Updated on 2024/05/01

写真a

 
AKAGI Takashi
 
Organization
Faculty of Environmental, Life, Natural Science and Technology Professor
Position
Professor
Contact information
メールアドレス
External link

Degree

  • PhD in Agricultural Science ( 2011.3   Kyoto University )

  • 博士(農学) ( 京都大学 )

  • 修士(農学) ( 京都大学 )

Research Areas

  • Environmental Science/Agriculture Science / Horticultural science

  • Life Science / Plant molecular biology and physiology

  • Life Science / Evolutionary biology

 

Papers

  • Rapid and dynamic evolution of a giant Y chromosome inSilene latifolia

    Takashi Akagi, Naoko Fujita, Kanae Masuda, Kenta Shirasawa, Kiyotaka Nagaki, Ayano Horiuchi, Eriko Kuwada, Riko Kunou, Koki Nakamura, Yoko Ikeda, Koichiro Ushijima, Deborah Charlesworth

    2023.9

  • Ongoing Rapid Evolution of a Post-Y Region Revealed by Chromosome-Scale Genome Assembly of a Hexaploid Monoecious Persimmon (Diospyros kaki). International journal

    Ayano Horiuchi, Kanae Masuda, Kenta Shirasawa, Noriyuki Onoue, Naoko Fujita, Koichiro Ushijima, Takashi Akagi

    Molecular biology and evolution   40 ( 7 )   2023.7

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

    Plants have evolved sex chromosomes independently in many lineages, and loss of separate sexes can also occur. In this study, we assembled a monoecious recently hexaploidized persimmon (Diospyros kaki), in which the Y chromosome has lost the maleness-determining function. Comparative genomic analysis of D. kaki and its dioecious relatives uncovered the evolutionary process by which the nonfunctional Y chromosome (or Ymonoecy) was derived, which involved silencing of the sex-determining gene, OGI, approximately 2 million years ago. Analyses of the entire X and Ymonoecy chromosomes suggested that D. kaki's nonfunctional male-specific region of the Y chromosome (MSY), which we call a post-MSY, has conserved some characteristics of the original functional MSY. Specifically, comparing the functional MSY in Diospyros lotus and the nonfunctional "post-MSY" in D. kaki indicated that both have been rapidly rearranged, mainly via ongoing transposable element bursts, resembling structural changes often detected in Y-linked regions, some of which can enlarge the nonrecombining regions. The recent evolution of the post-MSY (and possibly also MSYs in dioecious Diospyros species) therefore probably reflects these regions' ancestral location in a pericentromeric region, rather than the presence of male-determining genes and/or genes controlling sexually dimorphic traits.

    DOI: 10.1093/molbev/msad151

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  • Application of deep learning diagnosis for multiple traits sorting in peach fruit

    Kanae Masuda, Rika Uchida, Naoko Fujita, Yoshiaki Miyamoto, Takahiro Yasue, Yasutaka Kubo, Koichiro Ushijima, Seiichi Uchida, Takashi Akagi

    Postharvest Biology and Technology   201   112348 - 112348   2023.7

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

    DOI: 10.1016/j.postharvbio.2023.112348

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  • A leaf-emanated signal orchestrates grain size and number in response to maternal resources. Reviewed International journal

    Kim Nhung Ta, Sae Shimizu-Sato, Ayumi Agata, Yuri Yoshida, Ken-Ichiro Taoka, Hiroyuki Tsuji, Takashi Akagi, Yasuhiro Tanizawa, Ryosuke Sano, Misuzu Nosaka-Takahashi, Toshiya Suzuki, Taku Demura, Atsushi Toyoda, Yasukazu Nakamura, Yutaka Sato

    The Plant journal : for cell and molecular biology   115 ( 1 )   175 - 189   2023.7

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

    In plants, variations in seed size and number are outcomes of different reproductive strategies. Both traits are often environmentally influenced, suggesting that a mechanism exists to coordinate these phenotypes in response to available maternal resources. Yet, how maternal resources are sensed and influence seed size and number is largely unknown. Here, we report a mechanism that senses maternal resources and coordinates grain size and number in the wild rice Oryza rufipogon, a wild progenitor of Asian cultivated rice. We showed that FT-like 9 (FTL9) regulates both grain size and number and that maternal photosynthetic assimilates induce FTL9 expression in leaves to act as a long-range signal that increases grain number and reduces size. Our findings highlight a strategy that benefits wild plants to survive in a fluctuating environment. In this strategy, when maternal resources are sufficient, wild plants increase their offspring number while preventing an increase in offspring size by the action of FTL9, which helps expand their habitats. In addition, we found that a loss-of-function allele (ftl9) is prevalent among wild and cultivated populations, offering a new scenario in the history of rice domestication.

    DOI: 10.1111/tpj.16219

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  • Genetic basis of lineage-specific evolution of fruit traits in hexaploid persimmon. International journal

    Ayano Horiuchi, Kanae Masuda, Kenta Shirasawa, Noriyuki Onoue, Ryusuke Matsuzaki, Ryutaro Tao, Yasutaka Kubo, Koichiro Ushijima, Takashi Akagi

    DNA research : an international journal for rapid publication of reports on genes and genomes   2023.6

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    Frequent polyploidization events in plants have led to the establishment of many lineage-specific traits representing each species. Little is known about the genetic bases for these specific traits in polyploids, presumably due to plant genomic complexity and their difficulties of applying genetic approaches. Hexaploid Oriental persimmon (Diospyros kaki) has evolved specific fruit characters, including wide variations in fruit shapes and astringency. In this study, using whole-genome diploidized/quantitative genotypes from ddRAD-Seq data of 173 persimmon cultivars, we examined their population structures and potential correlations between their structural transitions and variations in nine fruit traits. The population structures of persimmon cultivars were highly randomized and not substantially correlated with the representative fruit traits focused on in this study, except for fruit astringency. With genome-wide association analytic tools considering polyploid alleles, we identified the loci associated with the nine fruit traits; we mainly focused on fruit-shape variations, which have been numerically characterized by principal component analysis of elliptic Fourier descriptors. The genomic regions that putatively underwent selective sweep exhibited no overlap with the loci associated with these persimmon-specific fruit traits. These insights will contribute to understanding of the genetic mechanisms by which fruit traits are independently established, possibly due to polyploidization events.

    DOI: 10.1093/dnares/dsad015

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  • Transcriptomic interpretation on explainable AI-guided intuition uncovers premonitory reactions of disordering fate in persimmon fruit.

    Kanae Masuda, Eriko Kuwada, Maria Suzuki, Tetsuya Suzuki, Takeshi Niikawa, Seiichi Uchida, Takashi Akagi

    Plant & cell physiology   2023.5

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    Deep neural network (DNN) techniques, as an advanced machine learning framework, have allowed various image diagnoses in plants, which often achieve better prediction performance than human experts in each specific field. Notwithstanding, in plant biology, the application of deep neural networks is still mostly limited to rapid and effective phenotyping. Recent development of explainable CNN frameworks has allowed visualization of the features in the prediction by convolutional neural network (CNN), which potentially contributes to the understanding of physiological mechanisms in objective phenotypes. In this study, we propose an integration of explainable CNN and transcriptomic approach to make a physiological interpretation of a fruit internal disorder in persimmon, rapid over-softening. We constructed CNN models to accurately predict the fate to be rapid softening in persimmon cv. Soshu, only with photo images. The explainable CNNs, such as Grad-CAM and Guided Grad-CAM, visualized specific featured regions relevant to the prediction of rapid-softening, which would correspond to the premonitory symptoms in a fruit. Transcriptomic analyses to compare the featured regions of predicted rapid-softening and control fruits suggested that rapid softening is triggered by precocious ethylene signal-dependent cell wall modification, despite exhibiting no direct phenotypic changes. Further transcriptomic comparison between the featured and non-featured regions in predicted rapid-softening fruit suggested that premonitory symptoms reflected hypoxia and the related stress signals finally to induce ethylene signals. These results would provide a good example for the collaboration of image analysis and omics approaches in plant physiology, which uncovered a novel aspect of fruit premonitory reactions in the rapid softening fate.

    DOI: 10.1093/pcp/pcad050

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  • Evolution of sex in crops: recurrent scrap and rebuild.

    Kanae Masuda, Takashi Akagi

    Breeding science   73 ( 2 )   95 - 107   2023.4

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    Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.

    DOI: 10.1270/jsbbs.22082

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  • Recurrent neo-sex chromosome evolution in kiwifruit

    Takashi Akagi, Erika Varkonyi-Gasic, Kenta Shirasawa, Andrew Catanach, Isabelle M. Henry, Daniel Mertten, Paul Datson, Kanae Masuda, Naoko Fujita, Eriko Kuwada, Koichiro Ushijima, Kenji Beppu, Andrew C. Allan, Deborah Charlesworth, Ikuo Kataoka

    Nature Plants   2023.3

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    Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1038/s41477-023-01361-9

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    Other Link: https://www.nature.com/articles/s41477-023-01361-9

  • 1-Methylcyclopropene Pretreatment in ‘La France’ Pears to Extend Postharvest Life and Maximize Fruit Quality Reviewed

    Abdul H. Kazimi, Oscar W. Mitalo, Azimullah Azimi, Kanae Masuda, Chikara Yano, Takashi Akagi, Koichiro Ushijima, Yasutaka Kubo

    2023.1

  • ウメの青果流通期間拡大に向けた台湾ウメ,日本ウメの収穫後果実の低温応答と1-MCP処理効果の調査

    Tomoaki Kashiwamoto, Takashi Kawai, Takaaki Oe, Yasuhisa Tsuchida, Chikara Yano, Maqsood Muqadas, Takashi Akagi, Fumio Fukuda, Yasutaka Kubo, Koichiro Ushijima

    Horticultural Research (Japan)   22 ( 4 )   303 - 311   2023

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    Publishing type:Research paper (scientific journal)   Publisher:Japanese Society for Horticultural Science  

    DOI: 10.2503/hrj.22.303

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  • Deep Learning on Images and Genetic Sequences in Plants: Classifications and Regressions

    Kanae Masuda, Takashi Akagi

    Plant Omics   224 - 233   2022.12

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    Publishing type:Part of collection (book)   Publisher:CABI  

    DOI: 10.1079/9781789247534.0017

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  • Polyploidy before and after domestication of crop species. International journal

    Takashi Akagi, Katharina Jung, Kanae Masuda, Kentaro K Shimizu

    Current opinion in plant biology   69   102255 - 102255   2022.10

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    Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species.

    DOI: 10.1016/j.pbi.2022.102255

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  • Sexual System and Its Evolution

    Kanae Masuda, Takashi Akagi

    Compendium of Plant Genomes   97 - 107   2022.9

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    Publishing type:Part of collection (book)   Publisher:Springer International Publishing  

    DOI: 10.1007/978-3-031-05584-3_8

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  • Effect of storage temperature on development of chilling injury and its transcriptome analysis in ‘Fuyu’ persimmon fruit with or without 1-MCP treatment

    T. Furuta, O.W. Mitalo, T. Otsuki, R. Okada, K. Ohashi, K. Masuda, T. Akagi, K. Ushijima, R. Nakano, Y. Kubo

    Acta Horticulturae   ( 1338 )   343 - 350   2022.4

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    Publishing type:Research paper (scientific journal)   Publisher:International Society for Horticultural Science (ISHS)  

    DOI: 10.17660/actahortic.2022.1338.49

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

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

    The Plant cell   34 ( 6 )   2174 - 2187   2022.3

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    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. International journal

    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   2022.3

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    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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  • The effect of layer-by-layer edible coating on the shelf life and transcriptome of ‘Kosui’ Japanese pear fruit Reviewed

    Natsuki Hira, Oscar W. Mitalo, Rui Okada, Momoka Sangawa, Kanae Masuda, Naoko Fujita, Koichiro Ushijima, Takashi Akagi, Yasutaka Kubo

    Postharvest Biology and Technology   185   111787 - 111787   2022.3

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    Publishing type:Research paper (scientific journal)   Publisher:Elsevier {BV}  

    DOI: 10.1016/j.postharvbio.2021.111787

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

    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   2022.1

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    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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  • Examining the Role of Low Temperature in Satsuma Mandarin Fruit Peel Degreening via Comparative Physiological and Transcriptomic Analysis. International journal

    Oscar W Mitalo, William O Asiche, Seung W Kang, Hiroshi Ezura, Takashi Akagi, Yasutaka Kubo, Koichiro Ushijima

    Frontiers in plant science   13   918226 - 918226   2022

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    Peel degreening is the most conspicuous aspect of fruit ripening in many citrus fruits because of its importance for marketability. In this study, peel degreening in response to propylene (an ethylene analog) and at varying storage temperatures was characterized in Satsuma mandarin (Citrus unshiu Marc.) fruit. Propylene treatment triggered rapid peel degreening (within 4-6 days), indicated by an increase in the citrus color index (CCI) and chlorophyll loss. Peel degreening was also observed in fruit at 10°C and 15°C after 28-42 days, with gradual CCI increase and chlorophyll reduction. However, fruit at 5°C, 20°C, and 25°C remained green, and no substantial changes in peel CCI and chlorophyll content were recorded during the 42-day storage duration. The transcriptomes of peels of fruit treated with propylene for 4 days and those stored at varying temperatures for 28 days were then analyzed by RNA-Seq. We identified three categories of differentially expressed genes that were regulated by (i) propylene (and by analogy, ethylene) alone, (ii) low temperature (5°C, 10°C, or 15°C vs. 25°C) alone, and (iii) either propylene or low temperature. Gene-encoding proteins associated with chlorophyll degradation (such as CuSGR1, CuNOL, CuACD2, CuCAB2, and CuLHCB2) and a transcription factor (CuERF114) were differentially expressed by propylene or low temperature. To further examine temperature-induced pathways, we also monitored gene expression during on-tree fruit maturation vs. postharvest. The onset of on-tree peel degreening coincided with autumnal drops in field temperatures, and it was accompanied by differential expression of low temperature-regulated genes. On the contrary, genes that were exclusively regulated by propylene (such as CuCOPT1 and CuPOX-A2) displayed insignificant expression changes during on-tree peel degreening. These findings indicate that low temperatures could be involved in the fruit ripening-related peel degreening independently of ethylene.

    DOI: 10.3389/fpls.2022.918226

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  • Deep Learning Predicts Rapid Over-softening and Shelf Life in Persimmon Fruits

    Maria Suzuki, Kanae Masuda, Hideaki Asakuma, Kouki Takeshita, Kohei Baba, Yasutaka Kubo, Koichiro Ushijima, Seiichi Uchida, Takashi Akagi

    Horticulture Journal   91 ( 3 )   408 - 415   2022

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    In contrast to the progress in the research on physiological disorders relating to shelf life in fruit crops, it has been difficult to non-destructively predict their occurrence. Recent high-tech instruments have gradually enabled non-destructive predictions for various disorders in some crops, while there are still issues in terms of efficiency and costs. Here, we propose application of a deep neural network (or simply deep learning) to simple RGB images to predict a severe fruit disorder in persimmon, rapid over-softening. With 1,080 RGB images of ‘Soshu’ persimmon fruits, three convolutional neural networks (CNN) were examined to predict rapid over-softened fruits with a binary classification and the date to fruit softening. All of the examined CNN models worked successfully for binary classification of the rapid over-softened fruits and the controls with > 80% accuracy using multiple criteria. Furthermore, the prediction values (or confidence) in the binary classification were correlated to the date to fruit softening. Although the features for classification by deep learning have been thought to be in a black box by conventional standards, recent feature visualization methods (or “explainable” deep learning) has allowed identification of the relevant regions in the original images. We applied Grad-CAM, Guided backpropagation, and layer-wise relevance propagation (LRP), to find early symptoms for CNNs classification of rapid over-softened fruits. The focus on the relevant regions tended to be on color unevenness on the surface of the fruit, especially in the peripheral regions. These results suggest that deep learning frameworks could potentially provide new insights into early physiological symptoms of which researchers are unaware.

    DOI: 10.2503/hortj.UTD-323

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

    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   2021.5

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    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

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    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. International journal

    Raffaele Testolin, Sarah M Pilkington, Takashi Akagi

    Frontiers in plant science   12   719588 - 719588   2021

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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   2020.12

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

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

    The Plant Journal   104 ( 6 )   1551 - 1567   2020.10

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    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.

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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   2020.8

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    <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.

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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   2020.8

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    © 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.

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

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

    Nature   584 ( 7819 )   109 - 114   2020.8

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    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.

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

    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 )   2020.6

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    <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.

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  • Correction: The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. Reviewed International journal

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

    PLoS genetics   16 ( 5 )   e1008845   2020.5

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

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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   2020.2

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    <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.

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  • The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. Reviewed International journal

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

    PLoS genetics   16 ( 2 )   e1008566   2020.2

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    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.

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  • Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon. International journal

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

    Frontiers in plant science   11   567249 - 567249   2020

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    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.

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

    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   158   110949 - 110949   2019.12

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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   2019.11

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    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.

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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   2019.10

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    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.

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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   2019.9

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  • Two Y-encoded genes determine sex in kiwifruit Reviewed International journal

    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   2019.8

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    Dioecy, the presence of male and female individuals, has evolved independently in multiple flowering plant lineages1-3. Although theoretical models for the evolution of dioecy, such as the 'two-mutations' model, are well established4,5, little is known about the specific genes determining sex and their evolutionary history3. Kiwifruit, a major tree crop consumed worldwide, is a dioecious species. In kiwifruit we previously identified a Y-encoded sex-determinant candidate gene acting as the suppressor of feminization (SuF), named Shy Girl (SyGI)6. Here, we identify a second Y-encoded sex-determinant that we named Friendly Boy (FrBy), which exhibits strong expression in tapetal cells. Gene-editing and complementation analyses in Arabidopsis thaliana and Nicotiana tabacum indicated that FrBy acts for the maintenance of male (M) functions, independently of SyGI, and that these functions are conserved across angiosperm species. We further characterized the genomic architecture of the small (<1 megabase pairs (Mb)) male-specific region of the Y chromosome (MSY), which harbours only two genes expressed extensively in developing gynoecia and androecia, respectively: SyGI and FrBy. Re-sequencing of the genome of a natural hermaphrodite kiwifruit revealed that this individual is genetically male but carries deletion(s) of parts of the Y chromosome, including SyGI. Additionally, expression of FrBy in female kiwifruit resulted in hermaphrodite plants. These results clearly indicate that Y-encoded SyGI and FrBy act independently as the SuF and M factors in kiwifruit, respectively, and provide insight into not only the evolutionary path leading to a two-factor sex-determination system, but also a new breeding approach for dioecious species.

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

    Yang HW, Akagi T, Kawakatsu T, Tao R

    The Plant journal : for cell and molecular biology   98 ( 1 )   97 - 111   2019.4

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    Separating male and female sex organs is one of the main strategies used to maintain genetic diversity within a species. However, the genetic determinants and their regulatory mechanisms have been identified in only a few species. In dioecious persimmons, the homeodomain transcription factor, MeGI, which is the target of a Y chromosome-encoded small-RNA, OGI, can determine floral sexuality. The basic features of this system are conserved in the monoecious hexaploid Oriental persimmon, in which an additional epigenetic regulation of MeGI determines floral sexuality. The downstream regulatory pathways of MeGI remain uncharacterized. In this study, we examined transcriptomic data for male and female flowers from monoecious persimmon cultivars to unveil the gene networks orchestrated by MeGI. A network visualization and cistrome assessment suggested that class-1 KNOTTED-like homeobox (KNOX)/ovate family protein (OFP)/growth regulating factors (GRFs) and short vegetative phase (SVP) genes mediate the differences in gynoecium and androecium development between male and female flowers, respectively. The expression of these genes is directly controlled by MeGI. The gene networks also suggested that some cytokinin, auxin, and gibberellin signaling genes function cooperatively in the KNOX/OFP/GRF pathway during gynoecium differentiation. Meanwhile, SVP may repress PI expression in developing androecia. Overall, our results suggest that MeGI evolved the ability to promote gynoecium development and suppress androecium development by regulating KNOX/OFP/GRF and SVP expression levels, respectively. These insights may help to clarify the molecular mechanism underlying the production of unisexual flowers, while also elucidating the physiological background enabling a single-factor system to establish dioecy in plants.

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

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

    Scientia Horticulturae   246   693 - 699   2019.2

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  • Evolution and diversification of the plant gibberellin receptor GID1. Reviewed International journal

    Hideki Yoshida, Eiichi Tanimoto, Takaaki Hirai, Yohei Miyanoiri, Rie Mitani, Mayuko Kawamura, Mitsuhiro Takeda, Sayaka Takehara, Ko Hirano, Masatsune Kainosho, Takashi Akagi, Makoto Matsuoka, Miyako Ueguchi-Tanaka

    Proceedings of the National Academy of Sciences of the United States of America   115 ( 33 )   E7844-E7853 - E7853   2018.8

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    The plant gibberellin (GA) receptor GID1 shows sequence similarity to carboxylesterase (CXE). Here, we report the molecular evolution of GID1 from establishment to functionally diverse forms in eudicots. By introducing 18 mutagenized rice GID1s into a rice gid1 null mutant, we identified the amino acids crucial for GID1 activity in planta. We focused on two amino acids facing the C2/C3 positions of ent-gibberellane, not shared by lycophytes and euphyllophytes, and found that adjustment of these residues resulted in increased GID1 affinity toward GA4, new acceptance of GA1 and GA3 carrying C13-OH as bioactive ligands, and elimination of inactive GAs. These residues rendered the GA perception system more sophisticated. We conducted phylogenetic analysis of 169 GID1s from 66 plant species and found that, unlike other taxa, nearly all eudicots contain two types of GID1, named A- and B-type. Certain B-type GID1s showed a unique evolutionary characteristic of significantly higher nonsynonymous-to-synonymous divergence in the region determining GA4 affinity. Furthermore, these B-type GID1s were preferentially expressed in the roots of Arabidopsis, soybean, and lettuce and might be involved in root elongation without shoot elongation for adaptive growth under low-temperature stress. Based on these observations, we discuss the establishment and adaption of GID1s during plant evolution.

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

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

    Plant and Cell Physiology   59 ( 6 )   1265 - 1275   2018.6

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    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.

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

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

    Annual Review of Plant Biology   69   553 - 575   2018.4

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    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.

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

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

    Plant Cell   30 ( 4 )   780 - 795   2018.4

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    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.

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

    T. Akagi, R. Tao

    Acta Horticulturae   1195   71 - 74   2018.3

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    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.

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

    Haruka Maeda, Takashi Akagi, Ryutaro Tao

    SCIENTIA HORTICULTURAE   228   41 - 48   2018.1

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    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.

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

    Takashi Akagi

    GENES & GENETIC SYSTEMS   91 ( 6 )   317 - 317   2016.12

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

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

    PLANT CELL   28 ( 12 )   2905 - 2915   2016.12

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    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.

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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) Reviewed

    Takashi Akagi, Takashi Kawai, Ryutaro Tao

    SCIENTIA HORTICULTURAE   213   243 - 251   2016.12

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    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.

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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 Reviewed

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

    PLANT AND CELL PHYSIOLOGY   57 ( 6 )   1281 - 1294   2016.6

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    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.

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

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

    DNA RESEARCH   23 ( 3 )   271 - 282   2016.6

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    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.

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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. Reviewed

    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 ( 2 )   121 - 126   2015

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    Most persimmon (Diospyros kaki Thunb.) cultivars bear only female flowers, which limits persimmon cross-breeding. Although the genetic and molecular bases of sexuality in persimmon have yet to be determined, a maleness-associated region, DlSx-AF4S, was recently identified in D. lotus L., which is a wild diploid relative of hexaploid/nonaploid D. kaki. This finding suggests that D. lotus has a heterogametic male (XY-type) dioecious sexual system. Here, we investigated the association between DlSx-AF4S genotypes and the maleness (sexuality) of 174 persimmon cultivars. DlSx-AF4S was detected in all but three cultivars that bear male flowers, suggesting that the maleness of persimmon is controlled by a genetic factor similar to that in D. lotus. On the other hand, DlSx-AF4S was also found in 17% of the tested cultivars that were reported to bear only female flowers. Considering that the sexuality of persimmon is more susceptible to environmental factors, some cultivars may hardly bear male flowers under certain conditions even though they have male determinants. In addition, a higher ploidy level in persimmon may also complicate sex expression. This elusive sex expression system in persimmon will be better understood when a male determinant(s) linked to DlSx-AF4S is identified and characterized in the future.

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

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

    SCIENCE   346 ( 6209 )   646 - 650   2014.10

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    In plants, multiple lineages have evolved sex chromosomes independently, providing a powerful comparative framework, but few specific determinants controlling the expression of a specific sex have been identified. We investigated sex determinants in the Caucasian persimmon, Diospyros lotus, a dioecious plant with heterogametic males (XY). Male-specific short nucleotide sequences were used to define a male-determining region. A combination of transcriptomics and evolutionary approaches detected a Y-specific sex-determinant candidate, OGI, that displays male-specific conservation among Diospyros species. OGI encodes a small RNA targeting the autosomal MeGI gene, a homeodomain transcription factor regulating anther fertility in a dosage-dependent fashion. This identification of a feminizing gene suppressed by a Y-chromosome-encoded small RNA contributes to our understanding of the evolution of sex chromosome systems in higher plants.

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

    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   2014.7

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    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.

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

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

    V INTERNATIONAL SYMPOSIUM ON PERSIMMON   996   133 - 137   2013

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    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 Reviewed

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

    TREE GENETICS & GENOMES   8 ( 1 )   195 - 204   2012.2

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    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 Reviewed

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

    PLANT PHYSIOLOGY   158 ( 2 )   1089 - 1102   2012.2

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    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 Reviewed

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

    PLANT PHYSIOLOGY   157 ( 1 )   485 - 497   2011.9

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    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 Reviewed

    Takashi Akagi, Ayako Katayama-Ikegami, Keizo Yonemori

    SCIENTIA HORTICULTURAE   130 ( 2 )   373 - 380   2011.9

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    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 Reviewed

    Takashi Akagi, Tomoyuki Tsujimoto, Ayako Ikegami, Keizo Yonemori

    PLANTA   233 ( 5 )   883 - 894   2011.5

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    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.) Reviewed

    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   2011.4

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    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 Reviewed

    Takashi Akagi, Ayako Ikegami, Keizo Yonemori

    PLANTA   232 ( 5 )   1045 - 1059   2010.10

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    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 Reviewed

    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   2010.7

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    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.

    DOI: 10.2503/jjshs1.79.275

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

    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   2010.4

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    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.

    DOI: 10.2503/jjshs1.79.150

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

    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   2010.1

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    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 Reviewed

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

    PLANT PHYSIOLOGY   151 ( 4 )   2028 - 2045   2009.12

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    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 Reviewed

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

    PLANTA   230 ( 5 )   899 - 915   2009.10

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    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.) Reviewed

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

    PLANTA   230 ( 4 )   841 - 855   2009.9

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    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 Reviewed

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

    TREE GENETICS & GENOMES   5 ( 3 )   483 - 492   2009.7

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    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.) Reviewed

    K. Yonemori, T. Akagi, S. Kanzaki

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

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    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 Reviewed

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

    IV INTERNATIONAL SYMPOSIUM ON PERSIMMON   833   151 - 156   2009

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    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.

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

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

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

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Books

  • 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)  2019.2  ( ISBN:9784910389066

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    Total pages:542p   Language:Japanese

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  • The future of genetic resources and breeding science brightened by genomics and new technologies

    Sato Yutaka, Kusaba Makoto, Naito Ken, Isobe Sachiko, Ariizumi Tohru, Sato Shusei, Sato Kazuhiro, Niikura Satoshi, Akagi Takashi

    Breeding Research   25 ( 1 )   33 - 40   2023.6

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    Language:Japanese   Publisher:Japanese Society of Breeding  

    DOI: 10.1270/jsbbr.25.s01

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  • Recurrent neo-sex chromosome evolution in the genus Actinidia (II)

    赤木剛士, 赤木剛士, VARKONYI-GASIC Erika, 白澤健太, CATANACH Andrew, HENRY Isabelle M., MERTTEN Daniel, DATSON Paul, 増田佳苗, 藤田尚子, 桑田恵理子, 牛島幸一郎, 別府賢治, ALLAN Andrew C., CHARLESWORTH Deborah, 片岡郁雄

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    堀内綾乃, 増田佳苗, 白澤健太, 尾上典之, 藤田尚子, 牛島幸一郎, 赤木剛士

    園芸学研究 別冊   22 ( 1 )   2023

  • Recurrent neo-sex chromosome evolution in the genus Actinidia (I)

    赤木剛士, 赤木剛士, VARKONYI-GASIC Erika, 白澤健太, CATANACH Andrew, HENRY Isabelle M., DATSON Paul, 増田佳苗, 藤田尚子, 桑田恵理子, 牛島幸一郎, 別府賢治, ALLAN Andrew C., COMAI Luca, CHARLESWORTH Deborah, 片岡郁雄

    園芸学研究 別冊   21 ( 2 )   2022

  • Population genetic analysis for fruit shape diversity specific to hexaploid persimmon cultivars

    堀内綾乃, 増田佳苗, 増田佳苗, 尾上典之, 松崎隆介, 白澤健太, 久保康隆, 牛島幸一郎, 赤木剛士

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  • Comparative genome analysis of two Silene species with and without sex chromosomes

    藤田尚子, 白澤健太, 牛島幸一郎, 赤木剛士

    園芸学研究 別冊   21 ( 2 )   2022

  • Deep learning predicts complex fruit internal traits for peach sorting

    内田里佳, 藤田尚子, 増田佳苗, 安江隆浩, 宮本善秋, 内田誠一, 赤木剛士, 赤木剛士

    園芸学研究 別冊   21 ( 1 )   2022

  • Comparative analysis on somaclonal mutants for fruit shape determination in persimmon

    堀内綾乃, 増田佳苗, 松崎隆介, 尾上典之, 久保康隆, 牛島幸一郎, 赤木剛士

    育種学研究   24   2022

  • Variety differentiation in hexaploid persimmon, with a wide fruit shape diversity

    堀内綾乃, 増田佳苗, 増田佳苗, 尾上典之, 松崎隆介, 白澤健太, 久保康隆, 牛島幸一郎, 赤木剛士

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  • Prediction and premonitory symptoms characterization for rapid over-softening in persimmon fruit, with deep learning

    鈴木茉莉亜, 増田佳苗, 杉浦真由, 鈴木哲也, 新川猛, 久保康隆, 牛島幸一郎, 内田誠一, 赤木剛士, 赤木剛士

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    藤田尚子, 白澤健太, 牛島幸一郎, 赤木剛士

    日本植物学会大会研究発表記録(CD-ROM)   86th   2022

  • The genetic control and transcriptome analyses of the slow softening strain of melon

    合田駿平, 池田和生, 小林和真, 赤木剛士, 加藤鎌司, 久保康隆, 中野龍平, 牛島幸一郎

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  • Reinvention of hermaphroditism triggered by activation of a RADIALIS-like gene in hexaploid persimmon

    増田佳苗, 池田陽子, 松浦恭和, 川勝泰二, 田尾龍太郎, 久保康隆, 牛島幸一郎, HENRY Isabelle M., 赤木剛士, 赤木剛士

    園芸学研究 別冊   20 ( 2 )   2021

  • Comparative analysis for persimmon fruit shape determination in ‘Hiratanenashi’ and the bud sport ‘Koushimaru’

    堀内綾乃, 増田佳苗, 松崎隆介, 尾上典之, 久保康隆, 牛島幸一郎, 赤木剛士

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    化学と生物   59 ( 1 )   2021

  • Susceptibility to black spot of peach in peach genetic resources and hybrid populations

    浅野貴洋, 河井崇, 伊藤那月, 芦田祐里, 飯島彩加, 鵜木悠治郎, 高田大輔, 中野龍平, 福田文夫, 久保康隆, 赤木剛士, 山本幹博, 牛島幸一郎

    園芸学研究 別冊   19 ( 1 )   2020

  • Estimation of locus region associated with susceptibility to black spot of peach

    浅野貴洋, 河井崇, 鵜木悠治郎, 日原誠介, 高田大輔, 白澤健太, 赤木剛士, 福田文夫, 中野龍平, 久保康隆, 山本幹博, 牛島幸一郎

    育種学研究   22   2020

  • Deep learning on genomes (I): application to short sequences in the persimmon genome

    赤木剛士, 増田佳苗, 馬場康平, 内田誠一

    園芸学研究 別冊   19 ( 1 )   2020

  • Image diagnosis of rapid softening in perssimon fruit with deep learning

    鈴木茉莉亜, 増田佳苗, 竹下孔喜, 朝隈英昭, 鈴木哲也, 杉浦真由, 新川猛, 内田誠一, 赤木剛士

    育種学研究   22   2020

  • Study on prediction of early ripening of persimmon

    馬場康平, 増田佳苗, 鈴木茉莉亜, 赤木剛士, 内田誠一

    電子情報通信学会大会講演論文集(CD-ROM)   2020   2020

  • ヒロハノマンテマにおける性と花芽形成の関係

    藤田尚子, 増田佳苗, 赤木剛士

    Plant Morphology   32 ( 1 )   2020

  • Polyploid-specific reinvention of hermaphroditism in persimmon is triggered by stress-induced NGATHA

    増田佳苗, 牛島幸一郎, 久保康隆, 赤木剛士

    育種学研究   22   2020

  • 作物ゲノムへのディープラーニングによるcis配列デコーディング

    赤木剛士, 増田佳苗, 内田誠一

    日本植物学会大会研究発表記録(CD-ROM)   84th   2020

  • 性の可塑化を規定する遺伝子ネットワーク:六倍体カキにおける両性花派生機構

    増田佳苗, 牛島幸一郎, 久保康隆, 赤木剛士

    日本植物学会大会研究発表記録(CD-ROM)   84th   2020

  • 非モデル雌雄異株植物群における遺伝子機能評価系の開発

    藤田尚子, 桑田恵理子, 増田佳苗, 赤木剛士, 赤木剛士

    日本植物学会大会研究発表記録(CD-ROM)   84th   2020

  • 六倍体カキの樹内雌雄バランスに関する倍数体用GWAS解析

    増田佳苗, 白澤健太, 山本英司, 河井崇, 尾上典之, 河野淳, 牛島幸一郎, 久保康隆, 田尾龍太郎, 赤木剛士

    育種学研究   21   31   2019.9

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  • Epigenetic flexibility underlies bud-sport male expression in a persimmon cultivar, Saijo

    18 ( 1 )   37   2019.3

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  • Dynamic epigenetic flexibility underlies somaclonal sex conversions in hexaploid persimmon tree

    MASUDA Kanae, AKAGI Takashi, ESUMI Tomoya, TAO Ryutaro

    日本植物生理学会年会(Web)   60th   352 (WEB ONLY)   2019

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  • 深層学習によるカキ果実における生理障害の画像診断および判断要因の可視化

    赤木剛士, 赤木剛士, 黒木陵平, 大西信徳, 鈴木哲也, 新川猛, 田尾龍太郎, 内田誠一, 伊勢武史

    園芸学研究 別冊   18 ( 1 )   2019

  • ヒロハノマンテマにおいてオス因子様機能を果たす菌エフェクターの探索

    藤田尚子, 増田佳苗, 赤木剛士

    日本植物学会大会研究発表記録   83rd   2019

  • カキ品種の果実生育・成熟に関する倍数体用ゲノムワイドアソシエーション解析

    赤木剛士, 増田佳苗, 牛島幸一郎, 久保康隆

    園芸学研究 別冊   18 ( 2 )   2019

  • カキの両性花派生に関する共発現ネットワーク解析

    増田佳苗, 牛島幸一郎, 久保康隆, 田尾龍太郎, 赤木剛士

    園芸学研究 別冊   18 ( 2 )   2019

  • カキの雌雄花比に関するゲノムワイドアソシエーション解析

    増田佳苗, 赤木剛士, 赤木剛士, 白澤健太, 河井崇, 尾上典之, 河野淳, 田尾龍太郎

    園芸学研究 別冊   17 ( 2 )   90   2018.9

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  • サクラ属の配偶体型自家不和合性における花粉側共通因子の同定

    大野健太朗, 赤木剛士, 森本拓也, WUENSCH Ana, 田尾龍太郎

    園芸学研究 別冊   17 ( 1 )   36   2018.3

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  • カキ属の全ゲノム情報が明らかにする性の多様性を駆動した古倍化

    赤木剛士, 赤木剛士, 白澤健太, 長崎英樹, 平川英樹, 田尾龍太郎, COMAI Luca, HENRY Isabelle M

    園芸学研究 別冊   17 ( 1 )   37   2018.3

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  • カキにみられる多様な果実形状の数値化

    前田春香, 赤木剛士, 赤木剛士, 田尾龍太郎

    園芸学研究 別冊   16 ( 2 )   142   2017.9

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  • カキ属の全ゲノム配列解読(第1報):系統特異的なゲノム進化

    赤木剛士, 赤木剛士, 白澤健太, 長崎英樹, 平川英樹, COMAI Luca, 田尾龍太郎, HENRY Isabelle M

    園芸学研究 別冊   16 ( 2 )   139   2017.9

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  • キウイフルーツにおける性決定因子の同定(第2報):雌化抑制因子のcis進化

    赤木剛士, 赤木剛士, 別府賢治, 片岡郁雄, 田尾龍太郎

    園芸学研究 別冊   16 ( 1 )   38   2017.3

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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の進化成立過程の解析

    森本拓也, 赤木剛士, 田尾龍太郎

    園芸学研究 別冊   16 ( 1 )   34   2017.3

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  • 全ゲノムシークエンス解析によるカンカオウトウの花粉側自家不和合性共通因子の探索

    大野健太朗, 森本拓也, WUENSCH A, 赤木剛士, 田尾龍太郎

    園芸学研究 別冊   16 ( 1 )   33   2017.3

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  • Diversity of the Sex Determination in Seed Plants : From a Finding of the Sex Determinant in Persimmon

    55 ( 1 )   35 - 41   2017.1

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  • Sexuality of seed plants, from a standpoint of the sex determination system of persimmons

    52 ( 1 )   31 - 38   2017

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  • エピジェネティックな記憶によるカキの可塑的な性決定(第2報)

    赤木剛士, 赤木剛士, HENRY Isabelle M, COMAI Luca, 田尾龍太郎

    園芸学研究 別冊   15 ( 2 )   80   2016.9

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  • キウイフルーツにおける性決定因子の同定(第一報)

    大谷遥, 赤木剛士, 赤木剛士, 森本拓也, 別府賢治, 片岡郁雄, 田尾龍太郎

    園芸学研究 別冊   15 ( 2 )   82   2016.9

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  • エピジェネティックな記憶によるカキの可塑的な性決定(第1報)

    赤木剛士, 赤木剛士, HENRY Isabelle M, 河井崇, COMAI Luca, 田尾龍太郎

    園芸学研究 別冊   15 ( 1 )   36   2016.3

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  • 全ゲノムワイド連鎖・発現解析によるカンカオウトウにおける花粉側non‐S自家和合化因子の探索

    森本拓也, WUENSCH A, 渡辺美佳子, 赤木剛士, 赤木剛士, 田尾龍太郎

    園芸学研究 別冊   15 ( 1 )   95   2016.3

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  • 果樹における先端ゲノム解析と新しい研究の展開 No.12 カキの性決定

    赤木剛士, 田尾龍太郎

    果実日本   71 ( 1 )   24 - 26   2016.1

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  • カキ属における性決定遺伝子相同因子群の重複進化

    赤木剛士, HENRY Isabelle M, COMAI Luca, 田尾龍太郎

    園芸学研究 別冊   14 ( 2 )   84   2015.9

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  • サクラ属およびリンゴ亜連植物におけるS遺伝子の進化系統解析

    森本拓也, 赤木剛士, 田尾龍太郎

    園芸学研究 別冊   14 ( 2 )   133   2015.9

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  • カキ属性決定相同因子群の組織特異的発現動態

    杉本綾香, 赤木剛士, 山根久代, 田尾龍太郎

    園芸学研究 別冊   14 ( 2 )   85   2015.9

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  • カキ品種の複雑な性表現におけるカキ属性決定因子の関与

    河井 崇, 赤木剛士, 田尾龍太郎

    園芸学会平成27年度春季大会   14 ( 1 )   2015.3

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  • Evolutionary analysis of genes for S-RNase-based self-incompatibility reveals S locus duplications in the Ancestral Rosaceae

    Takuya Morimoto, Takashi Akagi, Ryutaro Tao

    Horticulture Journal   84 ( 3 )   233 - 242   2015.1

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    © 2015 The Japanese Society for Horticultural Science (JSHS), All rights reserved.Flowering plants have developed a genetically determined self-incompatibility (SI) system to maintain genetic diversity within a species. The Solanaceae, the Rosaceae, and the Plantaginaceae have the S-RNase-based gametophytic SI (GSI) system, which uses S-RNase and F-box proteins as the pistil S and pollen S determinants, respectively. SI is associated with culture and breeding difficulties in rosaceous fruit trees, such as apple, pear, and stone fruit species; therefore, researchers in the pomology field have long studied the mechanism and genetics of SI in order to obtain clues to overcome these difficulties. Here, we investigated the evolutionary paths of the S-RNase genes by tracking their duplication patterns. Phylogenetic analysis and estimation of proxy ages for the establishment of S-RNase and its homologs in several rosaceous species showed that the divergence of S-RNase in the subtribe Malinae and the genus Prunus predated the gene in most recent common ancestors of Rosaceae species. Furthermore, the duplicated S-RNase-like genes were accompanied by duplicated pollen S-like F-box genes, suggesting segmental duplications of the S locus. Analysis of the expression patterns and evolutionary speeds of duplicated S-RNase-like genes in Prunus suggested that these genes have lost the SI recognition function, resulting in a single S locus. Furthermore, the S loci in the current Rosaceae species might have evolved independently from the duplicated S loci, which could explain the presence of genus-specific SI recognition mechanisms in the Rosaceae. The results of the present study should be valuable for the future development of artificial SI control and for self-compatible breeding in rosaceous horticultural plant species.

    DOI: 10.2503/hortj.MI-060

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  • 花粉F-box遺伝子の進化様式から示されたサクラ属特異的な自家不和合性機構の成立

    赤木剛士, 森本拓也, 渡辺美佳子, 田尾龍太郎

    園芸学研究 別冊   14 ( 1 )   2015

  • リンゴ小球形潜在ウイルスベクターを用いたサクラ属果樹の遺伝子機能評価系の開発

    河井 崇, 長山枝里香, 赤木剛士, 山根久代, 山岸紀子, 吉川信幸, 田尾龍太郎

    園芸学会平成24年度春季大会   11 ( 1 )   2012.3

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  • Development of the ALSV-mediated gene evaluation system for Prunus

    Kawai, T, E. Nagayama, T. Akagi, H. Yamane, R. Tao

    Plant & Animal Genome Conference XX   2012.1

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  • カキの甘渋性識別SCARマーカーを利用した完全甘ガキの選抜

    三谷宣仁, 河野淳, 山田昌彦, 神崎真哉, 佐藤明彦, 小林省藏, 伴雄介, 上野俊人, 白石美樹夫, 赤木剛士, 辻本誠幸, 米森敬三

    園芸学研究 別冊   10 ( 1 )   39   2011.3

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  • Development of a gene evaluation system with virus-induced gene silencing in Prunus

    Akagi, T, E. Nagayama, T. Kawai, H. Yamane, R. Tao

    5th International Rosaceae Genomics Conference   2010.11

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  • 季節的気温シグナルがDkMyb4の発現を介してカキの甘渋性制御に関与する

    赤木剛士, 池上礼子, 米森敬三

    園芸学研究 別冊   9 ( 1 )   2010

  • カキの甘渋性を決定するDkMyb4の季節的発現制御因子についての解析

    赤木剛士, 池上礼子, 小林省蔵, 佐藤明彦, 米森敬三

    園芸学研究 別冊   8 ( 2 )   2009

  • カキの甘渋性決定に関与する転写因子DkMyb4の同定

    赤木剛士, 池上礼子, 佐藤明彦, 小林省蔵, 米森敬三

    園芸学研究 別冊   8 ( 1 )   2009

  • Expression pattern of the genes involved in flavonoid biosynthesis between astringent and non-astringent persimmon

    AKAGI T., IKEGAMI A., YAMADA M., YONEMORI K.

    7 ( 1 )   79 - 79   2008.3

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  • Isolation of transcription factors involved in flavonoid biosynthesis of persimmon fruit and their relation to tannin accumulation

    AKAGI T., YOSHIDA J., YAMADA M., YONEMORI K.

    6 ( 2 )   88 - 88   2007.9

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  • Molecular marker linked to natural astringency-loss in Chinese-type PCNA persimmon (Diospyros kaki thunb.) fruit

    Keizo Yonemori, Sai Eguchi, Ayako Ikegami, Yoshihisa Sakaguchi, Takashi Akagi, Akira Kitajima, Masahiko Yamada, Dan E. Partitt

    HORTSCIENCE   42 ( 4 )   976 - 976   2007.7

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  • Genomic analysis of Japanese persimmon using molecular markers and real time PCR

    AKAGI T, TAO R, YONEMORI K

    園芸学研究. 別冊, 園芸学会大会研究発表要旨   6 ( 1 )   93 - 93   2007.3

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  • Segregation of fruit astringency type and selection of PCNA offspring using RFLP marker in the BC_1 progeny derived from 'Kurokuma' persimmon

    KANZAKI S., KIMURA M., YAMADA M., MITANI N., AKAGI T., UTSUNOMIYA N., YONEMORI K.

    6 ( 1 )   356 - 356   2007.3

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  • Possibility for identification of AST-locus in D. kaki by chromosome walking of D. lotus

    AKAGI T., MASUKO T., KANZAKI S., MITANI N., YAMADA M., YONEMORI K.

    75 ( 2 )   168 - 168   2006.9

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  • New molecular markers associated with the trait of astringency-loss in Japanese pollination-constant and non-astringent (PCNA) type persimmon

    OKAMOTO K., AKAGI T., MITANI N., YAMADA M., YONEMORI K.

    75 ( 2 )   167 - 167   2006.9

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Presentations

  • Boy meets Girl, everywhere? Mysteries in neo-sex chromosome evolution in kiwifruit Invited

    Takashi Akagi

    XI International Symposium on Kiwifruit  2024.2.23 

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  • 植物における性の収斂進化に潜む 「生理的な共通性」を求めて Invited

    赤木剛士

    植物化学調節学会 第58回大会  2023.11.18 

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  • ゲノム・遺伝情報への深層学習 ~X-AI協働研究 Invited

    赤木剛士

    令和5年度 野菜花き課題別研究会  2023.10.25 

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  • 古今ゲノム倍化が駆動する『植物の性の可塑性』~柿の進化に学ぶ Invited

    赤木剛士

    倍数体をどうにかする会 2023  2023.10.13 

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  • ゲノム x 進化 x AIの視点から見える「植物らしさ」 Invited

    赤木剛士

    第4回 木村資生記念進化学セミナー  2023.9.22 

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  • ゲノム・遺伝情報へのAI協働研究から見る「新機能」の 進化 Invited

    赤木剛士

    植物バイオテクノロジー学会 2023年度大会  2023.9.13 

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  • 『ゲノム・遺伝子倍化』が生み出す植物の新機能獲得進化 Invited

    赤木剛士

    日本植物学会 第87回大会  2023.9.9 

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  • Genome-wide cis-decoding for tomato fruit ripening with explainable deep learning Invited

    Takashi Akagi

    ETHYLENE 2023  2023.6.28 

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  • ゲノム・分子・画像への「AI の直感」活用法:wet研究者だって AI にあやかりたい!! Invited

    赤木剛士

    日本植物生理学会 64回年会  2023.3.15 

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  • 覆される定説 ~ 植物の「挑戦的」性染色体進化 Invited

    赤木剛士

    日本植物生理学会 64回年会  2023.3.15 

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  • Genome-Wide Cis-Decoding for Expression Design in Tomato Using Cistrome Data and Explainable Deep Learning Invited

    Takashi Akagi

    Plant and Animal Genome 30  2023.1.15 

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  • 『植物ゲノム進化×AI技術進化』から見る作物の新規デザイン Invited

    赤木剛士

    植物科学シンポジウム2022  2022.12.6 

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  • ゲノム・分子・イメージデータへの AI 協働研究 が拓く育種学の新視点 Invited

    赤木剛士

    日本育種学会 第142回講演会  2022.9.23 

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  • Wet植物研究者のための「AIとの協働研究」 Invited

    赤木剛士

    日本植物生理学会第63回年会  2022.3.24 

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  • ゲノム・遺伝子改変に向けたAI協働研究 Invited

    赤木剛士

    日本農薬学会第47回大会  2022.3.9 

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  • Takashi Akagi Invited

    2022.3.3 

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  • Plastic plant sex, orchestrated by epigenetic fluctuation Invited

    Takashi Akagi

    The 44th Annual Meeting of the Molecular Biology Society of Japan  2021.12.2 

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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 Invited

    赤木剛士

    明治大学農学部 特別講義  2021.10.21 

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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 Invited

    赤木剛士

    明治大学農学部 特別講義  2021.10.21 

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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 Invited

    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  2021.10.15 

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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 Invited

    赤木剛士

    第38回日本植物バイオテクノロジー学会  2021.9.11 

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    Presentation type:Symposium, workshop panel (nominated)  

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  • Genomic behaviors triggering the convergent evolution of plants sexualities Invited

    Takashi Akagi

    IPSR Web Forum 2021  2021.9.6 

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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 Invited

    赤木剛士

    東京大学 第1365回生物科学セミナー  2021.7.14 

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

    Takashi Akagi

    Philosophical Transactions B Royal Society, Online Conference  2021.6.24 

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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 Invited

    赤木剛士

    麦学オンラインセミナー  2021.6.4 

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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 Invited

    赤木剛士

    日本植物生理学会第62回  2021.3.14 

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  • 果樹のゲノム進化から紐解く「植物の性」 Invited

    赤木剛士

    岡山バイオアクティブ研究会  2020.10.21 

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  • 植物における性の成立と多様化の分子進化 Invited

    赤木剛士

    日本時間生物学会  2020.9.27 

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  • 植物の性の成立と揺らぎ Invited

    赤木剛士

    神戸大学理学部特別講義  2019.12.13 

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

    Takashi Akagi

    日本分子生物学会 第42回年会  2019.12.5 

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  • 果樹ゲノムが紐解く植物の性の成立と進化 Invited

    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  2019.11.29 

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  • 作物における性の成立と進化 Invited

    赤木剛士

    東京大学大学院農学生命科学研究科特別講義  2019.11.14 

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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 Invited

    赤木剛士

    果樹バイオテクノロジー研究会  2019.10.9 

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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 Invited

    赤木剛士

    NGSデータ解析シンポジウム  2019.9.24 

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  • ゲノム進化から紐解く植物の多様な性決定 Invited

    赤木剛士

    日本遺伝学会第91回大会  2019.9.11 

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  • Evolution of sexuality in tree crops Invited

    Takashi Akagi

    日本育種学会第136回講演会  2019.9.6 

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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 Invited

    赤木剛士

    第二回植物インフォマティクス研究会  2019.9.2 

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

    Takashi Akagi

    Botanical Seminar at University of Zurich  2019.6.28 

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  • Evolution of the plant sexuality, triggered by polyploidization Invited

    Invited seminar at Max Planck Institute Plant Breeding Research  2019.6.26 

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  • 植物における性の決定と進化 Invited

    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  2019.5.21 

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  • 柿における性決定の進化 Invited

    赤木剛士

    京都植物バイテクシンポジウム  2019.5.16 

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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 Invited

    赤木剛士

    日本植物生理学会第60回  2019.3.15 

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  • カキから紐解く「性」の進化と多様化機構 Invited

    赤木剛士

    日本植物生理学会第60回  2019.3.15 

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  • Diversification of sexual system: insights from the persimmon genome Invited International conference

    Takashi Akagi

    The Society for Molecular Biology & Evolution 2018  2018.7.10 

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  • キウイフルーツから紐解く性の進化 Invited

    赤木 剛士

    イネ遺伝学・分子生物学ワークショップ2018  2018.7.5 

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

    Takashi Akagi

    The 25th International Congress on Sexual Plant Reproduction  2018.6.16 

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  • Identification of the Y-encoded suppressor of feminization in kiwifruit. Invited International conference

    Takashi Akagi

    Plant and Animal Genome Conference XXV  2018.1.14 

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  • The persimmon genome unveils lineage-specific paleoduplication events driving diversification of sexual systems Invited International conference

    Takashi Akagi

    Plant and Animal Genome Conference XXV  2018.1.14 

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

    Takashi Akagi

    IX International Symposium on Kiwifruit  2017.9.6 

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  • Evolution of flexible sex determination system in polyploid persimmon Invited International conference

    Takashi Akagi

    XIX International Botanical Congress  2017.7.24 

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  • ゲノムから紐解く果樹作物の”性” Invited

    赤木 剛士

    NGS現場の会 第5回研究会  2017.5.23 

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  • 柿における性の成立と揺らぐ性への進化 Invited

    赤木 剛士

    植物科学シンポジウム  2016.12.7 

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

    Takashi Akagi

    Kyoto-Swiss Symposium 2016  2016.11.1 

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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 Invited

    赤木 剛士

    日本植物学会第80回大会  2016.9.16 

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  • カキ属の性決定を統御する転写因子 Invited

    赤木 剛士

    園芸学会平成28年度秋季大会  2016.9.11 

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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 Invited

    赤木 剛士

    日本遺伝学会第88回大会  2016.9.8 

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  • Evolution of a flexible sex determination system in polyploid persimmon. Invited International conference

    Takashi Akagi

    Plant and Animal Genome Conference XXIII  2016.1.10 

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  • 「柿」でみつかった性決定因子が示す可能性 Invited

    赤木 剛士

    日本植物学会第79回大会  2015.9.6 

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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~ Invited

    赤木 剛士

    園芸学会平成27年度春季大会  2015.3.28 

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  • 植物の性決定遺伝子 Invited

    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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Awards

  • 園芸学会奨励賞

    2023.3   園芸学会  

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  • 農学進歩賞

    2019.11   日本農学会  

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  • 文部科学大臣表彰 若手科学者省

    2019.4   文部科学省  

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Research Projects

  • Genomic dynamics underlying the plastic hermaphroditism in plants: the basis of exploratory reproductive adaptations.

    Grant number:22A303  2022.06 - 2027.03

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

    赤木 剛士

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  • Genomic dynamics underlying the plastic hermaphroditism in plants: the basis of exploratory reproductive adaptations

    Grant number:22H05172  2022.06 - 2027.03

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

    赤木 剛士, 藤井 壮太, 木下 哲, 伊藤 寿朗, 榊原 恵子, 奥田 哲弘, 清水 健太郎, 井澤 毅, 白澤 健太, 渡辺 正夫, 内田 誠一, 越阪部 晃永, 草野 修平, 遠藤 真咲, 小田原 瑛美子, 櫻庭 俊

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    Grant amount:\317590000 ( Direct expense: \244300000 、 Indirect expense:\73290000 )

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  • Genomic dynamics driving plastic sexuality in plants

    Grant number:22H05173  2022.06 - 2027.03

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

    赤木 剛士, 内田 誠一

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    Grant amount:\113880000 ( Direct expense: \87600000 、 Indirect expense:\26280000 )

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  • カキのゲノム進化に基づく果実の形状多様性獲得モデルの構築

    Grant number:22H02339  2022.04 - 2026.03

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

    赤木 剛士, 川勝 泰二, 尾上 典之

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    Grant amount:\17420000 ( Direct expense: \13400000 、 Indirect expense:\4020000 )

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  • Simultaneous expression system of herbicide-metabolizing genes key to the expression of multiple-herbicide resistance in E. phyllopogon

    Grant number:22H02347  2022.04 - 2026.03

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

    岩上 哲史, 権藤 崇裕, 赤木 剛士, 宮下 正弘

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    Grant amount:\17160000 ( Direct expense: \13200000 、 Indirect expense:\3960000 )

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  • 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

    2020.12 - 2024.03

    JST  JST-PRESTO 

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  • New Frontier of Fruit Postharvest Physiology-Low Temperature modulated Ripening and its application

    Grant number:20H02977  2020.04 - 2024.03

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

    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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    Grant amount:\17810000 ( Direct expense: \13700000 、 Indirect expense:\4110000 )

    本研究は、低温誘導成熟機構を、温帯性果実種横断的にゲノム・トランスクリプトーム解析、メタボローム解析、遺伝子組換え技術などを駆使して解析し、その統合的理解を目指す先駆的学術的取り組みである。低温誘導成熟果はエチレン誘導果よりも品質保持期間が長く、低温感受性の品種間差異は成熟の早生・晩生性に密接に関与している。本研究は、収穫後ロス低減に直結する新品質保持技術開発と分子マーカー開発による育種への貢献を目的とする。
    本年度は第1段階として、カキ、温州ミカン、レモン、セイヨウナシについて果実のエチレン処理および温度処理に対する応答性を解析した。レモンではエチレン処理と10-15℃温度処理によって、カロテノイド合成のs苦心とクロロフィル分解の顕著な促進が見られた。また、それらの反応に対応する遺伝子は発現の変化を捉えた。カキでは15℃以下で低温障害発生の兆候が見られ、RNAseq解析により低温特異的に応答する遺伝子群を特定した。また、温州ミカンにおいて、早晩性の異なる4品種を用いて、次世代シーケンサーによるゲノム解析を行なった。
    ‘宮川早生‘ウンシュウミカン果実と’小原紅早生’ウンシュウミカン果実のゲノムを比較すると、‘宮川早生’特異的なcontigが45個得られた。これらのcontigのうち半数ほどはトランスポゾン様の動きをしており、ゲノム中の複数箇所へ変異をもたらしていた。今回の結果では具体的に両品種の色に違いを決定する因子の特定には至らなかったが、他の植物で色の違いをもたらす原因となっているトランスポゾンの存在を確認できたこと、またアポカロテノイドを生成するCCD4と似たような二重結合を酸化開裂する働きをもつ2OG-Fe(II)oxygenase family proteinなどに変異がある可能性が示唆されたことは、重要な進展と考えている。

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  • 開花・性・花寿命を変える菌因子の特定

    Grant number:20K06016  2020.04 - 2023.03

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

    本研究では、Silene属植物における菌感染による花の表現型の変化に着目し、外的要因による重要花形質「性表現」「開花期」「寿命」の表現型変動の原因因子の特定および分子機構の解明を目指している。
    1年目の本年度は、「性表現」と「開花期」を制御する候補因子を得るため、花器官分化のごく初期の花芽メリステムを解剖・サンプリングし、RNA-seq解析に供した。得られたRNA-seqデータから感染花特異的な発現変動遺伝子群を抽出し、候補因子を抽出した。
    花の「寿命」(保存性)に関しては、多くの植物種で花弁老化にはエチレンが主導的な役割を果たしていることから、トランスクリプトーム解析に先行して、菌感染花におけるエチレン生成量と感受性を調査した。プロピレン処理により花弁のエチレン感受性を検証したところ、処理翌日には全ての花弁に萎れがみられたことから、エチレン感受性であることが示された。多くの植物でみられる受粉・受精の刺激によるエチレン生成量の上昇も観察され、未受粉の花は1週間程度の花寿命を保持するのに対し、受粉後の花では翌日に花弁の萎れが確認された。一方、菌感染花においては、プロピレン処理下においても寿命が1日程度延びたことから、菌感染がエチレン感受性を抑制することが示唆された。さらに、健全花において花弁の萎れがみられる直前に観察されるエチレン生成量の上昇ピークが菌感染花には確認されず、菌感染花の寿命は健全花に比べて有意に延びることが見出された。

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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

    Grant number:20K20454  2019.06 - 2025.03

    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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    Grant amount:\26000000 ( Direct expense: \20000000 、 Indirect expense:\6000000 )

    本研究では,カキ属植物の基礎および応用研究を加速化するために,1)大量シークエンシング技術を活用したゲノム情報と発現遺伝子情報の整備,2)機械計測と機械学習による形質評価法の開発,3)遺伝子機能評価系の開発, 4)遺伝資源の調査と収集,の4種類のサブテーマにより支えられるコモンプラットフォームを整備するものである.本年度の成果は以下の通りである.
    (ゲノム情報と発現遺伝子情報の整備)昨年度に引き続いて,PacBioおよび10xGenomics社のGemCode Technologyを利用し六倍体カキのドラフトゲノムの構築をした.加えて,九倍体の平核無およびその枝変わり品種である突核無のゲノムシークエンスを行うとともに,果実の発現情報を収集した.
    (機械計測と機械学習による形質評価法の開発)昨年度に引き続いて,果実の写真からの三次元構築を行い,カキ果実のサイズと形状の三次元情報を数値化して評価する方法を検討した.また樹体に着果したカキ果実を見つけ出す方法の開発に着した.深層学習を利用した品質解析法に関する結果をとりまとめて論文発表した.
    (遺伝子機能評価系の開発)昨年度までに開発したカキの近縁二倍体種のマメガキ(D. lotus)やアブラガキ(D. oleifera)のアグロバクテリウム法による形質転換系によって,雌雄性関連遺伝子による形質転換を行った.カキ属におけるCEN相同遺伝子のノックアウトによる,カキ属植物の早期開花系の開発を検討した.
    (遺伝資源の収集と整備)本年度はCOVID19の影響のため,予定していた国外での調査は行うことが出来ず,文献調査のみを行った.

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  • Comparative genomics for the sex chromosomes evolutions in woody crops

    2019.06 - 2022.03

    JSPS  二国間交流事業 

    赤木剛士

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  • Elucidation of coordinated regulation mechanism of cytochrome P450 genes: key genes for multiple-herbicide resistance in Echinochloa phyllopogon

    Grant number:19H02955  2019.04 - 2022.03

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

    Iwakami Satoshi

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    Grant amount:\17680000 ( Direct expense: \13600000 、 Indirect expense:\4080000 )

    We analyzed the resistance mechanism of Echinochloa phyllopogon, a paddy field weed that has acquired resistance to various herbicides by simultaneously overexpressing enzymes that detoxify herbicides, and clarified the followings: (1) The genome of the multiple-herbicide resistant line was sequenced and highly contiguous genome was obtained. Genetic analysis using the genome revealed that the multiple-herbicide resistance was caused by a single region of the genome. (2) We have selected one E. phyllopogon line that produces callus with excellent culture characteristics. This line will be a valuable resource for the establishment of E. phyllopogon transformation system. (3) Resistance to the VLCFAE inhibitor thiobencarb was independent of resistance to many other herbicides.

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  • Evolutionary paths to establish flexibility in plant sexuality

    Grant number:19H04862  2019.04 - 2021.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    赤木 剛士

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    Grant amount:\9100000 ( Direct expense: \7000000 、 Indirect expense:\2100000 )

    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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  • Genome-wide model to regulate the wide diversity of fruit shape in persimmon

    Grant number:18H02199  2018.04 - 2022.03

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

    Akagi Takashi

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    Grant amount:\16510000 ( Direct expense: \12700000 、 Indirect expense:\3810000 )

    We here attempted to identify genetic factors and evolutionary mechanisms to drive fruit shape diversity, which is specific to persimmon cultivars, from a genome-wide viewpoint. The draft whole-genome in a wild relative close to cultivated persimmon (Diospyros lotus) was assembled. With this reference genome, we identified gene co-expression networks associated with the fruit shape diversity, quantified with principal components of elliptic Fourier descriptors. Some cytokinin-related transcription factors, including KNAT1, exhibited persimmon-specific expression fluctuation in fruit, which was not observed in other fruit crops. This persimmon specific expression behaviors may be a key to express dynamic fruit shape diversities amongst the cultivars.

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  • Characterization of interspecific cross incompatibility in the genus Prunus

    Grant number:17K19265  2017.06 - 2019.03

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

    Akagi Takashi, MORIMOTO Takuya

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    Grant amount:\5980000 ( Direct expense: \4600000 、 Indirect expense:\1380000 )

    We attempted to unveil the molecular mechanism to cause inter-crossing male sterility, with a cross of Japanese apricot and Japanese plum. In this study, we performed morphological observation with microscope, transcriptome and methylome analyses, using anthers from a representative cross of Japanese plum cv. Soldam x Japanese apricot cv. Jizo-ume, and its offspring sel. Sumomo-ume no. 1.
    The inter-crossed sel. Sumomo-ume no. 1 showed specific irregularity in tapetum development and no degradation of tapetum layers, which is indispensable for pollen fertility. Transcriptome analysis suggested that expression imbalances between nuclei genome and organelle genome, and some non-additive regulatory genes, which showed unexpected expression patterns from those in the parents, involved the male sterility in this inter-specific crossing.

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  • Species barriers in endosperm: key molecular mechanisms of epigenetic regulation

    Grant number:16H06471  2016.06 - 2021.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    Kinoshita Tetsu

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    Grant amount:\115960000 ( Direct expense: \89200000 、 Indirect expense:\26760000 )

    The mechanism of species hybridization barrier is arranged in the plant endosperm to avoid heterologous fertilization with different species, which is controlled by not only nucleotide sequence but also epigenetic mechanisms. In this study, in order to elucidate the principle of the birth of new plant species, we clarified the role of FACT histone chaperones, which are essential for DNA demethylation to epigenetically induce reproductive barriers in the endosperm. We also identified basics that species barrier can be overcome by increased ploidy levels in one parent.

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  • Comprehensive analysis of full length cDNA and alternative splicing for the genes related to fruit development and ripening

    Grant number:16K14854  2016.04 - 2018.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research  Grant-in-Aid for Challenging Exploratory Research

    Ushijima Koichiro

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    Grant amount:\3640000 ( Direct expense: \2800000 、 Indirect expense:\840000 )

    3rd generation sequences promotes not only genome sequencing but also transcript analysis. Iso-seq analysis using PacBio are very useful method for reading full length cDNA and detecting alternative splicing. In this analysis, we carried out Iso-seq analysis for melon fruits. We used three different methods for construction of full length cDNA library. The libraries were sequenced by PacBio sequel and Nanopore MinION. Isoforms were mapped on the reference genome of melon and compared them. PacBio and Nanopore isoforms fell into ~ 6,500 and 12,000 loci respectively. 509 loci of them were located at intergenic region and predicted novel loci.

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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

    2015.12 - 2019.03

    JST  JST-PRESTO 

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    Authorship:Principal investigator 

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  • Studies on the molecular basis and evolution of Prunus-specific self-incompatibility recognition system

    Grant number:15H02431  2015.04 - 2019.03

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

    Tao Ryutaro

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    Grant amount:\41990000 ( Direct expense: \32300000 、 Indirect expense:\9690000 )

    Genome-wide analysis of the evolutional radiation of S locus-related F-box genes were conducted to elucidate the evolutionary path to the establishment of the Prunus-specific S-RNase-based gametophytic self-incompatibility (GSI) system. The analysis indicated that the Prunus pollen S F-box gene, SFB, diverged from pollen S F-box genes of the Malinae (Rosaceae), Solanaceae, and Plantaginaceae. early after the establishment of the Eudicots. The analysis also indicated the Prunus SFB gene originated in a recent Prunus-specific gene duplication event, which could contribute to the establishment of the Prunus-specific GSI recognition mechanism. Both evolutional and biochemical analyses conducted strongly indicated that pollen expressed F-box genes (SLFLs) located close to the S locus of Prunus may be the so-called general inhibitor (GI) of the GI model explaining Prunus-specific GSI recognition mechanism.

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  • Diversification of agriculturally important traits accelerated by polyploidization in Diospyros

    Grant number:15K14654  2015.04 - 2017.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research  Grant-in-Aid for Challenging Exploratory Research

    Akagi Takashi

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    Grant amount:\3900000 ( Direct expense: \3000000 、 Indirect expense:\900000 )

    In diploid persimmons, we previously elucidated the mechanism of sex determination that a Y-encoded pseudo-gene called OGI, via the production of small-RNAs against the gene encoding the female-determining factor MeGI, derives separate male and female individuals. On the other hand, in hexaploid Diospyros kaki, this regulatory mechanism leads to the formation of both male and female flowers (monoeocy), in genetically male individuals. Here we revealed that, in monoecious hexaploid persimmon, the DNA methylation levels on the MeGI is the key factor to determine flowert sexuality. Instead, OGI expression is generally undetectable, due to the SINE-like transposon insertion of a transposon in the 5' region of its promoter. This transposon insertion is highly methylated as is reported SINE families in other plant species, and is conserved in all Y-carrying D. kaki cultivars, suggesting either natural selection or a strong bottleneck for the silenced OGI gene during polyploidization.

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  • Genome-wide modeling of fruit development and maturation in persimmons

    Grant number:26712005  2014.04 - 2018.03

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

    Akagi Takashi

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    Grant amount:\22620000 ( Direct expense: \17400000 、 Indirect expense:\5220000 )

    We attempted to quantitatively characterize the pattern of fruit shape development and to identify genetic factors contributing to that pattern, in a wide variety of persimmon cultivars.
    We developed a method to quantify the pattern of fruit development by separating the principal components of complex shape of persimmon fruits, with "SHAPE" software. In the stage of fruit shape development, transcriptomic data in persimmon cultivars/segregated populations were assessed with Pearson correlation or co-expression network analyses, to identify the genetic factors associated with fruit shapes. Lastly, we found some candidate genes and potential molecular pathways which contribut to fruit shape determining in a wide variety of persimmon accessions.

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  • Molecular Analysis for heterostyly by using genomics and transcriptmics approches

    Grant number:25292023  2013.04 - 2017.03

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

    Ushijima Koichiro

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    Grant amount:\18980000 ( Direct expense: \14600000 、 Indirect expense:\4380000 )

    Heterostyly is one of self-incompatibility that is a genetic system to reject the self-pollen and be linked to floral morph polymorphism.In this study, to elucidate the molecular mechanism of Linum heterostyly, we isolated the candidate gene controlling heterostyly and characterized the S locus region. Four candidate gene were newly isolated by transcriptome analysis. Genome analysis revealed the S haplotype specific region at least reached more that 1 Mbp. All candidate genes were included in this region but the relative locations were unclear. We further shotgun sequenced the genome of Linum grandiflorum and de novo assembly. The assembled contigs will give new insights on the study of heterostyly.

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  • Studies on MADS-box transcription factors associated with bud dormancy regulation in the fruit tree species of Prunus

    Grant number:23380017  2011.04 - 2015.03

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

    YAMANE Hisayo, TAO Ryutaro, HABU Tsuyoshi, AKAGI Takashi, NAGAYAMA Erika, HOSAKA Yukari, SASAKI Ryuta, TAKEUCHI Nozomi

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    Grant amount:\16510000 ( Direct expense: \12700000 、 Indirect expense:\3810000 )

    Bud dormancy of temperate fruit trees is one of the important agronomic traits that affects next season’s annual growth. In this study, we used 454-pyrosequencing technique to gather sequence information of dormant bud ESTs in Prunus mume and to search for the candidate genes that are involved in endodormancy regulation. As a result, PmDAM4 and PmDAM5 were found to be up-regulated in endodormant buds as is the case with PmDAM6 which has already been identified as endodormancy-related gene in our previous studies. All six PmDAM genes were up-regulated when chilling exposure was avoided and down-regulated during cold treatment. Among them, PmDAM4, PmDAM5, and PmDAM6 were down-regulated by cold treatment in chilling requirement-dependent manner. These results suggested that PmDAMs play roles in genetic control of chilling requirement of Prunus mume.

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  • Analysis on Genomic Evolution via Domestication Steps of Amygdalus subgenus

    Grant number:23880013  2011

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Research Activity Start-up  Grant-in-Aid for Research Activity Start-up

    AKAGI Takashi

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    Grant amount:\1690000 ( Direct expense: \1300000 、 Indirect expense:\390000 )

    Genome-wide genetic structural analysis was conducted to 96 species of Amygdalus subgenus by using the SNPs information from ca. 9000 loci in the genome. It was suggested that current domesticated peach(Prunus persica) cultivars formed multiple clusters which had been under the historical artificial selections, to which wild cultivars have not been subjected. Comparison of differences in the genetic diversities among the clusters showed some specific selective sweeps on certain genomic regions of each cluster. Importantly, the clusters of the ornamental flower peaches and the main fruit peaches gave clues for artificial selective pressure on their certain genomic regions, respectively. These genomic regions contained genes apparently related to the characteristics specific to each cluster. It would be suggested that these genes importantly play substantial rolls to maintain the characteristics of each peach cluster and to lead them under the domestication.

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  • カキの甘渋性に関する研究

    Grant number:09J02989  2009 - 2010

    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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    Grant amount:\1400000 ( Direct expense: \1400000 )

    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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