2022/04/16 更新

写真a

アカギ タカシ
赤木 剛士
AKAGI Takashi
所属
環境生命科学学域 准教授
職名
准教授
連絡先
メールアドレス
外部リンク

学位

  • 農学博士 ( 2011年3月   京都大学 )

  • 博士(農学) ( 京都大学 )

  • 修士(農学) ( 京都大学 )

研究分野

  • 環境・農学 / 園芸科学

  • ライフサイエンス / 植物分子、生理科学

  • ライフサイエンス / 進化生物学

 

論文

  • Genome-wide cis-decoding for expression design in tomato using cistrome data and explainable deep learning. 国際誌

    Takashi Akagi, Kanae Masuda, Eriko Kuwada, Kouki Takeshita, Taiji Kawakatsu, Tohru Ariizumi, Yasutaka Kubo, Koichiro Ushijima, Seiichi Uchida

    The Plant cell   2022年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    In the evolutionary history of plants, variation in cis-regulatory elements (CREs) resulting in diversification of gene expression has played a central role in driving the evolution of lineage-specific traits. However, it is difficult to predict expression behaviors from CRE patterns to properly harness them, mainly because the biological processes are complex. In this study, we used cistrome datasets and explainable convolutional neural network (CNN) frameworks to predict genome-wide expression patterns in tomato (Solanum lycopersicum) fruit from the DNA sequences in gene regulatory regions. By fixing the effects of trans-acting factors using single cell-type spatiotemporal transcriptome data for the response variables, we developed a prediction model for crucial expression patterns in the initiation of tomato fruit ripening. Feature visualization of the CNNs identified nucleotide residues critical to the objective expression pattern in each gene, and their effects were validated experimentally in ripening tomato fruit. This cis-decoding framework will not only contribute to the understanding of the regulatory networks derived from CREs and transcription factor interactions, but also provides a flexible means of designing alleles for optimized expression.

    DOI: 10.1093/plcell/koac079

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  • Reinvention of hermaphroditism via activation of a RADIALIS-like gene in hexaploid persimmon. 国際誌

    Kanae Masuda, Yoko Ikeda, Takakazu Matsuura, Taiji Kawakatsu, Ryutaro Tao, Yasutaka Kubo, Koichiro Ushijima, Isabelle M Henry, Takashi Akagi

    Nature plants   8 ( 3 )   217 - 224   2022年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    In flowering plants, different lineages have independently transitioned from the ancestral hermaphroditic state into and out of various sexual systems1. Polyploidizations are often associated with this plasticity in sexual systems2,3. Persimmons (the genus Diospyros) have evolved dioecy via lineage-specific palaeoploidizations. More recently, hexaploid D. kaki has established monoecy and also exhibits reversions from male to hermaphrodite flowers in response to natural environmental signals (natural hermaphroditism, NH), or to artificial cytokinin treatment (artificial hermaphroditism, AH). We sought to identify the molecular pathways underlying these polyploid-specific reversions to hermaphroditism. Co-expression network analyses identified regulatory pathways specific to NH or AH transitions. Surprisingly, the two pathways appeared to be antagonistic, with abscisic acid and cytokinin signalling for NH and AH, respectively. Among the genes common to both pathways leading to hermaphroditic flowers, we identified a small-Myb RADIALIS-like gene, named DkRAD, which is specifically activated in hexaploid D. kaki. Consistently, ectopic overexpression of DkRAD in two model plants resulted in hypergrowth of the gynoecium. These results suggest that production of hermaphrodite flowers via polyploidization depends on DkRAD activation, which is not associated with a loss-of-function within the existing sex determination pathway, but rather represents a new path to (or reinvention of) hermaphroditism.

    DOI: 10.1038/s41477-022-01107-z

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  • Evolutionary alterations in gene expression and enzymatic activities of gibberellin 3-oxidase 1 in Oryza. 国際誌

    Kyosuke Kawai, Sayaka Takehara, Toru Kashio, Minami Morii, Akihiko Sugihara, Hisako Yoshimura, Aya Ito, Masako Hattori, Yosuke Toda, Mikiko Kojima, Yumiko Takebayashi, Hiroyasu Furuumi, Ken-Ichi Nonomura, Bunzo Mikami, Takashi Akagi, Hitoshi Sakakibara, Hidemi Kitano, Makoto Matsuoka, Miyako Ueguchi-Tanaka

    Communications biology   5 ( 1 )   67 - 67   2022年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Proper anther and pollen development are important for plant reproduction. The plant hormone gibberellin is important for anther development in rice, but its gametophytic functions remain largely unknown. Here, we report the functional and evolutionary analyses of rice gibberellin 3-oxidase 1 (OsGA3ox1), a gibberellin synthetic enzyme specifically expressed in the late developmental stages of anthers. Enzymatic and X-ray crystallography analyses reveal that OsGA3ox1 has a higher GA7 synthesis ratio than OsGA3ox2. In addition, we generate an osga3ox1 knockout mutant by genome editing and demonstrate the bioactive gibberellic acid synthesis by the OsGA3ox1 action during starch accumulation in pollen via invertase regulation. Furthermore, we analyze the evolution of Oryza GA3ox1s and reveal that their enzyme activity and gene expression have evolved in a way that is characteristic of the Oryza genus and contribute to their male reproduction ability.

    DOI: 10.1038/s42003-022-03008-5

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  • Shy Girl, a kiwifruit suppressor of feminization, restricts gynoecium development via regulation of cytokinin metabolism and signalling. 国際誌

    Erika Varkonyi-Gasic, Tianchi Wang, Janine Cooney, Subin Jeon, Charlotte Voogd, Mikaela J Douglas, Sarah M Pilkington, Takashi Akagi, Andrew C Allan

    The New phytologist   230 ( 4 )   1461 - 1475   2021年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Kiwifruit (Actinidia chinensis) is a dioecious, long-living woody perennial vine. Reduced generation time and induction of hermaphroditism can accelerate crop improvement and facilitate alternative farming for better food security in the face of climate change. Previous studies identified that CENTRORADIALIS genes CEN and CEN4 act to repress flowering, whilst the male-specific Shy Girl (SyGl) gene with homology to type-C cytokinin response regulators could repress gynoecium development in model plants. Here we use CRISPR/Cas9 to mutagenize CEN, CEN4 and SyGl in the male kiwifruit A. chinensis 'Bruce'. Biallelic mutations of CEN and CEN4 generated rapid-flowering male plants, and simultaneous targeting of CEN4 and SyGl gave rise to rapid-flowering hermaphrodites with restored gynoecial function and viable pollen, providing functional evidence for the role of SyGl in suppression of feminization. Analysis of ovary tissues identified genes that contribute to carpel development and revealed that SyGl affected both cytokinin profiles and the expression of genes involved in cytokinin metabolism and signalling. The plant lines generated by CEN4/SyGl knockout could self-pollinate and produce fast-flowering offspring. These results establish that SyGI acts as the suppressor of feminization in kiwifruit and demonstrate the potential for accelerated breeding in an outcrossing horticultural woody perennial.

    DOI: 10.1111/nph.17234

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  • Noninvasive diagnosis of seedless fruit using deep learning in persimmon

    Kanae Masuda, Maria Suzuki, Kohei Baba, Kouki Takeshita, Tetsuya Suzuki, Mayu Sugiura, Takeshi Niikawa, Seiichi Uchida, Takashi Akagi

    Horticulture Journal   90 ( 2 )   172 - 180   2021年

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    掲載種別:研究論文(学術雑誌)  

    Noninvasive diagnosis of internal traits in fruit crops is a high unmet need; however it generally requires time, costs, and special methods or facilities. Recent progress in deep neural network (or deep learning) techniques would allow easy, but highly accurate diagnosis with single RGB images, and the latest applications enable visualization of “the reasons for each diagnosis” by backpropagation of neural networks. Here, we propose an application of deep learning for image diagnosis on the classification of internal fruit traits, in this case seedlessness, in persimmon fruit (Diospyros kaki). We examined the classification of seedlessness in persimmon fruit by using four convolutional neural networks (CNN) models with various layer structures. With only 599 pictures of ‘Fuyu’ persimmon fruit from the fruit apex side, the neural networks successfully made a binary classification of seedless and seeded fruits with up to 85% accuracy. Among the four CNN models, the VGG16 model with the simplest layer structure showed the highest classification accuracy of 89%. Prediction values for the binary classification of seeded fruits were significantly increased in proportion to seed numbers in all four CNN models. Furthermore, explainable AI methods, such as Gradient-weighted Class Activation Mapping (Grad-CAM) and Guided Grad-CAM, allowed visualization of the parts and patterns contributing to the diagnosis. The results indicated that finer positions surrounding the apex, which correspond to hypothetical bulges derived from seeds, are an index for seeded fruits. These results suggest the novel potential of deep learning for noninvasive diagnosis of fruit internal traits using simple RGB images and also provide novel insights into previously unrecognized features of seeded/seedless fruits.

    DOI: 10.2503/hortj.UTD-248

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  • Editorial: Dioecy in Fruit Crops: The Gender Rise and Decline and Its Agronomic Impact. 国際誌

    Raffaele Testolin, Sarah M Pilkington, Takashi Akagi

    Frontiers in plant science   12   719588 - 719588   2021年

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  • Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon

    Kanae Masuda, Naoko Fujita, Ho-Wen Yang, Koichiro Ushijima, Yasutaka Kubo, Ryutaro Tao, Takashi Akagi

    FRONTIERS IN PLANT SCIENCE   11   2020年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:FRONTIERS MEDIA SA  

    Sex expression in plants is often flexible and contributes to the maintenance of genetic diversity within a species. In diploid persimmons (the genus Diospyros), the sexuality is controlled by the Y chromosome-encoded small-RNA gene, OGI, and its autosomal counterpart, MeGI. Hexaploid Oriental persimmon (Diospyros kaki) evolved more flexible sex expression, where genetically male individuals carrying OGI can produce both male and female flowers (monoecy). This is due to (semi-)inactivation of OGI by the Kali-SINE retrotransposon insertion on the promoter region and the resultant DNA methylations. Instead, flower sex determination in Oriental persimmon is also dependent on DNA methylation states of MeGI. Here, we focused on a cultivar, Kumemaru, which shows stable male flower production. Our results demonstrated that cv. Kumemaru carries OGI with Kali-SINE, which was highly methylated as well as in other monoecious cultivars; nevertheless, OGI gene could have a basal expression level. Transcriptomic analysis between cv. Kumemaru and 14 cultivars that predominantly produce female flowers showed differentially expressed genes (DEGs) specific to cv. Kumemaru, which is mainly involved in stress responses. Co-expression gene networks focusing on the DEGs also suggested the involvement of stress signals, mainly via gibberellin (GA), salicylic acid (SA), and especially jasmonic acid (JA) signal pathways. We also identified potential regulators of this co-expression module, represented by the TCP4 transcription factor. Furthermore, we attempted to identify cv. Kumemaru-specific transcript polymorphisms potentially contributing to derepressed OGI expression by cataloging subsequences (k-mers) in the transcriptomic reads from cv. Kumemaru and the other 14 female cultivars. Overall, although the direct genetic factor to activate OGI remains to be solved, our results implied the involvement of stress signals in the release of silenced OGI and the resultant continuous male production.

    DOI: 10.3389/fpls.2020.567249

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  • Interspecific introgression and natural selection in the evolution of Japanese apricot ( Prunus mume ) 国際誌

    Koji Numaguchi, Takashi Akagi, Yuto Kitamura, Ryo Ishikawa, Takashige Ishii

    The Plant Journal   104 ( 6 )   1551 - 1567   2020年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Wiley  

    Domestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity. We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome-wide single-nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution. These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selections.

    DOI: 10.1111/tpj.15020

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  • Explainable deep learning reproduce a “professional eye” on the diagnosis of internal disorders in persimmon fruit

    Takashi Akagi, Masanori Onishi, Kanae Masuda, Ryohei Kuroki, Kohei Baba, Kouki Takeshita, Tetsuya Suzuki, Takeshi Niikawa, Seiichi Uchida, Takeshi Ise

    Plant and Cell Physiology   61 ( 11 )   1967 - 1973   2020年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    <title>Abstract</title>
    Recent rapid progress in deep neural network techniques have allowed various object recognitions and classifications, which often exceed the performance with human eyes. In plant biology and crop sciences, some deep neural network frameworks have been applied mainly to effective and rapid phenotyping. In this study, beyond simple optimizations of phenotyping, we propose an application of deep neural networks to make image-based internal disorder diagnosis that is hard even for experts, and to visualize the reasons of each diagnosis to provide biological interpretations. Here we exemplified classification of calyx-end cracking in persimmon fruit by using five convolutional neural network models with various layer structures, and examined potential analytic options involved in the diagnostic qualities. With 3,173 visible RGB images from the fruit apex side, the neural networks successfully made the binary classification of each degree of disorders, with up to 90% accuracy. Furthermore, feature visualizations, such as Grad-CAM and LRP, visualize the image regions that contribute to the diagnosis. They suggest that specific patterns of color unevenness, such as in fruit peripheral area, can be indexes of calyx-end cracking. These results not only provided novel insights into indexes of fruit internal disorders but proposed potential applicability of deep neural networks in plant biology.

    DOI: 10.1093/pcp/pcaa111

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  • Low temperature modulates natural peel degreening in lemon fruit independently of endogenous ethylene

    Oscar W. Mitalo, Takumi Otsuki, Rui Okada, Saeka Obitsu, Kanae Masuda, Yuko Hojo, Takakazu Matsuura, Izumi C. Mori, Daigo Abe, William O. Asiche, Takashi Akagi, Yasutaka Kubo, Koichiro Ushijima

    Journal of Experimental Botany   71 ( 16 )   4778 - 4796   2020年8月

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    掲載種別:研究論文(学術雑誌)  

    © 2020 Oxford University Press. All rights reserved. Peel degreening is an important aspect of fruit ripening in many citrus fruit, and previous studies have shown that it can be advanced by ethylene treatment or by low-temperature storage. However, the important regulators and pathways involved in natural peel degreening remain largely unknown. To determine how natural peel degreening is regulated in lemon fruit (Citrus limon), we studied transcriptome and physiochemical changes in the flavedo in response to ethylene treatment and low temperatures. Treatment with ethylene induced rapid peel degreening, which was strongly inhibited by the ethylene antagonist, 1-methylcyclopropene (1-MCP). Compared with 25 ºC, moderately low storage temperatures of 5-20 °C also triggered peel degreening. Surprisingly, repeated 1-MCP treatments failed to inhibit the peel degreening induced by low temperature. Transcriptome analysis revealed that low temperature and ethylene independently regulated genes associated with chlorophyll degradation, carotenoid metabolism, photosystem proteins, phytohormone biosynthesis and signalling, and transcription factors. Peel degreening of fruit on trees occurred in association with drops in ambient temperature, and it coincided with the differential expression of low temperature-regulated genes. In contrast, genes that were uniquely regulated by ethylene showed no significant expression changes during on-tree peel degreening. Based on these findings, we hypothesize that low temperature plays a prominent role in regulating natural peel degreening independently of ethylene in citrus fruit.

    DOI: 10.1093/jxb/eraa206

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  • Antagonistic regulation of the gibberellic acid response during stem growth in rice 国際誌

    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年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    The size of plants is largely determined by growth of the stem. Stem elongation is stimulated by gibberellic acid(1-3). 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 nameACCELERATOR 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 ofDECELERATOR OF INTERNODE ELONGATION 1(DEC1), which encodes a zinc-finger transcription factor, suppresses internode elongation, whereas downregulation ofDEC1allows internode elongation. We also show that the mechanism of internode elongation that is mediated byACE1andDEC1is conserved in the Gramineae family. Furthermore, an analysis of genetic diversity suggests that mutations inACE1andDEC1have 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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    その他リンク: http://www.nature.com/articles/s41586-020-2501-8

  • Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon 国際誌

    Kanae Masuda, Eiji Yamamoto, Kenta Shirasawa, Noriyuki Onoue, Atsushi Kono, Koichiro Ushijima, Yasutaka Kubo, Ryutaro Tao, Isabelle M Henry, Takashi Akagi

    DNA Research   27 ( 3 )   2020年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    <title>Abstract</title>
    Sexuality is one of the fundamental mechanisms that work towards maintaining genetic diversity within a species. In diploid persimmons (Diospyros spp.), separated sexuality, the presence of separate male and female individuals (dioecy), is controlled by the Y chromosome-encoded small-RNA gene, OGI. On the other hand, sexuality in hexaploid Oriental persimmon (Diospyros kaki) is more plastic, with OGI-bearing genetically male individuals, able to produce both male and female flowers (monoecy). This is thought to be linked to the partial inactivation of OGI by a retrotransposon insertion, resulting in DNA methylation of the OGI promoter region. To identify the genetic factors regulating branch sexual conversion, genome-wide correlation/association analyses were conducted using ddRAD-Seq data from an F1 segregating population, and using both quantitative and diploidized genotypes, respectively. We found that allelic ratio at the Y-chromosomal region, including OGI, was correlated with male conversion based on quantitative genotypes, suggesting that OGI can be activated in cis in a dosage-dependent manner. Genome-wide association analysis based on diploidized genotypes, normalized for the effect of OGI allele dosage, detected three fundamental loci associated with male conversion. These loci underlie candidate genes, which could potentially act epigenetically for the activation of OGI expression.

    DOI: 10.1093/dnares/dsaa012

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    その他リンク: http://academic.oup.com/dnaresearch/article-pdf/27/3/dsaa012/33571384/dsaa012.pdf

  • Correction: The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. 査読 国際誌

    Takashi Akagi, Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle M Henry

    PLoS genetics   16 ( 5 )   e1008845   2020年5月

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    記述言語:英語  

    [This corrects the article DOI: 10.1371/journal.pgen.1008566.].

    DOI: 10.1371/journal.pgen.1008845

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  • Epigenetic Flexibility Underlies Somaclonal Sex Conversions in Hexaploid Persimmon

    Kanae Masuda, Takashi Akagi, Tomoya Esumi, Ryutaro Tao

    Plant and Cell Physiology   61 ( 2 )   393 - 402   2020年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    <title>Abstract</title>
    Epigenetic regulation adds a flexible layer to genetic variations, potentially enabling long-term, but reversible, changes to a trait, while maintaining genetic information. In the hexaploid Oriental persimmon (Diospyros kaki), genetically monoecious cultivars bearing male flowers require the Y-encoded small RNA (smRNA) gene, OGI. This gene represses the expression of its autosomal counterpart gene, MeGI, as part of the canonical male production system. However, a D. kaki cultivar, Saijo, which lacks the OGI gene and originally bears only female flowers, occasionally produces somaclonal mutant male and revertant female (RF) branches. In this study, we investigated the mechanisms underlying these somaclonal sex conversions in persimmon. Specifically, we aimed to unravel how a genetically female tree without the OGI gene can produce male flowers and RF flowers. Applying multi-omics approaches, we revealed that this noncanonical male production system is basically consistent with the canonical system, in which the accumulation of smRNA targeting MeGI and the considerable DNA methylation of MeGI are involved. The epigenetic status of MeGI on CGN and CHG was synchronized to the genome-wide methylation patterns, both in transition to and from the male production system. These results suggest that the somaclonal sex conversions in persimmon are driven by the genome-wide epigenetic regulatory activities. Moreover, flexibility in the epigenetic layers of long-lived plant species (e.g. trees) is important for overcoming genetic robustness.

    DOI: 10.1093/pcp/pcz207

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    その他リンク: http://academic.oup.com/pcp/article-pdf/61/2/393/32741507/pcz207.pdf

  • The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. 査読 国際誌

    Takashi Akagi, Kenta Shirasawa, Hideki Nagasaki, Hideki Hirakawa, Ryutaro Tao, Luca Comai, Isabelle M Henry

    PLoS genetics   16 ( 2 )   e1008566   2020年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Most angiosperms bear hermaphroditic flowers, but a few species have evolved outcrossing strategies, such as dioecy, the presence of separate male and female individuals. We previously investigated the mechanisms underlying dioecy in diploid persimmon (D. lotus) and found that male flowers are specified by repression of the autosomal gene MeGI by its paralog, the Y-encoded pseudo-gene OGI. This mechanism is thought to be lineage-specific, but its evolutionary path remains unknown. Here, we developed a full draft of the diploid persimmon genome (D. lotus), which revealed a lineage-specific whole-genome duplication event and provided information on the architecture of the Y chromosome. We also identified three paralogs, MeGI, OGI and newly identified Sister of MeGI (SiMeGI). Evolutionary analysis suggested that MeGI underwent adaptive evolution after the whole-genome duplication event. Transformation of tobacco plants with MeGI and SiMeGI revealed that MeGI specifically acquired a new function as a repressor of male organ development, while SiMeGI presumably maintained the original function. Later, a segmental duplication event spawned MeGI's regulator OGI on the Y-chromosome, completing the path leading to dioecy, and probably initiating the formation of the Y-chromosome. These findings exemplify how duplication events can provide flexible genetic material available to help respond to varying environments and provide interesting parallels for our understanding of the mechanisms underlying the transition into dieocy in plants.

    DOI: 10.1371/journal.pgen.1008566

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  • Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon. 国際誌

    Kanae Masuda, Naoko Fujita, Ho-Wen Yang, Koichiro Ushijima, Yasutaka Kubo, Ryutaro Tao, Takashi Akagi

    Frontiers in plant science   11   567249 - 567249   2020年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Sex expression in plants is often flexible and contributes to the maintenance of genetic diversity within a species. In diploid persimmons (the genus Diospyros), the sexuality is controlled by the Y chromosome-encoded small-RNA gene, OGI, and its autosomal counterpart, MeGI. Hexaploid Oriental persimmon (Diospyros kaki) evolved more flexible sex expression, where genetically male individuals carrying OGI can produce both male and female flowers (monoecy). This is due to (semi-)inactivation of OGI by the Kali-SINE retrotransposon insertion on the promoter region and the resultant DNA methylations. Instead, flower sex determination in Oriental persimmon is also dependent on DNA methylation states of MeGI. Here, we focused on a cultivar, Kumemaru, which shows stable male flower production. Our results demonstrated that cv. Kumemaru carries OGI with Kali-SINE, which was highly methylated as well as in other monoecious cultivars; nevertheless, OGI gene could have a basal expression level. Transcriptomic analysis between cv. Kumemaru and 14 cultivars that predominantly produce female flowers showed differentially expressed genes (DEGs) specific to cv. Kumemaru, which is mainly involved in stress responses. Co-expression gene networks focusing on the DEGs also suggested the involvement of stress signals, mainly via gibberellin (GA), salicylic acid (SA), and especially jasmonic acid (JA) signal pathways. We also identified potential regulators of this co-expression module, represented by the TCP4 transcription factor. Furthermore, we attempted to identify cv. Kumemaru-specific transcript polymorphisms potentially contributing to derepressed OGI expression by cataloging subsequences (k-mers) in the transcriptomic reads from cv. Kumemaru and the other 14 female cultivars. Overall, although the direct genetic factor to activate OGI remains to be solved, our results implied the involvement of stress signals in the release of silenced OGI and the resultant continuous male production.

    DOI: 10.3389/fpls.2020.567249

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  • Passe Crassane’ pear fruit (Pyrus communis L.) ripening: revisiting the role of low temperature via integrated physiological and transcriptome analysis 査読

    Oscar Witere MITALO, Yasuaki Tosa, Sumire Tokiwa, Yuki Kondo, Azimullah Azimi, Yuko Hojo, Takakazu Matsuura, Izumi Mori, Ryohei NAKANO, Takashi Akagi, Koichiro Ushijima, Yasutaka Kubo

    Postharvest Biology and Technology   2019年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1016/j.postharvbio.2019.110949

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  • Evolution of Lineage-Specific Gene Networks Underlying the Considerable Fruit Shape Diversity in Persimmon

    Haruka Maeda, Takashi Akagi, Noriyuki Onoue, Atsushi Kono, Ryutaro Tao

    Plant and Cell Physiology   60 ( 11 )   2464 - 2477   2019年11月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press (OUP)  

    <title>Abstract</title>
    The shapes of plant organs reflect the evolution of each lineage and have been diversified according to lineage-specific adaptations to environment. Research on the molecular pathways responsible for organ shapes has traditionally been focused mainly on leaves or flowers. Thus, little is known about the pathways controlling fruit shapes, despite their diversity in some plant species. In this study, we analyzed oriental persimmon (Diospyros kaki), which exhibits considerable diversity in fruit shapes among cultivars, to elucidate the underlying molecular mechanism using transcriptomic data and quantitative evaluation. First, to filter the candidate genes associated with persimmon fruit shapes, the whole gene expression patterns obtained using mRNA-Seq analysis from 100 individuals, including a segregated population and various cultivars, were assessed to detect correlations with principal component scores for fruit shapes characterized with elliptic Fourier descriptors. Next, a gene co-expression network analysis with weighted gene co-expression network analysis (WGCNA) package revealed that class 1 KNOX family genes and SEEDSTICK function as integrators along with some phytohormone-related genes, to regulate the fruit shape diversity. On the other hand, the OVATE family genes also contribute to fruit shape diversity, of which pathway would be potentially shared with other plant species. Evolutionary aspects suggest that acquisition of a high lineage-specific and variable expression of class 1 KNOX gene, knotted-like homeobox of Arabidopsis thaliana 1 (KNAT1), in young fruit is important for establishing the persimmon-specific mechanism that determines fruit shape diversity.

    DOI: 10.1093/pcp/pcz139

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  • Pleiotropic effects of sex-determining genes in the evolution of dioecy in two plant species

    Takashi Akagi, Deborah Charlesworth

    Proceedings of the Royal Society B: Biological Sciences   286 ( 1913 )   20191805 - 20191805   2019年10月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:The Royal Society  

    One reason for studying sex chromosomes of flowering plants is that they have often evolved separate sexes recently, and the genomes of dioecious species may not yet have evolved adaptations to their changes from the ancestral state. An unstudied question concerns the relative importance of such adaptation, versus the effects of the mutations that led to separate sexes in the first place. Theoretical models for such an evolutionary change make the prediction that the mutations that created males must have sexually antagonistic effects, not only abolishing female functions, but also increasing male functions relative to the ancestral functional hermaphrodites. It is important to test this critical assumption. Moreover, the involvement of sexual antagonism also implies that plant sex-determining genes may directly cause some of the sexual dimorphisms observed in dioecious plants. Sex-determining genes are starting to be uncovered in plants, including species in the genera
    <italic>Diospyros</italic>
    and
    <italic>Actinidia</italic>
    (families Ebenaceae and Actinidiaceae, respectively). Here, we describe transgenic experiments in which the effects of the very different male-determining genes of these two dioecious species were studied in a non-dioecious plant,
    <italic>Nicotiana tabacum</italic>
    . The results indeed support the critical assumption outlined above.

    DOI: 10.1098/rspb.2019.1805

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  • Detection of a novel locus involved in non-seed-shattering behaviour of Japonica rice cultivar, Oryzasativa ‘Nipponbare’

    Yuki Tsujimura, Shohei Sugiyama, Kotaro Otsuka, Than Myint Htun, Koji Numaguchi, Cristina Castillo, Takashi Akagi, Takashige Ishii, Ryo Ishikawa

    Theoretical and Applied Genetics   132 ( 9 )   2615 - 2623   2019年9月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    DOI: 10.1007/s00122-019-03376-3

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  • Two Y-encoded genes determine sex in kiwifruit 査読 国際誌

    Takashi Akagi, Sarah M. Pilkington, Erika Varkonyi-Gasic, Isabelle M. Henry, Shigeo S. Sugano, Minori Sonoda, Alana Firl, Mark A. McNeilage, Mikaela J. Douglas, Tianchi Wang, Ria Rebstock, Charlotte Voogd, Paul Datson, Andrew C. Allan, Kenji Beppu, Ikuo Kataoka, Ryutaro Tao

    Nature Plants   5 ( 5 )   801 - 809   2019年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1038/s41477-019-0489-6

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  • Gene networks orchestrated by MeGI: a single-factor mechanism underlying sex determination in persimmon. 査読

    Yang HW, Akagi T, Kawakatsu T, Tao R

    The Plant journal : for cell and molecular biology   98 ( 1 )   97 - 111   2019年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1111/tpj.14202

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  • Characterization of post-mating interspecific cross-compatibility in Prunus (Rosaceae) 査読

    Takuya Morimoto, Yuto Kitamura, Koji Numaguchi, Takashi Akagi, Ryutaro Tao

    Scientia Horticulturae   246   693 - 699   2019年2月

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    掲載種別:研究論文(学術雑誌)   出版者・発行元:Elsevier BV  

    DOI: 10.1016/j.scienta.2018.11.045

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  • Genome re-sequencing of diverse sweet cherry (Prunus avium) individuals reveals a modifier gene mutation conferring pollen-part self-compatibility 査読

    Kentaro Ono, Takashi Akagi, Takuya Morimoto, Ana Wónsch, Ryutaro Tao

    Plant and Cell Physiology   59 ( 6 )   1265 - 1275   2018年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Oxford University Press  

    The S-RNase-based gametophytic self-incompatibility (GSI) reproduction barrier is important for maintaining genetic diversity in species of the families Solanaceae, Plantaginaceae and Rosaceae. Among the plant taxa with S-RNase-based GSI, Prunus species in the family Rosaceae exhibit Prunus-specific self-incompatibility (SI). Although pistil S and pollen S determinants have been identified, the mechanism underlying SI remains uncharacterized in Prunus species. A putative pollen-part modifier was identified in this study. Disruption of this modifier supposedly confers self-compatibility (SC) to sweet cherry (Prunus avium) 'Cristobalina'. To identify the modifier, genome re-sequencing experiments were completed involving sweet cherry individuals from 18 cultivars and 43 individuals in two segregating populations. Cataloging of subsequences (35 bp kmers) from the obtained genomic reads, while referring to the mRNA sequencing data, enabled the identification of a candidate gene [M locus-encoded GST (MGST)]. Additionally, the insertion of a transposon-like sequence in the putative MGST promoter region in 'Cristobalina' down-regulated MGST expression levels, probably leading to the SC of this cultivar. Phylogenetic, evolutionary and gene expression analyses revealed that MGST may have undergone lineage-specific evolution, and the encoded protein may function differently from the corresponding proteins encoded by GST orthologs in other species, including members of the subfamily Maloideae (Rosaceae). Thus, MGST may be important for Prunus-specific SI. The identification of this novel modifier will expand our understanding of the Prunus-specific GSI system. We herein discuss the possible functions of MGST in the Prunus-specific GSI system.

    DOI: 10.1093/pcp/pcy068

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  • One Hundred Ways to Invent the Sexes: Theoretical and Observed Paths to Dioecy in Plants 査読

    Isabelle M. Henry, Takashi Akagi, Ryutaro Tao, Luca Comai

    Annual Review of Plant Biology   69   553 - 575   2018年4月

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    記述言語:英語   出版者・発行元:Annual Reviews Inc.  

    Dioecy, the presence of male and female flowers on separate individuals, is both widespread and uncommon within flowering plants, with only a few percent of dioecious species spread across most major phylogenetic taxa. It is therefore safe to assume that dioecy evolved independently in these different groups, which allows us to ask questions regarding the molecular and developmental mechanisms underlying these independent transitions to dioecy. We start this review by examining the problem from the standpoint of a genetic engineer trying to develop dioecy, discuss various potential solutions, and compare them to models proposed in the past and based on genetic and evolutionary considerations. Next, we present recent information regarding candidate sex determinants in three species, acquired using newly established genomic approaches. Although such specific information is still scarce, it is slowly becoming apparent that various genes or pathways can be altered to evolve dioecy.

    DOI: 10.1146/annurev-arplant-042817-040615

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  • A Y-encoded suppressor of feminization arose via lineage-specific duplication of a cytokinin response regulator in kiwifruit 査読

    Takashi Akagi, Isabelle M. Henry, Haruka Ohtani, Takuya Morimoto, Kenji Beppu, Ikuo Kataoka, Ryutaro Tao

    Plant Cell   30 ( 4 )   780 - 795   2018年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Society of Plant Biologists  

    Dioecy, the presence of male and female flowers on distinct individuals, has evolved independently in multiple plant lineages, and the genes involved in this differential development are just starting to be uncovered in a few species. Here, we used genomic approaches to investigate this pathway in kiwifruits (genus Actinidia). Genome-wide cataloging of male-specific subsequences, combined with transcriptome analysis, led to the identification of a type-C cytokinin response regulator as a potential sex determinant gene in this genus. Functional transgenic analyses in two model systems, Arabidopsis thaliana and Nicotiana tabacum, indicated that this gene acts as a dominant suppressor of carpel development, prompting us to name it Shy Girl (SyGI). Evolutionary analyses in a panel of Actinidia species revealed that SyGI is located in the Y-specific region of the genome and probably arose from a lineage-specific gene duplication. Comparisons with the duplicated autosomal counterpart, and with orthologs from other angiosperms, suggest that the SyGI-specific duplication and subsequent evolution of cis-elements may have played a key role in the acquisition of separate sexes in this species.

    DOI: 10.1105/tpc.17.00787

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  • A pathway from conventional to next generation methods to identify the sex determinant in persimmon 査読

    T. Akagi, R. Tao

    Acta Horticulturae   1195   71 - 74   2018年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:International Society for Horticultural Science  

    Cultivated Diospyros kaki, otherwise known as persimmon or kaki, is a polygamous species, whereas most other Diospyros species are dioecious. Most commercial cultivars of D. kaki bear only female flowers
    however, some cultivars bear male flowers as well. Elucidation of the genetic and molecular basis of sex expression in D. kaki may lead to the development of artificial control of sex expression in this important fruit species. To this end, Diospyros lotus was used as a model to study the sexuality of D. kaki. Using a population of 63 F1 offspring of D. lotus, a bulked segregant analysis with amplified fragment length polymorphisms (AFLP) showed that the sexuality of this species is controlled by a single locus or haploblock in a heterogametic male (XY) system. Male-specific subsequences from Illumina HiSeq genomic reads data obtained from male and female pools were cataloged and assembled. This enabled comprehensive isolation of the male-determining regions on the Y-chromosome of D. lotus. Integration of transcriptome and evolutionary analyses led to the identification of one Y-specific sex-determinant candidate gene, OGI. This gene encodes a small RNA that triggers a transitive RNAi on the feminizing gene, MeGI, which is located on the autosome or the pseudoautosomal region of the sex chromosome. Molecular markers developed from the OGI sequence and its flanking regions indicated that the genetic control of maleness expression in D. kaki is based essentially on the OGI/MeGI system.

    DOI: 10.17660/ActaHortic.2018.1195.12

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  • Quantitative characterization of fruit shape and its differentiation pattern in diverse persimmon (Diospyros kaki) cultivars 査読

    Haruka Maeda, Takashi Akagi, Ryutaro Tao

    SCIENTIA HORTICULTURAE   228   41 - 48   2018年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    There is considerable diversity in fruit shapes among persimmon (Diospyros kaki) cultivars. Although fruit shape is one of the most important traits affecting the commercial quality of fruits, quantitatively characterizing fruit shape features remains difficult. The objective of this study was to develop a reliable method for quantitatively analyzing persimmon fruit shapes, and to clarify the fruit development patterns as well as their relationships to the shapes of other organs across cultivars. Using 153 persimmon cultivars and two wild Diospyros relatives, we evaluated two-dimensional pictures of longitudinal and transverse fruit sections with elliptical Fourier descriptors (EFDs) and the SHAPE program. Principal component analysis (PCA) using each EFD generated representative vectors, which elucidated the fruit shape diversity among the cultivars. Additionally, a PCA of the EFDs quantified two major components of the variability in the shapes of longitudinal fruit sections, namely the ratio of length to diameter and the fruit apex shape. Seasonal characterizations of the first principal component revealed the fruit shape development patterns. The fundamental shapes in the longitudinal direction were coordinately determined during the early developmental stages across cultivars. Furthermore, a quantitative characterization of persimmon fruit, seed, and leaf shapes unveiled correlations between these traits. The data presented herein indicate that combining EFDs and PCA enables the quantitative analysis of persimmon organ shapes, which may be related to various quantitative indices.

    DOI: 10.1016/j.scienta.2017.10.006

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  • Flexible "sex determinations in persimmons: evolution from a genetic to an epigenetic regulation" 査読

    Takashi Akagi

    GENES & GENETIC SYSTEMS   91 ( 6 )   317 - 317   2016年12月

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    記述言語:英語   出版者・発行元:GENETICS SOC JAPAN  

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  • Epigenetic Regulation of the Sex Determination Gene MeGI in Polyploid Persimmon 査読

    Takashi Akagi, Isabelle M. Henry, Takashi Kawai, Luca Comai, Ryutaro Tao

    PLANT CELL   28 ( 12 )   2905 - 2915   2016年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER SOC PLANT BIOLOGISTS  

    Epigenetic regulation can add a flexible layer to genetic variation, potentially enabling long-term but reversible cis-regulatory changes to an allele while maintaining its DNA sequence. Here, we present a case in which alternative epigenetic states lead to reversible sex determination in the hexaploid persimmon Diospyros kaki. Previously, we elucidated the molecular mechanismof sex determination in diploid persimmon and demonstrated the action of a Y-encoded sex determinant pseudogene called OGI, which produces small RNAs targeting the autosomal gene MeGI, resulting in separate male and female individuals (dioecy). We contrast these findings with the discovery, in hexaploid persimmon, of an additional layer of regulation in the form of DNA methylation of the MeGI promoter associated with the production of both male and female flowers in genetically male trees. Consistent with this model, developing male buds exhibited higher methylation levels across the MeGI promoter than developing female flowers from either monoecious or female trees. Additionally, a DNA methylation inhibitor induced developing male buds to form feminized flowers. Concurrently, in Y-chromosome-carrying trees, the expression of OGI is silenced by the presence of a SINE (short interspersed nuclear element)-like insertion in the OGI promoter. Our findings provide an example of an adaptive scenario involving epigenetic plasticity.

    DOI: 10.1105/tpc.16.00532

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  • A male determinant gene in diploid dioecious Diospyros, OGI, is required for male flower production in monoecious individuals of Oriental persimmon (D-kaki) 査読

    Takashi Akagi, Takashi Kawai, Ryutaro Tao

    SCIENTIA HORTICULTURAE   213   243 - 251   2016年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    The sexuality of crops is an important trait affecting production and breeding efficiencies. Recently, a Y-chromosome-encoded gene, designated Oppressor of MeGI (OGI), has been shown to play a central role in dioecious sex determination in diploid persimmons (Diospyros spp.). However, little is known about the relationship between OGI and the irregular sexuality in polyploid persimmon (D. kaki). D. kaki, which is mostly hexaploid with some nonaploid individuals, is mainly constituted of monoecious and female individuals. In this study, we attempted to investigate the association of sexuality with OGI allele diversities/dosages in a wide range of D. kaki cultivars. The results indicated that OGI is indispensable for the monoecious phenotype producing male flowers, which suggested a conserved role for OGI as a key to expressing maleness in D. kaki, as in dioecious diploid Diospyros. However, the existence of OGI alleles did not always lead to production of male flowers in D. kaki. The dosage or composition of OGI alleles had no substantial effect on the sexuality of the cultivars tested. We discuss the potential use of the obtained information on OGI allele diversities dosages for breeding of D. kaki cultivars. (C) 2016 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.scienta.2016.10.046

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  • Insights into the Prunus-Specific S-RNase-Based Self-Incompatibility System from a Genome-Wide Analysis of the Evolutionary Radiation of S Locus-Related F-box Genes 査読

    Takashi Akagi, Isabelle M. Henry, Takuya Morimoto, Ryutaro Tao

    PLANT AND CELL PHYSIOLOGY   57 ( 6 )   1281 - 1294   2016年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    Self-incompatibility (SI) is an important plant reproduction mechanism that facilitates the maintenance of genetic diversity within species. Three plant families, the Solanaceae, Rosaceae and Plantaginaceae, share an S-RNase-based gametophytic SI (GSI) system that involves a single S-RNase as the pistil S determinant and several F-box genes as pollen S determinants that act via non-self-recognition. Previous evidence has suggested a specific self-recognition mechanism in Prunus (Rosaceae), raising questions about the generality of the S-RNase-based GSI system. We investigated the evolution of the pollen S determinant by comparing the sequences of the Prunus S haplotype-specific F-box gene (SFB) with those of its orthologs in other angiosperm genomes. Our results indicate that the Prunus SFB does not cluster with the pollen S of other plants and diverged early after the establishment of the Eudicots. Our results further indicate multiple F-box gene duplication events, specifically in the Rosaceae family, and suggest that the Prunus SFB gene originated in a recent Prunus-specific gene duplication event. Transcriptomic and evolutionary analyses of the Prunus S paralogs are consistent with the establishment of a Prunus-specific SI system, and the possibility of subfunctionalization differentiating the newly generated SFB from the original pollen S determinant.

    DOI: 10.1093/pcp/pcw077

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  • Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication 査読

    Takashi Akagi, Toshio Hanada, Hideaki Yaegaki, Thomas M. Gradziel, Ryutaro Tao

    DNA RESEARCH   23 ( 3 )   271 - 282   2016年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:OXFORD UNIV PRESS  

    Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops.

    DOI: 10.1093/dnares/dsw014

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  • マメガキ(Diospyros lotus L.)で同定された雄性決定因子連鎖領域とカキ(D. kaki Thunb.)品種の雄花着生特性との関連性. 査読

    梶田啓, 赤木剛士, 山根久代, 田尾龍太郎, 米森敬三

    園芸学研究   14   121 - 126   2015年

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    記述言語:日本語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.2503/hrj.14.121

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  • A Y-chromosome–encoded small RNA acts as a sex determinant in persimmons 査読

    Takashi Akagi

    Science   346 ( 6209 )   646 - 650   2014年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1126/science.1257225

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  • Development of Molecular Markers Associated with Sexuality in Diospyros lotus L. and Their Application in D-kaki Thunb 査読

    Takashi Akagi, Kei Kajita, Takanori Kibe, Haruka Morimura, Tomoyuki Tsujimoto, Soichiro Nishiyama, Takashi Kawai, Hisayo Yamane, Ryutaro Tao

    JOURNAL OF THE JAPANESE SOCIETY FOR HORTICULTURAL SCIENCE   83 ( 3 )   214 - 221   2014年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:JAPAN SOC HORTICULTURAL SCI  

    Sexuality of crops affects both cultivation and breeding systems. Cultivated persimmon (Diospyros kaki Thunb) has a morphologically well-characterized polygamous or gyonodioecious sexual system. However, the genetic basis of sexuality in D. kaki has yet to be characterized. Here, we used dioecious D. lotus L., a diploid wild relative species to hexaploid or nonaploid D. kaki, as a model to clarify the genetic basis of sexuality in Diospyros and to develop molecular markers associated with the sexuality of individuals. Using 62 F-1 offspring segregated into distinct male/female phenotypes, we found two amplified fragment-length polymorphism markers, DlSx-AF4 and DlSx-AF7, which cosegregated with maleness. This could suggest that the sexuality of D. lotus is controlled by a single gene/haploblock, and the male is dominant over the female. Thus, D. lotus's sexuality can be described as the heterogametic male type, the ICY-type, as reported for most other dioecious plant species. For unknown reasons, segregation of the phenotype of a sequence-characterized amplified region marker developed from DlSx-AF4 (DlSx-AF4S) and/or the male/female phenotype in two different crosses in D. lotus showed an apparent bias towards femaleness and better fitted 1:2 than 1:1, which is the theoretical segregation for a single genetic locus or haploblock in diploid D. lotus. DlSx-AF4S could distinguish D. kaki cultivars with female and male flowers from cultivars with only female flowers, strongly indicating that the same genetic system controls D. kaki's sexuality and that DlSx-AF4S could be used as a genetic marker for sexuality in D. kaki breeding programs.

    DOI: 10.2503/jjshs1.CH-109

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  • Development of EST-SSR Markers Derived from Diospyros kaki 査読

    T. Tsujimoto, T. Akagi, K. Yonemori, S. Kanzaki

    V INTERNATIONAL SYMPOSIUM ON PERSIMMON   996   133 - 137   2013年

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    記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)   出版者・発行元:INT SOC HORTICULTURAL SCIENCE  

    For genetic analysis of persimmon (Diospyros kaki) and its relatives, we investigated the development of SSR markers with expression sequence tags (ESTs). Of 9475 EST data from the NCBI database which had isolated from D. kaki, 746 sequences contained SSRs which had more than four (tetranucleotide) or five (dinucleotide and trinucleotide) repeats. Tested on two species, D. kaki and D. lotus (a diploid relative of D. kaki), of primer pairs based on 65 SSR-containing EST sequences, 52 primer pairs resulted in proper PCR products. Some of these candidate EST-SSR markers showed polymorphism among cultivars and seedlings of D. kaki and D. lotus. Among tested seven clones of D. lotus, 32 of 52 candidate EST-SSR markers showed polymorphism. For molecular phylogenetic analysis, linkage mapping and whole genome mapping of Diospyros species, EST-SSR markers appear to be as useful as genomic SSR markers. In addition, development of EST-SSR markers seems to be easy and cost-effective when compared with genomic SSR markers.

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  • Fine genotyping of a highly polymorphic ASTRINGENCY-linked locus reveals variable hexasomic inheritance in persimmon (Diospyros kaki Thunb.) cultivars 査読

    Takashi Akagi, Ryutaro Tao, Tomoyuki Tsujimoto, Atsushi Kono, Keizo Yonemori

    TREE GENETICS & GENOMES   8 ( 1 )   195 - 204   2012年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER HEIDELBERG  

    Persimmon (Diospyros kaki Thunb.) is one of the major tree crops in East Asia and is generally hexaploid. A single ASTRINGENCY (AST) locus controls the astringency/non-astringency (A/NA) trait of persimmon fruit, one of the most important traits for consumption, on each of the six corresponding chromosomes. Although several molecular approaches are in progress to elucidate the molecular mechanisms of astringency trait in persimmon, the distinct polysomic behavior of the AST locus remains to be solved. The aim of this study was to perform fine genotyping of a highly polymorphic marker locus linked to the AST locus, detect the allele pairing in ten segregated F(1) lines derived from hybridization of A-type x NA-type cultivars, and identify the basis of hexaploid inheritance at the AST locus in persimmon. The results showed that persimmon cultivars frequently produce aneuploid offspring bearing an extra chromosome with the AST locus, with the incidence of aneuploidy varying among the cultivars. On the examination of hexasomic behavior in persimmon cultivars, the ratios of individuals bearing each allele pair segregated from A-type parents showed a good fit to the expected ratios in an autohexaploid inheritance model, except for cvs. Luo-tian-tian-shi and Sa-gok-shi which fitted to an autoallohexaploid inheritance model. These results suggest variable hexasomic behavior among persimmon cultivars.

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  • Seasonal Abscisic Acid Signal and a Basic Leucine Zipper Transcription Factor, DkbZIP5, Regulate Proanthocyanidin Biosynthesis in Persimmon Fruit 査読

    Takashi Akagi, Ayako Katayama-Ikegami, Shozo Kobayashi, Akihiko Sato, Atsushi Kono, Keizo Yonemori

    PLANT PHYSIOLOGY   158 ( 2 )   1089 - 1102   2012年2月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER SOC PLANT BIOLOGISTS  

    Proanthocyanidins (PAs) are secondary metabolites that contribute to plant protection and crop quality. Persimmon (Diospyros kaki) has a unique characteristic of accumulating large amounts of PAs, particularly in its fruit. Normal astringent-type and mutant nonastringent-type fruits show different PA accumulation patterns depending on the seasonal expression patterns of DkMyb4, which is a Myb transcription factor (TF) regulating many PA pathway genes in persimmon. In this study, attempts were made to identify the factors involved in DkMyb4 expression and the resultant PA accumulation in persimmon fruit. Treatment with abscisic acid (ABA) and an ABA biosynthesis inhibitor resulted in differential changes in the expression patterns of DkMyb4 and PA biosynthesis in astringent-type and nonastringent-type fruits depending on the development stage. To obtain an ABA-signaling TF, we isolated a full-length basic leucine zipper (bZIP) TF, DkbZIP5, which is highly expressed in persimmon fruit. We also showed that ectopic DkbZIP5 overexpression in persimmon calluses induced the up-regulation of DkMyb4 and the resultant PA biosynthesis. In addition, a detailed molecular characterization using the electrophoretic mobility shift assay and transient reporter assay indicated that DkbZIP5 recognized ABA-responsive elements in the promoter region of DkMyb4 and acted as a direct regulator of DkMyb4 in an ABA-dependent manner. These results suggest that ABA signals may be involved in PA biosynthesis in persimmon fruit via DkMyb4 activation by DkbZIP5.

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  • Functional and Expressional Analyses of PmDAM Genes Associated with Endodormancy in Japanese Apricot 査読

    Ryuta Sasaki, Hisayo Yamane, Tomomi Ooka, Hiroaki Jotatsu, Yuto Kitamura, Takashi Akagi, Ryutaro Tao

    PLANT PHYSIOLOGY   157 ( 1 )   485 - 497   2011年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER SOC PLANT BIOLOGISTS  

    Bud endodormancy in woody plants plays an important role in their perennial growth cycles. We previously identified a MADS box gene, DORMANCY-ASSOCIATED MADS box6 (PmDAM6), expressed in the endodormant lateral buds of Japanese apricot (Prunus mume), as a candidate for the dormancy-controlling gene. In this study, we demonstrate the growth inhibitory functions of PmDAM6 by overexpressing it in transgenic poplar (Populus tremula x Populus tremuloides). Transgenic poplar plants constitutively expressing PmDAM6 showed growth cessation and terminal bud set under environmental conditions in which control transformants continued shoot tip growth, suggesting the growth inhibitory functions of PmDAM6. In the Japanese apricot genome, we identified six tandemly arrayed PmDAM genes (PmDAM1-PmDAM6) that conserve an amphiphilic repression motif, known to act as a repression domain, at the carboxyl-terminal end, suggesting that they all may act as transcriptional repressors. Seasonal expression analysis and cold treatment in autumn indicated that all PmDAMs were repressed during prolonged cold exposure and maintained at low levels until endodormancy release. Furthermore, PmDAM4 to PmDAM6 responses to a short period of cold exposure appeared to vary between low-and high-chill genotypes. In the high-chill genotype, a short period of cold exposure slightly increased PmDAM4 to PmDAM6 expression, while in the low-chill genotype, the same treatment repressed PmDAM4 to PmDAM6 expression. Furthermore, PmDAM4 to PmDAM6 expression was negatively correlated with endodormancy release. We here discuss the genotype-dependent seasonal expression patterns of PmDAMs in relation to their involvement in endodormancy and variation in chilling requirements.

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  • Proanthocyanidin biosynthesis of persimmon (Diospyros kaki Thunb.) fruit 査読

    Takashi Akagi, Ayako Katayama-Ikegami, Keizo Yonemori

    SCIENTIA HORTICULTURAE   130 ( 2 )   373 - 380   2011年9月

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    記述言語:英語   出版者・発行元:ELSEVIER SCIENCE BV  

    Persimmon accumulates a large amount of condensed tannins (proanthocyanidins, PAs) in the vacuoles of specific cells called &apos;tannin cells&apos; during fruit development. PAs cause astringency, which is a dry or puckering sensation due to the coagulation of oral proteins. The composition of PAs in persimmon fruit can be analysed mainly by two methods, thiolysis degradation and acid catalysis in the presence of phloroglucinol. These methods indicate that epigallocatechin (EGC) and epigallocatechin-3-O-gallate (EGCG) constitute the main subunit components of PAs in astringent-type fruit. PAs are synthesised via the phenylpropanoid and flavonoid biosynthetic pathways, which originate from substrates derived from the shikimate pathway. Subunits EGC and EGCG possibly derive from active transcription offlavonoid 3&apos;5&apos; hydroxylase and anthocyanidin reductase, and from gallic acid synthesised via the shikimate pathway for galloylation. The reason for the formation of gallates and transport systems into cell vacuoles specifically accumulating these compounds remains unknown, as well as the processes for polymerisation of fiavan 3-ol units. In addition, two Myb transcription factors, DkMyb2 and DkMyb4, which have the ability to activate the transcription of enzymatic genes, are involved in PA regulation in persimmon. In particular, DkMyb4 has been suggested to facilitate substantial PA biosynthesis in fruit. A better understanding of the mechanisms involved in PA biosynthesis in persimmon fruit will provide the basis for the breeding of non-astringent-type cultivars for fresh consumption, or for the genetic engineering of PAs for human benefit. (C) 2011 Elsevier B.V. All rights reserved.

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  • Effects of seasonal temperature changes on DkMyb4 expression involved in proanthocyanidin regulation in two genotypes of persimmon (Diospyros kaki Thunb.) fruit 査読

    Takashi Akagi, Tomoyuki Tsujimoto, Ayako Ikegami, Keizo Yonemori

    PLANTA   233 ( 5 )   883 - 894   2011年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

    Persimmon fruits accumulate a large amount of proanthocyanidin (PA). Fruits of the mutant non-astringent (NA) type lose their ability to accumulate PA at an early stage of fruit development, whereas fruits of the normal astringent (A) type sustain PA accumulation until ripening. This allelotype is determined by the genotype of a single ASTRINGENCY (AST) locus. It is possible that the reduction in PA accumulation in NA-type fruits is due to phenological down-regulation of DkMyb4 (a PA regulator) and the resultant down-regulation of structural genes in the PA pathway. In this study, attempts were made to identify the regulatory mechanisms of phenological PA accumulation in A- and NA-type fruits, focusing particularly on the effects of ambient temperature. Continuous cool temperature conditions caused sustained expression of DkMyb4 in NA-type fruits, as well as in A-type fruits, resulting in increased expression of PA pathway genes and PA accumulation. However, the expression of some A/NA phenotypic marker genes was not significantly affected by the cool temperature conditions. In addition, PA composition in NA-type fruits exposed to cool temperatures differed from that in A-type fruits. These results indicate that a cool ambient temperature may have induced DkMyb4 expression and resultant PA accumulation, but did not directly affect the expression of the AST gene.

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  • Development of Molecular Markers Linked to the Allele Associated with the Non-astringent Trait of the Chinese Persimmon (Diospyros kaki Thunb.) 査読

    Ayako Ikegami, Sai Eguchi, Takashi Akagi, Akihiko Sato, Masahiko Yamada, Shinya Kanzaki, Akira Kitajima, Keizo Yonemori

    JOURNAL OF THE JAPANESE SOCIETY FOR HORTICULTURAL SCIENCE   80 ( 2 )   150 - 155   2011年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:JAPAN SOC HORTICULTURAL SCI  

    Persimmon cultivars are classified into four types depending on the nature of astringency loss of the fruit, namely pollination constant non-astringent (PCNA), pollination variant non-astringent (PVNA), pollination variant astringent (PVA), and pollination constant astringent (PCA). Among these four types, PCNA is the most important cultivar for persimmon breeding due to the stable loss of natural astringency on the tree. The trait of natural astringency loss is recessive in Japanese PCNA cultivars, while that in the Chinese PCNA cultivar, 'Luo tian tian shi', is dominant and the latter locus, termed CPCNA, is different from that in Japanese cultivars. In order to develop a molecular marker for the selection of the CPCNA-type cultivar, we performed amplified fragment length polymorphism (AFLP) in combination with bulked segregant analysis for F-1 offspring derived from 'Luo tian tian shi', which was used as the maternal parent. A total of 384 primer combinations were tested, and three AFLP markers, namely EACT-MCCC-222 (RO1), EGGC-MCTC-309 (RO2), and EGCC-MCGA-105 (RO3), linked to the CPCNA dominant allele were obtained. Among these markers, EGGC/MCTC-309 (RO2) was converted into a sequence-characterized amplified region (SCAR) marker. PCR analysis using F-1 offspring (n = 264) revealed that the relevance ratio of the SCAR marker was 94%. The polymorphism of the RO2 marker, which was strongly linked to the CPCNA dominant allele, was detected in only two Chinese PCNA cultivars, namely 'Luo tian tian shi' and 'Tian bao gai', among the Chinese, Korean, and Japanese cultivars tested. These results indicate that the RO2 marker contributes to marker-assisted selection for breeding programs of new PCNA cultivars having the CPCNA trait.

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  • DkMyb2 wound-induced transcription factor of persimmon (Diospyros kaki Thunb.), contributes to proanthocyanidin regulation 査読

    Takashi Akagi, Ayako Ikegami, Keizo Yonemori

    PLANTA   232 ( 5 )   1045 - 1059   2010年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

    Proanthocyanidins (PAs) are secondary metabolites that contribute to the protection of a plant against biotic and abiotic stresses. Persimmon (Diospyros kaki) accumulates abundant PAs in each plant organ, and some potential Myb-like transcription factors (Myb-TFs) involved in the production of PAs have been isolated. In this study, we aimed to molecularly characterize one of them, DkMyb2, which was placed in a subclade including a PA regulator of Arabidopsis (Arabidopsis thaliana), TRANSPARENT TESTA2 (TT2), and was co-induced with PA pathway genes after wound stress. Ectopic DkMyb2 overexpression caused significant up-regulation of PA pathway genes in transgenic persimmon calluses and significant accumulation of PA, and increased mean degree of polymerization of PAs in transgenic kiwifruit calluses. Analysis of the DNA-binding ability of DkMyb2 by electrophoretic mobility shift assays showed that DkMyb2 directly binds to the AC-rich cis-motifs known as AC elements in the promoters of the two PA pathway genes in persimmon, DkANR, and DkLAR. Furthermore, a transient reporter assay using a dual-luciferase system demonstrated direct transcriptional activation of DkANR and DkLAR by DkMyb2. We also discuss subfunctionalization of two PA regulators in persimmon, DkMyb2 and DkMyb4, as well as PA regulators in other plant species from the viewpoint of their ability to bind to cis-motifs and their functions in transcriptional activation. Our results provide insight into the multiple regulatory mechanisms that control PA metabolism by Myb-TFs in persimmon.

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  • Condensed Tannin Composition Analysis in Persimmon (Diospyros kaki Thunb.) Fruit by Acid Catalysis in the Presence of Excess Phloroglucinol 査読

    Takashi Akagi, Yasuhiko Suzuki, Ayako Ikegami, Hiroshi Kamitakahara, Toshiyuki Takano, Fumiaki Nakatsubo, Keizo Yonemori

    JOURNAL OF THE JAPANESE SOCIETY FOR HORTICULTURAL SCIENCE   79 ( 3 )   275 - 281   2010年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:JAPAN SOC HORTICULTURAL SCI  

    Persimmon (Diospyros kaki Thunb.) accumulates soluble condensed tannin (CT) in fruit which is responsible for its astringency trait. In this study, we analyzed the CT composition in persimmon fruit with phloroglucinol, and identified and characterized novel epigallocatechin-3-O-gallate-phloroglucinol (EGCG-P) adducts as one of the main CT components of persimmon fruit. Analysis with phloroglucinol in persimmon cultivars revealed the different tendencies of the CT composition and component ratio among the four astringency types (PCNA, PVNA, PVA, and PCA), which are categorized by their patterns of astringency loss. The concentration of the main CT component in persimmon fruit, epigallocatechin-3-O-gallate (EGCG), was particularly different among astringency types. Further analysis of the fruit at various maturation stages will help in understanding the different mechanisms of CT accumulation among astringent types. Our results demonstrated that the phloroglucinol methodology is useful for CT composition analysis in persimmon fruit and will contribute to future studies on the astringency trait in this fruit.

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  • SCAR Markers for Practical Application of Marker-assisted Selection in Persimmon (Diospyros kaki Thunb.) Breeding 査読

    Shinya Kanzaki, Takashi Akagi, Takuya Masuko, Miyuki Kimura, Masahiko Yamada, Akihiko Sato, Nobuhito Mitani, Naoki Ustunomiya, Keizo Yonemori

    JOURNAL OF THE JAPANESE SOCIETY FOR HORTICULTURAL SCIENCE   79 ( 2 )   150 - 155   2010年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:JAPAN SOC HORTICULTURAL SCI  

    In previous studies, we have developed molecular markers linked to the AST locus that controls fruit astringency type in persimmon; however, these markers are not feasible for practical application to breeding programs since they are not fully effective for discriminating the pollination constant and non-astringent (PCNA) genotype from the non-PCNA genotype in a progeny derived from 'Kurokuma'. Here we developed new sequence characterized amplified region (SCAR) markers that enable easy and reliable selection of the PCNA genotype from breeding populations. Genomic regions adjacent to probe 5R, which showed polymorphic fragments between PCNA and non-PCNA genotypes in restriction fragment length polymorphism (RFLP) analysis, were isolated from the genomic libraries of 'Nishimura-wase', 'Jiro', and 'Kurokuma'-derived offspring. The isolated genomic regions were characterized and 3 insertion/deletion mutations were observed between ast- and AST-linked regions. Several primers were designed in the flanking region of Indel-3 and, in multiplex PCR, it was shown that using 2 forward primers, AST-F and PCNA-F and a reverse primer, 5R3R, is the most useful and reliable primer set. The AST-linked 220-bp fragment proved to be a common marker of 'Kurokuma'-, 'Nisimura-wase'- and 'Aizumishirazu'- derived progenies. This multiplex PCR is considered the most practical tool for marker-assisted selection (MAS) and can enhance and accelerate progress in persimmon breeding.

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  • Quantitative Genotyping for the Astringency Locus in Hexaploid Persimmon Cultivars using Quantitative Real-time PCR 査読

    Takashi Akagi, Yumi Takeda, Keizo Yonemori, Ayako Ikegami, Atsushi Kono, Masahiko Yamada, Shinya Kanzaki

    JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE   135 ( 1 )   59 - 66   2010年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER SOC HORTICULTURAL SCIENCE  

    Persimmon (Diospyros kaki Thunb.) is generally hexaploid, and a single AST locus controls the pollination-constant non-astringency trait on each of six corresponding chromosomes. The pollination-constant non-astringent (PCNA) genotype is nulliplex and requires homozygous recessive alleles (ast) at the AST locus. There are several non-PCNA cultivars/selections that could be cross parents; however, the probability of yielding nulliplex offspring depends on the number of recessive alleles (ast). In genotyping for the AST locus in hexaploid persimmon, in contrast to the situation in diploid plants, we need to detect the AST/ast allele dosage; this cannot be detected by common codominant markers. In this study, we detected the allele dosage of M(ast), which is a marker allele strongly linked to the ast allele among cultivars, by quantitative real-time polymerase chain reaction (qPCR) using three reference sites, actin (DkAct), anthocyanin reductase (DkANR), and L5R, whose sequences are conserved in the genome of persimmon cultivars. Based on the allele dosage of the M(ast), AST/ast genotypes were estimated for 63 non-astringent cultivars/selections, of which only five cultivars/selections were estimated to be simplex or duplex. The quantitative genotyping method using qPCR may be generally effective for polyploid plants.

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  • DkMyb4 Is a Myb Transcription Factor Involved in Proanthocyanidin Biosynthesis in Persimmon Fruit 査読

    Takashi Akagi, Ayako Ikegami, Tomoyuki Tsujimoto, Shozo Kobayashi, Akihiko Sato, Atsushi Kono, Keizo Yonemori

    PLANT PHYSIOLOGY   151 ( 4 )   2028 - 2045   2009年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:AMER SOC PLANT BIOLOGISTS  

    Proanthocyanidins (PAs) are secondary metabolites that contribute to the protection of the plant and also to the taste of the fruit, mainly through astringency. Persimmon (Diospyros kaki) is unique in being able to accumulate abundant PAs in the fruit flesh. Fruits of the nonastringent (NA)-type mutants lose their ability to produce PA at an early stage of fruit development, while those of the normal astringent (A) type remain rich in PA until fully ripened. The expression of many PA pathway genes was coincidentally terminated in the NA type at an early stage of fruit development. The five genes encoding the Myb transcription factor were isolated from an A-type cultivar (Kuramitsu). One of them, DkMyb4, showed an expression pattern synchronous to that of the PA pathway genes in A-and NA-type fruit flesh. The ectopic expression of DkMyb4 in kiwifruit (Actinidia deliciosa) induced PA biosynthesis but not anthocyanin biosynthesis. The suppression of DkMyb4 in persimmon calluses caused a substantial down-regulation of the PA pathway genes and PA biosynthesis. Furthermore, analysis of the DNA-binding ability of DkMyb4 showed that it directly binds to the MYBCORE cis-motif in the promoters of the some PA pathway genes. All our results indicate that DkMyb4 acts as a regulator of PA biosynthesis in persimmon and, therefore, suggest that the reduction in the DkMyb4 expression causes the NA-type-specific down-regulation of PA biosynthesis and resultant NA trait.

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  • Expression balances of structural genes in shikimate and flavonoid biosynthesis cause a difference in proanthocyanidin accumulation in persimmon (Diospyros kaki Thunb.) fruit 査読

    Takashi Akagi, Ayako Ikegami, Yasuhiko Suzuki, Junya Yoshida, Masahiko Yamada, Akihiko Sato, Keizo Yonemori

    PLANTA   230 ( 5 )   899 - 915   2009年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

    Persimmon fruits accumulate a large amount of proanthocyanidin (PA) during development. Fruits of pollination-constant and non-astringent (PCNA) type mutants lose their ability to produce PA at an early stage of fruit development, while fruits of the normal (non-PCNA) type remain rich in PA until fully ripened. To understand the molecular mechanism for this difference, we isolated the genes involved in PA accumulation that are differentially expressed between PCNA and non-PCNA, and confirmed their correlation with PA content and composition. The expression of structural genes of the shikimate and flavonoid biosynthetic pathways and genes encoding transferases homologous to those involved in the accumulation of phenolic compounds were downregulated coincidentally only in the PCNA type. Analysis of PA composition using the phloroglucinol method suggested that the amounts of epigallocatechin and its 3-O-gallate form were remarkably low in the PCNA type. In the PCNA type, the genes encoding flavonoid 3&apos;5&apos; hydroxylase (F3&apos;5&apos;H) and anthocyanidin reductase (ANR) for epigallocatechin biosynthesis showed remarkable downregulation, despite the continuous expression level of their competitive genes, flavonoid 3&apos; hydroxylation (F3&apos;H) and leucoanthocyanidin reductase (LAR). We also confirmed that the relative expression levels of F3&apos;5&apos;H to F3&apos;H, and ANR to LAR, were considerably higher, and the PA composition corresponded to the seasonal expression balances in both types. These results suggest that expressions of F3&apos;5&apos;H and ANR are important for PA accumulation in persimmon fruit. Lastly, we tested enzymatic activity of recombinant DkANR in vitro, which is thought to be an important enzyme for PA accumulation in persimmon fruits.

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  • Molecular identification of 1-Cys peroxiredoxin and anthocyanidin/flavonol 3-O-galactosyltransferase from proanthocyanidin-rich young fruits of persimmon (Diospyros kaki Thunb.) 査読

    Ayako Ikegami, Takashi Akagi, Daniel Potter, Masahiko Yamada, Akihiko Sato, Keizo Yonemori, Akira Kitajima, Kentaro Inoue

    PLANTA   230 ( 4 )   841 - 855   2009年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER  

    Fruits of persimmon (Diospyros kaki Thunb.) accumulate large amounts of proanthocyanidins (PAs) in the early stages of development. Astringent (A)-type fruits remain rich in soluble PAs even after they reach full-mature stage, whereas non-astringent (NA)-type fruits lose these compounds before full maturation. As a first step to elucidate the mechanism of PA accumulation in this non-model species, we used suppression subtractive hybridization to identify transcripts accumulating differently in young fruits of A- and NA-type. Interestingly, only a few clones involved in PA biosynthesis were identified in A-NA libraries. Represented by multiple clones were those encoding a novel 1-Cys peroxiredoxin and a new member of family 1 glycosyltransferases. Quantitative RT-PCR analyses confirmed correlation of the amount of PAs and accumulation of transcripts encoding these proteins in young persimmon fruits. Furthermore, the new family 1 glycosyltransferase was produced in Escherichia coli and shown to efficiently catalyze galactosylation at 3-hydroxyl groups of several anthocyanidins and flavonols. These findings suggest a complex mechanism of PA accumulation in persimmon fruits.

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  • Quantitative real-time PCR to determine allele number for the astringency locus by analysis of a linked marker in Diospyros kaki Thunb 査読

    Takashi Akagi, Shinya Kanzaki, Mai Gao, Ryutaro Tao, Dan E. Parfitt, Keizo Yonemori

    TREE GENETICS & GENOMES   5 ( 3 )   483 - 492   2009年7月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:SPRINGER HEIDELBERG  

    Persimmon (Diospyros kaki Thunb.) is a polyploidy fruit tree species of economic importance to East Asia. Natural astringency loss is an important trait in persimmon breeding programs. Quantitative real-time PCR was used to determine the number of AST/ast alleles for fruit astringency in persimmon (D. kaki Thunb.). To this end, the cultivar Jiro was transformed with one or two copies of a gene encoding NADP-dependent sorbitol-6-phosphate dehydrogenase (S6PDH), which was used as a standard for measuring the allele number of a sequenced marker tightly linked to the recessive ast locus for nonastringency. Primers for markers linked to the AST or ast allele were then used to measure the AST to ast ratio directly in the progeny of a full-sib cross. From determination of the AST to ast ratio and the results of the S6PDH copy number, the number of AST and ast alleles at the AST/ast locus was estimated. This research supported the hypothesis that D. kaki is a hexaploid with six AST and/or ast alleles. In addition to the determination of the allelic status of the AST locus, the application of real-time PCR for confirmation of the ploidy level and allelic composition of target genes in autopolyploids or allopolyploids was demonstrated.

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  • Construction of a Reliable PCR Marker for Selecting Pollination Constant and Non-Astringent (PCNA) Type Offspring among Breeding Population of Persimmon (Diospyros kaki Thunb.) 査読

    K. Yonemori, T. Akagi, S. Kanzaki

    I INTERNATIONAL SYMPOSIUM ON BIOTECHNOLOGY OF FRUIT SPECIES: BIOTECHFRUIT2008   839   625 - 629   2009年

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    記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)   出版者・発行元:INT SOC HORTICULTURAL SCIENCE  

    Pollination constant and non-astringent (PCNA) type persimmons, which lose their astringency naturally on the tree, are the most desirable for fresh fruit consumption. The trait of natural astringency-loss in PCNA type is recessive and controlled by a single locus, known as AST locus. Because PCNA type cultivars are of recent origin and exist only in a small number of cultivars, inbreeding depression resulting from repeated crosses among very few cultivars and/or selections is a major challenge facing the current breeding of new PCNA type cultivars. One solution to overcome this inbreeding depression is to include non-PCNA cultivars in the breeding project to extend the genetic pool by utilizing the wide diversity found in non-PCNA cultivars. However, to date, F-1 populations resulting from crosses between PCNA and non-PCNA type cultivars/selections have yielded only non-PCNA offspring. To obtain PCNA offspring, F-1 progeny needs to be backcrossed to PCNA type cultivars/selections. As persimmon is hexaploid, the obtainable rate of PCNA offspring in a backcross population is only 10-15%. Although we identified AFLP and RFLP markers tightly linked to the trait of natural astringency-loss in persimmon, these markers could not distinguish some non-PCNA progenies in other breeding populations. Previously, we demonstrated that RFLP markers derived from fosmid clones of D. lotus, diploid relatives of D. kaki, could be used to distinguish between PCNA and non-PCNA types of D. kaki, and established the possibility of extending this approach to PCR based markers. In this study, we describe the development of PCR-based markers derived from fosmid clones of D. kaki and D. lotus, and confirm their effectiveness across diverse progenies to select PCNA type.

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  • Analysis of Differentially Expressed Genes in Astringent Fruit Using Suppression Subtractive Hybridization 査読

    A. Ikegami, T. Akagi, K. Yonemori, M. Yamada, A. Kitajima

    IV INTERNATIONAL SYMPOSIUM ON PERSIMMON   833   151 - 156   2009年

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    記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)   出版者・発行元:INT SOC HORTICULTURAL SCIENCE  

    Persimmon fruit accumulates a quantity of proanthocyanidins (PAs) into "tannin cells" during development. In order to isolate genes involved in PA accumulation, suppression subtractive hybridization (SSH) libraries were constructed from astringent and non-astringent fruit as tester and driver populations for reciprocal SSH procedures. Three populations; (i) the fruit of F-1 individuals derived from the cross between Chinese and Japanese PCNA, (ii) BC1 individuals derived from the cross between F1 (Japanese PCNA x astringent cultivar) and Japanese PCNA, and (iii) astringency-removed fruit on the tree by ethanol treatment and untreated astringent fruit, were used for the SSH analysis. We identified several cDNA fragments which have similarity to flavonoid biosynthetic genes, such as PAL CHS, DFR and ANR. Additionally, we isolated gene fragments including F3GalTase, DHQ/SDH, SCPL, 1-CysPer and GST, which have not been identified for their role in PA biosynthesis. RNA gel blot analysis revealed that these genes were coincidentally expressed with PA accumulation during fruit development both in astringent and PCNA types. These genes, identified as being differentially expressed in astringent fruit by SSH, may help further study on the molecular mechanism of PA biosynthesis and its accumulation in tannin cells.

    Web of Science

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  • Phylogeny and cultivar development of Diospyros kaki: A survey based on molecular analyses 査読

    K. Yonemori, S. Kanzaki, C. Honsho, T. Akagi, D.E. Parfitt

    Advances in Horticultural Science   22 ( 4 )   261 - 268   2008年

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    記述言語:英語  

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書籍等出版物

  • 遺伝子から解き明かす性の不思議な世界 : 科学が明らかにした多様性と進化の仕組み

    田中, 実(生物学), 大久保, 範聡, 宮副, 大地, 伊藤, 道彦, 三浦, 郁夫, 松原, 和純, 戸張, 靖子, 金井, 克晃, 平松, 竜司, 菊水, 健史, 深見, 真紀, 勝間, 進, 赤木, 剛士, 菊池, 潔

    一色出版,悠書館 (発売)  2019年2月  ( ISBN:9784910389066

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    総ページ数:542p   記述言語:日本語

    CiNii Books

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MISC

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講演・口頭発表等

  • Plastic plant sex, orchestrated by epigenetic fluctuation 招待

    Takashi Akagi

    The 44th Annual Meeting of the Molecular Biology Society of Japan  2021年12月2日 

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    会議種別:口頭発表(招待・特別)  

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  • ヒトvs AI? ~植物研究者がゼロから始める ディープラーニングのススメ 招待

    赤木剛士

    明治大学農学部 特別講義  2021年10月21日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • 果樹作物のゲノムから紐解く 「植物の性」の成立と揺らぎの進化 招待

    赤木剛士

    明治大学農学部 特別講義  2021年10月21日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • 農林水産業における画像・ゲノム情報へのディープラーニング:AIとの協働研究 招待

    赤木剛士

    近畿大学アグリ技術革新研究所 第16回オープンセミナー  2021年10月15日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • 進化過程は設計図~進化的力学から見る植物における形質多様化の原動力 招待

    赤木剛士

    第38回日本植物バイオテクノロジー学会  2021年9月11日 

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    会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • Genomic behaviors triggering the convergent evolution of plants sexualities 招待

    Takashi Akagi

    IPSR Web Forum 2021  2021年9月6日 

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    会議種別:口頭発表(招待・特別)  

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  • 植物における 「性」の成立と揺らぎを駆動するゲノム進化 招待

    赤木剛士

    東京大学 第1365回生物科学セミナー  2021年7月14日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • Lineage-specific inventions of the sex in plants, triggered via independent gene/genome duplication events 招待

    Takashi Akagi

    Philosophical Transactions B Royal Society, Online Conference  2021年6月24日 

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    会議種別:口頭発表(基調)  

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  • ゲノム・遺伝子重複が駆動する新機能獲得を紐解く ~ 進化学・情報学・農学合わせワザ 招待

    赤木剛士

    麦学オンラインセミナー  2021年6月4日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • ヒト vs AI ? : 深層学習から見抜く植物の生理反応とゲノム情報のパターン 招待

    赤木剛士

    日本植物生理学会第62回  2021年3月14日 

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    会議種別:シンポジウム・ワークショップ パネル(公募)  

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  • 果樹のゲノム進化から紐解く「植物の性」 招待

    赤木剛士

    岡山バイオアクティブ研究会  2020年10月21日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • 植物における性の成立と多様化の分子進化 招待

    赤木剛士

    日本時間生物学会  2020年9月27日 

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    会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • 植物の性の成立と揺らぎ 招待

    赤木剛士

    神戸大学理学部特別講義  2019年12月13日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • Genome evolutions driving the sexual diversity and plasticity in plants 招待

    Takashi Akagi

    日本分子生物学会 第42回年会  2019年12月5日 

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    会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • 果樹ゲノムが紐解く植物の性の成立と進化 招待

    赤木剛士

    神戸大学農学部インタージェノミクスセミナー  2019年11月29日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • 作物における性の成立と進化 招待

    赤木剛士

    東京大学大学院農学生命科学研究科特別講義  2019年11月14日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • ディープラーニングによる青果物の品質評価や嗜好性の予測 招待

    赤木剛士

    果樹バイオテクノロジー研究会  2019年10月9日 

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    会議種別:口頭発表(基調)  

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  • 果樹ゲノムが紐解いた植物における性決定の進化 招待

    赤木剛士

    NGSデータ解析シンポジウム  2019年9月24日 

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    会議種別:口頭発表(基調)  

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  • ゲノム進化から紐解く植物の多様な性決定 招待

    赤木剛士

    日本遺伝学会第91回大会  2019年9月11日 

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    会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • Evolution of sexuality in tree crops 招待

    Takashi Akagi

    日本育種学会第136回講演会  2019年9月6日 

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    会議種別:口頭発表(招待・特別)  

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  • 進化とゲノムの有効活用:植物の性決定を紐解く 招待

    赤木剛士

    第二回植物インフォマティクス研究会  2019年9月2日 

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    会議種別:口頭発表(基調)  

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  • Evolution of the plant sexuality via independent genome/gene duplications 招待

    Takashi Akagi

    Botanical Seminar at University of Zurich  2019年6月28日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • Evolution of the plant sexuality, triggered by polyploidization 招待

    Takashi Akagi

    Invited seminar at Max Planck Institute Plant Breeding Research  2019年6月26日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • 植物における性の決定と進化 招待

    赤木剛士

    九州大学大学院システム情報科学研究院 特別講義  2019年5月21日 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • 柿における性決定の進化 招待

    赤木剛士

    京都植物バイテクシンポジウム  2019年5月16日 

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    会議種別:口頭発表(基調)  

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  • Wet研究者の視点から始める深層学習~画像診断と判断要因の可視化 招待

    赤木剛士

    日本植物生理学会第60回  2019年3月15日 

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    会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • カキから紐解く「性」の進化と多様化機構 招待

    赤木剛士

    日本植物生理学会第60回  2019年3月15日 

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    会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • Diversification of sexual system: insights from the persimmon genome 招待

    赤木 剛士

    The Society for Molecular Biology & Evolution 2018  2018年7月10日 

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    記述言語:英語   会議種別:口頭発表(基調)  

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  • キウイフルーツから紐解く性の進化 招待

    赤木 剛士

    イネ遺伝学・分子生物学ワークショップ2018  2018年7月5日 

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    会議種別:口頭発表(基調)  

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  • A Y-encoded sex determinant arose via linage-speicific duplication of a cytokinin response regulator in kiwifruit 招待

    赤木 剛士

    The 25th International Congress on Sexual Plant Reproduction  2018年6月16日 

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    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • Identification of the Y-encoded suppressor of feminization in kiwifruit. 招待

    赤木 剛士

    Plant and Animal Genome Conference XXV  2018年1月14日 

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    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • The persimmon genome unveils lineage-specific paleoduplication events driving diversification of sexual systems 招待

    赤木 剛士

    Plant and Animal Genome Conference XXV  2018年1月14日 

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    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • Rapid cis-evlution of a Y-encoded suppressor of feminization derived the dioecious sex determination inkiwifruits 招待

    赤木 剛士

    IX International Symposium on Kiwifruit  2017年9月6日 

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    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • Evolution of flexible sex determination system in polyploid persimmon 招待

    赤木 剛士

    XIX International Botanical Congress  2017年7月24日 

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    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • ゲノムから紐解く果樹作物の”性” 招待

    赤木 剛士

    NGS現場の会 第5回研究会  2017年5月23日 

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    会議種別:口頭発表(招待・特別)  

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  • 柿における性の成立と揺らぐ性への進化 招待

    赤木 剛士

    植物科学シンポジウム  2016年12月7日 

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    会議種別:口頭発表(招待・特別)  

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  • Evolution of a flexible sex determination system in polyploid persimmon 招待

    赤木 剛士

    Kyoto-Swiss Symposium 2016  2016年11月1日 

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    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • 木本性植物における性決定機構の多様性と一般性 招待

    赤木 剛士

    日本植物学会第80回大会  2016年9月16日 

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    会議種別:口頭発表(招待・特別)  

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  • カキ属の性決定を統御する転写因子 招待

    赤木 剛士

    園芸学会平成28年度秋季大会  2016年9月11日 

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    会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • カキ属植物における「柔軟な」性決定~遺伝的制御からエピジェネティック性への進化 招待

    赤木 剛士

    日本遺伝学会第88回大会  2016年9月8日 

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    会議種別:口頭発表(招待・特別)  

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  • Evolution of a flexible sex determination system in polyploid persimmon. 招待

    赤木 剛士

    Plant and Animal Genome Conference XXIII  2016年1月10日 

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    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • 「柿」でみつかった性決定因子が示す可能性 招待

    赤木 剛士

    日本植物学会第79回大会  2015年9月6日 

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    会議種別:口頭発表(招待・特別)  

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  • カキ属における性決定因子の同定 ~非モデル植物への全ゲノムワイド解析と進化遺伝学的アプローチ~ 招待

    赤木 剛士

    園芸学会平成27年度春季大会  2015年3月28日 

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    会議種別:口頭発表(基調)  

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  • 植物の性決定遺伝子 招待

    赤木剛士

    広島県立大学生命環境学部 大学院特別講義 

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    会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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受賞

  • 農学進歩賞

    2019年11月   日本農学会  

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  • 文部科学大臣表彰 若手科学者省

    2019年4月   文部科学省  

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共同研究・競争的資金等の研究

  • ゲノム・遺伝子倍化が駆動する植物分子の新機能の探索とデザイン

    2020年12月 - 2024年03月

    科学技術振興機構  JSTさきがけ 

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    担当区分:研究代表者 

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  • 果実ポストハーベスト研究のニューフロンティア-低温誘導成熟機構解明とその利用

    研究課題/領域番号:20H02977  2020年04月 - 2024年03月

    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)

    久保 康隆, 矢野 健太郎, 阿部 大吾, 加藤 雅也, 牛島 幸一郎, 赤木 剛士, 河井 崇

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    配分額:17810000円 ( 直接経費:13700000円 、 間接経費:4110000円 )

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  • 開花・性・花寿命を変える菌因子の特定

    研究課題/領域番号:20K06016  2020年04月 - 2023年03月

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

    藤田 尚子, 赤木 剛士

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    配分額:4290000円 ( 直接経費:3300000円 、 間接経費:990000円 )

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  • 作物科学研究へのパラダイムシフトを誘起するカキ属植物の研究加速化のための基盤形成

    研究課題/領域番号:20K20454  2019年06月 - 2025年03月

    日本学術振興会  科学研究費助成事業 挑戦的研究(開拓)  挑戦的研究(開拓)

    田尾 龍太郎, 岩田 洋佳, 赤木 剛士, 西山 総一郎, 山根 久代

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    配分額:26000000円 ( 直接経費:20000000円 、 間接経費:6000000円 )

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  • 大規模比較ゲノミクスによる木本性作物の性染色体進化解析

    2019年06月 - 2022年03月

    日本学術振興会  二国間交流事業 

    赤木剛士

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    担当区分:研究代表者 

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  • タイヌビエ多剤抵抗性の鍵となるシトクロムP450遺伝子の協調的発現制御機構の解明

    研究課題/領域番号:19H02955  2019年04月 - 2022年03月

    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)

    岩上 哲史, 赤木 剛士

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    配分額:17680000円 ( 直接経費:13600000円 、 間接経費:4080000円 )

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  • 植物における性表現の揺らぎを成立させる進化機構

    研究課題/領域番号:19H04862  2019年04月 - 2021年03月

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    赤木 剛士

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    配分額:9100000円 ( 直接経費:7000000円 、 間接経費:2100000円 )

    本研究では、六倍体の栽培ガキにおける「雌雄同株性」および「偶発的な両性花着花性」に着目し、本年は、1. GWAS解析による雌雄花の着生バランス決定要因の探索、2. 共発現ネットワーク解析による雄花から両性花の派生機構の解明、3. Y染色体性決定因子OGIを有さない個体群での偶発的な雄花着花機構の解明、の3点における研究を行った。
    1. に関して、交雑分離後代およびカキ品種群におけるGWAS解析から、幅広い品種間において共通する2つの雌雄バランス制御ゲノム領域の同定に至った。これらの領域にはヒストンリモデリング関連遺伝子が多く蓄積しており、既に報告されている栽培ガキのエピジェネティックな性表現制御 (Akagi et al. 2016) と関連する可能性が示唆された。
    2. に関して、カキ25品種における雌雄花・両性花分化時期のトランスクリプトーム解析データから、両性花が派生する特異的な条件として、雄花にストレスシグナル、特にエチレン・ABAに関連する発現制御が重要な役割を担っている可能性が示唆された。これらの植物ホルモンの外的処理を含む共発現ネットワーク解析より、これらのストレスシグナルを統御して雄花における雌器官形成促進を担う因子候補として、シロイヌナズナのNAGTHA1オーソログが同定された。
    3. に関して、制決定遺伝子OGIを有さないカキ品種西条において、出雲地域で頻出する雄花着花系統について、雄花形成過程およびその原因として、全ゲノムワイドなDNAメチレーションレベルの揺らぎがOGIの標的遺伝子であるメス化統御因子MeGIに及ぶことで、MeGIの発現抑制が偶発的に生じ、遺伝的因子を持たなくても雄花を着花できる「非正規」な制御系の同定に至った。

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  • カキの果実形状多様性を制御する全ゲノムワイドモデルの構築

    研究課題/領域番号:18H02199  2018年04月 - 2022年03月

    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)

    赤木 剛士

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    配分額:16510000円 ( 直接経費:12700000円 、 間接経費:3810000円 )

    カキ品種192品種およびカキ属近縁野生種3種に対して、ddRAD-Seqベースの全ゲノムジェノタイピングを行った。栽培ガキは同質六倍体であるため、遺伝子型決定に倍数体用の基準を設け、二値および量的遺伝子型を決定した。このデータをもとに集団遺伝学的視点からPCAやSTRUCTUREなどを用いた集団構造解析・野生種-栽培種間の遺伝子流入の検定を行い、同時に、果実成熟期およびフーリエ記述子の主成分得点によって表現した果実形値と連関した遺伝子座を同定するための二値ジェノタイプを用いたrrBRUPによるGWAS解析、および量値ジェノタイプを用いたピアソン線形相関解析を行った。
    カキ品種群において、遺伝子型に関して二値・量値間での集団構造解析の結果に大きな差異はなかった。品種群の分化に顕著な構造化は見られなかったが、完全甘ガキ品種群に共通した遺伝的要因が潜在している可能性が示唆され、単一のクラスターを形成していた。得られた集団構造データによる補正の元、二値ジェノタイプによるGWAS解析を行った結果、果実縦形および成熟期に関して有意に連関する遺伝子座が得られた。さらに、量値ジェノタイプと果実形値間における線形相関解析より、GWAS解析とは独立したピークが得られ、これはアレルの量依存的に果実縦形に関与する遺伝子座であることが示唆された。このようなアレル量依存形質は倍数体に特異な特徴であり、カキ属の進化において、六倍体の栽培ガキが特異的に有する果実形多様性の獲得に寄与する因子である可能性が考えられた。

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  • サクラ属植物における種間交雑障壁の特性化と打破

    研究課題/領域番号:17K19265  2017年06月 - 2019年03月

    日本学術振興会  科学研究費助成事業 挑戦的研究(萌芽)  挑戦的研究(萌芽)

    赤木 剛士, 北村 祐人, 森本 拓也

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    配分額:5980000円 ( 直接経費:4600000円 、 間接経費:1380000円 )

    本研究ではウメ・スモモ間の交雑を対象として、種間交雑時に生じる交雑不稔性の原因究明を目指した。この種間交雑においては後代系統において雄性不稔性を生じるため、本研究では、ウメ品種「地蔵梅」スモモ品種「ソルダム」とその交雑系統であるスモモウメ一号をモデルとして、葯の経時的形態観察、トランスクリプトーム解析およびメチローム解析を行った。
    スモモウメ一号では両親系統では見られないタペート層の生育異常が見られ、花粉稔性に必須であるタペート層の崩壊が生じなかった。この原因として、オルガネラゲノムの発現バランス異常、および非相加的調節遺伝子の発現が関与している可能性が示された。

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  • 胚乳における種の障壁:エピゲノム制御の鍵分子機構

    研究課題/領域番号:16H06471  2016年06月 - 2021年03月

    日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型)  新学術領域研究(研究領域提案型)

    木下 哲, 赤木 剛士

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    配分額:115960000円 ( 直接経費:89200000円 、 間接経費:26760000円 )

    植物の生殖過程では、「他の植物種と交雑することなく自らのゲノムの維持するシステム」が生殖障壁として機能している。このシステムは、受精に至る多段階に配置される「鍵と鍵穴」の分子認証の総体として捉えることができる。興味深いことに、受精前の分子認証を突破した場合でも、受精後の胚乳において、極めて鋭敏な異種ゲノムを感知する分子認証システムが配置されている。ここでは、両親ゲノムの塩基配列レベルの違いのみならず、可塑性の高いエピジェネティックな制御機構が重要な位置をしめていることを、我々は科研費を中心とした研究費支援により一連の分子機構を明らかにしてきた。本研究計画では、植物新種誕生原理の解明のため、(1)受精後の胚乳の生殖障壁をエピジェネティックに誘導するDNA脱メチル化の役割と(2)受精後の胚乳が自らを崩壊させることにより異種ゲノムを排除する機構を明らかにすることを目的とする。

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  • 果実発育・成熟関連遺伝子の完全長cDNA配列と選択的スプライシングの網羅的解析

    研究課題/領域番号:16K14854  2016年04月 - 2018年03月

    日本学術振興会  科学研究費助成事業 挑戦的萌芽研究  挑戦的萌芽研究

    牛島 幸一郎, 門田 有希, 赤木 剛士

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    配分額:3640000円 ( 直接経費:2800000円 、 間接経費:840000円 )

    第3世代の次世代シークエンサーの普及により,ゲノム解読だけではなく転写産物の解読に利用されている.本研究ではメロン果実のIso-seq解析を行い,完全長cDNA配列と選択的スプライシングについて解析を行った.3つの異なる方法で完全長cDNA配列ライブラリーを構築し,PacBioとNanoporeを用いて配列解読を行った.得られたIsoformをメロンゲノムにマッピングして比較した結果,PacBioの解読では 約6,500遺伝子座,Nanoporeの解読では12,000の遺伝子座からの転写産物が得られた.そのうち,509遺伝子座が新規の遺伝子座であった.

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  • カキ属をモデルとした環境応答性の性表現多様化機構の解明

    2015年12月 - 2019年03月

    科学技術振興機構  JSTさきがけ 

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    担当区分:研究代表者 

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  • バラ科サクラ属に特異な自家不和合性認識機構とその進化遺伝学的な成立過程の解明

    研究課題/領域番号:15H02431  2015年04月 - 2019年03月

    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)

    田尾 龍太郎, 赤木 剛士

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    配分額:41990000円 ( 直接経費:32300000円 、 間接経費:9690000円 )

    本研究は,バラ科サクラ属に特異なS-RNase依存性配偶体型自家不和合性の成立過程ならびにその特異な不和合性認識機構の分子基盤の解明を試みたものであり,以下の結果を得た.1)サクラ属の花粉SであるF-box遺伝子(SFB)は,バラ科リンゴ亜連,ナス科,オオバコ科植物の花粉S遺伝子のF-box遺伝子とは異なる進化を遂げており,これがサクラ属特異な自家不和合性機構の確立を駆動した可能性を示した.2)生化学的な実験から,サクラ属のS遺伝子座近傍に座乗する花粉発現のF-box遺伝子(SLFLs)がサクラ属の不和合性認識モデルの中で重要な役割を果たすジェネラルインヒビターである可能性を示した.

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  • カキ属のゲノム倍化に伴う重要形質多様化機構の解明

    研究課題/領域番号:15K14654  2015年04月 - 2017年03月

    日本学術振興会  科学研究費助成事業 挑戦的萌芽研究  挑戦的萌芽研究

    赤木 剛士

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    配分額:3900000円 ( 直接経費:3000000円 、 間接経費:900000円 )

    本研究では主に、二倍体カキ属野生種と六倍体の栽培ガキの性表現の変化に着目し研究を行った。二倍体種は基本的に明確な雌雄異株性を示すのに対し、六倍体栽培ガキは雌雄の両者が同一の個体に着花する個体が現れ、より柔軟な性表現を示す。調査の結果、カキ属の性決定遺伝子であるsmall-RNAをコードする「OGI」の発現が、六倍体種ではSINE様配列によって抑制されており、その代わりに、OGIの標的となるMeGIのプロモーター領域におけるDNAメチル化が花単位の性決定の鍵因子であることを明らかにした。さらに栽培ガキの倍数化においてOGIに挿入されたSINE様配列への強い選抜が生じていることが明らかになった。

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  • カキ果実の生育・成熟機構に関する全ゲノムワイドモデルの構築

    研究課題/領域番号:26712005  2014年04月 - 2018年03月

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

    赤木 剛士

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    配分額:22620000円 ( 直接経費:17400000円 、 間接経費:5220000円 )

    本研究ではカキの果実形状における品種間多様性を量的に評価する手法を確立して果実の形状発達パターンを特性化するとともに、形状決定に寄与する遺伝的要因の同定を目指した。
    SHAPEソフトウエアにより、カキ品種間における果実の複雑形状を幾つかの主要な成分へと展開し、その変化パターンを数値化した。カキ果実の形状決定時期においてトランスクリプトームデータと果実形状変化パターンの相関解析や共発現ネットワーク解析を行い、カキ品種・分離後代間に共通する果実形状決定遺伝子候補や、その分子経路を特定した。

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  • ゲノミクス・トランスクリプトミクス的アプローチによる異形花型不和合性の機構解明

    研究課題/領域番号:25292023  2013年04月 - 2017年03月

    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)

    牛島 幸一郎, 鈴木 孝征, 赤木 剛士, 池田 和生

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    配分額:18980000円 ( 直接経費:14600000円 、 間接経費:4380000円 )

    異形花型自家不和合性(HetSI)は自己花粉を排除する自家不和合性形質と花の形(花型)と連鎖した現象である.アマ科植物のHetSIの機構解明のために原因遺伝子であるS遺伝子候補の単離とS遺伝子座領域の解析を行った.トランスクリプトームの解析からは,あらたに4つの候補遺伝子の単離に成功した.ゲノム解析からS遺伝子座領域が1Mbp以上にわたることを明らかとした.すべての候補遺伝子はこの領域に含まれるが,その相対的な配置は明らかになっていない.そこで,ベニバナアマのゲノム配列を明らかにするためにショットガンシークエンシングとde novo assemblyを行い,今後の新たな研究基盤を構築した.

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  • MADS-box転写因子を介したバラ科サクラ属果樹の休眠制御機構の解明

    研究課題/領域番号:23380017  2011年04月 - 2015年03月

    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)

    山根 久代, 田尾 龍太郎, 羽生 剛, 赤木 剛士, 長山 枝里香, 保坂 友香里, 佐々木 隆太, 竹内 希

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    配分額:16510000円 ( 直接経費:12700000円 、 間接経費:3810000円 )

    永年生温帯落葉果樹の1年のライフサイクルを制御する重要な生理現象のひとつが休眠である。本研究では、サクラ属果樹の自発休眠に関わる主導遺伝子の単離を目的とし、ウメを材料に454-pyrosequencing法を利用したEST解析をおこなった。その結果、先行研究で単離したPmDAM6遺伝子に加えて、PmDAM4, PmDAM5遺伝子が自発休眠芽で多く発現する遺伝子として単離された。DAM遺伝子は低温に遭遇しなければ発現が低下しないこと、特にPmDAM4,5,6は品種特異的な低温要求量に遭遇することで発現が低下することが明らかとなり、ウメの低温要求性制御に重要な役割を担っていることが示唆された。

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  • モモ亜属の栽培化に伴うゲノム進化機構の解明

    研究課題/領域番号:23880013  2011年

    日本学術振興会  科学研究費助成事業 研究活動スタート支援  研究活動スタート支援

    赤木 剛士

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    配分額:1690000円 ( 直接経費:1300000円 、 間接経費:390000円 )

    モモ亜属(Amygdalus subgenus)の植物96種に対して約9000ローカスのSNPsタイピングを行い,全ゲノムワイドな遺伝的構造解析を行った.現在の栽培モモ品種群は,野生品種とは明らかに異なる,歴史的な人為的選抜を受けた複数のクラスター群を形成する事が示唆された.クラスター間における多様性度の推移を比較することにより,各クラスターに特徴的なゲノム部分領域へのselective sweepを検出した.観賞用ハナモモ,および主要食用モモのクラスターにおいて,特定のゲノム領域に人為的選択圧が見られ,それぞれのクラスターの特徴と非常に関連性の考えられる遺伝子群が存在していた.これらの遺伝子は各モモ品種群の特徴を維持し,栽培化の原動力となった重要遺伝子であると考えられた.

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  • カキの甘渋性に関する研究

    研究課題/領域番号:09J02989  2009年 - 2010年

    日本学術振興会  科学研究費助成事業 特別研究員奨励費  特別研究員奨励費

    赤木 剛士

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    配分額:1400000円 ( 直接経費:1400000円 )

    カキ(Diospyros kaki)果実の渋味成分であるプロアントシアニジン(PA)蓄積制御機構の解明を目的とし,完全甘ガキ(PCNA)と非完全甘ガキ(non-PCNA)間の甘渋性形質の発現差異を決定する要因についての検討を行った。今年度はカキ果実内においてPA合成制御遺伝子群を総括的に統御する単一の転写因子であるDkMyb4の発現制御機構に関わる環境因子の特定を目指し、季節的な外気温シグナル、および外気温と連動したカキ果実のアブシシン酸(ABA)とそれに関与したシグナリング因子群によってカキ果実内部のDkMyb4の発現調節が行われる事を示唆した。また、そのシグナリング経路における律速因子となるbZIP転写因子DkbZIP5を同定し、この遺伝子がカキにおいてABAシグナル依存的にDkMyb4を制御する基礎的分子機構を解明した.これらの知見はこれまでに分子生物学的観点からの解析の少ない植物の特定器官におけるPA蓄積制御機構についても寄与するものであり、基礎生物学的にも価値の高いものである。
    また、本研究では順遺伝学的アプローチによりPCNA/non-PCNAのPA蓄積差異を遺伝的に決定するAST遺伝子座の同定を目指した。今年度はreal-time PCRを用いた量的遺伝子型決定法に基づき、六倍体であるカキのAST遺伝子座を含む染色体群の詳細な遺伝様式を明らかにするとともに、その知見を利用してカキと二倍体近縁種(Diospyros lotus)間における比較ゲノム解析によってAST遺伝子座の存在領域を特定し、候補遺伝子の同定に成功した。

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  • 研究科目演習2 (2021年度) 3・4学期  - その他

  • 農産物利用学演習 (2021年度) 前期  - その他

  • 農産物利用学演習 (2021年度) 後期  - その他

  • 農産物利用学演習 (2021年度) 後期  - その他

  • 農産物利用学演習 (2021年度) 前期  - その他

  • 農産物利用学1 (2021年度) 第3学期  - 金3,金4

  • 農産物利用学2 (2021年度) 第4学期  - 金3,金4

  • 青果物保蔵生理学 (2021年度) 後期  - その他

  • コース演習3 (2020年度) 1・2学期  - その他

  • コース演習3 (2020年度) 1・2学期  - その他

  • コース演習4 (2020年度) 3・4学期  - その他

  • コース演習4 (2020年度) 3・4学期  - その他

  • 卒業論文 (2020年度) 1~4学期  - その他

  • 卒業論文 (2020年度) 1~4学期  - その他

  • 生物情報処理学特論 (2020年度) 前期  - 金3,金4

  • 生物生産科学特別研究 (2020年度) 通年  - その他

  • 研究科目演習1 (2020年度) 1・2学期  - その他

  • 研究科目演習1 (2020年度) 1・2学期  - その他

  • 研究科目演習2 (2020年度) 3・4学期  - その他

  • 研究科目演習2 (2020年度) 3・4学期  - その他

  • 農産物利用学演習 (2020年度) 前期  - その他

  • 農産物利用学演習 (2020年度) 後期  - その他

  • 農産物利用学演習 (2020年度) 後期  - その他

  • 農産物利用学演習 (2020年度) 前期  - その他

  • 農産物利用学1 (2020年度) 第3学期  - 金3,金4

  • 農産物利用学2 (2020年度) 第4学期  - 金3,金4

  • 青果物保蔵生理学 (2020年度) 後期  - その他

▼全件表示