Directory of Researchers

FUJIMOTO Ryo
Graduate School of Agricultural Science / Department of Bioresource Science
Associate Professor
Agriculture
Last Updated :2021/04/12

Researcher Profile and Settings

Affiliation

  • <Faculty / Graduate School / Others>

    Graduate School of Agricultural Science / Department of Bioresource Science
  • <Related Faculty / Graduate School / Others>

    Faculty of Agriculture / Department of Bioresource Science

Teaching

Research at Kobe

  • 20 Aug. 2019, The mechanism that controls Chinese cabbage flowering
  • 27 Oct. 2016, DNA methylation affects superiority of hybrid plants -Discovery could be used in efficient breeding of high-yield vegetables-

Research Activities

Research Areas

  • Environmental science/Agricultural science / Plant genetics and breeding
  • Environmental science/Agricultural science / Horticulture

Awards

  • Jan. 2018 神戸大学, 平成29年度優秀若手研究賞, 雑種強勢研究

    FUJIMOTO RYO

    Others

  • Oct. 2017 神戸大学農学部同窓会六篠会, 六篠論文賞, PNAS誌に掲載された論文

    FUJIMOTO RYO

    Others

  • Mar. 2017 日本育種学会, 平成28年度日本育種学会奨励賞, アブラナ科植物におけるゲノム多様性および雑種強勢に関する研究

    FUJIMOTO RYO

    Japan society

Published Papers

  • Naomi Miyaji, Motoki Shimizu, Takeshi Takasaki-Yasuda, Elizabeth S Dennis, Ryo Fujimoto

    KEY MESSAGE: Fusarium yellows resistant and susceptible lines in Brassica rapa showed different salicylic acid responses; the resistant line showed a similar response to previous reports, but the susceptible line differed. Fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans (Foc) is an important disease. Previous studies showed that genes related to salicylic acid (SA) response were more highly induced following Foc infection in Brassica rapa Fusarium yellows resistant lines than susceptible lines. However, SA-induced genes have not been identified at the whole genome level and it was unclear whether they were up-regulated by Foc inoculation. Transcriptome analysis with and without SA treatment in the B. rapa Fusarium yellows susceptible line 'Misugi' and the resistant line 'Nanane' was performed to obtain insights into the relationship between SA sensitivity/response and Fusarium yellows resistance. 'Nanane's up-regulated genes were related to SA response and down-regulated genes were related to jasmonic acid (JA) or ethylene (ET) response, but differentially expressed genes in 'Misugi' were not. This result suggests that Fusarium yellows resistant and susceptible lines have a different SA response and that an antagonistic transcription between SA and JA/ET responses was found only in a Fusarium yellows resistant line. SA-responsive genes were induced by Foc inoculation in Fusarium yellows resistant (RJKB-T23) and susceptible lines (RJKB-T24). By contrast, 39 SA-induced genes specific to RJKB-T23 might function in the defense response to Foc. In this study, SA-induced genes were identified at the whole genome level, and the possibility, the defense response to Foc observed in a resistant line could be mediated by SA-induced genes, is suggested. These results will be useful for future research concerning the SA importance in Foc or other diseases resistance in B. rapa.

    Corresponding, Apr. 2021, Plant cell reports, 40 (4), 605 - 619, English, International magazine

    [Refereed]

    Scientific journal

  • Hasan Mehraj, Daniel J Shea, Satoshi Takahashi, Naomi Miyaji, Ayasha Akter, Motoaki Seki, Elizabeth S Dennis, Ryo Fujimoto, Kenji Osabe

    Long noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels when both were present. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. B. rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and identified a suite of candidate lncRNAs that may be epigenetically regulated in the Brassica genus.

    2021, PloS one, 16 (3), e0242530, English, International magazine

    [Refereed]

    Scientific journal

  • Hasan Mehraj, Ayasha Akter, Naomi Miyaji, Junji Miyazaki, Daniel J Shea, Ryo Fujimoto, Md Asad-Ud Doullah

    The genus Brassica contains important vegetable crops, which serve as a source of oil seed, condiments, and forages. However, their production is hampered by various diseases such as clubroot and Fusarium wilt, especially in Brassica vegetables. Soil-borne diseases are difficult to manage by traditional methods. Host resistance is an important tool for minimizing disease and many types of resistance (R) genes have been identified. More than 20 major clubroot (CR) disease-related loci have been identified in Brassica vegetables and several CR-resistant genes have been isolated by map-based cloning. Fusarium wilt resistant genes in Brassica vegetables have also been isolated. These isolated R genes encode the toll-interleukin-1 receptor/nucleotide-binding site/leucine-rice-repeat (TIR-NBS-LRR) protein. DNA markers that are linked with disease resistance allele have been successfully applied to improve disease resistance through marker-assisted selection (MAS). In this review, we focused on the recent status of identifying clubroot and Fusarium wilt R genes and the feasibility of using MAS for developing disease resistance cultivars in Brassica vegetables.

    09 Jun. 2020, Plants (Basel, Switzerland), 9 (6), English, International magazine

    [Refereed]

    Scientific journal

  • In Arabidopsis thaliana Heterosis Level Varies among Individuals in an F1 Hybrid Population

    Hasan Mehraj, Takahiro Kawanabe, Motoki Shimizu, Naomi Miyaji, Ayasha Akter, Elizabeth S. Dennis and Ryo Fujimoto

    Corresponding, Mar. 2020, Plants, 9 (4), 414

    [Refereed]

    Scientific journal

  • Ayasha Akter, Etsuko Itabashi, Tomohiro Kakizaki, Keiichi Okazaki, Elizabeth S Dennis, Ryo Fujimoto

    The genus Brassica includes oil crops, vegetables, condiments, fodder crops, and ornamental plants. Brassica species underwent a whole genome triplication event after speciation between ancestral species of Brassica and closely related genera including Arabidopsis thaliana. Diploid species such as Brassica rapa and Brassica oleracea have three copies of genes orthologous to each A. thaliana gene, although deletion in one or two of the three homologs has occurred in some genes. The floral transition is one of the crucial events in a plant's life history, and time of flowering is an important agricultural trait. There is a variation in flowering time within species of the genus Brassica, and this variation is largely dependent on a difference in vernalization requirements. In Brassica, like in A. thaliana, the key gene of vernalization is FLOWERING LOCUS C (FLC). In Brassica species, the vernalization response including the repression of FLC expression by cold treatment and the enrichment of the repressive histone modification tri-methylated histone H3 lysine 27 (H3K27me3) at the FLC locus is similar to A. thaliana. B. rapa and B. oleracea each have four paralogs of FLC, and the allotetraploid species, Brassica napus, has nine paralogs. The increased number of paralogs makes the role of FLC in vernalization more complicated; in a single plant, paralogs vary in the expression level of FLC before and after vernalization. There is also variation in FLC expression levels between accessions. In this review, we focus on the regulatory circuits of the vernalization response of FLC expression in the genus Brassica.

    Corresponding, 2020, Frontiers in plant science, 11, 619417 - 619417, English, International magazine

    [Refereed]

    Scientific journal

  • Ayasha Akter, Junji Miyazaki, Daniel J. Shea, Namiko Nishida, Satoko Takada, Naomi Miyaji, Hasan Mehraj, Motoki Shimizu, Md. Asad-ud Doullah, Takeshi Takasaki-Yasuda, Keiichi Okazaki, Ryo Fujimoto

    Last, Japanese Society for Horticultural Science, 2020, The Horticulture Journal, 89 (3), 268 - 277, English

    [Refereed]

    Scientific journal

  • Comparison of Cold Responses for Orthologs of Cabbage Vernalization-related Genes

    Etsuko Itabashi, Daniel J. Shea, Nobuko Fukino, Ryo Fujimoto, Keiichi Okazaki, Tomohiro Kakizaki, Takayoshi Ohara

    Oct. 2019, The Horticulture Journal, 88 (4), 462 - 470, English

    [Refereed]

    Scientific journal

  • Ayasha Akter, Satoshi Takahashi, Weiwei Deng, Daniel J Shea, Etsuko Itabashi, Motoki Shimizu, Naomi Miyaji, Kenji Osabe, Namiko Nishida, Yutaka Suzuki, Chris A Helliwell, Motoaki Seki, William James Peacock, Elizabeth S Dennis, Ryo Fujimoto

    Brassica rapa L. is an important vegetable and oilseed crop. We investigated the distribution of the histone mark tri-methylation of H3K27 (H3K27me3) in B. rapa and its role in the control of gene expression at two stages of development (2-day cotyledons and 14-day leaves) and among paralogs in the triplicated genome. H3K27me3 has a similar distribution in two inbred lines, while there was variation of H3K27me3 sites between tissues. Sites that are specific to 2-day cotyledons have increased transcriptional activity, and low levels of H3K27me3 in the gene body region. In 14-day leaves, levels of H3K27me3 were associated with decreased gene expression. In the triplicated genome, H3K27me3 is associated with paralogs that have tissue-specific expression. Even though B. rapa and Arabidopsis thaliana are not closely related within the Brassicaceae, there is conservation of H3K27me3-marked sites in the two species. Both B. rapa and A. thaliana require vernalization for floral initiation with FLC being the major controlling locus. In all four BrFLC paralogs, low-temperature treatment increases H3K27me3 at the proximal nucleation site reducing BrFLC expression. Following return to normal temperature growth conditions, H3K27me3 spreads along all four BrFLC paralogs providing stable repression of the gene.

    01 Oct. 2019, DNA research : an international journal for rapid publication of reports on genes and genomes, 26 (5), 433 - 443, English, International magazine

    [Refereed]

    Scientific journal

  • Satoko Takada, Ayasha Akter, Etsuko Itabashi, Namiko Nishida, Daniel J Shea, Naomi Miyaji, Hasan Mehraj, Kenji Osabe, Motoki Shimizu, Takeshi Takasaki-Yasuda, Tomohiro Kakizaki, Keiichi Okazaki, Elizabeth S Dennis, Ryo Fujimoto

    There is a wide variation of flowering time among lines of Brassica rapa L. Most B. rapa leafy (Chinese cabbage etc.) or root (turnip) vegetables require prolonged cold exposure for flowering, known as vernalization. Premature bolting caused by low temperature leads to a reduction in the yield/quality of these B. rapa vegetables. Therefore, high bolting resistance is an important breeding trait, and understanding the molecular mechanism of vernalization is necessary to achieve this goal. In this study, we demonstrated that BrFRIb functions as an activator of BrFLC in B. rapa. We showed a positive correlation between the steady state expression levels of the sum of the BrFLC paralogs and the days to flowering after four weeks of cold treatment, suggesting that this is an indicator of the vernalization requirement. We indicate that BrFLCs are repressed by the accumulation of H3K27me3 and that the spreading of H3K27me3 promotes stable FLC repression. However, there was no clear relationship between the level of H3K27me3 in the BrFLC and the vernalization requirement. We also showed that if there was a high vernalization requirement, the rate of repression of BrFLC1 expression following prolonged cold treatments was lower.

    25 Sep. 2019, Scientific reports, 9 (1), 13843 - 13843, English, International magazine

    [Refereed]

    Scientific journal

  • Allele specific DNA marker for fusarium resistance gene FocBo1 in Brassica oleracea

    Maho Sato, Motoki Shimizu, Daniel J. Shea, Mozammel Hoque, Takahiro Kawanabe, Naomi Miyaji, FUJIMOTO RYO, Eigo Fukai, Keiichi Okazaki

    Jul. 2019, Breeding Science, 69, 308 - 315, English

    [Refereed]

    Scientific journal

  • Long noncoding RNAs in Brassica rapa L. following vernalization

    Daniel J Shea, Namiko Nishida, Satoko Takada, Etsuko Itabashi, Satoshi Takahashi, Ayasha Akter, Naomi Miyaji, Kenji Osabe, Hasan Mehraj, Motoki Shimizu, Motoaki Seki, Tomohiro Kakizaki, Keiichi Okazaki, Elizabeth S. Dennis, FUJIMOTO RYO

    Jun. 2019, Scientific Reports, 9 (1), 9302, English

    [Refereed]

    Scientific journal

  • アブラナ科植物における自家不和合性研究の最前線と育種現場での利用

    土松 隆志, 安田 晋輔, 高田 美信, 北柴 大泰, 新倉 聡, FUJIMOTO RYO, 柿崎 智博

    Jun. 2019, 育種学研究, 21 (1), 61 - 68, Japanese

  • Genome-Wide Analysis of Parent-of-Origin Allelic Expression in Endosperms of Brassicaceae Species, Brassica rapa.

    Takanori Yoshida, Takahiro Kawanabe, Yina Bo, FUJIMOTO RYO, Akira Kawabe

    Dec. 2018, Plant & Cell Physiology, 59 (12), 2590 - 2601, English

    [Refereed]

    Scientific journal

  • Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.

    Satoshi Takahashi, Kenji Osabe, Naoki Fukushima, Shohei Takuno, Naomi Miyaji, Motoki Shimizu, Takeshi Takasaki-Yasuda, Yutaka Suzuki, Elizabeth S Dennis, Motoaki Seki, FUJIMOTO RYO

    Oct. 2018, DNA Research, 25 (5), 511 - 520, English

    [Refereed]

    Scientific journal

  • How Brassica oleracea FLOWERING LOCUS C 2 works in Brassica rapa genetic background

    Namiko Nishida, Daniel J. Shea, Keiichi Okazaki, FUJIMOTO RYO

    Sep. 2018, AusCanola 2018 Proceedings E-book, 127 - 131, English

    [Invited]

  • Characterization of FLOWERING LOCUS C genes in leafy Brassica rapa vegetables

    FUJIMOTO RYO, Ayasha Akter, Namiko Nishida, Takeshi Takasaki-Yasuda, Elizabeth S Dennis

    Sep. 2018, AusCanola 2018 Proceedings E-book, 71 - 75, English

    [Invited]

  • The production and characterization of a BoFLC2 introgressed Brassica rapa by repeated backcrossing to an F1

    Daniel J. Shea, Yuki Tomaru, Etsuko Itabashi, Yuri Nakamura, Toshio Miyazaki, Tomohiro Kakizaki, Tonu Nazmoon Naher, Motoki Shimizu, FUJIMOTO RYO, Eigo Fukai, Keiichi Okazaki

    Aug. 2018, Breeding Science, 68 (3), 316 - 325, English

    [Refereed]

    Scientific journal

  • Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of a commercial F1 hybrid cultivar of Chinese cabbage

    Daniel J. Shea, Motoki Shimizu, Etsuko Itabashi, Naomi Miyaji, Junji Miyazaki, Kenji Osabe, Makoto Kaji, Keiichi Okazaki, FUJIMOTO RYO

    Aug. 2018, Breeding Science, 68 (3), 375 - 380, English

    [Refereed]

    Scientific journal

  • Daniel J. Shea, Etsuko Itabashi, Satoko Takada, Eigo Fukai, Tomohiro Kakizaki, Ryo Fujimoto, Keiichi Okazaki

    As climatic changes occur over the coming decades, our scientific understanding of plant responses to environmental cues will become an increasingly important consideration in the breeding of agricultural crops. This review provides a summary of the literature regarding vernalization research in Brassicaceae, covering both the historical origins of vernalization research and current understanding of the molecular mechanisms behind the regulatory pathways involved in vernalization and subsequent inflorescence. We discuss the evolutionarily conserved biology between the model organism Arabidopsis thaliana and the Brassica genus of crop cultivars and contrast the differences between the genera to illustrate the importance of Brassica-specific research into vernalization.

    CSIRO, 2018, Crop and Pasture Science, 69 (1), 30 - 39, English

    [Refereed]

    International conference proceedings

  • Satoshi Takahashi, Naoki Fukushima, Kenji Osabe, Etsuko Itabashi, Motoki Shimizu, Naomi Miyaji, Takeshi Takasaki-Yasuda, Yutaka Suzuki, Motoaki Seki, Ryo Fujimoto

    DNA methylation is an epigenetic gene regulatory mechanism that plays an essential role in gene expression, transposon silencing, genome imprinting and plant development. We investigated the influence of DNA methylation on gene expression in Brassica rapa L., to understand whether epigenetic differences exist between inbred lines. Genome-wide DNA methylation was analysed by methylated DNA immunoprecipitation sequencing (MeDIP-seq) of 14-day-old first and second leaves from two inbred lines of Chinese cabbage, one susceptible and one resistant to fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans. MACS (model-based analysis for ChIP-seq) identified DNA methylation peaks in genic regions including 2kb upstream, exon, intron and 2kb downstream. More than 65% of genes showed similar patterns of DNA methylation in the genic regions in the two inbred lines. DNA methylation states of the two inbred lines were compared with their transcriptome. Genes having DNA methylation in the intron and in the 200bp upstream and downstream regions were associated with a lower expression level in both lines. A small number of genes showed a negative correlation between differences in DNA methylation levels and differences in transcriptional levels in the two inbred lines, suggesting that DNA methylation in these genes results in transcriptional suppression.

    CSIRO, 2018, Crop and Pasture Science, 69 (1), 107 - 120, English

    [Refereed]

    International conference proceedings

  • Etsuko Itabashi, Kenji Osabe, Ryo Fujimoto, Tomohiro Kakizaki

    Epigenetic regulation, covalent modification of DNA and changes in histone proteins are closely linked to plant development and stress response through flexibly altering the chromatin structure to regulate gene expression. In this review, we will illustrate the importance of epigenetic influences by discussing three agriculturally important traits of Brassicaceae. (1) Vernalization, an acceleration of flowering by prolonged cold exposure regulated through epigenetic silencing of a central floral repressor, FLOWERING LOCUS C. This is associated with cold-dependent repressive histone mark accumulation, which confers competency of consequence vegetative-to-reproductive phase transition. (2) Hybrid vigor, in which an F1 hybrid shows superior performance to the parental lines. Combination of distinct epigenomes with different DNA methylation states between parental lines is important for increase in growth rate in a hybrid progeny. This is independent of siRNA-directed DNA methylation but dependent on the chromatin remodeler DDM1. (3) Self-incompatibility, a reproductive mating system to prevent self-fertilization. This is controlled by the S-locus consisting of SP11 and SRK which are responsible for self/non-self recognition. Because self-incompatibility in Brassicaceae is sporophytically controlled, there are dominance relationships between S haplotypes in the stigma and pollen. The dominance relationships in the pollen rely on de novo DNA methylation at the promoter region of a recessive allele, which is triggered by siRNA production from a flanking region of a dominant allele.

    Springer Verlag, 01 Jan. 2018, Plant Cell Reports, 37 (1), 87 - 101, English

    [Refereed]

    Scientific journal

  • Ryo Fujimoto, Kosuke Uezono, Wsonoko Ishikura, Kenji Osabe, W. James Peacock, Elizabeth S. Dennis

    Heterosis or hybrid vigor is a phenomenon where hybrid progeny have superior performance compared to their parental inbred lines. This is important in the use of F1 hybrid cultivars in many crops and vegetables. However, the molecular mechanism of heterosis is not clearly understood. Gene interactions between the two genomes such as dominance, overdominance, and epistasis have been suggested to explain the increased biomass and yield. Genetic analyses of F1 hybrids in maize, rice, and canola have defined a large number of quantitative trait loci, which may contribute to heterosis. Recent molecular analyses of transcriptomes together with reference to the epigenome of the parents and hybrids have begun to uncover new facts about the generation of heterosis. These include the identification of gene expression changes in hybrids, which may be important for heterosis, the role of epigenetic processes in heterosis, and the development of stable high yielding lines.

    Japanese Society of Breeding, 2018, Breeding Science, 68 (2), 145 - 158, English

    [Refereed][Invited]

    Scientific journal

  • Daniel J. Shea, Motoki Shimizu, Namiko Nishida, Eigo Fukai, Takashi Abe, Ryo Fujimoto, Keiichi Okazaki

    Background: Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species. In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling. Results: We show the accurate identification of introgressed genomic regions using both in silico simulated genomes, and a hybridized cultivar data set using our pipeline. Additionally we show, through targeted marker-based assays, validation of the IntroMap predicted regions for the hybrid cultivar. Conclusions: This approach can be used to automate the screening of large populations, reducing the time and labor required, and can improve the accuracy of the detection of introgressed regions in comparison to a marker-based approach. In contrast to other approaches that generally rely upon a variant calling step, our method achieves accurate identification of introgressed regions without variant calling, relying solely upon alignment.

    BIOMED CENTRAL LTD, Dec. 2017, BMC GENETICS, 18, 101, English

    [Refereed]

    Scientific journal

  • Naomi Miyaji, Motoki Shimizu, Junji Miyazaki, Kenji Osabe, Maho Sato, Yusuke Ebe, Satoko Takada, Makoto Kaji, Elizabeth S. Dennis, Ryo Fujimoto, Keiichi Okazaki

    Resistant and susceptible lines in Brassica rapa have different immune responses against Fusarium oxysporum inoculation.Fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans (Foc) is an important disease of Brassicaceae; however, the mechanism of how host plants respond to Foc is still unknown. By comparing with and without Foc inoculation in both resistant and susceptible lines of Chinese cabbage (Brassica rapa var. pekinensis), we identified differentially expressed genes (DEGs) between the bulked inoculated (6, 12, 24, and 72 h after inoculation (HAI)) and non-inoculated samples. Most of the DEGs were up-regulated by Foc inoculation. Quantitative real-time RT-PCR showed that most up-regulated genes increased their expression levels from 24 HAI. An independent transcriptome analysis at 24 and 72 HAI was performed in resistant and susceptible lines. GO analysis using up-regulated genes at 24 HAI indicated that Foc inoculation activated systemic acquired resistance (SAR) in resistant lines and tryptophan biosynthetic process and responses to chitin and ethylene in susceptible lines. By contrast, GO analysis using up-regulated genes at 72 HAI showed the overrepresentation of some categories for the defense response in susceptible lines but not in the resistant lines. We also compared DEGs between B. rapa and Arabidopsis thaliana after F. oxysporum inoculation at the same time point, and identified genes related to defense response that were up-regulated in the resistant lines of Chinese cabbage and A. thaliana. Particular genes that changed expression levels overlapped between the two species, suggesting that they are candidates for genes involved in the resistance mechanisms against F. oxysporum.

    SPRINGER, Dec. 2017, PLANT CELL REPORTS, 36 (12), 1841 - 1854, English

    [Refereed]

    Scientific journal

  • アブラナ科植物におけるゲノム多様性および雑種強勢に関する研究

    FUJIMOTO RYO

    Sep. 2017, 育種学研究, 19 (3), 116 - 123, Japanese

    [Invited]

    Scientific journal

  • Mozammel Hoque, Daniel J. Shea, Mitsuru Asada, Md. Asad-ud-Doullah, Motoki Shimizu, Ryo Fujimoto, Eigo Fukai, Keiichi Okazaki

    The tuberous stem of kohlrabi is an important quantitative trait, which affects its yield and quality. Genetic control of this trait has not yet been unveiled. To identify the QTLs controlling stem swelling of kohlrabi, a BC 1 population of 92 plants was developed from a cross of broccoli DH line GCP04 and kohlrabi var. Seine. A wide range of variation in tuberous stem diameter was observed among the mapping populations. We constructed a genetic map of nine linkage groups (LGs) with different types of markers, spanning a total length of 913.5 cM with an average marker distance of 7.55 cM. Four significant QTLs for radial enlargement of kohlrabi stem, namely, REnBo1, REnBo2, REnBo3, and REnBo4 were detected on C02, C03, C05, and C09, respectively, and accounted for the phenotypic variation of 59% for the stem diameter and 55% for the qualitative grading of tuberous stem in classes. Then, we confirmed the stability of identified QTLs using BC1S1 populations derived from the BC1 plants having heterozygous alleles at the target QTL and homozygous kohlrabi alleles at the remaining QTLs. REnBo1 and REnBo2 using 128 plants of BC(1)68S(1) and 94 plants of BC(1)43S(1), respectively, and REnBo3 and REnBo4 using 152 plants of BC(1)57S(1) were detected at the same positions as the respective QTLs of the BC1 population. Confirmation of QTLs in two successive generations indicates that the QTLs are persistent. The QTLs obtained in this study could be useful in marker-assisted selection of kohlrabi breeding, and to understand the genetic mechanisms of stem swelling and storage organ development in kohlrabi and other Brassica species.

    SPRINGER, Sep. 2017, MOLECULAR BREEDING, 37 (9), 109, English

    [Refereed]

    Scientific journal

  • アブラナ科植物の基礎研究と応用研究のネットワーク構築を目指して

    山本 雅也, 藤井 壮太, 柿崎 智博, FUJIMOTO RYO, 彦坂 幸毅, 畠山 勝徳, 伊藤 秀臣, 岡崎 桂一

    日本育種学会, Apr. 2017, 育種学研究, 19 (1), 21 - 29, Japanese

    [Invited]

  • Kazutaka Kawamura, Motoki Shimizu, Takahiro Kawanabe, Zujing Pu, Taro Kodama, Makoto Kaji, Kenji Osabe, Ryo Fujimoto, Keiichi Okazaki

    Cabbage (Brassica oleracea L. var. capitata) is an important vegetable worldwide. Most Japanese commercial cultivars of cabbage use an F-1 hybrid seed production system. The purity of F-1 hybrid seeds is important and the assessment of purity based on DNA markers can be highly accurate. In addition, selection of agronomically important traits such as disease resistance based on DNA markers is useful for breeding of cabbage. The aim of this study is to demonstrate the effectiveness of DNA marker-assisted selection in cabbage. In this study we distinguished the parental S haplotypes in 35 F-1 hybrid cultivars by combining several linked DNA markers. Thirty-one highly polymorphic simple sequence repeats (SSR) markers were screened from 175 reported SSR markers, which are useful for assessment of the purity of F-1 hybrid seeds. We examined the relationship between the DNA marker based genotype and the phenotype by an inoculation test of clubroot disease. A co-dominant PCR-RFLP marker was developed for selection of Fusarium yellows resistance and the genotypes using this marker were consistent with inoculation test in all tested samples.

    SPRINGER, Jan. 2017, EUPHYTICA, 213 (1), 28, English

    [Refereed]

    Scientific journal

  • Takahiro Kawanabe, Sonoko Ishikura, Naomi Miyaji, Taku Sasaki, Li Min Wu, Etsuko Itabashi, Satoko Takada, Motoki Shimizu, Takeshi Takasaki-Yasuda, Kenji Osabe, W. James Peacock, Elizabeth S. Dennis, Ryo Fujimoto

    Hybrid vigor or heterosis refers to the superior performance of F-1 hybrid plants over their parents. Heterosis is particularly important in the production systems of major crops. Recent studies have suggested that epigenetic regulation such as DNA methylation is involved in heterosis, but the molecular mechanism of heterosis is still unclear. To address the epigenetic contribution to heterosis in Arabidopsis thaliana, we used mutant genes that have roles in DNA methylation. Hybrids between C24 and Columbia-0 (Col) without RNA polymerase IV (Pol IV) or methyltransferase I (MET1) function did not reduce the level of biomass heterosis (as evaluated by rosette diameter). Hybrids with a mutation in decrease in dna methylation 1 (ddm1) showed a decreased heterosis level. Vegetative heterosis in the ddm1 mutant hybrid was reduced but not eliminated; a complete reduction could result if there was a change in methylation at all loci critical for generating the level of heterosis, whereas if only a proportion of the loci have methylation changes there may only be a partial reduction in heterosis.

    NATL ACAD SCIENCES, Oct. 2016, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 113 (43), E6704 - E6711, English

    [Refereed]

    Scientific journal

  • Genome-wide analysis of DNA methylation in Chinese cabbage

    Naoki Fukushima, Satoshi Takahashi, Etsuko Itabashi, Motoki Shimizu, Kenji Osabe, Takeshi Yasuda, Yutaka Suzuki, Motoaki Seki, Elizabeth S. Dennis, FUJIMOTO RYO

    Oct. 2016, Brassica 2016 Abstract Book, 172 - 177, English

    International conference proceedings

  • Identification of the Fusarium yellows resistance genes; its application for marker-assisted selection in Brassica rapa

    Naomi Miyaji, Motoki Shimizu, Satoko Takada, Takeshi Takasaki-Yasuda, Makoto Kaji, Kenji Osabe, Elizabeth S. Dennis, Keiichi Okazaki, FUJIMOTO RYO

    Oct. 2016, Brassica 2016 Abstract Book, 185 - 190, English

  • The epigenetic regulation of FLC expression by vernalization in Brassica rapa L

    Satoko Takada, Etsuko Itabashi, Naomi Miyaji, Takeshi Takasaki-Yasuda, Kenji Osabe, Elizabeth S. Dennis, FUJIMOTO RYO

    Oct. 2016, Brassica 2016 Abstract Book, 220 - 225, English

  • Characterization of early developmental and yield heterosis in Chinese cabbage

    FUJIMOTO RYO, Motoki Shimizu, Naomi Miyaji, Satoko Takada, Naoki Fukushima, Makoto Kaji, W. James Peacock, Elizabeth S. Dennis

    Oct. 2016, Brassica 2016 Abstract Book, 166 - 171, English

  • Kaoru Tonosaki, Kenji Osabe, Takahiro Kawanabe, Ryo Fujimoto

    Inter-specific hybrids are a useful source for increasing genetic diversity. Some reproductive barriers before and/or after fertilization prevent production of hybrid plants by inter-specific crossing. Therefore, techniques to overcome the reproductive barrier have been developed, and have contributed to hybridization breeding. In recent studies, identification of molecules involved in plant reproduction has been studied to understand the mechanisms of reproductive barriers. Revealing the molecular mechanisms of reproductive barriers may allow us to overcome reproductive barriers in inter-specific crossing, and to efficiently produce inter-specific hybrids in cross-combinations that cannot be produced through artificial techniques. Inter-specific hybrid plants can potentially serve as an elite material for plant breeding, produced through the merging of genomes of parental species by allopolyploidization. Allopolyploidization provides some benefits, such as heterosis, increased genetic diversity and phenotypic variability, which are caused by dynamic changes of the genome and epigenome. Understanding of allopolyploidization mechanisms is important for practical utilization of inter-specific hybrids as a breeding material. This review discusses the importance of reproductive barriers and the effect of allopolyploidization in crop breeding programs.

    JAPANESE SOC BREEDING, Jun. 2016, BREEDING SCIENCE, 66 (3), 333 - 349, English

    [Refereed]

    Scientific journal

  • Ultrastructural Changes in the stigma and upper style during floral development of Japanese pear.

    Li Lily, Okamura Ayaha, Nakanishi Tetsu, Fujimoto Ryo, TAKASAKI-YASUDA TAKESHI

    Mar. 2016, J. Electr. Microsc.Technol. Med. Biol., 29 (2), 1 - 7, English

    [Refereed]

    Scientific journal

  • Kazutaka Kawamura, Takahiro Kawanabe, Motoki Shimizu, Atsushi J. Nagano, Natsumi Saeki, Keiichi Okazaki, Makoto Kaji, Elizabeth S. Dennis, Kenji Osabe, Ryo Fujimoto

    Chinese cabbage (Brassica rapa L. var. pekinensis) is an important vegetable in Asia. Most Japanese commercial cultivars of Chinese cabbage use an F1 hybrid seed production system because of the high yielding cultivars produced. An efficient method for predicting hybrid performance in the parental generations is desired, and genetic distance between parental lines might be a good indicator of the level of hybrid vigor in a cross. Information concerning the genetic relationships among parental candidate inbred lines is useful for variety protection. The number of DNA markers available that can be used to assess the purity of inbred lines is limited in B. rapa. The aim of this study is to use DNA markers to assess the genetic distance between inbred lines to examine early developmental and yield heterosis so as to develop methods for selecting the best parental lines for the production of hybrids. We screened highly polymorphic SSR and CAPS markers to assess the genetic uniformity of inbred lines and characterize their genetic relationship. We examined the early size and yield heterosis in 32 F1 hybrids of Chinese cabbage. There was a moderate correlation in mid-parent heterosis between leaf size at 21 days after sowing and harvested biomass but not in best-parent heterosis. In contrast there was no correlation between genetic distance and mid-parent or best-parent heterosis, indicating that genetic distance does not predict the heterosis phenotype.

    Elsevier B.V., 01 Mar. 2016, Plant Gene, 5, 1 - 7, English

    [Refereed]

    Scientific journal

  • Genetic characterization of inbred lines of Chinese cabbage by DNA markers; towards the application of DNA markers to breeding of F1 hybrid cultivars.

    Kazutaka Kawamura, Takahiro Kawanabe, Motoki Shimizu, Keiichi Okazaki, Makoto Kaji, Elizabeth S Dennis, Kenji Osabe, FUJIMOTO RYO

    Mar. 2016, Data in Brief, 11 (6), 229 - 237, English

    [Refereed]

    Scientific journal

  • Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage

    Natsumi Saeki, Takahiro Kawanabe, Hua Ying, Motoki Shimizu, Mikiko Kojima, Hiroshi Abe, Keiichi Okazaki, Makoto Kaji, Jennifer M. Taylor, Hitoshi Sakakibara, W. James Peacock, Elizabeth S. Dennis, FUJIMOTO RYO

    Feb. 2016, BMC Plant Biology, 16 (1), 45, English

    [Refereed]

    Scientific journal

  • Changes in the Proteome of Xylem Sap in Brassica oleracea in Response to Fusarium oxysporum Stress

    Zijing Pu, Yoko Ino, Yayoi Kimura, Asumi Tago, Motoki Shimizu, Satoshi Natsume, Yoshitaka Sano, FUJIMOTO RYO, Kentaro Kaneko, Daniel J Shea, Eigo Fukai, Shinichi Fujii, Hisashi Hirano, Keiichi Okazaki

    Feb. 2016, Frontiers in Plant Science, 7, 31, English

    [Refereed]

    Scientific journal

  • Takahiro Kawanabe, Kenji Osabe, Etsuko Itabashi, Keiichi Okazaki, Elizabeth S. Dennis, Ryo Fujimoto

    Epigenetic regulation is crucial for the development of plants and for adaptation to a changing environment. Recently, genome-wide profiles of histone modifications have been determined by a combination of chromatin immunoprecipitation (ChIP) and genomic tiling arrays (ChIP on chip) or ChIP and high-throughput sequencing (ChIP-seq) in species including Arabidopsis thaliana, rice and maize. Validation of ChIP analysis by PCR or qPCR using positive and negative regions of histone modification is necessary. In contrast, information about histone modifications is limited in Chinese cabbage, Brassica rapa. The aim of this study was to develop positive and negative control primer sets for H3K4me3 (trimethylation of the 4th lysine of H3), H3K9me2, H3K27me3 and H3K36me3 in B. rapa. The expression and histone modification of four FLC paralogs in B. rapa, before and after vernalization, were examined using the method developed here. After vernalization, expression of all four BrFLC genes was reduced, and accumulation of H3K27me3 was observed in three of them. As with A. thaliana, the vernalization response and stability of FLC repression correlated with the accumulation of H3K27me3. These results suggest that the epigenetic state during vernalization is important for high bolting resistance in B. rapa. The positive and negative control primer sets developed here revealed positive and negative histone modifications in B. rapa that can be used as a control for future studies.

    GENETICS SOC JAPAN, Feb. 2016, GENES & GENETIC SYSTEMS, 91 (1), 1 - 10, English

    [Refereed]

    Scientific journal

  • Motoki Shimizu, Zi-jing Pu, Takahiro Kawanabe, Hiroyasu Kitashiba, Satoru Matsumoto, Yusuke Ebe, Monari Sano, Taketo Funaki, Eigo Fukai, Ryo Fujimoto, Keiichi Okazaki

    We identified the candidate gene conferring yellow wilt resistance (YR) in B. oleracea . This work will facilitate YR breeding programs for B. oleracea and its closely related species. Yellow wilt disease is one of the most serious diseases of cabbage worldwide. Type A resistance to the disease is controlled by a single dominant gene that is used in cabbage breeding. Our previous QTL study identified the FocBo1 locus controlling type A resistance. In this study, the FocBo1 locus was fine-mapped by using 139 recombinant F-2 plants derived from resistant cabbage (AnjuP01) and susceptible broccoli (GCP04) DH lines. As a result, we successfully delimited the location of FocBo1 within 1.00 cM between markers, BoInd 2 and BoInd 11. Analysis of BAC and cosmid sequences corresponding to the FocBo1 locus identified an orthologous gene of Bra012688 that was recently identified as an candidate gene that confers yellows resistance in Chinese cabbage. The candidate gene-specific DNA markers and phenotypes in F-1 cabbage cultivars and their selfed F-2 populations showed a perfect correlation. Our identification of the candidate gene for FocBo1 will assist introduction of fusarium resistance into B. oleracea cultivars and contribute further understanding of interaction between Brassica plants and fusarium.

    SPRINGER, Jan. 2015, THEORETICAL AND APPLIED GENETICS, 128 (1), 119 - 130, English

    [Refereed]

    Scientific journal

  • Motoki Shimizu, Ryo Fujimoto, Hua Ying, Zi-jing Pu, Yusuke Ebe, Takahiro Kawanabe, Natsumi Saeki, Jennifer M. Taylor, Makoto Kaji, Elizabeth S. Dennis, Keiichi Okazaki

    Fusarium yellows caused by Fusarium oxysporum f. sp. conglutinans is an important disease of Brassica worldwide. To identify a resistance (R) gene against Fusarium yellows in Chinese cabbage (Brassica rapa var. pekinensis), we analyzed differential expression at the whole genome level between resistant and susceptible inbred lines using RNA sequencing. Four hundred and eighteen genes were significantly differentially expressed, and these were enriched for genes involved in response to stress or stimulus. Seven dominant DNA markers at putative R-genes were identified. Presence and absence of the sequence of the putative R-genes, Bra012688 and Bra012689, correlated with the resistance of six inbred lines and susceptibility of four inbred lines, respectively. In F-2 populations derived from crosses between resistant and susceptible inbred lines, presence of Bra012688 and Bra012689 cosegregated with resistance, suggesting that Bra012688 and Bra012689 are good candidates for fusarium yellows resistance in Chinese cabbage.

    SPRINGER, Jun. 2014, PLANT MOLECULAR BIOLOGY, 85 (3), 247 - 257, English

    [Refereed]

    Scientific journal

  • Correlative gene/genome system in plant breeding

    Yuji Kishima, Ryohei Terauchi, Yoshinobu Takada, TAKUMI SHIGEO, FUJIMOTO RYO, Koji Murai

    日本育種学会, Jun. 2014, 育種学研究, 16 (2), 79 - 85, Japanese

    [Invited]

  • Md. Masud Karim, Asfakun Siddika, Nazmoon Naher Tonu, Delwar M. Hossain, Md. Bahadur Meah, Takahiro Kawanabe, Ryo Fujimoto, Keiichi Okazaki

    Brassica napus is a leading oilseed crop throughout many parts of the world. It is well adapted to long day photoperiods, however, it does not adapt well to short day subtropical regions. Short duration B. nap us plants were resynthesized through ovary culture from interspecific crosses in which B. rapa cultivars were reciprocally crossed with B. oleracea. From five different combinations, 17 hybrid plants were obtained in both directions. By self-pollinating the F-1 hybrids or introgressing them with cultivated B. napus, resynthesized (RS) F-3 and semi-resynthesized (SRS) F-2 generations were produced, respectively. In field trial in Bangladesh, the RS B. napus plants demonstrated variation in days to first flowering ranging from 29 to 73 days; some of which were similar to cultivated short duration B. napus, but not cultivated short duration B. rapa. The RS and SRS B. napus lines produced 2-4.6 and 1.6-3.7 times higher yields, respectively, as compared to cultivated short duration B. napus. Our developed RS lines may be useful for rapeseed breeding not only for subtropical regions, but also for areas such as Canada and Europe where spring rapeseed production can suffer from late spring frosts. Yield and earliness in RS lines are discussed.

    JAPANESE SOC BREEDING, Jan. 2014, BREEDING SCIENCE, 63 (5), 495 - 502, English

    [Refereed]

    Scientific journal

  • Hiroya Tomita, Motoki Shimizu, Md Asad-ud Doullah, Ryo Fujimoto, Keiichi Okazaki

    Throughout the world, clubroot disease is one of the most damaging diseases affecting Brassica oleracea. To develop marker-assisted selection (MAS) that could assist the incorporation of durable clubroot resistance (CR) into cultivars, previous genetic analyses have identified several CR quantitative trait loci (CR-QTL). However, the independent and cumulative effects of each CR locus against various isolates have rarely been tested. Previously, we identified one major CR-QTL and four minor CR-QTL in the F2 plants from broccoli doubled haploid (DH) line x cabbage DH line of B. oleracea. In the present study, to clarify their effectiveness for controlling disease involving various isolates, inoculation testing was conducted in genotypes with various combinations of the CR genes, which were selected using the DNA markers closely associated with each CR-QTL. In exploring the overall disease incidence, it was apparent that a single involvement of the major CR gene located in the PbBo(Anju)1 locus, or accumulation of CR genes in the minor CR-QTL, is not enough to confer sufficient resistance. One major CR gene in the QTL PbBo(Anju)1 locus plus two to three minor CR genes conferred moderate resistance. The genotype in which all of the CR genes locating in the five QTL including PbBo(Anju)1 were accumulated showed the highest resistance, and it was broadly resistant against six isolates. Accumulation of several CR genes by MAS is necessary to conduct CR breeding in B. oleracea. Our developed DNA markers can be used efficiently to make selections of required loci for the acquisition of resistance, and use of these markers will be a powerful tool for CR breeding in B. oleracea.

    SPRINGER, Dec. 2013, MOLECULAR BREEDING, 32 (4), 889 - 900, English

    [Refereed]

    Scientific journal

  • Michael Groszmann, Ian K. Greaves, Ryo Fujimoto, W. James Peacock, Elizabeth S. Dennis

    Hybrid vigour, or heterosis, refers to the increased yield and biomass of hybrid offspring relative to the parents. Although this has been exploited in plants for agriculture and horticulture, the molecular and cellular mechanisms underlying hybrid vigour are largely unknown. Genetic analyses show that there are a large number of quantitative trait loci (QTLs) that contribute to the heterotic phenotype, indicating that it is a complex phenomenon. Gene expression in hybrids is regulated by the interactions of the two parental epigenetic systems and the underlying genomes. Increasing understanding of the interplay of small RNA (sRNA) molecules, DNA methylation, and histone marks provides new opportunities to define the basis of hybrid vigour and to understand why F1 heterosis is not passed on to subsequent generations. We discuss recent findings that suggest the existence of several pathways that alter DNA methylation patterns, which may lead to transcriptional changes resulting in the heterotic phenotype.

    ELSEVIER SCIENCE LONDON, Dec. 2013, TRENDS IN GENETICS, 29 (12), 684 - 690, English

    [Refereed]

    Scientific journal

  • Comparison of Positions of QTLs Conferring Resistance to Xanthomonas campestris pv. campestris in Brassica oleracea

    TONU NAZMOON NAHER, DOULLAH MD. ASAD-UD, SHIMIZU MOTOKI, KARIM MD. MASUD, KAWANABE TAKAHIRO, FUJIMOTO RYO, OKAZAKI KEIICHI

    Black rot, caused by Xanthomonas campestris pv. campestris (Xcc) is possibly the most important disease of Brassica worldwide. To compare chromosomal positions of Xcc resistance loci in Brassica oleracea between the present and published studies and to develop marker assisted selection (MAS) to resistance against Xcc race 1, we constructed a B. oleracea map, including pW, pX an

    Scientific Research, Aug. 2013, American Journal of Plant Sciences, 4 (8), 11 - 20, English

    [Refereed]

    Scientific journal

  • Takahiro Kawanabe, Ryo Fujimoto, Taku Sasaki, Jennifer M. Taylor, Elizabeth S. Dennis

    Difference in the level of expression of genes is one of the factors contributing to plant phenotype. As well as being under genetic control, gene expression is regulated by epigenetic processes such as DNA methylation and histone modifications. We compared genome-wide gene expression between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera to understand which genes might contribute to species differences. Genes categorized into response to stress tended to show differential expression between species, suggesting that divergence of expression in these genes contributes to adaptation to environmental conditions following the divergence of species. Regions methylated in A. lyrata were identified from Methylated-DNA immunoprecipitation, and this DNA methylation profile together with transcriptome data revealed that gene body methylation was not associated with differential gene expression between A. thaliana and A. lyrata. The DNA methylation status of four putative imprinted genes of A. lyrata was examined and found to be conserved in vegetative tissues between A. thaliana and A. lyrata in FIS2, HDG3, and HDG9, but not in HDG8. (C) 2012 Elsevier B.V. All rights reserved.

    ELSEVIER SCIENCE BV, Sep. 2012, GENE, 506 (2), 301 - 309, English

    [Refereed][Invited]

    Scientific journal

  • Zi-jing Pu, Motoki Shimizu, Yan-ju Zhang, Tomohiko Nagaoka, Takeshi Hayashi, Hidetaka Hori, Satoru Matsumoto, Ryo Fujimoto, Keiichi Okazaki

    Fusarium wilt caused by Fusarium oxysporum f. sp. conglutinans is one of the most important diseases of Brassica crops, resulting in severe reductions in yield and quality. To characterize the inheritance pattern of fusarium resistance, a cross between a susceptible broccoli and a resistant cabbage was subjected to segregation analysis. Results indicated that resistance was controlled by a single dominant allele. This gene was named Foc-Bo1 and mapped to linkage group seven (O7) by both the segregation test and quantitative trait locus (QTL) analysis. The QTL on O7 was detected with a logarithm of odds score (LOD) of 19.5, which was above the threshold value with genome-wide 1% significance level (2.01). A minor QTL was also detected on O4 with a LOD score of 2.06. Inoculation tests indicated that stable expression of fusarium resistance at high temperatures required Foc-Bo1 homozygosity. The association between Foc-Bo1 and the closest simple sequence repeat marker (KBrS003O1N10) was analyzed in three F3 populations. Based on these studies, KBrS003O1N10 represents an effective marker-assisted selection (MAS) tool for breeding fusarium wilt resistance into Brassica oleracea crops. To our knowledge, this is the first paper to map the fusarium-resistance gene in Brassica species and to validate the effectiveness of MAS in improving fusarium resistance in these important plants.

    SPRINGER, Aug. 2012, MOLECULAR BREEDING, 30 (2), 809 - 818, English

    [Refereed]

    Scientific journal

  • Ryo Fujimoto, Taku Sasaki, Ryo Ishikawa, Kenji Osabe, Takahiro Kawanabe, Elizabeth S. Dennis

    Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve alteration to the nucleotide sequence, can also cause changes in gene activity by changing the structure of chromatin through DNA methylation or histone modifications. Now there is evidence based on induced or spontaneous mutants that epigenetic changes can cause altering plant phenotypes. Epigenetic changes have occurred frequently in plants, and some are heritable or metastable causing variation in epigenetic status within or between species. Therefore, heritable epigenetic variation as well as genetic variation has the potential to drive natural variation.

    MDPI AG, Aug. 2012, INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 13 (8), 9900 - 9922, English

    [Refereed][Invited]

    Scientific journal

  • Kenji Osabe, Takahiro Kawanabe, Taku Sasaki, Ryo Ishikawa, Keiichi Okazaki, Elizabeth S. Dennis, Tomohiko Kazama, Ryo Fujimoto

    An allopolyploid is an individual having two or more complete sets of chromosomes derived from different species. Generation of allopolyploids might be rare because of the need to overcome limitations such as co-existing populations of parental lines, overcoming hybrid incompatibility, gametic non-reduction, and the requirement for chromosome doubling. However, allopolyploids are widely observed among plant species, so allopolyploids have succeeded in overcoming these limitations and may have a selective advantage. As techniques for making allopolyploids are developed, we can compare transcription, genome organization, and epigenetic modifications between synthesized allopolyploids and their direct parental lines or between several generations of allopolyploids. It has been suggested that divergence of transcription caused either genetically or epigenetically, which can contribute to plant phenotype, is important for the adaptation of allopolyploids.

    MDPI, Jul. 2012, INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 13 (7), 8696 - 8721, English

    [Refereed][Invited]

    Scientific journal

  • Ryo Fujimoto, Jennifer M. Taylor, Sachiko Shirasawa, W. James Peacock, Elizabeth S. Dennis

    Arabidopsis thaliana shows hybrid vigor (heterosis) in progeny of crosses between Columbia-0 and C24 accessions. Hybrid vigor was evident as early as mature seeds and in seedlings 3 d after sowing (DAS). At 3 DAS, genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes that have greater than midparent values of expression in the hybrid. Many of these genes are involved in chlorophyll biosynthesis and photosynthesis. The rate of photosynthesis was constant per unit leaf area in parents and hybrids. Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll, and more photosynthesis. The increased transcription of the chloroplast-targeted genes was restricted to the 3-7 DAS period. At 10 DAS, only 118 genes had expression levels different from the expected midparent value in the hybrid, and only 12 of these genes were differentially expressed at 3 DAS. The early increase in activity of genes involved in photosynthesis and the associated phenomena of increases in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass. In support of this correlation, we found that an inhibitor of photosynthesis eliminated heterosis and that higher light intensities enhanced both photosynthesis and heterosis. In hybrids with low-level heterosis (Landsberg erecta x Columbia-0), chloroplast-targeted genes were not up-regulated and leaf areas were only marginally increased.

    NATL ACAD SCIENCES, May 2012, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109 (18), 7109 - 7114, English

    [Refereed][Invited]

    Scientific journal

  • Kawanabe T, Osabe K, Fujimoto R

    2012, Bulletin of the Faculty of Agriculture, Niigata University, 64 (2), 143 - 149

    [Refereed]

  • Ryo Fujimoto, Jennifer M. Taylor, Taku Sasaki, Takahiro Kawanabe, Elizabeth S. Dennis

    The merging of two different genomes occurs during the formation of amphidiploids, and the merged regulatory networks have the potential to generate a new gene expression pattern. We examined the genome-wide gene expression of two newly synthesized amphidiploids between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera. 1,137 (4.7%) and 1,316 (5.4%) of probesets showed differential gene expression in A. thaliana-A. halleri and A. thaliana-A. lyrata hybrids respectively, compared to the mid parent value and of these, 489 were in common. Genes that differed in expression between the parental lines tended to have an expression level in both hybrids differing from the mid parent value. In contrast to protein coding genes, there is little differential expression of transposons. Genes in the categories of chloroplast-targeted and response to stress were overrepresented in the non-additively expressed genes in both amphidiploids. As these genes have the potential to contribute directly to the plant phenotype, we suggest that rapid changes of gene expression in amphidiploids might be important for producing greater biomass.

    SPRINGER, Nov. 2011, PLANT MOLECULAR BIOLOGY, 77 (4-5), 419 - 431, English

    [Refereed]

    Scientific journal

  • Takahiro Kawanabe, Ryo Fujimoto

    Arabidopsis thaliana is a quantitative long-day plant with the timing of the floral transition being regulated by both endogenous signals and multiple environmental factors, fwa is a late-flowering mutant, and this phenotype is due to ectopic FWA expression caused by hypomethylation at the FWA locus. The floral transition results in the activation of the floral development process, the key regulators being the floral meristem identity genes, AP1 (APETALA1) and LFY (LEAFY). In this study, we describe inflorescence abnormalities in plants overexpressing the Arabidopsis lyrata FT (AIFT) and A. thaliana FWA (AtFWA) genes simultaneously. The inflorescence abnormality phenotype was present in only a proportion of plants. All plants overexpressing both AIFT and AtFWA flowered earlier than fwa, suggesting that the inflorescence abnormality and earlier flowering time are caused independently. The inflorescence abnormality phenotype was similar to that of the double mutant of ap1 and fly, and AP1 and LFY genes were down-regulated in the abnormal inflorescences. From these results, we suggest that not only does ectopic AtFWA expression inhibit AtFT/AIFT function to delay flowering but that overexpression of AtFWA and AIFT together inhibits AP1 and LFY function to produce abnormal inflorescences. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

    ELSEVIER IRELAND LTD, Oct. 2011, PLANT SCIENCE, 181 (4), 496 - 503, English

    [Refereed]

    Scientific journal

  • Michael Groszmann, Ian K. Greaves, Nicolas Albert, Ryo Fujimoto, Chris A. Helliwell, Elizabeth S. Dennis, W. James Peacock

    In this review we have analysed two major biological systems involving epigenetic control of gene activity. In the first system we demonstrate the interplay between genetic and epigenetic controls over the transcriptional activity of FLC, a major repressor of flowering in Arabidopsis. FLC is down-regulated by low temperature treatment (vernalisation) releasing the repressor effect on flowering. We discuss the mechanisms of the reduced transcription and the memory of the vernalisation treatment through vegetative development. We also discuss the resetting of the repressed activity level of the PLC gene, following vernalisation, to the default high activity level and show it occurs during both male and female gametogenesis but with different timing in each. In the second part of the review discussed the complex multigenic system which is responsible for the patterns of gene activity which bring about hybrid vigour in crosses between genetically similar but epigenetically distinct parents. The epigenetic systems that we have identified as contributing to the heterotic phenotype are the 24nt siRNAs and their effects on RNA dependent DNA methylation (RdDM) at the target loci leading to changed expression levels. We conclude that it is likely that epigenetic controls are involved in expression systems in many aspects of plant development and plant function. (C) 2011 Elsevier B.V. All rights reserved.

    ELSEVIER SCIENCE BV, Aug. 2011, BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, 1809 (8), 427 - 437, English

    [Refereed]

    Scientific journal

  • Ryo Fujimoto, Taku Sasaki, Hiroshi Kudoh, Jennifer M. Taylor, Tetsuji Kakutani, Elizabeth S. Dennis

    P>fwa is a late flowering epi-mutant in Arabidopsis thaliana. FWA is silenced by DNA methylation in vegetative tissue but is demethylated in the central cell of the female ovule and continues to be expressed in the endosperm from the maternal copy. FWA is stably silenced in A. thaliana, but in related Arabidopsis species, FWA expression and DNA methylation levels vary in vegetative tissue. In this study, we show that variation in FWA expression in field isolates having identical DNA sequences is associated with changes in DNA methylation and may change over time. Vegetative FWA expression is correlated with decreased methylation at non-CG sites in the region upstream of the transcription start site in species related to A. thaliana and we conclude that methylation of this region is critical for FWA silencing in these species. In A. thaliana, FWA expression is affected by methylation in regions both upstream and downstream of the transcription start site. Ectopic A. thaliana FWA expression causes a late flowering phenotype, but over-expression of Arabidopsis lyrata FWA does not. In A. thaliana, stable silencing of FWA to prevent late flowering may have evolved through the selection of large tandem repeats and spread of the critical methylated region to include these repeats.

    WILEY-BLACKWELL, Jun. 2011, PLANT JOURNAL, 66 (5), 831 - 843, English

    [Refereed]

    Scientific journal

  • Taku Sasaki, Ryo Fujimoto, Sachie Kishitani, Takeshi Nishio

    DNA methylation is an important epigenetic modification regulating gene expression and transposon silencing. Although epigenetic regulation is involved in some agricultural traits, there has been relatively little research on epigenetic modifications of genes in Brassica rapa, which includes many important vegetables. In B. rapa, orthologs of DDM1, a chromatin remodeling factor required for maintenance of DNA methylation, have been characterized and DNA hypomethylated knock-down plants by RNAi (ddm1-RNAi plants) have been generated. In this study, we investigated differences of DNA methylation status at the genome-wide level between a wild-type (WT) plant and a ddm1-RNAi plant by methylation-sensitive amplification polymorphism (MSAP) analysis. MSAP analysis detected changes of DNA methylation of many repetitive sequences in the ddm1-RNAi plant. Search for body methylated regions in the WT plant revealed no difference in gene body methylation levels between the WT plant and the ddm1-RNAi plant. These results indicate that repetitive sequences are preferentially methylated by DDM1 genes in B. rapa.

    SPRINGER, Jan. 2011, PLANT CELL REPORTS, 30 (1), 81 - 88, English

    [Refereed]

    Scientific journal

  • Ryo Fujimoto, Yuki Kinoshita, Akira Kawabe, Tetsu Kinoshita, Kazuya Takashima, Magnus Nordborg, Mikhail E. Nasrallah, Kentaro K. Shimizu, Hiroshi Kudoh, Tetsuji Kakutani

    A central question in genomic imprinting is how a specific sequence is recognized as the target for epigenetic marking. In both mammals and plants, imprinted genes are often associated with tandem repeats and transposon-related sequences, but the role of these elements in epigenetic gene silencing remains elusive. FWA is an imprinted gene in Arabidopsis thaliana expressed specifically in the female gametophyte and endosperm. Tissue-specific and imprinted expression of FWA depends on DNA methylation in the FWA promoter, which is comprised of two direct repeats containing a sequence related to a SINE retroelement. Methylation of this element causes epigenetic silencing, but it is not known whether the methylation is targeted to the SINE-related sequence itself or the direct repeat structure is also necessary. Here we show that the repeat structure in the FWA promoter is highly diverse in species within the genus Arabidopsis. Four independent tandem repeat formation events were found in three closely related species. Another related species, A. halleri, did not have a tandem repeat in the FWA promoter. Unexpectedly, even in this species, FWA expression was imprinted and the FWA promoter was methylated. In addition, our expression analysis of FWA gene in vegetative tissues revealed high frequency of intra-specific variation in the expression level. In conclusion, we show that the tandem repeat structure is dispensable for the epigenetic silencing of the FWA gene. Rather, SINE-related sequence is sufficient for imprinting, vegetative silencing, and targeting of DNA methylation. Frequent independent tandem repeat formation events in the FWA promoter led us to propose that they may be a consequence, rather than cause, of the epigenetic control. The possible significance of epigenetic variation in reproductive strategies during evolution is also discussed.

    PUBLIC LIBRARY SCIENCE, Apr. 2008, PLOS GENETICS, 4 (4), English

    [Refereed]

    Scientific journal

  • Ryo Fujimoto, Yuki Kinoshita, Akira Kawabe, Tetsu Kinoshita, Kazuya Takashima, Magnus Nordborg, Mikhail E. Nasrallah, Kentaro K. Shimizu, Hiroshi Kudoh, Tetsuji Kakutani

    A central question in genomic imprinting is how a specific sequence is recognized as the target for epigenetic marking. In both mammals and plants, imprinted genes are often associated with tandem repeats and transposon-related sequences, but the role of these elements in epigenetic gene silencing remains elusive. FWA is an imprinted gene in Arabidopsis thaliana expressed specifically in the female gametophyte and endosperm. Tissue-specific and imprinted expression of FWA depends on DNA methylation in the FWA promoter, which is comprised of two direct repeats containing a sequence related to a SINE retroelement. Methylation of this element causes epigenetic silencing, but it is not known whether the methylation is targeted to the SINE-related sequence itself or the direct repeat structure is also necessary. Here we show that the repeat structure in the FWA promoter is highly diverse in species within the genus Arabidopsis. Four independent tandem repeat formation events were found in three closely related species. Another related species, A. halleri, did not have a tandem repeat in the FWA promoter. Unexpectedly, even in this species, FWA expression was imprinted and the FWA promoter was methylated. In addition, our expression analysis of FWA gene in vegetative tissues revealed high frequency of intra-specific variation in the expression level. In conclusion, we show that the tandem repeat structure is dispensable for the epigenetic silencing of the FWA gene. Rather, SINE-related sequence is sufficient for imprinting, vegetative silencing, and targeting of DNA methylation. Frequent independent tandem repeat formation events in the FWA promoter led us to propose that they may be a consequence, rather than cause, of the epigenetic control. The possible significance of epigenetic variation in reproductive strategies during evolution is also discussed. © 2008 Fujimoto et al.

    Apr. 2008, PLoS Genetics, 4 (4), e1000048, English

    [Refereed]

    Scientific journal

  • Ryo Fujimoto, Taku Sasaki, Hisashi Inoue, Takeshi Nishio

    DNA methylation and histone modification play important roles in regulating gene expression. The DDM1 gene in Arabidopsis thaliana (AtDDM1) is required for the maintenance of DNA methylation level and histone H3 methylation pattern. We isolated DDM1 homologs of Brassica rapa, BrDDM1a and BrDDM1b, which have 84.4% and 84.1% deduced amino acid sequence identities with AtDDM1, respectively. Both the BrDDM1a and BrDDM1b genes were found to be expressed in vegetative and reproductive tissues. B. rapa ddm1-RNAi transgenic plants with reduced levels of BrDDM1a/BrDDM1b expression showed genome-wide and non-tissue-specific demethylation. These results suggest that the BrDDM1a and BrDDM1b genes are orthologs of AtDDM1 and are required for the maintenance of DNA methylation as is AtDDM1. Despite genome-wide demethylation, developmental abnormalities were not found in the ddm1-RNAi transgenic plants. Dominance relationships of SP11/SCR alleles, the determinant of pollen recognition specificity in Brassica self-incompatibility, in S heterozygotes in B. rapa were not influenced by the low level of the BrDDM1 expression. Transcriptional reactivation of retrotransposon-like sequences observed in the ddm1-RNAi transgenic plants indicates that BrDDM1a and BrDDM1b participate in silencing of retrotransposons. Hypomethylation states of the ddm1-RNAi transgenic plants were inherited by plants of the next generation even by plants which had lost the RNAi construct by segregation. Remethylation was observed in a few progenies. Efficiencies of remethylation in the progenies without the RNAi construct were different between 18S rDNA, BoSTF12a/15a, and BrTto1 sequences.

    SPRINGER, Mar. 2008, PLANT MOLECULAR BIOLOGY, 66 (5), 463 - 473, English

    [Refereed]

    Scientific journal

  • The pattern of amplification and differentiation of Ty1-copia and Ty3-gypsy retrotransposons in Brassicaceae species

    Ryo Fujimoto, Shohei Takuno, Taku Sasaki, Takeshi Nishio

    One of the causes of genome size expansion is considered to be amplification of retrotransposons. We determined nucleotide sequences of 24 PCR products for each of six retrotransposons in Brassica rapa and Brassica oleracea. Phylogenetic trees of these sequences showed species-specific clades. We also sequenced STF7a homologs and Tto1 homologs, 24 PCR products each, in nine diploids and three allopolyploids, and constructed phylogenetic trees. In these phylogenetic trees, species-specific clades of diploid species were also formed, but retrotransposons of allopolyploids were clustered into the clades of their original genomes, indicating that these two retrotransposons amplified after speciation of the nine diploids. Genetic variation in these retrotransposons may have arisen before emergence of allopolyploid species. There was a positive correlation between the genome size and the average number of substitutions of STF7a and Tto1 homologs in at least seven diploids. The implications of these results in the genome evolution of Brassicaceae are herein discussed.

    GENETICS SOC JAPAN, Feb. 2008, GENES & GENETIC SYSTEMS, 83 (1), 13 - 22, English

    [Refereed]

    Scientific journal

  • Akira Kawabe, Ryo Fujimoto, Deborah Charlesworth

    Molecular imprinting is the differential expression and/or silencing of alleles according to their parent of origin [1, 2]. Conflicts between parents, or parents and offspring, should cause "arms races," with accelerated evolution of the genes involved in imprinting. This should be detectable in the evolution of imprinting genes' protein sequences and in the promoter regions of imprinted genes. Previous studies, however, found no evidence of more amino acid substitutions in imprinting genes [1, 3]. We have analyzed sequence diversity of the Arabidopsis lyrata Medea (MEA) gene and divergence from the A. thaliana sequence, including the first study of the promoter region. In A. thaliana, MEA is imprinted, with paternal alleles silenced in endosperm cells [4, 5], and also functions in the imprinting machinery [4, 6]; MEA protein binding at the MEA promoter region indicates self-regulated imprinting [7-9]. We find the same paternal MEA allele silencing in A. lyrata endosperm but no evidence for adaptive evolution in the coding region, whereas the 5' flanking region displays high diversity, with distinct haplotypes, suggesting balancing selection in the promoter region.

    CELL PRESS, Nov. 2007, CURRENT BIOLOGY, 17 (21), 1885 - 1889, English

    [Refereed]

    Scientific journal

  • Shohei Takuno, Ryo Fujimoto, Tetsu Sugimura, Keiichi Sato, Shunsuke Okamoto, Shao-Ling Zhang, Takeshi Nishio

    In self-incompatibility, a number of S haplotypes are maintained by frequency-dependent selection, which results in trans-specific S haplotypes. The region of several kilobases (similar to 40-60 kb) from SP6 to SP2, including self-incompatibility-related genes and some adjacent genes in Brassica rapa, has high nucleotide diversity due to the hitchhiking effect, and therefore we call this region the "S-locus complex." Recombination in the S-locus complex is considered to be suppressed. We sequenced regions of >50 kb of the S-locus complex of three S haplotypes in B. rapa and found higher nucleotide diversity in intergenic regions than in coding regions. Two highly similar regions of >10 kb were found between BrS-8 and BrS-46 Phylogenetic analysis using trans-specific S haplotypes (called interspecific pairs) of B. rapa and B. oleracea suggested that recombination reduced the nucleotide diversity in these two regions and that the genes not involved in self-incompatibility in the S-locus complex and the kinase domain, but not the S domain, of SRK have also experienced recombination. Recombination may reduce hitchhiking diversity in the S-locus complex, whereas the region from the S domain to SP11 would disfavor recombination.

    GENETICS, Oct. 2007, GENETICS, 177 (2), 949 - 958, English

    [Refereed]

    Scientific journal

  • Y. Hori, R. Fujimoto, Y. Sato, T. Nishio

    DNA polymorphism of the Wx gene in glutinous rice cultivars was investigated by PCR-RF-SSCP and heteroduplex cleavage analysis using Brassica petiole extract, and the nucleotide sequence variations were identified. Most japonica-type glutinous rice was found to have a 23-bp duplication in the second exon, which causes loss of the function of granule-bound starch synthase (GBSS) encoded by the Wx gene. Without the 23-bp duplication, there was an insertion of 7,764 bp in the ninth exon of the wx allele of 'Oragamochi'. Expression analysis of the wx allele using RT-PCR and Northern blot analysis revealed that transcripts of the 'Oragamochi' wx allele are about 1-kb shorter and that the deduced amino acid sequence of the transcript lacks a motif important for GBSS. Therefore, this insertion was considered to be the cause of the glutinous trait of 'Oragamochi'. This 7,764-bp insertion had long terminal repeats, a primer binding site, and a polypurine tract, but no sequence homologous with gag and pol, suggesting that it is a non-autonomous element. Furthermore, it had a structure similar to Dasheng and may be a member of Dasheng.

    SPRINGER, Jul. 2007, THEORETICAL AND APPLIED GENETICS, 115 (2), 217 - 224, English

    [Refereed]

    Scientific journal

  • Shunsuke Okamoto, Masashi Odashima, Ryo Fujimoto, Yutaka Sato, Hiroyasu Kitashiba, Takeshi Nishio

    Brassica napus is an amphidiploid species with the A genome from Brassica rapa and the C genome from Brassica oleracea. Although B. rapa, B. oleracea and artificially synthesized amphidiploids with the AC genome are self-incompatible, B. napus is self-compatible. Six S genotypes were identified in B. napus, five of which had class I S haplotypes from one species and a class II S haplotype from the other species, and mutations causing self-compatibility were identified in three of these S genotypes. The most predominant S genotype (BnS-1;BnS-6), which is that of cv. 'Westar', had a class I S haplotype similar to B. rapa S-47 (BrS-47) and a class II S haplotype similar to B. oleracea S-15 (BoS-15). The stigmas of 'Westar' rejected the pollen grains of both BrS-47 and BoS-15, while reciprocal crossings were compatible. Insertion of a DNA fragment of about 3.6 kb was found in the promoter region of the SP11/SCR allele of BnS-1, and transcripts of SP11/SCR were not detected in 'Westar'. The nucleotide sequence of the SP11 genomic DNA of BnS-6 was 100% identical to that of SP11 of BoS-15. Class I SP11 alleles from one species showed dominance over class II SP11 alleles from the other species in artificially synthesized B. napus lines, suggesting that the non-functional dominant SP11 allele suppressed the expression of the recessive SP11 allele in 'Westar'. Two other S genotypes in B. napus also had non-functional class I S haplotypes together with recessive BnS-6. These observations suggest independent origins of self-compatibility in B. napus.

    BLACKWELL PUBLISHING, May 2007, PLANT JOURNAL, 50 (3), 391 - 400, English

    [Refereed]

    Scientific journal

  • Ryo Fujimoto, Takeshi Nishio

    Self-incompatibility system has been most intensively studied in Brassica because of the advantage as plant materials and the importance as crop species. The determinants of self-recognition specificity in the stigma and the pollen are SRK and SP11/SCR, respectively. The genes of SRK and SP11 have many alleles in a species and are closely linked with each other in the S-locus complex. A set of SRK and SP11 alleles are referred to as S haplotype. Sequence analyses of many alleles of SRK and SP11 in Brassica species revealed pairs of S haplotypes having highly similar SRK and SP11 alleles between different species. The interspecific pair of S haplotypes is considered to be derived from the same ancestral S haplotype and to have maintained the same recognition specificity. The structure of the S-locus complex is highly variable, and this high structural polymorphism is considered to be important for suppressing the recombination between SRK and SP11, which may result in the breakdown of self-incompatibility. The first candidate protein identified as the female S determinant was SLG, which is abundant on the stigma surface, but the function of SLG in self-incompatibility is unclear. The dominance relationships of the SRK alleles are different from those of the SP11 alleles, and dominance order of S haplotypes is nonlinear. Recently, methylation of the promoter region of SP11 has been reported to be responsible for transcriptional suppression of recessive SP11. Several mutations in SP11 and SRK causing self-compatibility have been identified, and other genes controlling self-incompatibility have also been reported. These molecular studies can contribute to the development of the F(1) hybrid breeding using the self-incompatibility system in Brassica crops.

    ACADEMIC PRESS LTD-ELSEVIER SCIENCE LTD, 2007, ADVANCES IN BOTANICAL RESEARCH: INCORPORATING ADVANCES IN PLANT PATHOLOGY, VOL 45, 45, 139 - 154, English

    [Refereed]

    In book

  • Characterization of DNA methyltransferase genes in Brassica rapa

    Ryo Fujimoto, Taku Sasaki, Takeshi Nishio

    DNA methylation is essential for normal development and plays important roles in regulating gene expression in plants. Analysis of the key enzymes catalyzing DNA methylation is important to understand epigenetic phenomena. In this study, three putative methyltransferase genes, BrMET1a, BrMET1b, and BrCMT, were isolated from a genome library of Brassica rapa. Structural conservation of the amino acid sequence between BrMET1a/BrMET1b and AtMET1 and that between BrCMT and AtCMT3 suggests that they may function as DNA methyltransferase. BrMET1a was expressed in vegetative and reproductive organs, while BrMET1b was expressed only in pistils, indicating that these two genes have different functions. BrCMT was expressed especially in stamens at the stage of 2-4 days before anthesis. We isolated three DNA methyltransferase genes in Brassica rapa and indicated differences of expression patterns of these DNA methyltransferase genes and expression levels in different tissues and developmental stages, suggesting that these genes might play important roles in epigenetic gene regulation in B. rapa.

    GENETICS SOC JAPAN, Aug. 2006, GENES & GENETIC SYSTEMS, 81 (4), 235 - 242, English

    [Refereed]

    Scientific journal

  • Characterization of DNA methyltransferase genes in Brassica rapa.

    FUJIMOTO RYO, Taku Sasaki, Takeshi Nishio

    Aug. 2006, Genes Genetics and Systems, 81 (4), 235 - 242, English

    [Refereed]

    Scientific journal

  • Ryo Fujimoto, Tetsu Sugimura, Eigo Fukai, Takeshi Nishio

    Mutations in the S locus of a self-compatible cultivar Yellow Sarson in Brassica rapa, which has a self-compatible class-I S haplotype, S-f2, were investigated. S-28 in Brassica oleracea was found to be a member of an interspecific pair with S-f2 in B. rapa. The original S haplotype of S-f2 was identified to be S-54 in B. rapa. Sequence comparison of alleles in S-f2 with those in S-54 and B. oleracea S-28 revealed insertion of a retrotransposon-like sequence in the first intron of SRK and 89-bp deletion in the promoter region of SP11. No transcripts of SRK and SP11 were detected in S-f2 homozygotes, suggesting that the insertion and the deletion in SRK and SP11, respectively, caused the loss of the function of these genes. Promoter assay using transgenic plants indicated that the SP11 promoter of S-f2 has no activity. Heterozygotes of S-f2 and a normal class-II S haplotype, S-60, in B. rapa were found to be self-compatible. Interestingly, transcription of SP11-60 was revealed to be suppressed in the S-f2/S-60 heterozygotes, suggesting that an untranscribed class-I SP11 allele suppresses the expression of a recessive class-II SP11 allele in the anthers of S heterozygotes. Similar phenomenon was observed in heterozygotes of a self-compatible class-I S haplotype and a self-incompatible class-II S haplotype in B. oleracea.

    SPRINGER, Jul. 2006, PLANT MOLECULAR BIOLOGY, 61 (4-5), 577 - 587, English

    [Refereed]

    Scientific journal

  • T Shinada, Y Kikuchi, R Fujimoto, S Kishitani

    Nuclear so-called fertility-restorer genes reverse the pollen sterility of cytoplasmic male-sterile (CMS) plants caused by disturbed mitochondrial-nuclear interactions. We identified a CMS-associated chimeric mitochondrial gene in an alloplasmic CMS line of Brassica oleracea in the 'mur' system. This novel chimeric gene, orf72, was found in the mitochondrial genome of donor cytoplasm. It was located downstream of normal rps7 and contained part of atp9 (atp9-b). It was expressed specifically on the nuclear background of CMS B. oleracea, partially suppressed in the fertility-restored line and entirely suppressed in the cytoplasmic donor.

    OXFORD UNIV PRESS, Apr. 2006, PLANT AND CELL PHYSIOLOGY, 47 (4), 549 - 553, English

    [Refereed]

    Scientific journal

  • R Fujimoto, T Sugimura, T Nishio

    Self-compatible S-54 homozygotic plants were found in progenies of an F-1 hybrid cultivar in Chinese cabbage. Pollination tests revealed that this self-compatibility is controlled by the S locus and caused by the loss of the recognition function of the stigma. SRK, the gene for the recognition molecule in the stigma, was normally transcribed and translated in the self-compatible plants. The 1034-bp region in the receptor domain of SRK in the self-compatible plants was 100% identical to SLG in S-54, while that in self-incompatible S-54 homozygotic plants was 95.1% identical. These results suggest that the self-compatibility of the S-54 homozygotes is due to amino-acid changes caused by gene conversion from SLG to SRK. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

    ELSEVIER SCIENCE BV, Jan. 2006, FEBS LETTERS, 580 (2), 425 - 430, English

    [Refereed]

    Scientific journal

  • Ryo Fujimoto, Keiichi Okazaki, Eigo Fukai, Makoto Kusaba, Takeshi Nishio

    The determinants of recognition specificity of self-incompatibility in Brassica are SRK in the stigma and SP11/SCR in the pollen, both of which are encoded in the S locus. The nucleotide sequence analyses of many SRK and SP11/SCR alleles have identified several interspecific pairs of S haplotypes having highly similar sequences between B. oleracea and B. rapa. These interspecific pairs of S haplotypes are considered to be derived from common ancestors and to have maintained the same recognition specificity after speciation. In this study, the genome structures of three interspecific pairs of S haplotypes were compared by sequencing SRK, SP11/SCR, and their flanking regions. Regions between SRK and SP11/SCR in B. oleracea were demonstrated to be much longer than those of B. rapa and several retrotransposon-like sequences were identified in the S locus in B. oleracea. Among the seven retrotransposon-like sequences, six sequences were found to belong to the ty3 gypsy group. The gag sequences of the retrotransposon-like sequences were phylogenetically different from each other. In Southern blot analysis using retrotransposon-like sequences as probes, the B. oleracea genome showed more signals than the B. rapa genome did. These findings suggest a role for the S locus and genome evolution in self-incompatible plant species. Copyright © 2006 by the Genetics Society of America.

    2006, Genetics, 173 (2), 1157 - 1167, English

    [Refereed]

    Scientific journal

  • E Fukai, R Fujimoto, T Nishio

    The nucleotide sequence of an 86.4-kb region that includes the SP11, SRK, and SLG genes of Brassica rapa S-60 (a class-II S haplotype) was determined. In the sequenced region, 13 putative genes were found besides SP11-60, SRK-60, and SLG-60. Five of these sequences were isolated as cDNAs, five were homologues of known genes, cDNAs, or ORFs, and three are hypothetical ORFs. Based on their nucleotide sequences, however, some of them are thought to be non-functional. Two regions of colinearity between the class-II S-60 and Brassica class-I S haplotypes were identified, i.e., S flanking region 1 which shows partial colinearity of non-genic sequences and S flanking region 2 which shows a high level of colinearity. The observed colinearity made it possible to compare the order of SP-11, SRK, and SLG genes in the S locus between the five sequenced S haplotypes. It emerged that the order of SRK and SLG in class-II S-60is the reverse of that in the four class-I S haplotypes reported so far, and the order of SP11, SRK and SLG is the opposite of that in the class-I haplotype S-910. The possible gene designated as SAN1 ( S locus Anther-expressed Non-coding RNA like-1), which is located in the region between SP11-60 and SRK-60, has features reminiscent of genes for non-coding RNAs (ncRNAs), but no homologous sequences were found in the databases. This sequence is transcribed in anthers but not in stigmas or leaves. These features of the genomic structure of S-60 are discussed with special reference to the characteristics of class-II S haplotypes.

    SPRINGER-VERLAG, Jun. 2003, MOLECULAR GENETICS AND GENOMICS, 269 (3), 361 - 369, English

    [Refereed]

    Scientific journal

  • Commonality of self-recognition specificity of S haplotypes between Brassica oleracea and Brassica rapa

    Y Sato, R Fujimoto, K Toriyama, T Nishio

    We have identified several interspecific pairs of S haplotypes having highly similar SRK and SP11/SCR sequences between Brassica oleracea and Brassica rapa. The recognition specificities of S haplotypes in these pairs were examined with three different methods. Stigmas of interspecific hybrids between an S-32 homozygote in B. oleracea and an S-60 homozygote in B. rapa, which were produced to avoid the interspecific incompatibility between the two species, showed incompatibility to the pollen of an S-8 homozygote in B. rapa and to the pollen of an S-15 homozygote in B. oleracea, while it showed compatibility to the pollen of other S haplotypes, suggesting B. oleracea S-32 and B. rapa S-60 have the same recognition specificity as B. rapa S-8 and B. oleracea S-15. Pollen grains of transgenic S-60 homozygous plants in B. rapa carrying a transgene of SP11-24 from B. oleracea were incompatible to B. rapa S-36 stigma, indicating that B. oleracea S-24 and B. rapa S-36 have the same recognition specificity. Application of the SP11 protein of B. rapa S-41 and S-47 onto the surface of B. oleracea S-64 stigmas and S-12 stigmas, respectively, resulted in the incompatibility reaction to pollen grains of another S haplotype, but application onto the stigmas of other S haplotypes did not, suggesting that B. oleracea S-64 stigmas and S-12 stigmas recognized the B. rapa SP11-41 and SP11-47 proteins as self SP11 proteins, respectively. Besides having evolutionary implications, finding of many interspecific pairs of S haplotypes can provide insight into the molecular mechanism of self-recognition. Comparing deduced amino-acid sequences of SP11 proteins and SRK proteins in the pairs, regions of SP11 and SRK important for self-recognition are discussed.

    KLUWER ACADEMIC PUBL, Jun. 2003, PLANT MOLECULAR BIOLOGY, 52 (3), 617 - 626, English

    [Refereed]

    Scientific journal

  • R. Fujimoto, T. Nishio

    A self-incompatibility system is used for F(1) hybrid breeding in Brassicaceae vegetables. The determinants of recognition specificity of self-incompatibility in Brassica are SRK in the stigma and SP11/SCR in the pollen. Nucleotide sequences of SP11 alleles are more highly variable than those of SRK. We analyzed the S haplotype specificity of SP11 DNA by Southern-blot analysis and dot-blot analysis using 16 S haplotypes in Brassica oleracea, and found that DNA fragments of a mature protein region of SP11 cDNA, SP11(m), of eight S haplotypes can detect only the SP11 alleles of the same S haplotypes. This specificity makes these methods useful for S haplotype identification. Therefore, we developed two methods of dot-blot analysis for SP11. One is dot blotting of DNA samples, i.e. plant genomic DNA probed with labeled SP11(m), and the other is dot blotting of SP11(m) DNA fragments probed with labeled DNA samples, i.e. the SP11 coding region labeled by PCR using a template of plant genomic DNA. The former is useful for testing many plant materials. The latter is suitable, if there is no previous information on the S haplotypes of plant materials.

    SPRINGER, May 2003, THEORETICAL AND APPLIED GENETICS, 106 (8), 1433 - 1437, English

    [Refereed]

    Scientific journal

  • Recognition specificity of self-incompatibility maintained after the divergence of Brassica oleracea and Brassica rapa

    R Kimura, K Sato, R Fujimoto, T Nishio

    The determinants of recognition specificity of self-incompatibility in Brassica are SRK in the stigma and SP11/SCR in the pollen, respectively, In the pair of S haplotypes BrS46 (S-46 in B. rapa) and BoS(7) (S-7 in B. oleracea), which have highly similar SRK alleles, the SP11 alleles were found to be similar, with 96.1% identity in the deduced amino acid sequence. Two other pairs of S haplotypes, BrS47 and BoS(12), and BrS8 and BoS(32), having highly similar SRK and SP11 alleles between the two species were also found. The haplotypes in each pair are considered to have been derived from a single S haplotype in the ancestral species. The allotetraploid produced by interspecific hybridization between homozygotes of BrS46 and BoS(15) showed incompatibility with a BoS(7) homozygote and compatibility with other B. oleracea S haplotypes in reciprocal crossings. This result indicates that BrS46 and BoS(7) have maintained the same recognition specificity after the divergence of the two species and that amino acid substitutions found in such cases in both SRK alleles and SP11 alleles do not after the recognition specificity. DNA blot analysis of SRK, SP11, SLG and other S-locus genes showed different DNA fragment sizes between the interspecific pairs of S haplotypes. A much lower level of sequence similarity was observed outside the genes of SRK and SP11 between BrS46 and BoS(7). These results suggest that the DNA sequences of the regions intervening between the S-locus genes were diversified after or at the time of speciation. This is the first report demonstrating the presence of common S haplotypes in different plant species and presenting definite evidence of the trans-specific evolution of self-incompatibility genes.

    BLACKWELL PUBLISHING LTD, Jan. 2002, PLANT JOURNAL, 29 (2), 215 - 223, English

    [Refereed]

    Scientific journal

MISC

  • アブラナ科におけるFLCパラログ間の発現量比について

    西田菜美子, AKTER A, 板橋悦子, 宮路直実, MEHRAJ H, 柿崎智博, 岡崎桂一, 藤本龍

    06 Sep. 2019, 育種学研究, 21, 52, Japanese

  • キャベツにおける葉齢依存的な春化応答性のトランスクリプトーム解析

    板橋悦子, SHEA D, 吹野伸子, 藤本龍, 岡崎桂一, 柿崎智博, 小原隆由

    Sep. 2018, 育種学研究, 20 (2), 212, Japanese

  • 結球野菜の開花調節機構に関する研究の現状と今後の展望について

    藤本龍, 高田紗都子, 西田菜美子, 板橋悦子, 安田剛志, 柿崎智博, 宇野雄一

    24 Mar. 2018, 園芸学研究 別冊, 17 (1), 131, Japanese

  • キャベツの緑体春化におけるFLOWERING LOCUS Cの役割

    板橋悦子, 柿崎智博, 吹野伸子, 岡崎桂一, 藤本龍, 小原隆由

    24 Mar. 2018, 園芸学研究 別冊, 17 (1), 132, Japanese

  • Brassica oleracea FLC2領域を移入交雑で導入したBrassica rapaの特性解析

    SHEA D, 戸丸祐貴, 戸丸祐貴, 板橋悦子, 宮崎俊夫, 柿崎智博, 清水元樹, 藤本龍, 深井英吾, 岡崎桂一

    Oct. 2017, 育種学研究, 19 (2), 123, Japanese

  • アブラナ科植物の雑種強勢に関する研究

    川辺 隆大, FUJIMOTO RYO

    Oct. 2017, アグリバイオ, 1 (11), 43 - 44, Japanese

    [Invited]

    Introduction commerce magazine

  • Brassica rapa L.におけるアブラナ科植物白さび病抵抗性遺伝子の探索と検出

    西本良太, 宮路直実, 藤本龍, 土佐幸雄, 中馬いづみ

    12 Apr. 2017, 日本植物病理学会大会プログラム・講演要旨予稿集, 2017, 64, Japanese

  • アブラナ科植物白さび病菌Albugo candidaに対する抵抗性遺伝子同定に向けたBrassica rapa抵抗性品種の選抜

    西本良太, 宮路直実, 駒寛子, 藤本龍, 土佐幸雄, 中馬いづみ

    24 Sep. 2016, 育種学研究, 18, 115, Japanese

  • For the identification of the molecular mechanism of heterosis by epigenetic approach in Brassica

    Takahiro Kawanabe, Ryo Fujimoto

    GENETICS SOC JAPAN, Dec. 2015, GENES & GENETIC SYSTEMS, 90 (6), 373 - 373, English

    Summary international conference

  • ハクサイ市販一代雑種品種“W77”における雑種強勢に関わるQTLの探索

    ABE HIROSHI, KAWANABE TAKAHIRO, SAEKI NATSUMI, SHIMIZU MOTOKI, KONNO SHUHEI, NAGANO ATSUSHI, HONJO MIE, YASUGI MASAKI, KUDO HIROSHI, HATAKEYAMA KATSUNORI, MATSUMOTO SATOSHI, OKAZAKI KEIICHI, KAJI MAKOTO, FUJIMOTO RYU

    26 Sep. 2014, 育種学研究, 16, 111, Japanese

  • Screening of DNA markers suitable for purity test of inbred lines in Brassica rapa

    Kawamura Kazutaka, Saeki Natsumi, Ebe Yusuke, Abe Hirofumi, Shimizu Motoki, Osabe Kenji, Okazaki Keiichi, Kawanabe Takahiro, Fujimoto Ryo

    親候補となる近交系統の作成は、植物の一代雑種(F1)品種の育成過程の最初の段階である。一般的に遺伝的に均一な近交系統の育成には5、6世代以上の自殖が必要であると考えられている。DNAマーカーを利用した近交系の純度検定は信頼性が高いが、Brassica rapa L. では、純度検定に有効なDNAマーカーの報告は少ない。本研究では、F1品種の両親系統間の多型を見分けることができるDNAマーカーを見出すために、321のSSRプライマー対を試した。F2集団では、両親系統のゲノムが分離することから、両親系統の塩基配列の多型を追跡することが可能となる。材料にはハクサイの市販F1品種であるW77のF2個体を用いた。59のDNAマーカーでF2集団の個体間で多型が見られたことから、これらのDNAマーカーは純度検定に有効的であると考えられた。

    新潟大学農学部, Mar. 2014, 新潟大学農学部研究報告, 66 (2), 111 - 124, English

  • 藤本 龍, 白澤 沙知子, 川辺 隆大, 岡本 俊介

    公益社団法人 日本農芸化学会, 01 May 2013, 化学と生物, 51 (5), 283 - 285, Japanese

  • Brassica oleraceaにおける近交系統の純度検定に最適なDNAマーカーのスクリーニング

    富田 寛也, 清水 元樹, 久米 千織, 川辺 隆大, 長部 謙二, 岡崎 桂一, 藤本 龍

    近交系統の作成は、植物のF1品種の育成過程の最初の段階である。遺伝的に均一な近交系統の育成には5、6世代以上の自殖が必要であると考えられている。DNAマーカーを利用した近交系の純度検定は信頼性が高いが、B. oleraceaでは、純度検定に有効なDNAマーカーの報告は少ない。本研究では、F1品種の両親系統間の多型を見分けることができるDNA マーカーを見出すために、175のSSRプライマー対を試した。F2集団では、両親系統のゲノムが分離することから、両親系統の塩基配列の多型を追跡することが可能となる。そこで、材料にはキャベツの市販F1品種であるYR錦秋協力152のF2個体を用いた。12のDNAマーカーでF2集団の個体間で多型が見られたことから、これらのマーカーは純度検定に有効的であると考えられた。

    新潟大学農学部, Mar. 2013, 新潟大学農学部研究報告 = Bulletin of the Faculty of Agriculture, Niigata University, 65 (2), 137 - 147

  • シロイヌナズナにおける葯特異的遺伝子のプロモーター解析

    川辺 隆大, 長部 謙二, 藤本 龍

    葯特異的遺伝子やそれらのプロモーター配列の解析は、葯発達に関わる遺伝子の同定や、遺伝子組換えによる雄性不稔植物の作出を目的として、これまで多くなされてきている。本研究では、6つのプロモーター配列の単離を行い、GUS遺伝子に連結してシロイヌナズナに導入することで、葯の発達段階における発現誘導様式を調べた。プロモーターGUSの発現は、様々な花粉発達ステージにおいて観察された。また、塩基配列の解析では葯/花粉特異的遺伝子の発現に必要とされるシス配列が多く含まれていたことから、これらのシス配列が葯特異的に発現誘導していることが示唆された。

    新潟大学農学部, Sep. 2012, 新潟大学農学部研究報告 = Bulletin of the Faculty of Agriculture, Niigata University, 65 (1), 31 - 37

  • 植物の細胞質雄性不稔性と核遺伝子による稔性の制御について

    板橋 悦子, 川辺 隆大, 藤本 龍

    細胞質雄性不稔性(Cytoplasmic male sterility:CMS)は、ミトコンドリアゲノム上に存在する特有のorfによって引き起こされ、母性遺伝する形質である。多くの場合、核ゲノムにコードされる稔性回復遺伝子(Restorer of fertility:Rf)の存在下で、稔性が回復する。CMSとCMSの維持系統、Rf遺伝子を保持する稔性回復系統を組合せて利用する事で一代雑種育種を行う事ができるため、CMSやその稔性回復は農業上重要な現象である。これまでに同定されているRf遺伝子の多くは、ミトコンドリアに局在するpentatricopeptide repeat(PPR)タンパク質をコードしており、CMS関連ミトコンドリア遺伝子の発現を抑制している。

    新潟大学農学部, Mar. 2012, 新潟大学農学部研究報告 = Bulletin of the Faculty of Agriculture, Niigata University, 64 (2), 135 - 142, Japanese

  • 白菜のSハプロタイプ間における自家不和合性の強度の比較

    川辺 隆大, 長部 謙二, 藤本 龍

    アブラナ科野菜の自家不和合性の強度は、F1種子の生産において、自殖種子の混入を避けるために重要な要素である。アブラナ科植物の自家不和合性は、1つの複合遺伝子座(S複合座)によって胞子体型に制御されており、Sハプロタイプ間で優劣性が見られる。しかし、自家不和合性の強度と優劣性との関連性はあまり研究されていない。本研究では、Brassica rapa(白菜)のF1品種に由来するSホモ個体を作成し、3つの独立なSハプロタイプの組合せについて自家不和合性の強度を比較した。優劣性の有無にかかわらず、2つのclass IのSハプロタイプ間では自家不和合性の強度に違いが見られなかった。しかし、花粉において優劣性があるclass Iとclass IIのSハプロタイプ間では、class II Sハプロタイプの自家不和合性の強度はclass I Sハプロタイプに比べて弱かった。これらの結果から、Sハプロタイプ間における自家不和合性の強度は優劣性とは独立していることが示唆された。

    新潟大学農学部, Mar. 2012, 新潟大学農学部研究報告 = Bulletin of the Faculty of Agriculture, Niigata University, 64 (2), 143 - 149

  • エピジェネティクスが制御する植物の形質

    藤本 龍, ISHIKAWA RYO

    2010, 育種学研究, 12, 123 - 131, Japanese

    [Refereed]

    Introduction scientific journal

  • Recent molecular biological studies on Brassica self-incompatibility and future perspectives

    Fujimoto R, Nishio T

    Mar. 2008, Breeding Research, 10 (1), 1 - 9, Japanese

    Introduction other

Books etc

  • Breeding for Disease Resistance in Brassica Vegetables Using DNA Marker Selection

    Mst Arjina Akter, Hasan Mehraj, Takeru Itabashi, Tomoe Shindo, Masaaki Osaka, Ayasha Akter, Naomi Miyaji, Naoki Chiba, Junji Miyazaki, Ryo Fujimoto

    Joint work, IntechOpen, Feb. 2021

  • The Importance of Genetic and Epigenetic Research in the Brassica Vegetables in the Face of Climate Change

    Honghao Lv, Naomi Miyaji, Kenji Osabe, Ayasha Akter, Hasan Mehraj, Daniel J. Shea and Ryo Fujimoto

    Joint work, 161-256, Springer, Mar. 2020

  • Chapter 8 Hybrid Vigor: Importance of Epigenetic Processes and Consequences for Breeding

    Naomi Miyaji, FUJIMOTO RYO

    Joint work, Advances in Botanical Research-Plant Epigenetics Coming of Age for Breeding Applications, Nov. 2018, English

    Scholarly book

  • Genetic and Epigenetic Regulation of Vernalization in Brassicaceae

    Ayasha Akter, Namiko Nishida, Satoko Takada, Etsuko Itabashi, Kenji Osabe, Daniel J Shea, FUJIMOTO RYO

    Joint work, IntechOpen, Oct. 2018, English

    Scholarly book

  • 遺伝学の基礎 14章 エピジェネティクス

    FUJIMOTO RYO

    Others, 朝倉書店, Sep. 2018, Japanese

    Textbook

  • 育種学研究

    貴島 祐治, 寺内 良平, 高田 美信, 宅見 薫雄, FUJIMOTO RYO, 村井 耕二

    Joint work, 日本育種学会, Jul. 2014, Japanese

    Scholarly book

  • 植物の雑種強勢の分子生物学的な研究と展望

    FUJIMOTO RYOU, 白澤 沙知子, 川辺 隆大, 岡本 俊介

    Joint work, 日本農芸化学会, May 2013, Japanese

    Scholarly book

  • Self‐Incompatibility

    FUJIMOTO RYO, Takeshi Nishio

    Joint work, Advances in Botanical Research, 2007, English

    Scholarly book

Presentations

  • アブラナ科野菜における白さび病抵抗性DNAマーカーの開発

    宮路直実, 清水元樹, 鈴鴨千鶴子, 勝又雅彦, 安田(高崎)剛志, 中馬いづみ, 藤本龍

    園芸学会令和3年度春季大会, 27 Mar. 2021, Japanese

    Poster presentation

  • アブラナ科野菜におけるサリチル酸応答遺伝子の同定

    宮路直実, 安田剛志, 藤本龍

    園芸学会令和3年度春季大会, 27 Mar. 2021, Japanese

    Poster presentation

  • ナバナ(Brassica napus L.)の春化に必要な低温要求量と春化応答を示す生育ステージの評価

    北村八祥, 小栗速斗, 小堀純奈, 藤本龍, 板橋悦子

    園芸学会令和3年度春季大会, 27 Mar. 2021, Japanese

    Poster presentation

  • Brassica rapa品種の萎黄病抵抗性とFocBr1抵抗性遺伝子の多型解析

    川又美祐, 佐藤真帆, シェイダニエル, 清水元樹, 藤本龍, 深井英吾, 岡崎桂一

    日本育種学会 第139回講演会, 19 Mar. 2021, Japanese

  • Brassica rapa L.における白さび病抵抗性遺伝子の同定

    宮路直実, 清水元樹, 鈴鴨千鶴子, 勝又雅彦, 安田(高崎) 剛志, 中馬いづみ, 藤本龍

    日本育種学会 第139回講演会, 19 Mar. 2021, Japanese

    Oral presentation

  • Brassica rapa L.における白さび病抵抗性機構について

    宮路直実, 清水元樹, 安田(高崎)剛志, 中馬いづみ, 藤本龍

    令和3年度日本植物病理学会大会, Mar. 2021, Japanese

    Oral presentation

  • DNAメチル化転移酵素によるシロイヌナズナの雑種強勢制御機構

    山下萌, 安田(高崎)剛志, 藤本龍

    日本育種学会 第138回講演会, 11 Oct. 2020, Japanese

    Oral presentation

  • シロイヌナズナにおけるヒストン脱アセチル化酵素HDA6が雑種強勢に及ぼす影響

    村上照実, 安田 (高崎) 剛志, 藤本龍

    日本育種学会 第138回講演会, 11 Oct. 2020, Japanese

    Oral presentation

  • キャベツにおける春化応答性の品種間差とBoFLC2遺伝子の関係

    板橋 悦子, シェイ ダニエル, 吹野 伸子, 藤 本 龍, 岡崎 桂一, 柿崎 智博, 小原 隆由

    日本育種学会第137回講演会, Mar. 2020

    Oral presentation

  • Brassica rapa L. における白さび病抵抗性遺伝子の遺伝様式の解明と抵抗性遺伝子候補の探索

    宮路 直実, 清水 元樹, 安田 ( 高崎 ) 剛志, 中 馬 いづみ, 藤本 龍

    日本育種学会第137回講演会, Mar. 2020

    Oral presentation

  • キャベツ BoFLC2 導入ハクサイ系統の春化特性

    西田 菜美子, 岡崎 桂一, 藤本 龍

    日本育種学会第137回講演会, Mar. 2020

    Poster presentation

  • コールラビ茎肥大性 QTL のファインマッピング

    佐藤 庄人 , モジャミール ホック , シェイ ダニエルジョン, 松村 涼介, 清水 元樹, 藤本 龍, 深井 英吾, 岡崎 桂一

    日本育種学会第137回講演会, Mar. 2020

    Poster presentation

  • Transcriptome analysis before and after salicylic acid treatments in Brassica rapa L.

    Naomi Miyaji, Ryo Fujimoto

    Improvement of important agricultural traits based on genomic information of horticultural crops, Jan. 2020

    Oral presentation

  • Comparison of the Transcriptome profile between F1 hybrid cultivar and it's parental lines at two early developmental stages in Chinese cabbage.

    Mehraj Hasan, Ryo Fujimoto

    Improvement of important agricultural traits based on genomic information of horticultural crops, Jan. 2020

    Oral presentation

  • Characterization of FLOWERLING LOCUS C parlors in a late flowering line of Brassica rapa.

    Ayasha Akter, Ryo Fujimoto

    Improvement of important agricultural traits based on genomic information of horticultural crops, Jan. 2020

    Oral presentation

  • Transcriptome analysis before and after salicylic acid treatments in Brassica rapa L.

    Naomi Miyaji, Takeshi Takasaki-Yasuda, Ryo Fujimoto

    Plant and Animal Genome XXVIII Conference, Jan. 2020, English

    Poster presentation

  • 春化によりキャベツ由来のFLC2がハクサイの遺伝的背景でどのように機能するか

    西田菜美子, シェア ダニエル, 板橋悦子, 安田剛志, 柿崎智博, 岡崎桂一, 藤本龍

    園芸学会令和元年度秋季大会, Sep. 2019

    Oral presentation

  • Comparison of the Transcriptome profile between F1 hybrid cultivar and its parental lines at two early developmental stages in Chinese cabbage

    メエラジ ハサン, 松尾康大, 安田剛志, 藤本龍

    園芸学会令和元年度秋季大会, Sep. 2019

    Oral presentation

  • Characterization of FLOWERING LOCUS C parlors in a late flowering line of Brassica rapa

    アクタ アヤシャ, 西田菜美子, 宮路直実, 安田剛志, 藤本龍

    園芸学会令和元年度秋季大会, Sep. 2019

    Oral presentation

  • ハクサイにおける長鎖非コードRNAとエピジェネティクスとの関係性

    西田菜美子, シェア ダニエル, 高橋聡史, 板橋悦子, アクタ アヤシャ, 宮路直実, メエラジ ハサン, 安田剛志, 柿崎智博, 関原明, 岡崎桂一, 藤本龍

    園芸学会令和元年度秋季大会, Sep. 2019

    Oral presentation

  • ペチュニア花粉におけるニホンナシSFBB融合タンパク質発現系の開発

    上野環太, 久保健一, 藤本龍, 高山誠司, 安田剛志

    園芸学会令和元年度秋季大会, Sep. 2019

    Oral presentation

  • ニホンナシSホモ系統の花粉RNAからのPsSFBB配列の再構築とクローニング

    野木彩未, 高畑宏基, 西村遼太郎, 藤本龍, 安田剛志

    園芸学会令和元年度秋季大会, Sep. 2019

    Oral presentation

  • トランスクリプトーム解析によるシロイヌナズナDDM1変異雑種における雑種強勢低減の改名について

    松尾康大, 宮路直実, 安田剛志, 藤本龍

    日本育種学会第136回講演会, Sep. 2019

    Oral presentation

  • アブラナ科におけるFLCパラログ間の発現量比について

    西田菜美子, アクタ アヤシャ, 板橋悦子, 宮路直実, メエラジ ハサン, 柿崎 智博, 岡崎 桂一, 藤本龍

    日本育種学会第136回講演会, Sep. 2019

    Oral presentation

  • Vernalization alters histone H3 lysine 27 trimethylation at FLC locus in Brassica rapa

    Ayasha Akter, Satoshi Takahashi, Namiko Nishida, Naomi Miyaji, Takeshi Yasuda, Yutaka Suzuki, Motoaki Seki, FUJIMOTO RYO

    2019 KSBB & SABRAO International Conference on Plant Breeding for Sustainable Development, Jul. 2019, English, Kimdaejung Convention Center, Gwangju, International conference

    Poster presentation

  • Identification of non-additively expressed genes at early developmental stages in an F1 hybrid cultivar of Chinese cabbage

    Hasan Mehraj, Kodai Matsuo, Motoki Shimizu, Takeshi Yasuda, FUJIMOTO RYO

    2019 KSBB & SABRAO International Conference on Plant Breeding for Sustainable Development, Jul. 2019, English, Kimdaejung Convention Center, Gwangju, International conference

    Poster presentation

  • Transcriptome analysis indicate mechanisms underlying the DDM1-mediated heterosis in Arabidopsis thaliana

    Kodai Matsuo, Naomi Miyaji, Takeshi Yasuda, FUJIMOTO RYO

    International Symposium; Principles of pluripotent stem cells underlying plant vitality, May 2019, English, Tohoku University, International conference

    Poster presentation

  • Characterization of the transcriptome in heterotic F1 hybrids in Arabidopsis thaliana

    Terumi Murakami, Kodai Matsuo, Naomi Miyaji, Takeshi Yasuda, FUJIMOTO RYO

    International Symposium; Principles of pluripotent stem cells underlying plant vitality 英文, May 2019, English, Tohoku University, International conference

    Poster presentation

  • 萎黄病抵抗性・感受性ハクサイ系統における萎黄病菌感染時の免疫応答

    宮路 直実, 清水 元樹, 加治 誠, 安田 剛志, 岡崎 桂一, FUJIMOTO RYO

    平成31年度日本植物病理学会大会, Mar. 2019, Japanese, つくば国際会議場, Domestic conference

    Oral presentation

  • ハクサイにおける全ゲノムメチル化解析

    FUJIMOTO RYO, 高橋 聡史, 鈴木 穣, 関 原明, 安田 剛志

    園芸学会平成31年度春季大会, Mar. 2019, Japanese, 明治大学, Domestic conference

    Oral presentation

  • ハクサイにおけるノンコーディングRNAの同定

    西田菜美子, Daniel J Shea, 板橋 悦子, Ayasha Akter, 宮路 直美, Hasan Mehraj, 柿崎 智博, 岡崎 桂一, FUJIMOTO RYO

    日本育種学会第135回講演会, Mar. 2019, Japanese, 千葉大学, Domestic conference

    Oral presentation

  • Distribution of histone H3 lysine 27 trimethylation in different tissues of Brassica rapa

    アクタ アヤシャ, 宮路 直実, 安田 剛志, FUJIMOTO RYO

    園芸学会平成31年度春季大会, Mar. 2019, English, 明治大学, Domestic conference

    Oral presentation

  • Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage.

    FUJIMOTO RYO

    Improvement of important agricultural traits based on genomic information of horticultural crops, Dec. 2018, English, Sunchon National University, International conference

    Public discourse

  • Epigenetics and heterosis

    Kodai Matsuo, FUJIMOTO RYO

    Improvement of important agricultural traits based on genomic information of horticultural crops, Dec. 2018, English, Sunchon National University, International conference

    Public discourse

  • Brassica oleraceaにおける異なる菌株に対する根こぶ病QTL解析

    斎藤 浩之, 小玉 太郎, Mozammel Hoque, Daniel John Shea, 清水 元樹, FUJIMOTO RYO, 深井 英吾, 岡崎 桂一

    第13回東北育種研究集会, Nov. 2018, Japanese, Domestic conference

    Poster presentation

  • アブラナ科野菜における雑種強勢研究の動向

    FUJIMOTO RYO

    平成30年度野菜花き課題別研究会 「アブラナ科野菜における育種と栽培の現状と展望」, Oct. 2018, Japanese, 愛知県産業労働センター, Domestic conference

    Oral presentation

  • ハクサイ初期生育期における子葉および本葉サイズ関連遺伝子の探索

    上園 倖輔, シェア ダニエル, 清水 元樹, 板橋 悦子, ハサン メエラジ, 岡崎 桂一, 安田, 高崎, 剛志, FUJIMOTO RYO

    日本育種学会第134回講演会, Sep. 2018, Japanese, Domestic conference

    Oral presentation

  • ニホンナシSホモ系統における花柱内の和合・不和合花粉管伸長

    高橋侑也, FUJIMOTO RYO, TAKASAKI-YASUDA TAKESHI

    園芸学会平成30年度秋季大会, Sep. 2018, Japanese, 鹿児島大学, Domestic conference

    Oral presentation

  • ニホンナシS3-RNase周辺領域のBACコンティグの拡張によるPpSFBB3の探索

    張競月, 武矢悠太郎, FUJIMOTO RYO, TAKASAKI-YASUDA TAKESHI

    平成30年度園芸学会近畿支部会大阪大会, Sep. 2018, Japanese, 大阪府立大学, Domestic conference

    Poster presentation

  • コールラビ茎肥大性のトランスクリプトーム解析

    ホック モジャミール, シェイ ダニエル, 佐藤 庄人, 松村 涼介, ドウラ モハメドアサドウド, 清水 元樹, FUJIMOTO RYO, 深井 英吾, 岡崎 桂一

    日本育種学会第134回講演会, Sep. 2018, Japanese, Domestic conference

    Poster presentation

  • キャベツにおける葉齢依存的な春化応答性のトランスクリプトーム解析

    板橋 悦子, シェイ ダニエル, 吹野 伸子, FUJIMOTO RYO, 岡崎 桂一, 柿崎 智博, 小原 隆由

    日本育種学会第134回講演会, Sep. 2018, Japanese, Domestic conference

    Poster presentation

  • アブラナ科植物におけるPCR-RFLP法によるSハプロタイプ判定法が直面する問題点

    FUJIMOTO RYO, 川辺 隆大, 岡崎 桂一

    日本育種学会第134回講演会, Sep. 2018, Japanese, Domestic conference

    Oral presentation

  • The molecular basis of vernalization in Brassica rapa

    FUJIMOTO RYO

    Seminar in AgriBio, Sep. 2018, English, La Trobe University, International conference

    Public discourse

  • How Brassica oleracea FLOWERING LOCUS C2 works in a Brassica rapa genetic background

    Namiko Nishida, Daniel J. Shea, Keiichi Okazaki, FUJIMOTO RYO

    AusCanola2018, Sep. 2018, English, Rendezvous Hotel Scarborough, International conference

    Poster presentation

  • Characterization of FLOWERING LOCUS C genes in leafy Brassica rapa vegetables

    FUJIMOTO RYO, Ayasha Akter, Namiko Nishida, Takashi Takasaki-Yasuda, Elizabeth S. Dennis

    AusCanola2018, Sep. 2018, English, Rendezvous Hotel Scarborough, International conference

    Poster presentation

  • Brassica rapaにおけるメチローム解析

    高橋 聡史, 長部 謙二, 宮路 直実, 鈴木 穣, 関 原明, FUJIMOTO RYO

    日本育種学会第134回講演会, Sep. 2018, Japanese, Domestic conference

    Poster presentation

  • Brassica rapa L.における萎黄病・根こぶ病抵抗性DNAマーカー選抜系の応用

    宮路 直実, Hasan Mehraj, 清水 元樹, 加治 誠, 安田, 高崎, 剛志, FUJIMOTO RYO

    平成30年度園芸学会近畿支部大阪大会, Sep. 2018, Japanese, 大阪府立大学 中百舌鳥キャンパス, Domestic conference

    Oral presentation

  • Transcriptome Difference by Fusarium inoculation between Fusarium yellows resistant and susceptible lines in Brassica rapa L.

    Naomi Miyaji, Motoki Shimizu, Takeshi Takasaki-Yasuda, Keiichi Okazaki, FUJIMOTO RYO

    INTERNATIONAL PLANT MOLECULAR BIOLOGY 2018, Aug. 2018, English, International conference

    Poster presentation

  • QTL mapping combined with transcriptome analysis using broccoli and kohlrabi

    Mozammel Hoque, Daniel J. Shea, Masato Sato, Ryosuke Matsumura, Mohamad Asad- ud-doullah, Motoki Shimizu, FUJIMOTO RYO, Eigo Fukai, Keiichi Okazaki

    Brassica 2018, Jul. 2018, English, Saint-Malo, France, International conference

    Poster presentation

  • Characterization of epigenetic states in Brassica rapa L.

    FUJIMOTO RYO, Ayasha Akter, Satoshi Takahashi, Takeshi Takasaki-Yasuda, Yutaka Suzuki, Elizabeth S. Dennis, Motoaki Seki

    Brassica 2018, Jul. 2018, English, Saint-Malo, France, International conference

    Oral presentation

  • Identification of long non-coding RNAs before and after prolonged cold treatment in Brassica rapa L.

    Namiko Nishida, Daniel J. Shea, Satoko Takada, Etsuko Itabashi, Takeshi Takasaki-Yasuda, Keiichi Okazaki, Elizabeth S. Dennis, FUJIMOTO RYO

    The 25th International Congress on Sexual Plant Reproduction, Jun. 2018, English, Nagaragawa Convention Center, International conference

    Poster presentation

  • DDM1 has an important function on heterosis in Arabidopsis thaliana

    Naomi Miyaji, Etsuko Itabashi, Takeshi Takasaki-Yasuda, W. James Peacock, Elizabeth S. Dennis, FUJIMOTO RYO

    The 25th International Congress on Sexual Plant Reproduction, Jun. 2018, English, Nagaragawa Convention Center, International conference

    Poster presentation

  • Characterization of histone H3 lysine 27 tri-methylation in Brassica rapa L.

    FUJIMOTO RYO, Ayasha Akter, Satoshi Takahashi, Namiko Nishida, Takashi Takasaki-Yasuda, Yutaka Suzuki, Motoaki Seki, Elizabeth S. Dennis

    The 25th International Congress on Sexual Plant Reproduction, Jun. 2018, English, Nagaragawa Convention Center, International conference

    Poster presentation

  • 結球野菜の開花調節機構に関する研究の現状と今後の展望について

    FUJIMOTO RYO, 高田 紗都子, 西田 菜美子, 板橋 悦子, 安田 剛志, 柿崎 智博, 宇野 雄一

    園芸学会平成30年度春期大会, Mar. 2018, Japanese, 近畿大学農学部, Domestic conference

    Public symposium

  • 萎黄病菌キャベツ分離菌抵抗性遺伝子DNAマーカーで萎黄病菌コマツナ分離菌抵抗性を予測できるか?

    宮路 直実, 清水 元樹, 加治 誠, 安田 (高, 崎, 剛志, 岡崎 桂一, FUJIMOTO RYO

    園芸学会平成30年度春期大会, Mar. 2018, Japanese, Domestic conference

    Poster presentation

  • ハクサイ市販品種'W77'の両親系統間リシークエンスによる片親特異的遺伝子変異の同定

    上園 倖輔, Shea Daniel, 清水 元樹, 板橋 悦子, 宮路 直美, 岡崎 桂一, 安田, 高崎, 剛志, FUJIMOTO RYO

    園芸学会平成30年度春期大会, Mar. 2018, Japanese, Domestic conference

    Oral presentation

  • キャベツの緑体春化におけるFLOWERING LOCUS Cの役割

    板橋 悦子, 柿崎 智博, 吹野 伸子, 岡崎 桂一, FUJIMOTO RYO, 小原 隆由

    園芸学会平成30年度春期大会, Mar. 2018, Japanese, Domestic conference

    Public symposium

  • LncRNA BrFLC2as in Brassica rapa differs from Arabidopsis thaliana COOLAIR

    Shea Daniel, 高田 紗都子, 西田 菜美子, 板橋 悦子, 清水 元樹, 岡崎 桂一, FUJIMOTO RYO

    日本育種学会第133回講演会, Mar. 2018, Japanese, 九州大学, Domestic conference

    Poster presentation

  • Brassica rapaにおける春化経路関連遺伝子の機能解析

    西田 菜美子, 高田 紗都子, 板橋 悦子, 宮路 直実, 安田 剛志, FUJIMOTO RYO

    園芸学会平成30年度春期大会, Mar. 2018, Japanese, 近畿大学農学部, Domestic conference

    Oral presentation

  • 萎黄病抵抗性タンパク質と相互作用するタンパク質の同定に向けて

    梁瀬 拓雄, 上杉 百花, 神崎 洋之, 清水 元樹, Daniel J Shea, FUJIMOTO RYO, 深井 英吾, 岡崎 桂一

    第12回東北育種研究集会, Nov. 2017, Japanese, 秋田県立大学, Domestic conference

    Poster presentation

  • Brassica rapaにおける萎黄病抵抗性遺伝子FocBr1の多型解析と選抜マーカーの開発

    佐藤 真帆, Daniel J. Shea, 清水 元樹, FUJIMOTO RYO, 深井 英吾, 岡崎 桂一

    第12回東北育種研究集会, Nov. 2017, Japanese, 秋田県立大学, Domestic conference

    Poster presentation

  • Re-sequencing and SNP analysis of the parental lines of a commercial F1 hybrid cultivar of Chinese cabbage

    Daniel Shea, Motoki Shimizu, Etsuko Itabashi, Naomi Miyaji, Makoto Kaji, Keiichi Okazaki, FUJIMOTO RYO

    日本育種学会第132回講演会, Oct. 2017, English, Domestic conference

    Poster presentation

  • Brassica oleracea FLC2領域を移入交雑で導入したBrassica rapaの特性解析

    シェイ ダニエル, 戸丸 祐貴, 板橋 悦子, 宮崎 俊夫, 柿崎 智博, 清水 元樹, FUJIMOTO RYO, 深井 英吾, 岡崎 桂一

    日本育種学会第132回講演会, Oct. 2017, English, Domestic conference

    Oral presentation

  • 萎黄病抵抗性•感受性ハクサイ系統における萎黄病菌感染時転写応答の解明

    宮路 直実, 清水 元樹, 高田 紗都子, 加治 誠, 安田, 高崎, 剛志, 岡崎 桂一, FUJIMOTO RYO

    園芸学会平成29年度秋期大会, Sep. 2017, Japanese, Domestic conference

    Oral presentation

  • ハクサイ市販品種'W77'の両親系統のリシークエンスによるゲノム構造の系統間比較

    上園 倖輔, Shea Daniel, 清水 元樹, 板橋 悦子, 譚 永, 宮路 直美, 岡崎 桂一, 安田, 高崎, 剛志, FUJIMOTO RYO

    平成29年度園芸学会近畿支部滋賀大会, Sep. 2017, Japanese, Domestic conference

    Poster presentation

  • ハクサイ市販品種'W77'における初期生育の雑種強勢関連領域の同定にむけて

    譚 永, 上園 倖輔, 板橋 悦子, 安田, 高崎, 剛志, FUJIMOTO RYO

    平成29年度園芸学会近畿支部滋賀大会, Sep. 2017, Japanese, ピアザ淡海, Domestic conference

    Oral presentation

  • ニホンナシS2およびS4ハプロタイプ間のゲノム構造比較

    西村 遼太郎, 安藤 肇, FUJIMOTO RYO, 安田, 剛志

    園芸学会平成29年度秋期大会, Sep. 2017, Japanese, Domestic conference

    Oral presentation

  • MeDIP-seqによるハクサイ系統間のDNAメチル化比較解析

    FUJIMOTO RYO, 高橋 聡史, 鈴木 穣, 関 原明, 安田 剛志

    園芸学会平成29年度秋期大会, Sep. 2017, Japanese, Domestic conference

    Oral presentation

  • Brassica rapa L.における春化によるFLCのエピジェネティックな修飾変化の系統間比較

    高田 紗都子, 板橋 悦子, 宮路 直実, 安田 剛志, FUJIMOTO RYO

    園芸学会平成29年度秋期大会, Sep. 2017, Japanese, Domestic conference

    Oral presentation

  • Similar but different: the molecular basis of vernalization in Brassica rapa

    FUJIMOTO RYO

    THE PLANT EPIGENETICS CONSORTIUM IN JAPAN- SECOND MEETING, Aug. 2017, English, Domestic conference

    Oral presentation

  • DDM1 is required for a full level of heterosis in Arabidopsis thaliana

    Naomi Miyaji, Sonoko Ishikura, Satoko Takada, Takeshi Takasaki-Yasuda, W. James Peacock, Elizabeth S. Dennis, FUJIMOTO RYO

    Plant Biology 2017, Jun. 2017, English, International conference

    Poster presentation

  • ニホンナシ柱頭の表面および微細構造の変化と柱 頭浸出液の出現について

    高橋 侑也, 李 麗怡, 岡村 彩葉, FUJIMOTO RYO, 安田 (高, 崎, 剛志

    医学生物学電子顕微鏡技術学会第33回学術講演会, May 2017, Japanese, Domestic conference

    Oral presentation

  • Brassica rapa L. におけるアブラナ科 植物白さび病抵抗性遺伝子の探索と検 出

    西本 良太, 宮路 直実, FUJIMOTO RYO, 土佐 幸雄, 中馬 いづみ

    平成29年度日本植物病理学会大会, Apr. 2017, Japanese, Domestic conference

    Oral presentation

  • トランスクリプトーム解析を用いたハクサイの萎黄病菌感染時における免疫応答調査

    宮路 直実, 清水 元樹, 高田 紗都子, 加治 誠, 安田 剛志, 岡崎 桂一, FUJIMOTO RYO

    日本育種学会第131回講演会, Mar. 2017, Japanese, 名古屋大学, Domestic conference

    Oral presentation

  • シロイヌナズナの早期開花エピ変異体の形質評価

    高田 紗都子, 石倉 園子, 板橋 悦子, 宮路 直実, 清水 元樹, 安田 剛志, FUJIMOTO RYO

    日本育種学会第131回講演会, Mar. 2017, Japanese, 名古屋, Domestic conference

    Oral presentation

  • アブラナ科植物におけるゲノム多様性および雑種強勢に関する研究

    FUJIMOTO RYO

    日本育種学会第131回講演会, Mar. 2017, Japanese, 名古屋大学, Domestic conference

    [Invited]

    Invited oral presentation

  • Brassica oleraceaにおける萎黄病抵抗性遺伝子FocBo1の多型解析と選抜マーカー開発

    佐藤 真帆, 清水 元樹, FUJIMOTO RYO, 深井 英吾, 岡崎 桂一

    日本育種学会第131回講演会, Mar. 2017, Japanese, 名古屋大学, Domestic conference

    Poster presentation

  • The epigenetic regulation of FLC expression by vernalization in Brassica rapa L

    Satoko Takada, Etsuko Itabashi, Naomi Miyaji, Takeshi Takasaki-Yasuda, Kenji Osabe, Elizabeth S. Dennis, FUJIMOTO RYO

    Brassica 2016, Oct. 2016, English, International conference

    Poster presentation

  • QTL mapping for stem swelling trait of Kohlrabi (Brassica oleracea var. gongylodes)

    Mozammel Hoque, Mitsuru Asada, Daniel Shea, Motoki Shimizu, FUJIMOTO RYO, Eigo Fukai, Keiichi Okazaki

    Brassica 2016, Oct. 2016, English, International conference

    Oral presentation

  • Identification of the Fusarium yellows resistance genes; its application for marker-assisted selection in Brassica rapa

    Naomi Miyaji, Motoki Shimizu, Satoko Takada, Takeshi Takasaki-Yasuda, Makoto Kaji, Kenji Osabe, Elizabeth S. Dennis, Keiichi Okazaki, FUJIMOTO RYO

    Brassica 2016, Oct. 2016, English, International conference

    Oral presentation

  • Genome-wide analysis of DNA methylation in Chinese cabbage

    Naoki Fukushima, Satoshi Takahashi, Etsuko Itabashi, Motoki Shimizu, Kenji Osabe, Takeshi Yasuda, Yutaka Suzuki, Motoaki Seki, Elizabeth S. Dennis, FUJIMOTO RYO

    Brassica 2016, Oct. 2016, English, International conference

    Poster presentation

  • Characterization of early developmental and yield heterosis in Chinese cabbage

    FUJIMOTO RYO, Motoki Shimizu, Naomi Miyaji, Satoko Takada, Naoki Fukushima, Makoto Kaji, W. James Peacock, Elizabeth S. Dennis

    Brassica 2016, Oct. 2016, English, International conference

    Oral presentation

  • 萎黄病菌を接種したときの抵抗性と感受性ハクサイ系統のトランスクリプトームプロファイリング

    宮路 直実, 清水 元樹, 高田 紗都子, 加治 誠, 安田 剛志, 岡崎 桂一, FUJIMOTO RYO

    日本育種学会第130回講演会, Sep. 2016, Japanese, 鳥取大学, Domestic conference

    Poster presentation

  • ハクサイにおける萎黄病菌感染時のトランスクリプトーム解析による病害反応遺伝子の調査

    宮路 直実, 清水 元樹, 高田 紗都子, 加治 誠, 安田 剛志, 岡崎 桂一, FUJIMOTO RYO

    園芸学会平成28年度秋季大会, Sep. 2016, Japanese, 名城大学, Domestic conference

    Oral presentation

  • ハクサイにおけるメチローム解析

    福島 尚樹, 高橋 聡史, 板橋 悦子, 清水 元樹, 安田 剛志, 鈴木 穣, 関 原明, FUJIMOTO RYO

    日本育種学会第130回講演会, Sep. 2016, Japanese, Domestic conference

    Oral presentation

  • ハクサイにおけるエピゲノム解析

    FUJIMOTO RYO, 高橋 聡史, 板橋 悦子, 鈴木 穣, 関 原明

    日本育種学会第130回講演会, Sep. 2016, Japanese, 鳥取大学, Domestic conference

    Public symposium

  • ニホンナシS3-RNase 周辺BACコンティグの塩基配列解析

    武矢 悠太郎, 野村 直希, FUJIMOTO RYO, 安田, 剛志

    園芸学会平成28年度秋季大会, Sep. 2016, Japanese, 名城大学, Domestic conference

    Oral presentation

  • ニホンナシS2遺伝子座のゲノム構造および発現遺伝子解析

    西村 遼太郎, FUJIMOTO RYO, 安田, 剛志

    園芸学会平成28年度秋季大会, Sep. 2016, Japanese, 名城大学, Domestic conference

    Oral presentation

  • シロイヌナズナの雑種強勢に関与する遺伝子領域の探索

    宮路 直実, 石倉 園子, 高田 紗都子, 板橋 悦子, 安田 剛志, FUJIMOTO RYO

    日本育種学会第130回講演会, Sep. 2016, Japanese, Domestic conference

    Oral presentation

  • クロマチンリモデリング因子DDM1によるエピジェネティックな制御がシロイヌナズナのヘテローシスに及ぼす影響

    石倉 園子, 宮路 直実, 板橋 悦子, 高田 紗都子, 高橋 聡史, 清水 元樹, 安田 剛志, 関 原明, FUJIMOTO RYO

    日本育種学会第130回講演会, Sep. 2016, Japanese, 鳥取大学, Domestic conference

    Oral presentation

  • アブラナ科植物白さび病菌Albugo candidaに対する抵抗性遺伝子同定に向けたBrassica rapa抵抗性品種の選抜

    西本 良太, 宮路 直実, FUJIMOTO RYO, 土佐 幸雄, 中馬 いづみ

    日本育種学会第130回講演会, Sep. 2016, Japanese, 鳥取大学, Domestic conference

    Oral presentation

  • Whole genome bisulfite sequencingによるハクサイのDNAメチル化領域の探索

    福島 尚樹, 高橋 聡史, 板橋 悦子, 清水 元樹, 安田 剛志, 鈴木 穣, 関 原明, FUJIMOTO RYO

    園芸学会平成28年度秋季大会, Sep. 2016, Japanese, 名城大学, Domestic conference

    Oral presentation

  • Brassica rapa L.の開花期の決定におけるFRIGIDAとFLOWERING LOCUS Cの役割

    高田 紗都子, 板橋 悦子, 宮路 直実, 安田 剛志, FUJIMOTO RYO

    日本育種学会第130回講演会, Sep. 2016, Japanese, Domestic conference

    Oral presentation

  • Brassica rapa L.における春化によるFLOWERING LOCUS C のエピジェネティックな転写制御について

    高田 紗都子, 板橋 悦子, 宮路 直実, 清水 元樹, 安田 剛志, FUJIMOTO RYO

    園芸学会平成28年度秋季大会, Sep. 2016, Japanese, 名城大学, Domestic conference

    Poster presentation

  • Brassica rapa L.における開花関連遺伝子FRIGIDA の発現解析および全長配列の決定

    高田 紗都子, 板橋 悦子, 宮路 直実, 安田 剛志, FUJIMOTO RYO

    園芸学会平成28年度秋季大会, Sep. 2016, Japanese, 名城大学, Domestic conference

    Oral presentation

  • ニホンナシS3-RNase 周辺領域451kb のゲノム構造解析

    武矢 悠太郎, 野村 直希, FUJIMOTO RYO, 安田 剛志

    平成28 年度園芸学会近畿支部兵庫大会, Aug. 2016, Japanese, Domestic conference

    Oral presentation

  • ニホンナシS2-RNase 周辺領域663kb のゲノム構造解析

    西村 遼太郎, FUJIMOTO RYO, 安田 剛志

    平成28 年度園芸学会近畿支部兵庫大会, Aug. 2016, Japanese, 神戸大学 瀧川記念学術交流会館, Domestic conference

    Oral presentation

  • Brassica rapa における白さび病抵抗性遺伝子同定に向けた病害反応調査

    宮路 直美, 西本 良太, 清水 元樹, 高田 紗都子, 安田 剛志, 土佐 幸雄, 中馬 いづみ, FUJIMOTO RYO

    平成28 年度園芸学会近畿支部兵庫大会, Aug. 2016, Japanese, 神戸大学 瀧川記念学術交流会館, Domestic conference

    Oral presentation

  • Brassica rapa L.における春化経路関連遺伝子FLOWERING LOCUS C の発現解析および エピジェネティックな転写制御について

    高田 紗都子, 板橋 悦子, 宮路 直美, 安田 剛志, FUJIMOTO RYO

    平成28 年度園芸学会近畿支部兵庫大会, Aug. 2016, Japanese, Domestic conference

    Oral presentation

  • シロイヌナズナの雑種強勢の分子機構の解明に向けたRILの整備

    川辺 隆大, 宮路 直美, 高田 紗都子, 板橋 悦子, 安田 剛志, FUJIMOTO RYO

    日本育種学会第129回講演会, Mar. 2016, Japanese, 横浜市立大学, Domestic conference

    Oral presentation

  • ハクサイにおけるヒストンメチル化抗体を用いたクロマチン免疫沈降法のポジティブ ネガティブコントロールプライマーの作製

    FUJIMOTO RYO, 川辺 隆大, 板橋 悦子, 安田 剛志

    平成27年度園芸学会秋季大会, Sep. 2015, Japanese, 園芸学会, 徳島大学, 概要, Domestic conference

    Oral presentation

  • ハクサイにおけるヒストンメチル化抗体を用いたクロマチン免疫沈降法のポジティブ/ネガティブコントロールプライマーの作製

    FUJIMOTO RYO, 川辺 隆大, 板橋 悦子, 安田 剛志, 岡崎 桂一

    園芸学会平成27年度秋季大会, Sep. 2015, Japanese, Domestic conference

    Oral presentation

  • ハクサイにおいて、両親系統間の遺伝距離から雑種強勢を予測できるか?

    川村 和隆, 佐伯 なつみ, 今野 周平, 永野 敦, 本庄 三恵, 八杉 公基, 工藤 洋, 安田 剛志, 加治 誠, 岡崎 桂一, FUJIMOTO RYO

    日本育種学会第128回講演会, Sep. 2015, Japanese, Domestic conference

    Oral presentation

  • ハクサイにおいて、両親系統間の遺伝距離から雑種強勢を予測できるか?

    川村 和隆, 佐伯 なつみ, 今野 周平, 永野 敦, 本庄 三恵, 八杉 公基, 工藤 洋, 安田 剛志, 加治 誠, 岡崎 桂一, FUJIMOTO RYO

    育種学会第128回講演会, Sep. 2015, Japanese, 日本育種学会, 新潟大学, 概要, Domestic conference

    Oral presentation

  • ニホンナシSホモ系統の花粉cDNAからのPpSFBB2ホモログのクローニングII

    西村 遼太郎, FUJIMOTO RYO, 安田 剛志

    平成27年度秋季大会, Sep. 2015, Japanese, 園芸学会, 徳島大学, 概要, Domestic conference

    Oral presentation

  • アブラナ科の雑種強勢の分子機構の解明を目指した後成遺伝学的なアプローチ

    FUJIMOTO RYO, 川辺 隆大

    日本遺伝学会第87大会, Sep. 2015, Japanese, 東北大学, Domestic conference

    [Invited]

    Invited oral presentation

  • Brassica oleraceaの倍加半数体系統群を用いた連鎖地図の作成と根こぶ病レース特異的CR-QTLの同定

    小玉 太郎, 川村 和隆, モハマドアサドウドドウラ, 清水 元樹, FUJIMOTO RYO, 深井 英吾, 岡崎 桂一

    日本育種学会第128回講演会, Sep. 2015, Japanese, Domestic conference

    Poster presentation

  • Brassica oleracea における根こぶ病抵抗性遺伝子PbBo(Anju)1 のファインマッピング

    川村 和隆, 小玉 太郎, 清水 元樹, モハマドアサドウドドウラ, 富田 寛也, 佐々木 一嘉, FUJIMOTO RYO, 深井 英吾, 岡崎 桂一

    日本育種学会第128回講演会, Sep. 2015, Japanese, Domestic conference

    Oral presentation

  • Genetic and epigenetic approaches for identification of molecular mechanism of heterosis in Brassica

    FUJIMOTO RYO

    A consortium of plant epigenetisists in Japan – First Meeting, Jul. 2015, English, National Institute of Genetics, Domestic conference

    Public discourse

  • DNA marker-assisted breeding in F1 hybrid cultivar of Chinese cabbage

    FUJIMOTO RYO

    Symposium; Epigenetics and Gene expression for Crop improvement, Apr. 2015, English, ANU university House, International conference

    Oral presentation

  • Genetic and epigenetic approaches for identification of molecular mechanism of heterosis in Brassica

    FUJIMOTO RYO

    Institute of Plant Science and Recourses Workshop; Plant Epigenetics: From Emerging Phenomena to Novel Molecular Events, Jan. 2015, English, Kurashiki Geibun kan, Domestic conference

    Oral presentation

  • ハクサイ市販一代雑種品種‘W77’における雑種強勢に関わるQTLの探索

    阿部 寛史, 川辺 隆大, 佐伯 なつみ, 清水 元樹, 今野 周平, 永野 惇, 本庄 三恵, 八杉 公基, 工藤 洋, 畠山 勝徳, 松元 哲, 岡崎 桂一, 加治 誠, FUJIMOTO RYO

    日本育種学会第126回講演会, Sep. 2014, Japanese, 南九州大学, Domestic conference

    Oral presentation

  • ニホンナシ和合・不和合花粉管へのS-RNaseの取り込み

    李 麗怡, 時安 美奈, FUJIMOTO RYO, 安田 剛志

    平成26年度秋季大会, Sep. 2014, Japanese, 園芸学会, 佐賀大学, Domestic conference

    Oral presentation

  • ニホンナシSホモ系統の花粉cDNAからのPpSFBB2ホモログのクローニング

    西村 遼太郎, 今村 剛士, 加藤 大貴, FUJIMOTO RYO, 安田 剛志

    平成26年度秋季大会, Sep. 2014, Japanese, 園芸学会, 佐賀大学, Domestic conference

    Oral presentation

  • ニホンナシS4-RNase周辺BACコンティグの拡張によるPpSFBB遺伝子群の探索

    安藤 肇, 山下 翔人, FUJIMOTO RYO, 安田 剛志

    平成26年度秋季大会, Sep. 2014, Japanese, 園芸学会, 佐賀大学, Domestic conference

    Oral presentation

  • ニホンナシnon-S-RNaseの花柱組織における蓄積と花粉管への取り込み

    時安 美奈, 李 麗怡, 岡村 彩葉, FUJIMOTO RYO, 安田 剛志

    平成26年度秋季大会, Sep. 2014, Japanese, 園芸学会, 佐賀大学, Domestic conference

    Oral presentation

  • シロイヌナズナの雑種強勢に概日リズムは関わるか?

    川辺 隆大, 佐伯 なつみ, 阿部 寛史, FUJIMOTO RYO

    日本育種学会第126回講演会, Sep. 2014, Japanese, 南九州大学, Domestic conference

    Poster presentation

  • アブラナ科萎黄病菌(Fusarium oxysporum)のde novo全ゲノムシークエンス情報を用いた分化型特異的遺伝子領域の探索

    船木 武人, 田子 明日美, Pu ZI-JING, 深井 英吾, 佐野 義孝, 阿部 貴志, 藤 晋一, FUJIMOTO RYO, 清水 元樹, 夏目 俊, 寺内 良平, 岡崎 桂一

    日本育種学会第126回講演会, Sep. 2014, Japanese, 南九州大学, Domestic conference

    Poster presentation

  • DNAマーカーを用いたBrassica rapa近交系の基盤整備

    川村 和隆, 吉田 実央, 清水 元樹, 佐伯 なつみ, 阿部 寛史, 江部 裕介, 岡崎 桂一, FUJIMOTO RYO, 川辺 隆大

    日本育種学会第126回講演会, Sep. 2014, Japanese, 南九州大学, Domestic conference

    Poster presentation

  • Brassica oleracea近交系の遺伝的均一性評価およびF1種子純度検定に適したDNAマーカーの探索

    川村 和隆, 清水 元樹, 佐伯 なつみ, 阿部 寛史, 江部 裕介, 岡崎 桂一, 川辺 隆大, FUJIMOTO RYO

    園芸学会平成26年度秋期大会, Sep. 2014, Japanese, Domestic conference

    Poster presentation

  • ハクサイ市販一代雑種品種‘W39’における雑種強勢関連遺伝子の発現解析

    佐伯 なつみ, 川辺 隆大, 野瀬 笙子, 阿部 寛史, 加治 誠, 岡崎 桂一, FUJIMOTO RYO

    園芸学会平成26年度春季大会, Mar. 2014, Japanese, 筑波大学, Domestic conference

    Oral presentation

  • ハクサイ市販一代雑種品種W77及びそのF2後代の形質調査

    阿部 寛史, 川辺 隆大, 野瀬 笙子, 佐伯 なつみ, 清水 元樹, 今野 周平, 加治 誠, 岡崎 桂一, FUJIMOTO RYO

    日本育種学会第125回講演会, Mar. 2014, Japanese, 東北大学, Domestic conference

    Oral presentation

  • シロイヌナズナの初期生育時に見られる雑種強勢はPol4の機能とは独立である

    川辺 隆大, 佐伯 なつみ, 佐々木 卓, 阿部 寛史, FUJIMOTO RYO

    日本育種学会第125回講演会, Mar. 2014, Japanese, 日本育種学会, Domestic conference

    Poster presentation

  • RNA-sequencing法によるハクサイ市販F1品種の両親系統間のSNP同定

    佐伯なつみ, 野瀬 笙子, 川辺 隆大, 阿部 寛史, 岡崎 桂一, 加治 誠, FUJIMOTO RYO

    日本育種学会第125回講演会, Mar. 2014, Japanese, 東北大学, Domestic conference

    Oral presentation

  • Differential expression解析を用いたハクサイ萎黄病抵抗性候補遺伝子の同定

    清水 元樹, 江部 裕介, 川辺 隆大, 佐伯 なつみ, 加治 誠, 岡崎 桂一, FUJIMOTO RYO

    園芸学会平成26年度春季大会, Mar. 2014, Japanese, 筑波大学, Domestic conference

    Poster presentation

  • Brassica oleraceaにおける近交系の純度検定に最適なDNAマーカーのスクリーニングと汎用性

    川村 和隆, 玄田 真優, 佐々木 一嘉, 清水 元樹, 佐伯 なつみ, 岡崎 桂一, FUJIMOTO RYO, 川辺 隆大

    日本育種学会第125回講演会, Mar. 2014, Japanese, 東北大学, Domestic conference

    Poster presentation

  • ハクサイ市販F1品種‘W39’の生育初期に見られる雑種強勢について

    佐伯 なつみ, 川辺 隆大, 阿部 寛史, 加治 誠, 岡崎 桂一, FUJIMOTO RYO

    日本育種学会第124回講演会, Oct. 2013, Japanese, 鹿児島大学, Domestic conference

    Oral presentation

  • シロイヌナズナの子葉における雑種強勢を示すF1とその両親系統間での転写比較解析

    FUJIMOTO RYO, TAYLOR M. JENNIFER, 川辺 隆大, 佐伯 なつみ, 阿部 寛史, PEACOCK J. WILLIAM, DENNIS S. ELIZABETH

    日本育種学会第124回講演会, Oct. 2013, Japanese, 鹿児島大学, Domestic conference

    Oral presentation

  • シロイヌナズナのF1雑種にみられる雑種強勢の程度について

    川辺 隆大, 井出 千賀, 佐伯 なつみ, FUJIMOTO RYO

    日本育種学会第124回講演会, Oct. 2013, Japanese, 鹿児島大学, Domestic conference

    Oral presentation

  • アブラナ科植物一代雑種品種における両親系統の対立遺伝子間相互作用

    川辺 隆大, 佐伯 なつみ, 阿部 寛史, 今野 周平, 加治 誠, 岡崎 桂一, FUJIMOTO RYO

    日本育種学会第124回講演会, Oct. 2013, Japanese, 鹿児島大学, Domestic conference

    Public symposium

  • Brassica oleracea品種における萎黄病抵抗性遺伝子FocBo1連鎖DNA マーカーと抵抗性との関連性

    清水 元樹, 川辺 隆大, PU ZI-JING, FUJIMOTO RYO, 岡崎 桂一

    日本育種学会第124回講演会, Oct. 2013, Japanese, 鹿児島大学, Domestic conference

    Poster presentation

  • Brassica oleracea染色体添加型 B. rapa を用いた緑植物体春化の遺伝解析

    戸丸 祐貴, 中村 友理, 清水 元樹, FUJIMOTO RYO, 岡崎 桂一

    日本育種学会第124回講演会, Oct. 2013, Japanese, 鹿児島大学, Domestic conference

    Oral presentation

  • 初期生育時に見られるハクサイとシロイヌナズナの雑種強勢の相違点

    FUJIMOTO RYO, 佐伯 なつみ, 阿部 寛史, 加治 誠, 川辺 隆大

    園芸学会平成25年度秋期大会, Sep. 2013, Japanese, 岩手大学, Domestic conference

    Poster presentation

  • ハクサイF1品種W77における初期生育と収穫期の雑種強勢の評価

    川辺 隆大, 阿部 寛史, 佐伯 なつみ, 清水 元樹, 今野 周平, 加治 誠, FUJIMOTO RYO

    園芸学会平成25年度秋期大会, Sep. 2013, Japanese, 岩手大学, Domestic conference

    Oral presentation

  • ハクサイF1品種W39における生育初期及び収穫期の雑種強勢の評価

    佐伯 なつみ, 川辺 隆大, 阿部 寛史, 今野 周平, 清水 元樹, 加治 誠, FUJIMOTO RYO

    園芸学会平成25年度秋期大会, Sep. 2013, Japanese, 岩手大学, Domestic conference

    Oral presentation

  • Variation of the level of the heterosis among F1 hybrid individuals in Arabidopsis thaliana

    KAWANABE TAKAHIRO, SAEKI NATSUMI, FUJIMOTO RYO

    24th International Conference on Arabidopsis Research, Jun. 2013, English, Sydney, Australia, International conference

    Poster presentation

  • A large cotyledon area after germination is a common phenomenon in heterotic F1 hybrids of Arabidopsis thaliana and Chinese cabbage

    SAEKI NATSUMI, KAWANABE TAKAHIRO, ABE HIROFUMI, SHIMIZU MOTOKI, KONNO SHUHEI, KAJI MAKOTO, FUJIMOTO RYO

    24th International Conference on Arabidopsis Research, Jun. 2013, English, Sydney, Australia, International conference

    Poster presentation

  • アブラナ科植物の種内、種間雑種に見られる非相加的遺伝子発現

    FUJIMOTO RYO

    日本育種学会第123回講演会, Mar. 2013, Japanese, 東京農業大学, Domestic conference

    [Invited]

    Invited oral presentation

  • Establishment of heterosis at early developmental stage in Arabidopsis thaliana is independent from Pol4 activity

    FUJIMOTO RYO, SASAKI TAKU, KAWANABE TAKAHIRO, SAEKI NATSUMI, ABE HIROFUMI, PEACOCK J. WILLIAM, DENNIS S. ELIZABETH

    第54回日本植物生理学会年会, Mar. 2013, English, 岡山大学, Domestic conference

    Oral presentation

Research Projects

  • 藤本 龍

    学術研究助成基金助成金/国際共同研究加速基金(国際共同研究強化), Apr. 2017 - Mar. 2020, Principal investigator

    Competitive research funding

  • 安田 剛志

    科学研究費補助金/基盤研究(B), Apr. 2015 - Mar. 2019

    Competitive research funding

  • 藤本 龍

    科学研究費補助金/若手研究(A), Apr. 2015 - Mar. 2019, Principal investigator

    Competitive research funding

  • アブラナ科植物におけるDNAメチル化による雑種強勢発現機構の解明

    藤本 龍

    独立行政法人日本学術振興会, 二国間国際交流(オーストラリア(OP)との共同研究), 2017, Principal investigator

    Competitive research funding

  • アブラナ科野菜の白さび病抵抗性遺伝子の同定

    藤本 龍

    研究成果展開事業(マッチングプランナー プログラム), 2016, Principal investigator

    Competitive research funding

  • アブラナ科植物のヘテローシスの分子機構の解析

    藤本 龍

    独立行政法人日本学術振興会, 二国間交流事業(オープンパートナーシップ共同研究), 2016, Principal investigator

    Competitive research funding

  • 二国間交流「アブラナ科植物のヘテローシスの分子機構の解析」

    藤本 龍

    日本学術振興会, 二国間交流事業(オープンパートナーシップ共同研究), 2015, Principal investigator

    Competitive research funding

  • さきがけ「雑種強勢の分子機構の解明とその高バイオマス作物への活用」

    藤本 龍

    科学技術振興機構, 戦略的創造研究推進事業 個人型研究さきがけ, 2015, Principal investigator

    Competitive research funding

  • 藤本 龍

    学術研究助成基金助成金/若手研究(B), Apr. 2012 - Mar. 2014, Principal investigator

    Competitive research funding

  • 藤本 龍

    科学研究費補助金/新学術領域研究, Apr. 2012 - Mar. 2014, Principal investigator

    Competitive research funding

  • 二国間交流「アブラナ科植物のヘテローシスの分子機構の解析」

    藤本 龍

    二国間交流事業(オープンパートナーシップ共同研究), 2014, Principal investigator

    Competitive research funding

  • さきがけ「雑種強勢の分子機構の解明とその高バイオマス作物への活用」

    藤本 龍

    戦略的創造研究推進事業 個人型研究さきがけ, 2014, Principal investigator

    Competitive research funding

  • さきがけ「雑種強勢の分子機構の解明とその高バイオマス作物への活用」

    藤本 龍

    戦略的創造研究推進事業 個人型研究さきがけ, 2013, Principal investigator

    Competitive research funding