platform with 143-plex markers. Haplotypes for the 14 useful allele are unique and can discriminate among all other varieties. The genotyping consistency between the Affymetrix microarray and the Golden Gate array was 92.8%, and the accuracy of the Golden Gate array was confirmed in 3 F-2 segregating populations. The concept of the haplotype-based selection by using the constructed SNP array was proofed. (C) 2015 The Authors. Published by Elsevier Ireland Ltd.

    DOI: 10.1016/j.plantsci.2015.09.008

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  • Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci Reviewed

    Tomoyuki Furuta, Norio Komeda, Kenji Asano, Kanako Uehara, Rico Gamuyao, Rosalyn B. Angeles-Shim, Keisuke Nagai, Kazuyuki Doi, Diane R. Wang, Hideshi Yasui, Atsushi Yoshimura, Jianzhong Wu, Susan R. McCouch, Motoyuki Ashikari

    G3-GENES GENOMES GENETICS   5 ( 11 )   2267 - 2274   2015.11

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:GENETICS SOCIETY AMERICA  

    A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from Oryza nivara, Oryza rufipogon, and Oryza glaberrima donors. Phenotypic analyses of these libraries revealed the existence of three genes, Regulator of Awn Elongation 1 (RAE1), RAE2, and RAE3, involved in the loss of long awns in cultivated rice. Donor segments at two of these genes, RAE1 and RAE2, induced long awn formation in the CSSLs whereas an O. sativa segment at RAE3 induced long awn formation in O. glaberrima. These results suggest that the two cultivated rice species, O. sativa and O. glaberrima, have taken independent paths to become awnless.

    DOI: 10.1534/g3.115.020834

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    Other Link: http://orcid.org/0000-0002-0869-6626

  • Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice Reviewed

    Xian Jun Song, Takeshi Kuroha, Madoka Ayano, Tomoyuki Furuta, Keisuke Nagai, Norio Komeda, Shuhei Segami, Kotaro Miura, Daisuke Ogawa, Takumi Kamura, Takamasa Suzuki, Tetsuya Higashiyama, Masanori Yamasaki, Hitoshi Mori, Yoshiaki Inukai, Jianzhong Wu, Hidemi Kitano, Hitoshi Sakakibara, Steven E. Jacobsen, Motoyuki Ashikari

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   112 ( 1 )   76 - 81   2015.1

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATL ACAD SCIENCES  

    Grain weight is an important crop yield component; however, its underlying regulatory mechanisms are largely unknown. Here, we identify a grain-weight quantitative trait locus (QTL) encoding a new-type GNAT-like protein that harbors intrinsic histone acetyltransferase activity (OsglHAT1). Our genetic and molecular evidences pinpointed the QTL-OsglHAT1's allelic variations to a 1.2-kb region upstream of the gene body, which is consistent with its function as a positive regulator of the traits. Elevated OsglHAT1 expression enhances grain weight and yield by enlarging spikelet hulls via increasing cell number and accelerating grain filling, and increases global acetylation levels of histone H4. OsglHAT1 localizes to the nucleus, where it likely functions through the regulation of transcription. Despite its positive agronomical effects on grain weight, yield, and plant biomass, the rare allele elevating OsglHAT1 expression has so far escaped human selection. Our findings reveal the first example, to our knowledge, of a QTL for a yield component trait being due to a chromatin modifier that has the potential to improve crop high-yield breeding.

    DOI: 10.1073/pnas.1421127112

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  • Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from Oryza rufipogon in the genetic background of Oryza sativa L. Reviewed

    Tomoyuki Furuta, Kanako Uehara, Rosalyn B. Angeles-Shim, Junghyun Shim, Motoyuki Ashikari, Tomonori Takashi

    BREEDING SCIENCE   63 ( 5 )   468 - 475   2014.1

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:JAPANESE SOC BREEDING  

    The wild relatives of rice (Oryza sativa L.) are useful sources of alleles that have evolved to adapt in diverse environments around the world. Oryza rufipogon, the known progenitor of the cultivated rice, harbors genes that have been lost in cultivated varieties through domestication or evolution. This makes O. rufipogon an ideal source of value-added traits that can be utilized to improve the existing rice cultivars. To explore the potential of the rice progenitor as a genetic resource for improving O. sativa, 33 chromosome segment substitution lines (CSSLs) of O. rufipogon (W0106) in the background of the elite japonica cultivar Koshihikari were developed and evaluated for several agronomic traits. Over 90% of the entire genome was introgressed from the donor parent into the CSSLs. A total of 99 putative QTLs were detected, of which 15 were identified as major effective QTLs that have significantly large effects on the traits examined. Among the 15 major effective QTLs, a QTL on chromosome 10 showed a remarkable positive effect on the number of grains per panicle. Comparison of the putative QTLs identified in this study and previous studies indicated a wide genetic diversity between O. rufipogon accessions.

    DOI: 10.1270/jsbbs.63.468

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MISC

  • Evolutionary specificity of the hybrid sterility locus S1 in African cultivated rice O. glaberrima.

    Yamaguchi K, Koide Y, Yamagata Y, Furuta T, Kishima Y

    Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan   62   44 - 45   2021

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    Language:Japanese   Publisher:Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  

    DOI: 10.20751/hdanwakai.62.0_44

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

    山本敏央, 古田智敬, 小川大輔, 米丸淳一, 國吉大地, 貴島祐治

    作物研究   65   2020

  • Genotype and environmental interaction in heading date revealed by evaluation of rice MAGIC population under different locations

    山本敏央, 柏原壱成, 古田智敬, 小川大輔, 野々上慈徳, 常松浩史, 米丸淳一

    育種学研究   22   2020

  • イネの芒はどうして消失したか?~植物ホルモンとの関係~

    別所-上原奏子, 古田智敬, 芦苅基行

    生物の科学 遺伝   70 ( 5 )   58 - 62   2016

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Presentations

  • Development of R packages for accurate genotype calling and error correction in reduced representation sequencing based genotyping International conference

    Tomoyuki Furuta, Motoyuki Ashikari, Toshio Yamamoto

    Plant and Animal Genome 31  2024.1.15 

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    Event date: 2024.1.12 - 2024.1.17

    Language:English   Presentation type:Poster presentation  

    Venue:The U.S.A., San Diego  

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  • アジアイネゲノムとの網羅的オーソログ解析に基づくアフリカイネゲノムの特徴づけ

    古田 智敬, 佐藤 豊, 吉村 淳, 芦苅 基行

    日本育種学会第144回講演会  2023.9.16 

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    Event date: 2023.9.16 - 2023.9.17

    Presentation type:Oral presentation (general)  

    Venue:兵庫、神戸大学  

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  • Pipeline for accurate Genotype-by-Sequencing via eliminating error prone markers International conference

    Tomoyuki Furuta, Toshio Yamamoto

    The 19th International Symposium on Rice Functional Genomics  2022.11.4 

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    Event date: 2022.11.4 - 2022.11.7

    Language:English   Presentation type:Poster presentation  

    Venue:Thailand, Phuket  

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  • エラーを低減した Genotyping-by-Sequencing 解析パイプラインの構築

    古田 智敬

    第5回植物インフォマティクス研究会・年会  2022.10.18 

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    Event date: 2022.10.18

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン  

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  • Pipeline for accurate genotype calling via eliminating error prone markers. Invited

    2022.10.9 

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    Event date: 2022.10.8 - 2022.10.9

    Language:English   Presentation type:Oral presentation (invited, special)  

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  • 次世代シークエンスを用いたジェノタイピングにおける比較ゲノム情報に基づく誤判定の低減法

    古田 智敬, 鳥羽 大陽, 貴島 祐治, 山本 敏央

    日本育種学会第142回講演会  2022.9.23 

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    Event date: 2022.9.23 - 2022.9.24

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:北海道、帯広畜産大学  

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  • 他殖性作物の多型交雑集団にも対応した遺伝子型データエラー修正ツール「GBScleanR」の開発

    古田 智敬, 芦苅 基行, 山本 敏央

    日本育種学会第141回講演会  2022.3.21 

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    Event date: 2022.3.20 - 2022.3.21

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン  

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  • アフリカイネOryza glaberrima品種群を用いたゲノム育種基盤構築

    古田智敬, 佐藤豊, 芦苅基行

    日本育種学会第139回講演会  2021.3.21 

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    Event date: 2021.3.20 - 2021.3.21

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン  

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  • 隠れマルコフモデルに基づくGBSデータエラー修正ツールの開発

    古田智敬, Stefan Reuscher, 芦苅基行

    イネ遺伝学・分子生物学ワークショップ  2018.7.6 

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    Event date: 2018.7.5 - 2018.7.6

    Language:Japanese   Presentation type:Oral presentation (general)  

  • 隠れマルコフモデルを用いたエラー修正による低コスト育種のためのGBSパイプライン構築

    日本育種学会 第133回講演会  2018.3.25 

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    Event date: 2018.3.25 - 2018.3.26

    Language:Japanese   Presentation type:Oral presentation (general)  

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  • Exploring rhizome formation loci in Rice Invited International coauthorship International conference

    Tomoyuki Furuta

    Towards Increased Plant Productivity through Understanding of Environmental Responses and Epigenetic Regulation  2015.11.24 

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    Language:English   Presentation type:Oral presentation (invited, special)  

    Venue:RIKEN Yokohama Campus, Japan  

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  • GBSを利用した野生イネと 栽培イネの交雑に由来するF2 集団におけるQTL解析」 Invited

    古田智敬

    日本育種学会第128回講演会  2015.9.11 

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    Language:Japanese   Presentation type:Oral presentation (invited, special)  

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  • QTL analysis for rhizome formation loci using Genotyping-By-Sequencing on F2 population from the cross between Oryza sativa and Oryza longistaminata.

    Furuta T, Reuscher S, Uehara K, Kondo H, Shim-Angels RB, Doi K, Ashikari M

    International ERATO Higashiyama Live-Holonics Symposium & Technical Workshop 2015  2015.8 

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    Venue:Nagoya University, Japan  

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Awards

  • 第144回講演会日本育種学会優秀発表賞

    2023.9   日本育種学会   アジアイネゲノムとの網羅的オーソログ解析に基づくアフリカイネゲノムの特徴づけ

    古田 智敬, 佐藤 豊, 吉村 淳, 芦苅 基行

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  • 第141回講演会日本育種学会優秀発表賞

    2022.3   日本育種学会   他殖性作物の多系交雑集団にも対応した遺伝子型データエラー修正ツール「GBScleanR」の開発

    古田智敬, 芦苅基行, 山本敏央

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Research Projects

  • 有用遺伝子探索を革新するオミクスベースクローニング法の実証

    Grant number:23H02185  2023.04 - 2027.03

    日本学術振興会  科学研究費助成事業  基盤研究(B)

    古田 智敬, 鳥羽 大陽, 永井 啓祐, 黒羽 剛

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    Grant amount:\18850000 ( Direct expense: \14500000 、 Indirect expense:\4350000 )

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  • 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

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

    MAGIC集団が遺伝子型x環境相互作用(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継続している。緯度が似ているつくば市と倉敷市で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。令和元年度および2年度の調査では第6染色体のRFT1-Hd17ブロックのルリアオバハプロタイプで特異的な相互作用が示唆された。
    令和3年度は、この現象を確認するために両地点で作期を増やした栽培試験を行った。新たに設定したつくば市の遅植え区と倉敷市の早植え区はいずれも両地点の中間的な反応を示した。このことからRFT1-Hd17ブロックが引き起こす出穂期に関するGxEはルリアオバハプロタイプ特有の日長感受性によって引きこされるものと考えられた。
    他の出穂期関連QTLの検出に関する地域間差についても、令和元年度および2年度の結果を再現するものとなったが、感光性の違いによるものかどうかは明らかではない。またこれまでに検出された以外の新たなQTLは見いだされなかった。
    出穂期以外の形質として稈長、穂長、穂数を評価したが、その傾向は形質ごとに異なっていた。稈長は両地点および作期で特異的に検出される領域およびハプロタイプは認められなかった。穂長については主要なQTLは共通に検出されたが一部の地域特異的なQTLも見いだされた。穂数については両地点で共通なQTLは見いだされなかった。
    ゲノムシャッフリング集団(Cy3F5世代:165系統)の遺伝子型を8109か所のSNPマーカーで評価した。その結果、シャッフリング集団ではMAGIC集団と比較して一部の領域で特定のハプロタイプの減少や連鎖不平衡程度の減少が認められた。また主要な農業形質のGWAS解析結果をMAGIC集団と比較した結果、検出QTLのピークは低くなるとともに有意な領域数は減る傾向にあった。

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  • アフリカ栽培イネ特異的な高温ストレス耐性のゲノムワイド解析とGWASカタログ構築

    Grant number:20K15503  2020.04 - 2023.03

    日本学術振興会  科学研究費助成事業 若手研究  若手研究

    古田 智敬

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    Grant amount:\4290000 ( Direct expense: \3300000 、 Indirect expense:\990000 )

    令和2年度に引き続きアフリカ栽培イネ「グラベリマ」が保持する有用遺伝子を探索するため、172系統のグラベリマ品種集団を用いた表現型調査を行った。その結果、令和2年度と令和3年度の表現型データは概ね同様の結果を示すことが確認された。また前年度に得られた表現型データをもとにGWASを行ったところ、高温ストレス下における種子稔性に関与する可能性のある遺伝子座の他に、短日装置による開花誘導条件下で開花時期を制御する遺伝子座の存在も示唆された。一方で、グラべリマ品種群は土着品種が多く種子サイズや草丈などの形質が、品種群が持つ集団構造と相関しており既存のGWAS手法では表現型と統計的に有意な関連を示す遺伝子座の同定が困難なケースが散見されることが分かった。この結果は現行の統計手法の限界を示すものであり、異なる統計的アプローチによる手法の必要性が示された。
    2021年度には、上記に加えてグラベリマゲノムデータベースのさらなる整備を行った。具体的には、グラベリマのゲノム配列情報および172系統のDNA多型情報に基づき、遺伝子アノテーション情報の整備、系統樹解析や比較ゲノム解析によるグラべリマゲノムの特徴調査を実施した。解析の結果本研究で用いたグラべリマ品種「WK21」と既報のゲノム情報で用いられた品種「CG14」の間には遺伝子欠失を含めて様々な変異が存在し、同一種で複数系統のゲノム情報を得ることの有用性が示された。またゲノムデータベースの一般公開に向け、専用のウェブサーバーを用意し準備を行った。
    グラべリマ品種群の解析加えて派生的な研究として、次世代シークエンサーによる遺伝子型判定におけるエラーを修正するツール開発を実施しプレプリント・サーバーBioAxivに論文を掲載した。

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Class subject in charge

  • 資源植物学ラボマニュアル (2023academic year) 前期  - 火5~8

  • 資源植物学ラボマニュアル (2023academic year) 前期  - 火5~8

  • 資源植物学ラボマニュアル (2022academic year) 前期  - 火5~8

  • 資源植物学ラボマニュアル (2021academic year) 前期  - 火5~8