Researcher Profile and Settings

Master

Affiliation (Master)

• Research Faculty of Agriculture　Fundamental AgriScience Research　Applied Bioscience

Affiliation (Master)

• Research Faculty of Agriculture　Fundamental AgriScience Research　Applied Bioscience

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Profile and Settings

Profile and Settings

• Name (Japanese)

  Kishima

• Name (Kana)

  Yuji

• Name

  200901055937787372

Achievement

Research Interests

• 植物育種学、遺伝学、分子遺伝学   Plant Genetics   Plant Breeding   

Research Areas

• Environmental science/Agricultural science / Plant genetics and breeding

Awards

• 2022/03 Japanese Society of Breeding Award of Breeding Science paper in 2022
   Seed management using NGS technology to rapidly eliminate a deleterious allele from rice 

  受賞者: Elias G. Balimponya;Maria S. Dwiyanti;Toshiaki Ito;Shuntaro Sakaguchi;Koichi Yamamori;Yoshitaka Kanaoka;Yohei Koide;Yoshifumi Nagayoshi;Yuji Kishima
• 2002 第１回日本遺伝学会ベストペーパー賞
  
• 2001 平成１２年度日本育種学会奨励賞
  

Published Papers

• Cryptic cytoplasmic male sterility-causing gene in the mitochondrial genome of common japonica rice.

  Kinya Toriyama, Yuko Iwai, Shinya Takeda, Ayumu Takatsuka, Keisuke Igarashi, Tomoyuki Furuta, Sunlu Chen, Yoshitaka Kanaoka, Yuji Kishima, Shin-Ichi Arimura, Tomohiko Kazama

  The Plant journal : for cell and molecular biology 2024/09/09 [Refereed]
   

  Cytoplasmic male sterility (CMS) is an agronomically significant trait that causes dysfunction in pollen and anther development. It is often observed during successive backcrossing between distantly related species. Here, we show that Asian japonica cultivars (Oryza sativa) exhibit CMS when the nucleus is replaced with that of the African rice Oryza glaberrima. The CMS line produced stunted anthers and did not set any seeds. Mitochondrial orf288 RNA was detected in the anthers of CMS lines but not in fertility restorer lines. The mitochondrial genome-edited japonica rice that was depleted of orf288 did not exhibit male sterility when backcrossed with O. glaberrima. These results demonstrate that orf288 is a CMS-causing gene. As orf288 commonly occurs in the mitochondrial genomes of japonica rice, these results indicate that common japonica rice cultivars possess a cryptic CMS-causing gene hidden in their mitochondrial genomes.
• Stable early heading in photoperiod-insensitive rice varieties results from an extremely short photoperiod-sensitive phase and weak temperature sensitivity

  Shuntaro Sakaguchi, Md. Imdadul Hoque, Yuji Kishima

  Plant Stress 2024/09 [Refereed]
  
• TwoStabiliserloci inAntirrhinumsuppress the transposition of Tam3 without compromising transposase production

  Shasha Wang, Takako Uchiyama, Hiroyuki Kuwabara, Megumi Hirata, Ikumi Yuasa, Kenji Nakahara, Cathie Martin, Yuji Kishima

  2024/06/28
• Tetraploid interspecific hybrids between Asian and African rice species restore fertility depending on killer-protector loci for hybrid sterility.

  Daichi Kuniyoshi, Megumi Ishihara, Koichi Yamamori, Yohei Koide, Yuji Kishima

  Genetics 228 (1) iyae104  2024/06/28 [Refereed]
   

  Interspecific F1 hybrids between Asian (Oryza sativa) and African rice (Oryza glaberrima) exhibit severe sterility caused by the accumulation of hybrid sterility genes/loci at 15 or more loci. The mechanisms underlying the hybrid sterility genes are largely unknown; however, a few genes associated with the killer-protector system, which is the system most frequently associated with hybrid sterility genes, have been identified. We previously produced fertile plants as tetraploids derived from diploid interspecific F1 hybrids through anther culture; therefore, it was suggested that hybrid sterility could be overcome following tetraploidization. We investigated whether tetraploid interspecific plants produced by crossing are fertile and tested the involvement of hybrid sterility genes in the process. Fertile tetraploid interspecific F1 hybrid plants were obtained by crossing two tetraploids of Oryza sativa and Oryza glaberrima. To elucidate the relationships between pollen fertility and the hybrid sterility loci in the tetraploid F1 microspores, we performed genetic analyses of the tetraploid F2 hybrids and diploid plants obtained from the microspores of tetraploid interspecific hybrids by anther culture. The result suggested that the tetraploid interspecific hybrids overcame pollen and seed infertility based on the proportion of loci with the killer-protector system present in the tetraploids. The heterozygous hybrid sterility loci with the killer-protector system in the tetraploid segregate the homozygous killed allele (16.7-21.4%), with more than three-quarters of the gametes surviving. We theoretically and experimentally demonstrated that fertile rice progenies can be grown from tetraploid interspecific hybrids.
• The anther transcriptome of cold-tolerant rice cultivars is largely insensitive to temperature changes

  Koichi Yamamori, Seiya Ishiguro, Kei Ogasawara, Kayyis Lubba, Kaien Fujino, Kazumitsu Onishi, Yutaka Sato, Yuji Kishima

  2024/05/22 

  Abstract

  Many studies of stress tolerance in plants have characterized genes that show differences among a small number of lines with clearly distinct tolerance or sensitivity to the given stress. From the few cloned genes, it is difficult to genetically interpret intermediate tolerance or susceptibility levels and explain the complexity of stress responses and tolerance. In this study, we explored the changes in the transcriptome of anthers from 13 rice lines with different cold tolerance grown under control conditions or exposed to 4 days of cold stress to look for correlations between cold tolerance at the booting stage and expression levels. When examining the overall expression patterns in anthers at low temperature, the cold-tolerant lines tended to have relatively few highly expressed genes, and the expression levels of ribosome-related genes tended to be lower in cold-tolerant lines than in cold-sensitive lines. Importantly, we observed these different expression patterns between the cold-tolerant and -sensitive lines regardless of whether cold stress had been applied. Minimal expression changes under cold stress tended to be characteristic of the cold-tolerant lines, especially in repetitive sequences. We also identified unknown genes whose expression was cold responsive and common to all the lines studied. We conclude that rice lines whose transcriptome remains constant or insensitive in response to cold stress are more tolerant to low-temperature exposure during the booting stage than rice lines with more widespread expression changes.

• OlCHR, encoding a chromatin remodeling factor, is a killer causing hybrid sterility between rice species Oryza sativa and O. longistaminata.

  Zin Mar Myint, Yohei Koide, Wakana Takanishi, Tomohito Ikegaya, Choi Kwan, Kiwamu Hikichi, Yoshiki Tokuyama, Shuhei Okada, Kazumitsu Onishi, Ryo Ishikawa, Daisuke Fujita, Yoshiyuki Yamagata, Hideo Matsumura, Yuji Kishima, Akira Kanazawa

  iScience 27 (5) 109761 - 109761 2024/05/17 [Refereed]
   

  The genetic mechanisms of reproductive isolation have been widely investigated within Asian cultivated rice (Oryza sativa); however, relevant genes between diverged species have been in sighted rather less. Herein, a gene showing selfish behavior was discovered in hybrids between the distantly related rice species Oryza longistaminata and O. sativa. The selfish allele S13l in the S13 locus impaired male fertility, discriminately eliminating pollens containing the allele S13s from O. sativa in heterozygotes (S13s/S13l). Genetic analysis revealed that a gene encoding a chromatin-remodeling factor (CHR) is involved in this phenomenon and a variety of O. sativa owns the truncated gene OsCHR745, whereas its homologue OlCHR has a complete structure in O. longistaminata. CRISPR-Cas9-mediated loss of function mutants restored fertility in hybrids. African cultivated rice, which naturally lacks the OlCHR homologue, is compatible with both S13s and S13l carriers. These results suggest that OlCHR is a Killer gene, which leads to reproductive isolation.
• Different contributions of PROG1 and TAC1 to the angular kinematics of the main culm and tillers of wild rice (Oryza rufipogon)

  Yoshiki Tokuyama, Miku Omachi, Shiori Kushida, Kiwamu Hikichi, Shuhei Okada, Kazumitsu Onishi, Takashige Ishii, Yuji Kishima, Yohei Koide

  Planta 259 (1) 0032-0935 2023/12/12 [Refereed]
  
• Genetics of chilling response at early growth stage in rice: a recessive gene for tolerance and importance of acclimation.

  Akhil Ranjan Baruah, Hiroaki Bannai, Yan Meija, Ayumi Kimura, Haruka Ueno, Yohei Koide, Yuji Kishima, Jiwan Palta, Jun Kasuga, Masayuki P Yamamoto, Kazumitsu Onishi

  AoB PLANTS 15 (6) plad075  2023/12 [Refereed]
   

  Low-temperature adaptation in rice is mediated by the ability of a genotype to tolerate chilling temperatures. A genetic locus on chromosome 11 was analysed for chilling tolerance at the plumule stage in rice. The tolerant allele of A58, a japonica landrace in Japan, was inherited as a recessive gene (ctp-1A58), whereas the susceptible alleles from wild rice (Ctp-1W107) and modern variety (Ctp-1HY) were the dominant genes. Another recessive tolerant allele (ctp-1Silewah) was found in a tropical japonica variety (Silewah). Fine-mapping revealed that a candidate gene for the ctp-1 locus encoded a protein similar to the nucleotide-binding domain and leucine-rich repeat (NLR) protein, in which frameshift mutation by a 73 bp-deletion might confer chilling tolerance in ctp-1A58. Analysis of near-isogenic lines demonstrated that ctp-1A58 imparted tolerance effects only at severe chilling temperatures of 0.5 °C and 2 °C, both at plumule and seedling stages. Chilling acclimation treatments at a wide range of temperatures (8 °C-16 °C) for 72 h concealed the susceptible phenotype of Ctp-1W107 and Ctp-1HY. Furthermore, short-term acclimation treatment of 12 h at 8 °C was enough to be fully acclimated. These results suggest that the NLR gene induces a susceptible response upon exposure to severe chilling stress, however, another interacting gene(s) for acclimation response could suppress the maladaptive phenotype caused by the Ctp-1 allele. This study provides new insights for the adaptation and breeding of rice in a low-temperature environment.
• Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species.

  Nozomi Saito, Sunlu Chen, Katsuya Kitajima, Zhitong Zhou, Yohei Koide, Jaymee R Encabo, Maria Genaleen Q Diaz, Il-Ryong Choi, Kanako O Koyanagi, Yuji Kishima

  Frontiers in plant science 14 1261705 - 1261705 2023 [Refereed]
   

  INTRODUCTION: Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. These viral elements, known as endogenous RTBV-like sequences (eRTBVLs), comprise five subfamilies, eRTBVL-A, -B, -C, -D, and -X. Four subfamilies (A, B, C, and X) are present to a limited degree in the genomes of the Asian cultivated rice Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon. METHODS: The eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (Nipponbare) genome occur mostly at orthologous chromosomal positions in other AA-genome species. The eRTBVL-D sequences were inserted into the genomes just before speciation of the AA-genome species. RESULTS AND DISCUSSION: Ten eRTBVL-D segments are located at six loci, which were used for our evolutionary analyses during the speciation of the AA-genome species. The degree of genetic differentiation varied among the eRTBVL-D segments. Of the six loci, three showed phylogenetic trees consistent with the standard speciation pattern (SSP) of the AA-genome species (Type A), and the other three represented phylogenies different from the SSP (Type B). The atypical phylogenetic trees for the Type B loci revealed chromosome region-specific evolution among the AA-genome species that is associated with phylogenetic incongruences: complex genome rearrangements between eRTBVL-D segments, an introgression between the distant species, and low genetic diversity of a shared eRTBVL-D segment. Using eRTBVL-D as an indicator, this study revealed the phylogenetic incongruence of local chromosomal regions with different topologies that developed during speciation.
• Identification of a Saltol-Independent Salinity Tolerance Polymorphism in Rice Mekong Delta Landraces and Characterization of a Promising Line, Doc Phung.

  Tam Thanh Nguyen, Maria Stefanie Dwiyanti, Shuntaro Sakaguchi, Yohei Koide, Dung Viet Le, Toshihiro Watanabe, Yuji Kishima

  Rice (New York, N.Y.) 15 (1) 65 - 65 2022/12/18 [Refereed]
   

  The Mekong Delta River in Vietnam is facing salinity intrusion caused by climate change and sea-level rise that is severely affecting rice cultivation. Here, we evaluated salinity responses of 97 rice accessions (79 landraces and 18 improved accessions) from the Mekong Delta population by adding 100 mM NaCl to the nutrient solution for up to 20 days. We observed a wide distribution in salinity tolerance/sensitivity, with two major peaks across the 97 accessions when using the standard evaluation system (SES) developed by the International Rice Research Institute. SES scores revealed strong negative correlations (ranging from - 0.68 to - 0.83) with other phenotypic indices, such as shoot elongation length, root elongation length, shoot dry weight, and root dry weight. Mineral concentrations of Na+ in roots, stems, and leaves and Ca2+ in roots and stems were positively correlated with SES scores, suggesting that tolerant accessions lower their cation exchange capacity in the root cell wall. The salinity tolerance of Mekong Delta accessions was independent from the previously described salinity tolerance-related locus Saltol, which encodes an HKT1-type transporter in the salinity-tolerant cultivars Nona Bokra and Pokkali. Indeed, genome-wide association studies using SES scores and shoot dry weight ratios of the 79 accessions as traits identified a single common peak located on chromosome 1. This SNP did not form a linkage group with other nearby SNPs and mapped to the 3' untranslated region of gene LOC_Os01g32830, over 6.5 Mb away from the Saltol locus. LOC_Os01g32830 encodes chloroplast glycolate/glycerate translocator 1 (OsPLGG1), which is responsible for photorespiration and growth. SES and shoot dry weight ratios differed significantly between the two possible haplotypes at the causal SNP. Through these analyses, we characterize Doc Phung, one of the most salinity-tolerant varieties in the Mekong Delta population and a promising new genetic resource.
• Seed management using NGS technology to rapidly eliminate a deleterious allele from rice breeder seeds.

  Balimponya, E. G., Dwiyanti, M. S., Ito, T., Sakaguchi, S., Yamamori, K., Kanaoka, Y. Koide Y., Nagayoshi, Y., Kishima, Y.

  Breeding Science 1344-7610 2022/12 [Refereed]
  
• How to establish a mutually beneficial relationship between a transposon and its host: lessons from Tam3 in Antirrhinum

  Wang, S, Koide, Y. Kishima

  Genes & genetic systems 97 (4) 177 - 184 2022/12 [Refereed][Invited]
   

  The transposon Tam3 of Antirrhinum (snapdragon) has acquired properties that distinguish it from other transposons. Mobile DNA, commonly referred to as a transposable element or transposon, is considered to be synonymous with a selfish factor. That is, a transposable element increases in copy number and moves copies of itself independently of the survival of the host organism. Therefore, the host collectively regulates the transposition activities of most transposable elements in its genome by epigenetic means. However, our analyses of the structure and behavior of Tam3, as shown by the following five results, provide evidence that it does not behave in a selfish manner in relation to the host. 1) Active transposable elements normally increase the abundance of their non-autonomous elements, whereas Tam3 is known to have no non-autonomous elements, and a limited number of around 10 copies of autonomous elements present in the genome have been isolated as active copies. 2) Tam3 does not transpose at 25 ℃, which is the optimal growth temperature for Antirrhinum. Transposition of Tam3 occurs only at low temperatures of about 15 ℃, which is stressful for Antirrhinum. 3) Few strains of Antirrhinum have been found to contain genes that specifically suppress Tam3 transposition. 4) Most of the Tam3 insertions found in Antirrhinum genes do not affect the host genome, and the expression of these host genes is not completely suppressed. 5) Transcription and translation of the Tam3 transposase gene are not epigenetically regulated by the host. These five experimental results constitute evidence that Tam3 retains features that are dissimilar to those of many other transposons and that it does not behave in a selfish manner that is detrimental to the survival of the host. In this review, we consider what kinds of behavior are required if transposons are to establish a mutually beneficial relationship with their hosts, with reference to Tam3.
• Temporal changes in transcripts of miniature inverted-repeat transposable elements during rice endosperm development

  Nagata, H., Ono, A., Tonosaki, K., Kawakatsu, T., Sato, Y., Yano, K., Kishima, Y., Kinoshita, T.

  Plant Journal 109 (5) 1035 - 1047 1365-313X 2022/03 [Refereed][Not invited]
  
• Editorial: DNA virus and host plant interactions from antagonism to endogenization

  Richert-P{\"o}ggeler, K.R., Iskra-Caruana, M.-L., Kishima, Y.

  Frontiers in Plant Science 13 1664-462X 2022
• Effectiveness of Create ML in microscopy image classifications: a simple and inexpensive deep learning pipeline for non-data scientists

  Nagaki, K., Furuta, T., Yamaji, N., Kuniyoshi, D., Ishihara, M., Kishima, Y., Murata, M., Hoshino, A., Takatsuka, H.

  Chromosome Research 29 (3-4) 1573-6849 2021/10 [Refereed][Not invited]
  
• Revision of the relationship between anther morphology and pollen sterility by cold stress at the booting stage in rice.

  Koichi Yamamori, Kei Ogasawara, Seiya Ishiguro, Yohei Koide, Itsuro Takamure, Kaien Fujino, Yutaka Sato, Yuji Kishima

  Annals of botany 128 (5) 559 - 575 2021/07/07 [Refereed][Not invited]
   

  BACKGROUND AND AIMS: Cold stress in rice (Oryza sativa) plants at the reproductive stage prevents normal anther development and causes pollen sterility. Tapetum hypertrophy in anthers has been associated with pollen sterility in response to cold at the booting stage. Here, we reexamined whether the relationships between anther abnormality and pollen sterility caused by cold stress at the booting stage in rice can be explained by a monovalent factor such as tapetum hypertrophy. METHODS: After exposing plants to a 4-day cold treatment at the booting stage, we collected and processed anthers for transverse sectioning immediately and at the flowering stage. We anatomically evaluated the effect of cold treatment on anther internal morphologies, pollen fertilities and pollen numbers in the 13 cultivars with various cold sensitivities. KEY RESULTS: We observed four types of morphological anther abnormalities at each stage. Pollen sterility was positively correlated with the frequency of undeveloped locules, but not with tapetum hypertrophy as commonly believed. In cold-sensitive cultivars grown at low temperatures, pollen sterility was more frequent than anther morphological abnormalities, and some lines showed remarkably high pollen sterility without any anther morphological alterations. Most morphological anomalies occurred only in specific areas within large and small locules. Anther length tended to shorten in response to cold treatment and was positively correlated with pollen number. One cultivar showed a considerably reduced pollen number, but fertile pollen grains under cold stress. We propose three possible relationships to explain anther structure and pollen sterility and reduction due to cold stress. CONCLUSIONS: The pollen sterility caused by cold stress at the booting stage was correlated with the frequency of entire locule-related abnormalities, which might represent a phenotypic consequence, but not a direct cause of pollen abortion. Multivalent factors might underly the complicated relationships between anther abnormality and pollen sterility in rice.
• The mechanical origin of the radial shape in distichous phyllotaxy grass plants

  Tokuyama, Y., Koide, Y., Onishi, K., Hikichi, K., Omachi, M., Takamure, I., Kishima, Y.

  In Silico Plants 3 (2) 2517-5025 2021/07/01 [Refereed][Not invited]
   

  Three-dimensional plant shapes are influenced by their phyllotaxy, which plays a significant role in their environmental adaptation. Grasses with distichous phyllotaxy have linearly aligned culms and usually have vertical fan-like shapes. Counterintuitively, some distichous phyllotaxy grasses have radial shapes. Here, we investigate the organ-level mechanism underlying radial shape development in the distichous phyllotactic wild rice species (Oryza rufipogon). Detailed time-course phenotyping and three-dimensional micro-computed tomography showed that changes in the elevation angle in the main culm and azimuth angle in the primary tillers contribute to radial shape development. To infer the mechanical basis of the shape change, we simulated the movements of culms controlled by different kinematic factors. The computational models predicted that the combination of movements, including that controlled by negative gravitropism, produces the overall radial shape. This prediction was experimentally assessed. The analysis using a near-isogenic line of the gene, PROG1 for prostrate growth and the gravitropic mutant (lazy1) showed an association between genes and our model parameters. Our findings provide a simple, yet substantial, kinematic model for how the shape in distichous phyllotaxy plants changes as part of their adaptation to the surrounding environment.
• Genetic Mapping of the Gamete Eliminator Locus, S-2, Causing Hybrid Sterility and Transmission Ratio Distortion Found between Oryza sativa and Oryza glaberrima Cross Combination

  Myint Zin Mar, Yohei Koide, Mei Ogata, Daichi Kuniyoshi, Yoshiki Tokuyama, Kiwamu Hikichi, Mitsuhiro Obara, Yuji Kishima

  AGRICULTURE-BASEL 11 (3) 2021/03 [Refereed][Not invited]
   

  Hybrid sterility is a reproductive barrier that prevents gene flow between species. In Oryza species, some hybrid sterility loci, which are classified as gamete eliminators, cause pollen and seed sterility and sex-independent transmission ratio distortion (siTRD) in hybrids. However, the molecular basis of siTRD has not been fully characterized because of lacking information on causative genes. Here, we analyze one of the hybrid sterility loci, S-2, which was reported more than forty years ago but has not been located on rice chromosomes. Hybrids between African rice (Oryza glaberrima) and a near-isogenic line that possesses introgressed chromosomal segments from Asian rice (Oryza sativa) showed sterility and siTRD, which confirms the presence of the S-2 locus. Genome-wide SNP marker survey revealed that the near-isogenic line has an introgression on chromosome 4. Further substitution mapping located the S-2 locus between 22.60 Mb and 23.54 Mb on this chromosome. Significant TRD in this chromosomal region was also observed in a calli population derived from cultured anther in hybrids of another cross combination of African and Asian rice species. This indicates that the pollen abortion caused by the S-2 locus occurs before callus induction in anther culture. It also suggests the wide existence of the S-2-mediated siTRD in this interspecific cross combination. Chromosomal location of the S-2 locus will be valuable for identifying causative genes and for understanding of the molecular basis of siTRD.
• Analysis of microspores epigenome changes in cool treatment in rice anther culture

  Hoshi Sakura, Minouchi Yui, Yamamori Koichi, Kanaoka Yoshitaka, Koide Yohei, Kim Jong-Myong, Kijima Yuji

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本育種学会・日本作物学会北海道談話会 62 42 - 43 2021 [Not refereed][Not invited]
  
• Genome wide association study of seedling leaf length in Oryza glaberrima.

  Iguchi K, Koide Y, Yamagata Y, Fujita D, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本育種学会・日本作物学会北海道談話会 62 46 - 47 2021 [Not refereed][Not invited]
  
• Genetic comparative analysis of Notched-berry grain caused by low temperature at the Grain-filling stage in Hokkaido rice lines.

  Saitoh Ryosuke, Zhan Chengfang, Yamamori Koichi, Koide Yohei, Kishima Yuji

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本育種学会・日本作物学会北海道談話会 62 40 - 41 2021
• Evolutionary specificity of the hybrid sterility locus S1 in African cultivated rice O. glaberrima.

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

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本育種学会・日本作物学会北海道談話会 62 44 - 45 2021
• Effects of PROG1 and TAC1 loci on difference of culm angle dynamics between wild and cultivated rice

  Omachi M, Tokuyama Y, Onishi K, Ishii T, Kishima Y, Koide Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本育種学会・日本作物学会北海道談話会 62 38 - 39 2021
• Development of phenotyping system using low altitude UAV imagery and deep learning

  Suxing Lyu, Noboru Noguchi, Ricardo Ospina, Yuji Kishima

  INTERNATIONAL JOURNAL OF AGRICULTURAL AND BIOLOGICAL ENGINEERING 14 (1) 207 - 215 1934-6344 2021/01 [Refereed][Not invited]
   

  In this study, a lightweight phenotyping system that combined the advantages of both deep learning-based panicle detection and the photogrammetry based on light consumer-level UAVs was proposed. A two-year experiment was conducted to perform data collection and accuracy validation. A deep learning model, named Mask Region-based Convolutional Neural Network (Mask R-CNN), was trained to detect panicles in complex scenes of paddy fields. A total of 13 857 images were fed into Mask R-CNN, with 80% used for training and 20% used for validation. Scores, precision, recall, Average Precision (AP), and F1-score of the Mask R-CNN, were 82.46%, 80.60%, 79.46%, and 79.66%, respectively. A complete workflow was proposed to preprocess flight trajectories and remove repeated detection and noises. Eventually, the evident changed in rice growth during the heading stage was visualized with geographic distributions, and the total number of panicles was predicted before harvest. The average error of the predicted amounts of panicles was 33.98%. Experimental results showed the feasibility of using the developed system as the high-throughput phenotyping approach.
• Infection with an asymptomatic virus in rice results in a delayed drought response.

  Jaymee R Encabo, Reena Jesusa A Macalalad-Cabral, Jerlie Mhay K Matres, Sapphire Charlene Thea P Coronejo, Gilda B Jonson, Yuji Kishima, Amelia Henry, Il-Ryong Choi

  Functional plant biology : FPB 47 (3) 239 - 249 2020/02 [Refereed][Not invited]
   

  Infection of viruses in plants often modifies plant responses to biotic and abiotic stresses. In the present study we examined the effects of Rice tungro spherical virus (RTSV) infection on drought response in rice. RTSV infection delayed the onset of leaf rolling by 1-2 days. During the delay in drought response, plants infected with RTSV showed higher stomatal conductance and less negative leaf water potential under drought than those of uninfected plants, indicating that RTSV-infected leaves were more hydrated. Other growth and physiological traits of plants under drought were not altered by infection with RTSV. An expression analysis of genes for drought response-related transcription factors showed that the expression of OsNAC6 and OsDREB2a was less activated by drought in RTSV-infected plants than in uninfected plants, further suggesting improved water status of the plants due to RTSV infection. RTSV accumulated more in plants under drought than in well-watered plants, indicating the increased susceptibility of rice plants to RTSV infection by drought. Collectively, these results indicated that infection with RTSV can transiently mitigate the influence of drought stress on rice plants by increasing leaf hydration, while drought increased the susceptibility of rice plants to RTSV.
• Genetically-controlled morphological abnormality during endosperm maturation at low temperatures in a rice variety in Hokkaido

  Zhan C, Yamamori K, Koide Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本育種学会・日本作物学会北海道談話会 61 60 - 61 2020
• Occurrence of albinism trait in breeding seeds of rice and identification of the causative gene: insight into seed management approach

  Balimponya E, Kanaoka Y, Sakaguchi S, Koide Y, Nagayoshi Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本育種学会・日本作物学会北海道談話会 61 58 - 59 2020
• Diploid Male Gametes Circumvent Hybrid Sterility Between Asian and African Rice Species.

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

  Frontiers in plant science 11 579305 - 579305 2020 [Refereed]
   

  In F1 hybrids of Oryza sativa (Asian rice) and Oryza glaberrima (African rice), heterozygosity leads to a complete gamete abortion because of allelic conflict at each of the 13 hybrid sterility (HS) loci. We systematically produced 19 plants from the F1 hybrids of both the rice species by the anther culture (AC) method. Five of the 19 interspecific hybrid plants were partially fertile and able to produce seeds. Unlike ordinal doubled haploid plants resulting from AC, these regenerated plants showed various ploidy levels (diploid to pentaploid) and different zygosities (completely homozygous, completely heterozygous, and a combination). These properties were attributable to meiotic anomalies in the interspecific hybrid F1 plants. Examination of the genetic structures of the regenerated plants suggested meiotic non-reduction took place in the interspecific hybrid F1 plants. The centromeric regions in the regenerated plants revealed that the abnormal first and/or second divisions of meiosis, namely the first division restitution (FDR) and/or second division restitution (SDR), had occurred in the interspecific hybrid. Immunohistochemical observations also verified these phenomena. FDR and SDR occurrences at meiosis might strongly lead to the formation of diploid microspores. The results demonstrated that meiotic anomalies functioned as a reproductive barrier occurred before the HS genes acted in gamete of the interspecific hybrid. Although such meiotic anomalies are detrimental to pollen development, the early rescue of microspores carrying the diploid gamete resulted in the fertile regenerated plants. The five partially fertile plants carrying tetraploid genomes with heterozygous alleles of the HS loci produced fertile diploid pollens, implying that the diploid gametes circumvented the allelic conflicts at the HS loci. We also proposed how diploid male gametes avoid HS with the killer-protector model.
• Fertile Tetraploids: New Resources for Future Rice Breeding?

  Yohei Koide, Daichi Kuniyoshi, Yuji Kishima

  Frontiers in plant science 11 1231 - 1231 1664-462X 2020 [Refereed][Not invited]
   

  Ploidy manipulation is an efficient technique for the development of novel phenotypes in plant breeding. However, in rice (Oryza sativa L.), severe seed sterility has been considered a barrier preventing cultivation of autotetraploids since the 1930s. Recently, a series of studies identified two fertile autotetraploids, identified herein as the PMeS (Polyploid Meiosis Stability) and Neo-Tetraploid lines. Here, we summarize their characteristics, focusing on the recovery of seed fertility, and discuss potential future directions of study in this area, providing a comprehensive understanding of current progress in the study of fertile tetraploid rice, a classical, but promising, concept for rice breeding.
• Profiling SNP and Nucleotide Diversity to Characterize Mekong Delta Rice Landraces in Southeast Asian Populations.

  Nguyen Thanh Tam, Maria Stefanie Dwiyanti, Yohei Koide, Atsushi J Nagano, Huynh Ky, Huynh Quang Tin, Nguyen Loc Hien, Le Viet Dung, Yuji Kishima

  The plant genome 12 (3) 1 - 11 1940-3372 2019/11 [Refereed][Not invited]
   

  CORE IDEAS: Single nucleotide polymorphism (SNP) analyses are a powerful tool to examine structure of local rice population. 3000 dataset of IRRI facilitates SNP profiling of Southeast Asian rice populations. Mekong Delta population is featured by comparisons with the other populations. The low π-value SNPs well-profile unique genetic regions in their genomes. Recent analyses using single nucleotide polymorphism (SNP) are a feasible mean for local collections which potentially possess useful, but not large, genetic variations. Genomic sequences of more than 3000 accessions released by the International Rice Research Institute (IRRI) can be used to characterize various local rice (Oryza sativa) populations. The aim of this study was to develop a method to facilitate genomic characterization of local rice populations. We mainly used 99 indica rice accessions (81 landraces and 18 improved varieties) from the Mekong Delta Development Research Institute (MDI). We obtained 2301 SNPs after a genomic sequencing analysis of the 99 rice accessions and subsequent filtering. Within the IRRI's dataset, the landraces fell into a cluster consisting of accessions from Southeast Asian countries (Ind3 cluster), and the MDI improved varieties were grouped in a cluster containing IRRI improved varieties (Ind1B cluster). A principal component analysis suggested that geographical location strongly affects phylogenetic relationships, and the MDI landraces were placed into a Vietnam+Cambodia group. To detect the nucleotide diversity within a population, π-value is commonly used. We think that whole genome distribution of π-values representing the nucleotide diversity of each population can be used to characterize local populations. Our simple profiling using low π-value genomic regions was able to reveal regional characteristics of rice genomes and should be useful for identifying local rice populations.
• Genetic Properties Responsible for the Transgressive Segregation of Days to Heading in Rice.

  Yohei Koide, Shuntaro Sakaguchi, Takashi Uchiyama, Yuya Ota, Ayumi Tezuka, Atsushi J Nagano, Seiya Ishiguro, Itsuro Takamure, Yuji Kishima

  G3 (Bethesda, Md.) 9 (5) 1655 - 1662 2019/05/07 [Refereed][Not invited]
   

  Transgressive segregation produces hybrid progeny phenotypes that exceed the parental phenotypes. Unlike heterosis, extreme phenotypes caused by transgressive segregation are heritably stable. We examined transgressive phenotypes of flowering time in rice, and revealed transgressive segregation in F2 populations derived from a cross between parents with similar (proximal) days to heading (DTH). The DTH phenotypes of the A58 × Kitaake F2 progenies were frequently more extreme than those of either parent. These transgressive phenotypes were maintained in the F3 and F4 populations. Both A58 and Kitaake are japonica rice cultivars adapted to Hokkaido, Japan, which is a high-latitude region, and have a short DTH. Among the four known loci required for a short DTH, three loci had common alleles in A58 and Kitaake, implying there is a similar genetic basis for DTH between the two varieties. A genome-wide single nucleotide polymorphism (SNP) analysis based on the F4 population identified five new quantitative trait loci (QTL) associated with transgressive DTH phenotypes. Each of these QTL had different degrees of additive effects on DTH, and two QTL had an epistatic effect on each other. Thus, a genome-wide SNP analysis facilitated the detection of genetic loci associated with extreme DTH phenotypes, and revealed that the transgressive phenotypes were produced by exchanging the complementary alleles of a few minor QTL in the similar parental phenotypes.
• Innate vulnerability of Oryza glaberrima to rice tungro bacilliform virus

  Saito, N., Encabo, J.R., Chen, S., Jonson, G., Kishima, Y., Choi, I.-R.

  Japan Agricultural Research Quarterly 53 (1) 1 - 6 0021-3551 2019/01 [Refereed][Not invited]
  
• Ancient Endogenous Pararetroviruses in Oryza Genomes Provide Insights into the Heterogeneity of Viral Gene Macroevolution.

  Sunlu Chen, Nozomi Saito, Jaymee R Encabo, Kanae Yamada, Il-Ryong Choi, Yuji Kishima

  Genome biology and evolution 10 (10) 2686 - 2696 2018/10/01 [Refereed][Not invited]
   

  Endogenous viral sequences in eukaryotic genomes, such as those derived from plant pararetroviruses (PRVs), can serve as genomic fossils to study viral macroevolution. Many aspects of viral evolutionary rates are heterogeneous, including substitution rate differences between genes. However, the evolutionary dynamics of this viral gene rate heterogeneity (GRH) have been rarely examined. Characterizing such GRH may help to elucidate viral adaptive evolution. In this study, based on robust phylogenetic analysis, we determined an ancient endogenous PRV group in Oryza genomes in the range of being 2.41-15.00 Myr old. We subsequently used this ancient endogenous PRV group and three younger groups to estimate the GRH of PRVs. Long-term substitution rates for the most conserved gene and a divergent gene were 2.69 × 10-8 to 8.07 × 10-8 and 4.72 × 10-8 to 1.42 × 10-7 substitutions/site/year, respectively. On the basis of a direct comparison, a long-term GRH of 1.83-fold was identified between these two genes, which is unexpectedly low and lower than the short-term GRH (>3.40-fold) of PRVs calculated using published data. The lower long-term GRH of PRVs was due to the slightly faster rate decay of divergent genes than of conserved genes during evolution. To the best of our knowledge, we quantified for the first time the long-term GRH of viral genes using paleovirological analyses, and proposed that the GRH of PRVs might be heterogeneous on time scales (time-dependent GRH). Our findings provide special insights into viral gene macroevolution and should encourage a more detailed examination of the viral GRH.
• Anther culture in rice proportionally rescues microspores according to gametophytic gene effect and enhances genetic study of hybrid sterility.

  Yoshitaka Kanaoka, Daichi Kuniyoshi, Eri Inada, Yohei Koide, Yoshihiro Okamoto, Hideshi Yasui, Yuji Kishima

  Plant methods 14 102 - 102 2018 [Refereed][Not invited]
   

  Background: To investigate plant hybrid sterility, we studied interspecific hybrids of two cultivated rice species, Asian rice (Oryza sativa) and African rice (O. glaberrima). Male gametes of these hybrids display complete sterility owing to a dozen of hybrid sterility loci, termed HS loci, but this complicated genetic system remains poorly understood. Results: Microspores from these interspecific hybrids form sterile pollen but are viable at the immature stage. Application of the anther culture (AC) method caused these immature microspores to induce callus. The segregation distortion of 11 among 13 known HS loci was assessed in the callus population. Using many individual calli, fine mapping of the HS loci was attempted based on heterozygotes produced from chromosome segment substitution lines (CSSLs). Transmission ratio distortion (TRD) from microspores was detected at 6 of 11 HS loci in the callus population. The fine mapping of S 1 and S 19 loci using CSSLs revealed precise distances of markers from the positions of HS loci exhibiting excessive TRD. Conclusions: We demonstrated that AC to generate callus populations derived from immature microspores is a useful methodology for genetic study. The callus population facilitated detection of TRD at multiple HS loci and dramatically shortened the process for mapping hybrid sterility genes.
• Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences.

  Sunlu Chen, Huizhen Zheng, Yuji Kishima

  PLoS pathogens 13 (6) e1006413  1553-7366 2017/06 [Refereed][Not invited]
   

  The interplay of different virus species in a host cell after infection can affect the adaptation of each virus. Endogenous viral elements, such as endogenous pararetroviruses (PRVs), have arisen from vertical inheritance of viral sequences integrated into host germline genomes. As viral genomic fossils, these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus-virus interactions, but they have rarely been applied for this purpose. All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells. Here, we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through interplay between viruses. Our paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have participated in interplay with autonomous PRVs in a possible commensal partnership, or, alternatively, with one another in a possible mutualistic partnership. These partnerships, which have been established by the sharing of noncoding regulatory sequences (NRSs) in intergenic regions between two partner viruses, have been further maintained and altered by the sequence homogenization of NRSs between partners. Strikingly, we found that frequent region-specific recombination, rather than mutation selection, is the main causative mechanism of NRS homogenization. Our results, obtained from ancient DNA records of viruses, suggest that adaptation of PRVs has occurred by concerted evolution of NRSs between different virus species in the same host. Our findings further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.
• Alternative plant host defense against transposon activities occurs at the post-translational stage.

  Hua Zhou, Yuji Kishima

  Plant signaling & behavior 12 (5) e1318238  1559-2316 2017/05/04 [Refereed][Invited]
   

  The Antirrhinum DNA transposon Tam3 uniquely demonstrates low temperature-dependent transposition (LTDT), so transposition does not occur at high temperatures. We previously showed that the detainment of Tam3 transposase (TPase) at the plasma membrane occurs when transposition is inactive, and that TPase is released at the permissive state of Tam3 transposition. LTDT of Tam3 is attributed to interactions between Tam3 and its host. In this addendum, we propose a model to explain the LTDT of Tam3, which is regarded as an equilibrium state reached between the host and parasite to maximize the fitness of both.
• Detainment of Tam3 Transposase at Plasma Membrane by Its BED-Zinc Finger Domain.

  Hua Zhou, Megumi Hirata, Ryo Osawa, Kaien Fujino, Yuji Kishima

  Plant physiology 173 (2) 1492 - 1501 0032-0889 2017/02 [Refereed][Not invited]
   

  Transposable elements (TEs) are considered to be parasites of host genomes because they act as powerful mutagens. If not kept in check, they can cause gene disruption, genome rearrangement, and genomic takeover. Hence, activities of TEs are under the rigid control of hosts. To date, all identified TE regulations have been epigenetic dependent, with the exception of the DNA transposon Tam3. Blocking nuclear translocation of Tam3 transposase (TPase) is consistent with the suppression of Tam3 in Antirrhinum majus In this article, we discovered that epigenetic-independent regulation of Tam3 is mediated by the BED-zinc finger (Znf-BED) domain of Tam3 TPase. The host targets the N terminus of the Znf-BED domain, which contains two highly conserved aromatic amino acids, to detain Tam3 TPase at the plasma membrane and to silence Tam3. Zinc finger proteins perform broader functions in transcriptional regulation through their DNA binding ability. Our data revealed that the posttranslational epigenetic-independent silencing against TEs was a result of the protein binding ability of the Znf-BED domain.
• Endogenous pararetroviruses in rice genomes as a fossil record useful for the emerging field of palaeovirology.

  Sunlu Chen, Yuji Kishima

  Molecular plant pathology 17 (9) 1317 - 1320 1464-6722 2016/12 [Refereed][Invited]
  
• Genetic analyses of spikelet mutants for sterile lemma and rudimentary glume in rice

  Koyasaki K, Nara Y, Kodani M, Kishima Y, Takamure I

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (56) 38 - 39 2015/12
• Analysis of natural selection for endgenous pararetrovirus segments in rice genomes

  Yamada K, Saito N, Chen S, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (56) 36 - 37 2015/12
• High-temperature treatment at the booting stage reduces the pollen fertility and the spikelet fertility in rice

  Uchiyama T, Ishiguro S, Chen S, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (56) 34 - 35 2015/12
• Cytoplasmic genome diversity in the cultivated apple - Short Communication

  T. Mikami, K. Kitazaki, Y. Kishima

  HORTICULTURAL SCIENCE 42 (1) 47 - 51 0862-867X 2015 [Refereed][Not invited]
   

  The cultivated apple is one of the most common and important fruit crops in temperate regions. Phylogenetic analysis using a wide array of apple genotypes could give insights into the origin and domestication history of this crop. Maternally inherited mitochondrial and chloroplast DNAs have been utilised to characterise the cytoplasmic diversity within the apple germplasm collection and to elucidate the relationships between the cytoplasm types defined. This review focuses on the molecular basis of changes in the mitochondrial genome giving rise to diverse cytoplasm types. The possible maternal lineage of the cultivated apple is also discussed.
• Genome wide expression analysis of F1 plants with various combinations of rice varieties

  Hu N, Akhil Baruah, Ishiguro S, Sato Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (55) 11 - 12 2014/12
• Genetic analysis of rice cold-tolerance at booting stage in F2 populations from a Hokkaido local variety with indica varieties

  Sone Y, Ishiguro S, Sato T, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (55) 13 - 14 2014/12
• Isolation and sequence analysis of Old Stabiliser that suppresses activity of transposon Tam3 in Antirrhinum

  Hirata M, Ebinuma I, Fujino K, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (55) 15 - 16 2014/12
• Rice genomes recorded ancient pararetrovirus activities: Virus genealogy and multiple origins of endogenization during rice speciation.

  Sunlu Chen, Ruifang Liu, Kanako O Koyanagi, Yuji Kishima

  Virology 471-473 141 - 52 0042-6822 2014/12 [Refereed][Not invited]
   

  Viral fossils in rice genomes are a best entity to understand ancient pararetrovirus activities through host plant history because of our advanced knowledge of the genomes and evolutionary history with rice and its related species. Here, we explored organization, geographic origins and genealogy of rice pararetroviruses, which were turned into endogenous rice tungro bacilliform virus-like (eRTBVL) sequences. About 300 eRTBVL sequences from three representative rice genomes were clearly classified into six families. Most of the endogenization events of the eRTBVLs were initiated before differentiation of the rice progenitor (> 160,000 years ago). We successfully followed the genealogy of old relic viruses during rice speciation, and inferred the geographical origins for these viruses. Possible virus genomic sequences were explained mostly by recombinations between different virus families. Interestingly, we discovered that only a few recombination events among the numerous occasions had determined the virus genealogy.
• Correlative gene/genome system in plant breeding

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

  育種学研究 日本育種学会 16 (2) 79 - 85 1344-7629 2014/06 [Not refereed][Invited]
  
• Isolation of a major genetic interaction associated with an extreme phenotype using assorted F2 populations in rice

  Yuya Ota, Seiya Ishiguro, Eiko Aoyama, Ryosuke Aiba, Reika Iwashiro, Takanari Tanabata, Itsuro Takamure, Kaien Fujino, Yuji Kishima

  MOLECULAR BREEDING 33 (4) 997 - 1003 1380-3743 2014/04 [Refereed][Not invited]
   

  Detection of quantitative trait loci (QTLs) is dependent on the materials used in the analysis, as different combinations of parental materials may lead to different outcomes in QTLs for the same trait. On the other hand, an extreme phenotype associated with a given trait implies the potential involvement of a particular allele in various allelic interactions. A genetic factor associated with such an extreme phenotype may frequently be identified from various genetic populations consisting of different parental combinations. In this study, we attempted to uncover the genetic factor associated with extremely early heading date in rice, using various F2 populations. Heading date in rice has been characterized by at least 19 QTLs, from which 12 genes have been identified. A58, a rice strain with an extremely early heading date, is adapted to Hokkaido, the northernmost limit of rice cultivation. Six F2 populations derived from crosses of A58 with six other strains displayed a range of heading dates. Genotyping using 19 QTL markers indicated that the A58 allele of the Ghd7 locus was present in most F2 individuals exhibiting extremely early heading dates. This analysis also demonstrated that when the wild-type Ehd1 allele was present, the Ghd7 allele from A58 accelerated floral induction. The results of this study demonstrate that assorted F2 populations are valuable materials for comprehensive genotyping to explore major genetic factors for extreme phenotypes, and that this methodology is broadly applicable to other unknown traits.
• Low temperature-responsive changes in the anther transcriptome's repeat sequences are indicative of stress sensitivity and pollen sterility in rice strains.

  Seiya Ishiguro, Kei Ogasawara, Kaien Fujino, Yutaka Sato, Yuji Kishima

  Plant physiology 164 (2) 671 - 82 0032-0889 2014/02 [Refereed][Not invited]
   

  Genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine responses to low temperatures in rice (Oryza sativa). We focused particularly on the rice anther at the booting stage, because a low temperature at this stage can result in pollen abortion. The five rice strains examined in this study showed different pollen fertilities due to a low-temperature treatment during the booting stage. The microarray analyses demonstrated that the low-temperature stress caused genome-wide changes in the transcriptional activities not only of genes but also of repeat sequences in the rice anther. The degree of the temperature-responsive changes varied among the five rice strains. Interestingly, the low-temperature-sensitive strains revealed more changes in the transcriptome when compared with the tolerant strains. The expression patterns of the repeat sequences, including miniature inverted-repeat transposable elements, transposons, and retrotransposons, were correlated with the pollen fertilities of the five strains, with the highest correlation coefficient being 0.979. Even in the low-temperature-sensitive strains, the transcriptomes displayed distinct expression patterns. The elements responding to the low temperatures were evenly distributed throughout the genome, and the major cis-motifs involved in temperature-responsive changes were undetectable from the upstream sequences in the corresponding repeats. The genome-wide responses of transcription to the temperature shift may be associated with chromatin dynamics, which facilitates environmental plasticity. A genome-wide analysis using repeat sequences suggested that stress tolerance could be conferred by insensitivity to the stimuli.
• Establishment of endogenous pararetroviruses in the rice genome

  Liu, R., Kishima, Y.

  Plant Virus-Host Interaction: Molecular Approaches and Viral Evolution 2014
• Expression analysis of Antirrhinum genes, T3IF5 and T3IF6, controlling transposon Tam3

  Nakayama Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (54) 25 - 26 2013/12
• A malformed spikelet mutant [mls(t)] induced by two bases substitution at the zinc finger protein gene in rice

  Nakada A, Oshima K, Fukuroi K, Kodani M, Kishima Y, Takamure I

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (54) 15 - 16 2013/12
• Callus formation derived from anther culture of F1 hybrid between japonica and glaberrima species

  Kuniyoshi D, Iwashiro R, Okamoto Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (54) 17 - 18 2013/12
• Cytoplasmic diversity and possible maternal lineages in apples as revealed by analysis of the mitochondrial cox1 and atp9 loci

  Kazuyoshi Kitazaki, Seiya Ishigro, Sumie Kato, Akihito Wakatsuki, Yuji Kishima, Tetsuo Mikami

  SCIENTIA HORTICULTURAE 164 209 - 212 0304-4238 2013/12 [Refereed][Not invited]
   

  In apples, four cytoplasmic groups, 'Golden Delicious'-, 'Delicious'-, 'McIntosh'- and 'Dolgo Crab' cytotypes, are differentiated by variation in the mitochondrial cox1 and atp9 loci. The present study builds upon previous reports that (1) 'Golden Delicious' and 'Delicious' cytotype accessions each contain an intact cox1 (named as G-cox1 and D-cox1, respectively) and a pseudocopy (G-Psi cox1 and D-Psi cox1) at different stoichiometries and (2) the relative copy number of an atp9 pseudocopy (Psi atp9-1) is distinct in each cytotype. Here, the D-cox1 and D-Psi cox1 sequences were found as predominant forms in 'McIntosh' type germplasm accessions but as substoichiometric forms in 'Dolgo Crab' type accessions. The G-cox1 and G-Psi cox1 sequences were predominant in the 'Dolgo Crab' group whereas these two sequences were substoichiometric in the 'McIntosh' group. 'We also detected the presence of predominant form of Psi atp9-1 in 'McIntosh' and 'Dolgo Crab' groups. Moreover, the four cytotypes could be distinguished from one another by their own chloroplast DNA haplotypes. Using these data and those from our earlier publications, we attempted to construct a network of cytotypes representing possible maternal lineages of apples. (C) 2013 Elsevier B.V. All rights reserved.
• A pair of transposons coordinately suppresses gene expression, independent of pathways mediated by siRNA in Antirrhinum.

  Takako Uchiyama, Satoshi Hiura, Izuru Ebinuma, Mineo Senda, Tetsuo Mikami, Cathie Martin, Yuji Kishima

  The New phytologist 197 (2) 431 - 440 0028-646X 2013/01 [Refereed][Not invited]
   

  Our knowledge is limited regarding mechanisms by which transposable elements control host gene expression. Two Antirrhinum lines, HAM2 and HAM5, show different petal colors, pale-red and white, respectively, although these lines contain the same insertion of transposon Tam3 in the promoter region of the nivea (niv) locus encoding chalcone synthase. Among 1000 progeny from HAM5 grown under the preferred conditions for the Tam3 transposition, a few showed an intermediate petal color between HAM2 and HAM5. Transposon tagging using these progeny identified a causative insertion of Tam3 for the HAM5 type (white) petal color, which was found 1.6 kb downstream of the niv gene. Insertion of Tam3 at the position 1.6 kb downstream of niv alone showed nearly wildtype petal pigmentation, and the niv expression reduced by only 50%. Severe suppression of niv observed in HAM5 required interaction of two Tam3 copies on either side of the niv coding sequence. DNA methylation and small interfering RNAs (siRNAs) were not associated with the suppression of niv expression in HAM5. Insertion of a pair of transposons in close proximity can interfere with the expression of gene located between the two copies, and also provide evidence that this interference is not directly associated with pathways mediated by siRNAs.
• A pair of transposons coordinately suppresses gene expression at the nivea locus in Antirrhinum.

  Ebinuma I, Uchiyama T, Hiura S, Senda M, Mikami T, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (53) 79 - 80 2012/12
• Evolutionary force of AT-rich repeats to trap genomic and episomal DNAs into the rice genome: lessons from endogenous pararetrovirus.

  Ruifang Liu, Kanako O Koyanagi, Sunlu Chen, Yuji Kishima

  The Plant journal : for cell and molecular biology 72 (5) 817 - 28 0960-7412 2012/12 [Refereed][Not invited]
   

  In plant genomes, the incorporation of DNA segments is not a common method of artificial gene transfer. Nevertheless, various segments of pararetroviruses have been found in plant genomes in recent decades. The rice genome contains a number of segments of endogenous rice tungro bacilliform virus-like sequences (ERTBVs), many of which are present between AT dinucleotide repeats (ATrs). Comparison of genomic sequences between two closely related rice subspecies, japonica and indica, allowed us to verify the preferential insertion of ERTBVs into ATrs. In addition to ERTBVs, the comparative analyses showed that ATrs occasionally incorporate repeat sequences including transposable elements, and a wide range of other sequences. Besides the known genomic sequences, the insertion sequences also represented DNAs of unclear origins together with ERTBVs, suggesting that ATrs have integrated episomal DNAs that would have been suspended in the nucleus. Such insertion DNAs might be trapped by ATrs in the genome in a host-dependent manner. Conversely, other simple mono- and dinucleotide sequence repeats (SSR) were less frequently involved in insertion events relative to ATrs. Therefore, ATrs could be regarded as hot spots of double-strand breaks that induce non-homologous end joining. The insertions within ATrs occasionally generated new gene-related sequences or involved structural modifications of existing genes. Likewise, in a comparison between Arabidopsis thaliana and Arabidopsis lyrata, the insertions preferred ATrs to other SSRs. Therefore ATrs in plant genomes could be considered as genomic dumping sites that have trapped various DNA molecules and may have exerted a powerful evolutionary force.
• An apple atp9 pseudogene is maintained at high copy number in 'Golden Delicious'-type mitochondria but is present substoichiometrically in 'Delicious'-type mitochondria

  Sumie Kato, Kazuyoshi Kitazaki, Akihito Wakatsuki, Yuji Kishima, Tetsuo Mikami

  SCIENTIA HORTICULTURAE 134 237 - 240 0304-4238 2012/02 [Refereed][Not invited]
   

  In this study, the mitochondrial atp9 gene sequence of an apple cultivar 'Golden Delicious' was found to exist in one intact version and two truncated versions (termed phi atp9-1 and phi atp9-2). Interestingly, the phi atp9-1 sequence is maintained at high copy number in the six 'Golden Delicious'-cytotype cultivars examined but present substoichiometrically in eight 'Delicious'-cytotype cultivars. Our data also suggest that phi atp9-1 originated in a homologous recombination event mediated by the short repeat in a common ancestral mitochondrial genome of 'Golden Delicious' and 'Delicious', and was preferentially amplified in an evolutionary lineage that gave rise to the 'Golden Delicious'-type genome. On the other hand, phi atp9-2 was revealed to be present in high abundance in all 14 cultivars examined. (C) 2011 Elsevier B.V. All rights reserved.
• Rice repetitive sequences expressed in different tissues.

  Ogasawara K, Ishiguro S, Ezawa M, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (52) 41 - 42 2011/12
• An intact mitochondrial cox1 gene and a pseudogene with different genomic configurations are present in apple cultivars 'Golden Delicious' and 'Delicious': Evolutionary aspects

  Akihito Wakatsuki, Kazuyoshi Kitazaki, Sumie Kato, Yuji Kishima, Tetsuo Mikami

  SCIENTIA HORTICULTURAE 130 (1) 49 - 53 0304-4238 2011/08 [Refereed][Not invited]
   

  We have characterized the mitochondrial cox1 gene copies in two apple cultivars 'Golden Delicious' and 'Delicious'. Both the cultivars contained an intact copy and a truncated copy of cox1. The intact 'Golden Delicious' and 'Delicious' cox? genes, designated G-cox1 and D-cox 1, respectively, were both found to be actually transcribed to give an RNA of approximately 1.7 kb. The two intact cox1 and two truncated copies (G-phi cox1 and D-phi cox1)shared a common 1115-bp segment flanked by four combinations of two different 5'- and 3'-sequences. PCR assay demonstrated that the configurations bearing G-cox1 and G-phi cox1 existed in substoichiometric amounts within the mitochondria] genome of 'Delicious' whereas substoichiometric molecules carrying D-phi cox1 were present in the 'Golden Delicious' mitochondria] genome. Although ancestor/descendant relationships cannot be inferred between the G-cox1 and D-cox1 arrangements, the results led us to hypothesize that (1) the 1115-bp segment containing part of the progenitor cox1 was duplicated, thereby generating a pseudo-cox1 copy, and (2) this was followed by homologous recombination across a portion of the 1115-bp repeats which gave rise to the descendant cox1 and pseudo-cox1 arrangements. Crown Copyright (C) 2011 Published by Elsevier B.V. All rights reserved.
• Temperature controls nuclear import of Tam3 transposase in Antirrhinum.

  Kaien Fujino, Shin-Nosuke Hashida, Takashi Ogawa, Tomoko Natsume, Takako Uchiyama, Tetsuo Mikami, Yuji Kishima

  The Plant journal : for cell and molecular biology 65 (1) 146 - 155 0960-7412 2011/01 [Refereed][Not invited]
   

  It has been proposed that environmental stimuli can activate transposable elements (TEs), whereas few substantial mechanisms have been shown so far. The class-II element Tam3 from Antirrhinum majus exhibits a unique property of low-temperature-dependent transposition (LTDT). LTDT has proved invaluable in developing the gene isolation technologies that have underpinned much of modern plant developmental biology. Here, we reveal that LTDT involves differential subcellular localization of the Tam3 transposase (TPase) in cells grown at low (15°C) and high (25°C) temperatures. The mechanism is associated with the nuclear import of Tam3 TPase in Antirrhinum cells. At high temperature, the nuclear import of Tam3 TPase is severely restricted in Antirrhinum cells, whereas at low temperature, the nuclear localization of Tam3 TPase is observed in about 20% of the cells. However, in tobacco BY-2 and Allium cepa (onion) cells, Tam3 TPase is transported into most nuclei. In addition to three nuclear localization signals (NLSs), the Tam3 TPase is equipped with a nuclear localization inhibitory domain (NLID), which functions to abolish nuclear import of the TPase at high temperature in Antirrhinum. NLID in Tam3 TPase is considered to interact with Antirrhinum-specific factor(s). The host-specific regulation of the nuclear localization of transposase represents a new repertoire controlling class-II TEs.
• Change of the transposase expression in a hybrid of japonica rice

  Takahashi K, Takasu A, Ishiguro S, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (51) 23 - 24 2010/12
• Genetic differences within the japonica rice variety, Koshihikari, indicated by transposons.

  Yuji Kishima, Yuka Hotta, Seiya Ishiguro, Kazuteru Yamamura, Akira Hanawa, Satoshi Naito, Yoshio Sano

  Breeding Research 日本育種学会 12 (12) 81 - 86 1344-7629 2010 [Refereed][Not invited]
   

  Little is known about genetic variation, which follows the establishment of plant variety, and its accumulation process. Here, we collected samples from a total of 86 populations of a popular japonica rice variety, Koshihikari, from 15 prefectures in Japan and investigated genetic variation among these samples. In plants, insertion sites of transposable elements are of strong indications of genetic polymorphisms among different strains of the same species. Particularly, rice genomes contain at least seven potentially active transposable elements that could give rise to de novo insertions and mutations. In this study, transposon display (TD) experiments were performed with four transposable elements, which showed different banding profiles between the parents of Koshihikari, Norin 1 and Norin 22. In TDs involving three elements, 82 samples from the 86 populations examined showed common patterns, implying that these populations share an identity as Koshihikari. In contrast, TD involving the transposon mPing exhibited a number of polymorphisms among the 82 populations. These polymorphisms include population specific bands, which may result from recent de novo transpositions of mPing, indicating the activity of mPing in Koshihikari. Interestingly, the other polymorphisms due to two bands, A1 and A23, are able to classify Koshihikari populations into two types; the two bands distinguish Niigata or non-Niigata (Fukui) types where the samples originated. The A1 and A23 bands are derived from the Koshihikari parents, Norin 1 or Norin 22, respectively. The results suggest that the Koshihikari variety consists of two major populations (Niigata and Fukui types) with partially different genome structures that might be established during the breeding processes.
  
• Genetic differentiation among rice cultivar "Koshihikari" landraces by transposon

  Ishiguro S, Takasu A, Hotta Y, Sano Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (50) 27 - 28 2009/12
• Differnt behavior of transposon Tam3 between somatic and germ lines in Antirrhinum majus

  Tateo T, Asano M, Uchiyama T, Sano Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (50) 51 - 52 2009/12
• Analysis of stabiliser gene that inhibits transposition of Tam3 in Antirrhinum majus

  Kasahara T, Uchiyama T, Sano Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (50) 53 - 54 2009/12
• Stable transcription activities dependent on an orientation of Tam3 transposon insertions into Antirrhinum and yeast promoters occur only within chromatin.

  Takako Uchiyama, Kaien Fujino, Takashi Ogawa, Akihito Wakatsuki, Yuji Kishima, Tetsuo Mikami, Yoshio Sano

  Plant physiology 151 (3) 1557 - 69 0032-0889 2009/11 [Refereed][Not invited]
   

  Transposon insertions occasionally occur in the promoter regions of plant genes, many of which are still capable of being transcribed. However, it remains unclear how transcription of such promoters is able to occur. Insertion of the Tam3 transposon into various genes of Antirrhinum majus can confer leaky phenotypes without its excision. These genes, named Tam3-permissible alleles, often contain Tam3 in their promoter regions. Two alleles at different anthocyanin biosynthesis loci, nivea(recurrensTam3) (niv(rec)) and pallida(recurrensTam3) (pal(rec)), both contain Tam3 at a similar position immediately upstream of the promoter TATA-box; however, these insertions had different phenotypic consequences. Under conditions where the inserted Tam3 is immobilized, the niv(rec) line produces pale red petals, whereas the pal(rec) line produces no pigment. These pigmentation patterns are correlated with the level of transcripts from the niv(rec) or pal(rec) alleles, and these transcriptional activities are independent of DNA methylation in their promoter regions. In niv(rec), Tam3 is inserted in an orientation that results in the 3' end of Tam3 adjacent to the 5' region of the gene coding sequence. In contrast, the pal(rec) allele contains a Tam3 insertion in the opposite orientation. Four of five different nonrelated genes that are also Tam3-permissible alleles and contain Tam3 within the promoter region share the same Tam3 orientation as niv(rec). The different transcriptional activities dependent on Tam3 orientation in the Antirrhinum promoters were consistent with expression of luciferase reporter constructs introduced into yeast chromosomes but not with transient expression of these constructs in Antirrhinum cells. These results suggest that for Tam3 to sustain stable transcriptional activity in various promoters it must be embedded in chromatin.
• The analysis of mutation patern that is caused by transposon

  Asano M, Utiyama T, Sano Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (49) 101 - 102 2008/12
• Multiple regulatory mechanisms influence the activity of the transposon, Tam3, of Antirrhinum.

  Takako Uchiyama, Yumiko Saito, Hiroyuki Kuwabara, Kaien Fujino, Yuji Kishima, Cathie Martin, Yoshio Sano

  The New phytologist 179 (2) 343 - 355 0028-646X 2008/07 [Refereed][Not invited]
   

  In Antirrhinum, several unique regulations of the transposon, Tam3, have been described. Tam3 activity in Antirrhinum is strictly controlled by the growing temperature of plants (low-temperature-dependent transposition: LTDT), by chromosomal position of Tam3 copy and by two specific repressor genes Stabiliser (St) and New Stabiliser (NSt). Here, the effects of the St and NSt loci on Tam3 transposition are compared. In cotyledons and hypocotyls, Tam3 is active even at high growing temperatures, indicating that LTDT does not operate when these organs are developing. This developmental regulation of Tam3 activity is differentially influenced by the St and NSt loci: St permits Tam3 transposition in cotyledons and hypocotyls, whereas NSt suppresses it in these organs. The effects of these host genes on Tam3 activity at the molecular level were examined. It was found that neither of these genes inhibits the transcription of the Tam3 transposase gene nor its translation, and that the Tam3 transposase has the potential to catalyze transposition in the St and NSt lines. The differences between the effects of St and NSt imply that they regulate Tam3 activity independently. Our molecular data indicate that their influence on Tam3 transposition seems to be nonepigenetic; possible mechanisms for their activity are discussed.
• Rice transposable elements are characterized by various methylation environments in the genome.

  Miwako Takata, Akihiro Kiyohara, Atsuko Takasu, Yuji Kishima, Hisako Ohtsubo, Yoshio Sano

  BMC genomics 8 469 - 469 1471-2164 2007/12/20 [Refereed][Not invited]
   

  BACKGROUND: Recent studies using high-throughput methods have revealed that transposable elements (TEs) are a comprehensive target for DNA methylation. However, the relationship between TEs and their genomic environment regarding methylation still remains unclear. The rice genome contains representatives of all known TE families with different characteristics of chromosomal distribution, structure, transposition, size, and copy number. Here we studied the DNA methylation state around 12 TEs in nine genomic DNAs from cultivated rice strains and their closely related wild strains. RESULTS: We employed a transposon display (TD) method to analyze the methylation environments in the genomes. The 12 TE families, consisting of four class I elements, seven class II elements, and one element of a different class, were differentially distributed in the rice chromosomes: some elements were concentrated in the centromeric or pericentromeric regions, but others were located in euchromatic regions. The TD analyses revealed that the TE families were embedded in flanking sequences with different methylation degrees. Each TE had flanking sequences with similar degrees of methylation among the nine rice strains. The class I elements tended to be present in highly methylated regions, while those of the class II elements showed widely varying degrees of methylation. In some TE families, the degrees of methylation were markedly lower than the average methylation state of the genome. In two families, dramatic changes of the methylation state occurred depending on the distance from the TE. CONCLUSION: Our results demonstrate that the TE families in the rice genomes can be characterized by the methylation states of their surroundings. The copy number and degree of conservation of the TE family are not likely to be correlated with the degree of methylation. We discuss possible relationships between the methylation state of TEs and their surroundings. This is the first report demonstrating that TEs in the genome are associated with a particular methylation environment that is a feature of a given TE.
• Genetic variations in rice in vitro cultures at the EPSPs-RPS20 region

  Yuji Noro, Toshiyuki Takano-Shimizu, Kunihiko Syono, Yuji Kishima, Yoshio Sano

  THEORETICAL AND APPLIED GENETICS 114 (4) 705 - 711 0040-5752 2007/02 [Refereed][Not invited]
   

  In vitro cultures of plant cells have often been utilized to generate genetic variations, which are designated somaclonal variations. Little is known about the major genetic alterations in the cultured cells and the nature of these genetic changes. Here, we examined different lines of rice Oc cells that have been cultured for more than 20 years on agar media or in liquid media. We surveyed 35 clones obtained from PCR amplification of the 3-kb EPSPs-RPS20 region. The sequence divergence among the Oc cells was even greater than that between Japonica and Indica rice cultivars. The divergent sequences appeared to be maintained as multiple copies in a single cell. Surprisingly, the nucleotide substitutions in the Oc cells were characterized by an extremely high frequency of transition mutations of A/T-to-G/C, a feature which is similar to that of the mutations caused by chemical mutagens such as 5-bromouracil and 2-aminopurine. Although no replacements in the exons of this region were observed among the AA-genome Oryza species, our results revealed that the nucleotide substitutions of the cultured cell lines occurred more frequently at replacement sites in the exons than at synonymous sites. These distinct mutation biases found in rice in vitro cultures might contribute importantly to somaclonal variations.
• The temperature-dependent change in methylation of the Antirrhinum transposon Tam3 is controlled by the activity of its transposase

  SN Hashida, T Uchiyama, C Martin, Y Kishima, Y Sano, T Mikami

  PLANT CELL 18 (1) 104 - 118 1040-4651 2006/01 [Refereed][Not invited]
   

  The Antirrhinum majus transposon Tam3 undergoes low temperature-dependent transposition (LTDT). Growth at 15 degrees C permits transposition, whereas growth at 25 degrees C strongly suppresses it. The degree of Tam3 DNA methylation is altered somatically and positively correlated with growth temperature, an exceptional epigenetic system in plants. Using a Tam3-inactive line, we show that methylation change depends on Tam3 activity. Random binding site selection analysis and electrophoretic mobility shift assays revealed that the Tam3 transposase (TPase) binds to the major repeat in the subterminal regions of Tam3, the site showing the biggest temperature-dependent change in methylation state. Methylcytosines in the motif impair the binding ability of the TPase. Proteins in a nuclear extract from plants grown at 15 degrees C but not 25 degrees C bind to this motif in Tam3. The decrease in Tam3 DNA methylation at low temperature also requires cell division. Thus, TPase binding to Tam3 occurs only during growth at low temperature and immediately after DNA replication, resulting in a Tam3-specific decrease in methylation of transposon DNA. Consequently, the Tam3 methylation level in LTDT is regulated by Tam3 activity, which is dependent on the ability of its TPase to bind DNA and affected by growth temperature. Thus, the methylation/demethylation of Tam3 is the consequence, not the cause, of LTDT.
• Comparison of methylation degree of transposable elements in rice and the related species

  Kiyohara A, Takata M, Sano Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (46) 67 - 68 2005/12
• DNA methylation is not necessary for the inactivation of the Tam3 transposon at non-permissive temperature in Antirrhinum

  S Hashida, Y Kishima, T Mikami

  JOURNAL OF PLANT PHYSIOLOGY 162 (11) 1292 - 1296 0176-1617 2005/11 [Refereed][Not invited]
   

  It has been proposed that DNA methylation plays an important role in the inactivation of transposons. This view stems from a comparison of the degree of methylation of transposons in the active and inactive state. However, direct evidence for the degree of methylation required for the suppression of transposition has not been reported. Transposon Tam3 in Antirrhinum majus undergoes somatic reversal of its transposition activity, which is tightly controlled by temperature: low temperature around 15 degrees C permits transposition, high temperatures around 25 degrees C strongly inhibits it. Our previous study had shown that the methytation state of the Tam3 end regions is negatively correlated with the Tam3 transposition frequency. The results of the present study reveal that the inactive state of Tam3 copies at high temperature is unlikely to be directly coupled to the methytation state. Treatment with methylation inhibitors (5-azacytidine or 5-azacytidine+ethionine) does not affect Tam3 excision frequency in calli derived from Antirrhinum hypocotyls. The results suggest that methylation is not essential for the suppression of Tam3 transposition at high temperature, but rather that some other mechanism(s) involved in the control of Tam3 transposition may be obscured by methytation. (C) 2005 Elsevier GmbH. All rights reserved.
• DNA methylation polymorphisms in rice and wild rice strains: Detection of epigenetic markers

  M Takata, Y Kishima, Y Sano

  BREEDING SCIENCE 55 (1) 57 - 63 1344-7610 2005/03 [Refereed][Not invited]
   

  In plants, phenotypic variations have generally been found to be caused by genetic changes. However, it has recently been shown that phenotypic variations can also be potentially caused by epigenetic changes due to aberrant methylation states. To survey polymorphisms in methylation states in the genomic segments from nine strains of Oryza sativa and O. rufipogon, we employed the methylation-sensitive amplified polymorphism (MSAP) method based on AFLP analysis using isoschizomers differing in their methylation sensitivity, HpaII and MspI. In addition to MSAP analysis, we applied the MITE-transposon-display method to detect methylation-sensitive MITE-flanking polymorphisms (MSMPs) for surveying the methylation state of the genomes. The frequency of occurrence of the methylated fragments detected by these analyses varied depending on the three primers targeting two different MITE sequences for MSMP and EcoRI sites for MSAP. This suggests that MITEs are associated with the methylation state in their proximal regions. Comparison of the fragment patterns between any two of the nine strains revealed polymorphisms of the methylation state referred to as epigenetic markers (epi-markers). A phylogenetic tree based on epi-markers within non-polymorphic fragments was analogous to that based on genetic markers. On the other hand, the proportion of epi-markers in the total number of fragments was constant at 2-3% in all the combinations of two strains. Our results enabled us to predict that the epi-markers are potentially linked to phenotypic variations, and that this possibility is more likely to occur between closely related strains.
• Evidence for an evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with a short spacer

  S Kobayashi, Y Noro, H Nagano, KT Yoshida, T Takano-Shimizu, Y Kishima, Y Sano

  GENE 346 231 - 240 0378-1119 2005/02 [Refereed][Not invited]
   

  During the course of evolution, the genome should have toned down various types of genomic noise, such as those that cause the unstable expression or gene silencing observed in transgenic organisms. We found a rice genomic segment where two genes, encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPs) and ribosomal protein small subunit 20 (rps20), are located in a tail-to-tail orientation and separated by only 300 by of spacer. It is possible that this kind of structure would give rise to unstable expression due to antisense RNA derived from the neighboring gene. We examined this possibility using Northern blot, reverse transcription-polymerise chain reaction (RT-PCR), and 3' RACE analyses, but obtained no evidence for instability or antisense RNAs of these housekeeping genes. Comparison of the sequences in the corresponding regions among related rice species revealed a lower level of genetic divergence of both the 3'-untranslated region (3'-UTRs) than of the other noncoding regions; in particular both of the boundaries between the 3'-UTRs and the spacer were markedly conserved. The conservation of both the terminal regions is most likely the result of purifying selection, implying a functional role for the strict termination of the transcription of these genes to prevent gene-silencing-related events. (c) 2004 Elsevier B.V. All rights reserved.
• Genomics of rice: Markers as a tool for breeding

  Y. Kishima, K. Onishi, Y. Sano

  Biotechnology in Agriculture and Forestry 55 245 - 254 0934-943X 2005 [Refereed][Not invited]
  
• Polymorphisms in DNA methylation pattern among rice genomes and mapping.

  Komoda A, Takata M, Sano Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (45) 29 - 30 2004/12
• Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome: implications for integration and evolution

  M Kunii, M Kanda, H Nagano, Uyeda, I, Y Kishima, Y Sano

  BMC GENOMICS 5 80  1471-2164 2004/10 [Refereed][Not invited]
   

  Background: Plant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like sequences in plant genomes led us to set the objective of elucidating the origin of the repetitive sequences. Endogenous rice tungro bacilliform virus ( RTBV)-like sequences ( ERTBVs) have been found throughout the rice genome. Here, we reconstructed putative virus structures from RTBV-like sequences in the rice genome and characterized to understand evolutionary implication, integration manner and involvements of endogenous virus segments in the corresponding disease response. Results: We have collected ERTBVs from the rice genomes. They contain rearranged structures and no intact ORFs. The identified ERTBV segments were shown to be phylogenetically divided into three clusters. For each phylogenetic cluster, we were able to make a consensus alignment for a circular virus-like structure carrying two complete ORFs. Comparisons of DNA and amino acid sequences suggested the closely relationship between ERTBV and RTBV. The Oryza AA-genome species vary in the ERTBV copy number. The species carrying low-copy-number of ERTBV segments have been reported to be extremely susceptible to RTBV. The DNA methylation state of the ERTBV sequences was correlated with their copy number in the genome. Conclusions: These ERTBV segments are unlikely to have functional potential as a virus. However, these sequences facilitate to establish putative virus that provided information underlying virus integration and evolutionary relationship with existing virus. Comparison of ERTBV among the Oryza AA-genome species allowed us to speculate a possible role of endogenous virus segments against its related disease.
• ERTBV; Endogenous Rice Tungro Bacilliform Virus-like sequences in rice genome

  Kanda M, Kunii M, Nagano H, Sano Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (44) 11 - 12 2003/12
• Phenotypic observation of variegation patterns in Antirrhinum

  Murakami K, Sano Y, Kishima Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (44) 29 - 30 2003/12
• Analysis of hybrid sterility gene S1 detected between Asian and African species in rice

  Horigome A, Nishimoto D, Koide Y, Onishi K, Nagano H, Kishima Y, Sano Y

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (44) 3 - 4 2003/12
• Temperature shift coordinately changes the activity and the methylation state of transposon Tam3 in Antirrhinum majus

  S Hashida, K Kitamura, T Mikami, Y Kishima

  PLANT PHYSIOLOGY 132 (3) 1207 - 1216 0032-0889 2003/07 [Refereed][Not invited]
   

  The transposition frequency of Tam3 in Antirrhinum majus, unlike that of most other cut-and-paste-type transposons, is tightly controlled by temperature: Tam3 transposes rarely at 25degreesC, but much more frequently at 15degreesC. Here, we studied the mechanism of the low-temperature-dependent transposition (LTDT) of Tam3. Our results strongly suggest that LTDT is not likely to be due to either transcriptional regulation or posttranscriptional regulation of the Tam3 TPase gene. We found that temperature shift induced a remarkable change of the methylation state unique to Tam3 sequences in the genome: Higher temperature resulted in hypermethylation, whereas lower temperature resulted in reduced methylation. The methylation state was reversible within a single generation in response to a temperature shift. Although our data demonstrate a close link between LTDT and the methylation of Tam3, they also suggest that secondary factor(s) other than DNA methylation is involved in repression of Tam3 transposition.
• MITE-transposon display efficiently detects polymorphisms among the Oryza AA-genome species

  K Takagi, H Nagano, Y Kishima, Y Sano

  BREEDING SCIENCE 53 (2) 125 - 132 1344-7610 2003/06 [Refereed][Not invited]
   

  Miniature inverted repeat transposable elements (MITEs) are a major component of interspersed repetitive sequences in the rice genome. These elements serve as excellent tools for fine genomic analysis throughout the genome. Using the rice genome database, we evaluated MITEs present in a 200-kb region surrounding the rice waxy locus and selected four MITE subfamilies for MITE-transposon display (MITE-TD) analyses. MITE-TD, which is an AFLP-related technique based on MITE sequences, was applied to detect polymorphisms among the AA-genome Oryza species using the four selected MITEs. The MITE-TD used here enabled the most efficient detection of polymorphisms of all the molecular marker techniques applied to date in the Oryza species. Of the four MITEs, Mashu, a new MITE family, was found to be the best system for detecting the polymorphisms, with a detection frequency 3-1.5 times higher than that of the other three MITEs. The MITE-TDs also revealed information about genetic variations within the AA-genome species, and the complexity of the genetic relationships between O. sativa and O. rufipogon.
• Differentiation of iransposon-inducible variegation pattern in crossed lines of snapdragon

  Y Kishima, Y Itoh, Y Noro, Y Sano

  PROCEEDINGS OF THE INTERNATIONAL SYMPOSIUM ON CLASSICAL VERSUS MOLECULAR BREEDING OF ORNAMENTALS 612 (612) 67 - 71 0567-7572 2003 [Refereed][Invited]
   

  Two lines of snapdragon, HAM2 and HAM5, have an identical allele, nivea(recurrens:Tam3), that causes flower variegation due to excision of transposon Tam3. The Tam3 copy is inserted 64 bp upstream of the transcription start site. Despite of the same allele, HAM2 gives a light crimson in the petal background, while HAM5 shows white petals. We crossed each of the two lines with 8 lines of snapdragon carrying different genetic backgrounds. In the F2 progenies of each of the crossed lines, we selected plants that showed novel variegation patterns. After successive selfing for five generations, we produced 38 stable lines possessing novel variegation features in the petals. The characteristics of these lines were observed in the number of the spot, the spot colour, the localization of the spot and the form of the variegation. These petal phenotypes clearly differed from those of HAM2 and HAM5. The facts suggest that transposition of the element at nivea(recurrens:Tam3) are differentially controlled by the host genetic factor(s), and modification of the variegation pattern is potentially feasible.
• Genetic study of chromosome 7 regarding adaptive traits in wild rice using RILs

  Horiuchi Y., Ishigoh-Oka N., Takagi K., Onishi K., Kishima Y., Sano Y.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (43) 15 - 16 2002/11
• Germ line specific inheritance of rearranged structures in the nivea locus of Antirrhinum majus

  Tubota A., Noro Y., Tozaki T., Mikami T., Sano Y., Kishima Y.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (43) 1 - 2 2002/11
• Characterization of the repetitive sequences in a 200-kb region around the rice waxy locus: diversity of transposable elements and presence of veiled repetitive sequences

  H Nagano, M Kunii, T Azuma, Y Kishima, Y Sano

  GENES & GENETIC SYSTEMS 77 (2) 69 - 79 1341-7568 2002/04 [Refereed][Not invited]
   

  Repetitive genomic sequences might have various structural features and properties distinct from those of the known transposable elements (TE). Here, the content and properties of the repetitive sequences present in a 200-kb region around the rice waxy locus were analyzed using the available rice genomic database. In our previous Southern blotting analysis, 70% of the segments in this region showed smeared patterns, but according to the present database analysis, the proportion of repetitive sequences in this region was only 15%. The repetitive segments in this 200-kb region comprised 75 repetitive sequences that we classified into 46 subfamilies: 21 subfamilies were known TEs or repetitive sequences and 25 subfamilies consisted of newly identified TEs or novel types of repetitive sequences. The region contains no long terminal repeat (LTR) retrotransposable elements, but miniature inverted repeat transposable elements (MITEs) constituted a major class among the elements identified. These MITEs showed remarkable structural divergence: 12 elements were found to be new members of known MITE superfamilies, while five elements had novel terminal structures, and did not belong to any known TE families. Interestingly, about 10% of the repetitive sequences, including virus-like sequences did not have any of the usual characteristics of TEs, suggesting that a certain proportion of repetitive sequences that might not share the transpositional mechanisms of known elements are dispersed in the compact rice genome.
• Molecular basis of somaclonal variation in the epsps-rps20 region of rice

  Noro Y., Kobayashi S., Kishima Y., Sano Y.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (42) 11 - 12 2001/12
• Diversified genie actions reconfirmed in hybrid-sterility genes of rice

  Nishimoto D., Onishi K., Nagano H., Kishima Y., Sano Y.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (42) 13 - 14 2001/12
• 植物トランスポゾンの転移機構に関する分子育種学的研究

  貴島 祐治

  育種学研究 日本育種学会 3 (3) 169 - 175 1344-7629 2001
• Position effect of the excision frequency of the Antirrhinum transposon Tam3: implications for the degree of position-dependent methylation in the ends of the element

  K Kitamura, S Hashida, T Mikami, Y Kishima

  PLANT MOLECULAR BIOLOGY 47 (4) 475 - 490 0167-4412 2001 [Refereed][Not invited]
   

  We identified eight independent Tam3 copies residing in the same Antirrhinum majus genome. All the copies showed excision at 15 degreesC, but not at 25 degreesC. Under conditions promoting excision, each copy appeared to transpose in the leaves and flower lobes with a nearly constant frequency, whereas individual transposition abilities varied widely: the most active copy had an excision frequency more than 100-fold greater than that of the least active one. Despite the different transposition abilities, the structures of the eight Tam3 copies were almost identical. These results made it clear that the transpositional ability of Tam3 is regulated by chromosomal position, but they do not imply position-dependent transposase activity. The position effect of the Tam3 transposition was found to be correlated to the methylation state of the copy's end regions: DNA methylation in the Tam3 end regions tended to suppress the excision activity, and the degree of methylation was dependent on the chromosomal position. Our results also provide evidence of de novo methylation provoked by transposition of the endogenous element. We propose a mechanism of transpositional regulation of plant transposons that responds to the degree of methylation as determined by chromosomal position.
• Structural characterization of repetitive region for vicinity of Waxy locus

  Kunii M., Nagano H., Kishima Y., Sano Y.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (41) 17 - 18 2000/12
• Structural differences in the vicinity of the waxy locus among the Oryza species with the AA-genome: identification of variable regions

  H Nagano, S Kawasaki, Y Kishima, Y Sano

  THEORETICAL AND APPLIED GENETICS 100 (3-4) 376 - 383 0040-5752 2000/02 [Refereed][Not invited]
   

  We constructed a fine physical map for a 260-kb rice BAC contig surrounding the waxy locus. In order to identify variable regions within this 260-kb as to the restriction fragments length polymorphisms and copy numbers, sixty overlapping fragments derived from the 260-kb contig were used as probes to compare their corresponding structures among the Oryza species with AA-genome. According to the hybridization patterns, each fragment was classified into four types: true single copy (class 1), single copy with a smear background (class 2), multiple copy without a smear background (class 3), and only a smear background (class 4), Out of 16 single copy (class 1 and class 2) regions obtained in this map, the one site corresponding to wx gave rise to remarkable polymorphisms among AA-genome species in Oryza. In most of the fragments observed as repetitive segments (class 4), we could not find obvious differences in the hybridization pattern. However, interesting Iv, one site sorted into class-3 showed copy numbers varying among the lines. The lines belonging to O. sativa O. rufipogon, O. meridionalis, and O. longistaminata possessed high-copy numbers of this fragment, whereas only a few bands were detected in the lines from O. glaberrima, O. barthii, and O. glumaepatula. The two variable regions found within the AA-genome species represented genomic dynamisms.
• DNA sequences homologous to rice tungro bacilliform virus (RTBV) present in the rice genome.

  Nagano H, Oka A, Kishima Y, Sano Y

  Rice Genetics Newsletter 17 103 - 105 2000 [Refereed][Not invited]
  
• Comparative analysis of the epsps-rps40 spacer region in the Oryza genus

  Kobayashi S., Sato T., Nagano H., Kishima Y., Sano Y.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (40) 11 - 12 1999/12
• Resistance to gap repair of the transposon Tam3 in Antirrhinum majus: A role of the end regions

  S Yamashita, T Takano-Shimizu, K Kitamura, T Mikami, Y Kishima

  GENETICS 153 (4) 1899 - 1908 0016-6731 1999/12 [Refereed][Not invited]
   

  The extremely homogeneous organization of the transposon family Tam3 in Antirrhinum majus is in sharp contrast to the heterogeneity of the copies constituting many other transposon families. To address the issue of the Tam3 structural uniformity, we examined two possibilities: (1) recent invasion of Tam3 and (2) failure of gap repair, which is involved in conversion from autonomous forms to defective forms. The phylogenetic analysis of 17 Tam3 copies suggested that the invasion of Tam3 into the Antirrhinum genome occurred at least 5 mya, which is sufficiently long ago to have produced many aberrant copies by gap repair. Thus, we investigated gap repair events at the nivea(recurrens:Tam3) (niv(rec)::Tam3) allele, where Tam3 is actively excised. We show here that the gap repair of de novo somatic Tam3 excision was arrested immediately after initiation of the process. All of the identified gap repair products were short stretches, no longer than 150 bp from the ends. The Tam3 ends have hairpin structures with low free energies. We observed that the gap repair halted within the hairpin structure regions. Such small gap repair products appear to be distributed in the Antirrhinum genome, but:are unlikely to be active. Our data strongly suggest that the structural homogeneity of Tam3 was caused by immunity to gap repair at the hairpins in both of the end regions. The frequency of extensive gap repair of de novo excision products in eukaryotic transposons was found to be correlated with the free energies of the secondary structures in the end regions. This fact suggests that the fates of transposon families might depend on the structures of their ends.
• Genomic organization of the 260 kb surrounding the waxy locus in a Japonica rice

  H Nagano, LH Wu, S Kawasaki, Y Kishima, Y Sano

  GENOME 42 (6) 1121 - 1126 0831-2796 1999/12 [Refereed][Not invited]
   

  The present study was carried out to characterize the molecular organization in the vicinity of the waxy locus in rice. To determine the structural organization of the region surrounding waxy, contiguous clones covering a total of 260 kb were constructed using a bacterial artificial chromosome (BAC) library from the Shimokita variety of Japonica rice. This map also contains 200 overlapping subclones, which allowed construction of a fine physical map with a total of 64 HindIII sites. During the course of constructing the map, we noticed the presence of some repeated regions which might be related to transposable elements. We divided the 260-kb region into 60 segments (average size of 5.7 kb) to use as probes to determine their genomic organization. Hybridization patterns obtained by probing with these segments were classified into four types: class 1, a single or a few bands without a smeared background; class 2, a single or a few bands with a smeared background; class 3, multiple discrete bands without a smeared background; and class 4, only a smeared background. These classes constituted 6.5%, 20.9%, 3.7%, and 68.9% of the 260-kb region, respectively. The distribution of each class revealed that repetitive sequences are a major component in this region, as expected, and that unique sequence regions were mostly no longer than 6 kb due to interruption by repetitive sequences. We discuss how the map constructed here might be a powerful tool for characterization and comparison of the genome structures and the genes around the waxy locus in the Oryza species.
• Structural conservation of the transposon Tam3 family in Antirrhinum majus and estimation of the number of copies able to transpose

  Y Kishima, S Yamashita, C Martin, T Mikami

  PLANT MOLECULAR BIOLOGY 39 (2) 299 - 308 0167-4412 1999/01 [Refereed][Not invited]
   

  We have investigated the organization of the transposon Tam3 family in Antirrhinum majus. Genomic hybridization experiments and characterization of 40 independent Tam3 clones isolated from an A. majus plant revealed that the Tam3 family is quite conserved and the copy sizes are uniform. We did not find any copy with a deleted internal sequence, unlike what is usually observed in other transposons; This exceptionally conserved structure of the Tam3 family was confirmed by PCR and sequencing analyses. Sequencing analysis identified eight copies with sequences completely identical to that of the Tam3 transposase gene. These results suggested that a considerable number of autonomous Tam3 copies are present in the genome of A. majus. Among 24 copies which are surrounded by single copy regions of the genome, 14 copies are present as specific insertions in the line which we used, but absent in other lines. These copies are therefore predicted to be movable. If this ratio is the same for all Tam3 copies in a genome, then a maximum of 60% of the copies are estimated to be movable in the genome. The relatively high frequency of gene tagged by Tam3 might reflect the large number of movable copies in the genome.
• Rice EPSP synthase gene resides 45-kb downstream of the Waxy gene.

  Sato T, Wu L.-H, Nagano H, Kishima Y, Sano Y

  Rice Genetics Newsletter 16 108 - 110 1999 [Refereed][Not invited]
  
• Characterization of EPSPsynthase gene and rps40 gene and structural comparisons of their spacers in rice

  Sato T., Nagano H., Kishima Y., Sano Y.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (39) 3 - 4 1998/12
• Tam3 in Antirrhinum majus is exceptional transposon in resistant to alteration by abortive gap repair: identification of nested transposons

  S Yamashita, T Mikami, Y Kishima

  MOLECULAR AND GENERAL GENETICS 259 (5) 468 - 474 0026-8925 1998/09 [Refereed][Not invited]
   

  Most transposon families consist of heterogeneous copies with varying sizes. In contrast, the Tam3 copies in Antirrhinum majus are known to have exceptionally conserved structures of uniform size. Gap repair has been reported to be involved in the structural alteration of copies from several transposon families. In this study, we have asked whether or not gap repair has affected Tam3 copies. Five Tam3 copies carrying aberrant sequences were selected from 40 independent Tam3 clones and their sequences were analyzed. Two of the five copies contain insertions in the Tam3 sequence. These two insertions, designated Tam356 and Tam661, are typical transposon-like sequences, which have terminal inverted repeats and cause target site duplication. These nested transposons were obviously associated with transpositional events, and did not originate from the gap-repair process. The remaining three copies had lost large parts of the Tam3 sequence. We could not find any relationship between the deletions of Tam3 sequence in the three copies and gap repair. PCR analysis of a Tam3 excision site in the nivea(recurrence:Tam3) mutant also showed that most of the repair events after the Tam3 excision involved end-joining. In addition to the results obtained here, among the other clones isolated, we could not find any of the internally deleted copies that comprise a major part of other transposon families. All of these data suggest that some feature of the Tam3 structure suppresses the structural alterations that are otherwise generated during the gap repair process.
• Plant regeneration via somatic embryogenesis after somatic hybridization between Lycopersicon esculentum and L. peruvianum

  Chen L, Kinoshita T, Kishima Y, Akashi R, Adachi T

  SABRAO Journal of Breeding & Genetics 30 25 - 34 1998 [Refereed][Not invited]
  
• Organization of the 260 kb region in the vicinity of the waxy locus of rice.

  Nagano H, Kawasaki S, Kishima Y, Sano Y

  Rice Genetics Newsletter 15 167 - 168 1998 [Refereed][Not invited]
  
• Immobilized copies with a nearly intact structure of the transposon Tam3 in Antirrhinum majus: implications for the cis-element related to the transposition

  Y Kishima, S Yamashita, T Mikami

  THEORETICAL AND APPLIED GENETICS 95 (8) 1246 - 1251 0040-5752 1997/12 [Refereed][Not invited]
   

  In this study we have focused on two copies of the transposon Tam3 isolated from an Antirrhinum majus plant which has flower variegation due to the excision of Tam3 from the nivea locus. These two copies possess a high homology, over 95%, to an active Tam3 element found in the niven(recurrence:Tam3) allele. Although somatic excision of the Tam3 copy from the nivea locus can be detected at 15 degrees C by Southern blotting, neither of the two copies showed any sign of the excision. Both of the immobilized copies were also found in five varieties from different A. majus sources, all of which contain common fragments. The results suggest that the two copies have been fixed in the genomes of many A. majus varieties. Structural differences between these immobilized copies and the known active copy were mainly observed in the subterminal regions, including the terminal inverted repeats. The immobility of the two Tam3 copies might be due to mutations within the end regions of essential cis-elements in Tam3 transposition, as reported for Ac and En/Spm.
• Expansion of the IR in the chloroplast genomes of buckwheat species is due to incorporation of an SSC sequence that could be mediated by an inversion

  J Aii, Y Kishima, T Mikami, T Adachi

  CURRENT GENETICS 31 (3) 276 - 279 0172-8083 1997/03 [Refereed][Not invited]
   

  The chloroplast genomes in buckwheat species contain large inverted repeats which are at least 4 kbp longer than the majority of those in land plants. The length of the buckwheat inverted repeats was attributable to an additional region located adjacent to the borders of the small single-copy region. We have cloned and sequenced a 5.2-kbp SmaI fragment corresponding to this extra region in the inverted repeats. A homology search revealed that the sequence of the SmaI fragment is highly homologous to one side of the small single-copy region of the inverted repeats in dicot chloroplast DNAs such as tobacco and beechdrops. Interestingly, a 3.7-kbp segment in the middle of the SmaI fragment is inserted in the opposite orientation relative to those of the other dicot species, and 17-bp direct repeats are found located at both the ends of the additional region. These results suggest that expansion of the inverted repeats in buckwheat chloroplast DNA might have been associated with an inversion.
• Identification of the DNA fragments located in the vicinity of waxy locus responsible for gamate eliminatator.

  Wu L.-H, Nagano H, Kawasaki S, Kishima Y, Sano Y

  Rice Genetics Newsletter 14 123 - 124 1997 [Refereed][Not invited]
  
• Construction of a 300-kb BAC conting containing waxy locus in Japonica rice.

  Nagano H, Wu L.-H, Kawasaki S, Kishima Y, Sano Y

  Rice Genetics Newsletter 14 121 - 123 1997 [Refereed][Not invited]
  
• Molecular genetic studies on the waxy locus in rice.

  Wu L. H., Nagano H., Mikami I., Kawasaki S., Kishima Y., Sano Y.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (37) 14 - 15 1996/12
• Isolation and characterization of the transposon Tam3 family from Antiirhinum majus.

  Yamashita S., Kishima Y., Mikami T.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (37) 108 - 109 1996/12
• Transposon tagging for stabilizer gene in Antin-hinum majus

  Kishima Y.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (36) 80 - 81 1995/12
• Evidence that blue light induces betalain pigmentation in Portulaca callas

  Y Kishima, A Shimaya, T Adachi

  PLANT CELL TISSUE AND ORGAN CULTURE 43 (1) 67 - 70 0167-6857 1995/10 [Refereed][Not invited]
   

  The wavelength range that activates betalain pigmentation has been studied following selection of light inducible betalain producing callus lines originating from Portulaca sp. 'Jewel' seedlings. Light sources with different wavelengths were used to irradiate the callus, resulting in blue light being effective in inducing betalain pigmentation. In addition, when UV light was combined with blue light, some calluses from this cell line showed high production of the pigment. This is a first report that betalain pigmentation in callus was induced by blue and blue/UV lights.
• PHYSICAL MAPPING OF DIFFERENCES BETWEEN THE CHLOROPLAST DNAS OF BETA-VULGARIS AND B-WEBBIANA

  Y KISHIMA, Y YANAI, T KINOSHITA, T MIKAMI

  PLANT BREEDING 114 (4) 361 - 362 0179-9541 1995/08 [Refereed][Not invited]
   

  A physical map of Beta webbiana (a wild species of the section Procumbentes) chloroplast genome was constructed by localizing the cleavage sites of SmaI, PstI, PvuII, XhoI, and HindIII, and the map was then aligned with the map of sugarbeet (B. vulgaris) chloroplast DNA. This alignment shows 27 restriction-site changes and 11 insertions/deletions, most of which occur in the large single-copy region of the genome. A 0.7-kb long mutation,located within an unidentified open reading frame (ORF2280) in the inverted repeat, was also found.
• CHLOROPLAST DNA ANALYSIS IN BUCKWHEAT SPECIES - PHYLOGENETIC-RELATIONSHIPS, ORIGIN OF THE REPRODUCTIVE SYSTEMS AND EXTENDED INVERTED REPEATS

  Y KISHIMA, K OGURA, K MIZUKAMI, T MIKAMI, T ADACHI

  PLANT SCIENCE 108 (2) 173 - 179 0168-9452 1995/06 [Refereed][Not invited]
   

  We have constructed physical maps for the chloroplast genomes of buckwheat (Fagopyrum esculentum) and related species (F. tataricum and F. cymosum) by using six restriction enzymes. The genome sizes were found to be identical with approximately 155.5 kb. A comparison of physical maps revealed 11 altered restriction sites out of 259 analyzed. Phylogenetically, the chloroplast DNA of F. esculentum has been found to be quite distant from those of F. tataricum and F. cymosum. These results also suggest that the allogamous mode could be the ancestral reproductive system for Fagopyrum, whose present-day species display three different mechanisms of reproduction: allogamous, autogamous and vegetative, because both the distantly related species, F. esculentum and F. cymosum, maintain self-incompatibility due to heterostyly. We also observed that the unique 5.05-kb Sma-8 fragments, which extend the inverted repeats in buckwheat species, exhibit little homology with tobacco chloroplast DNA clones.
• Protoplast fusion in buckwheat: preliminary results on somatic hybridization.

  Lachmann S, Kishima Y, Adachi T

  Fagopyrum 14 7 - 12 1994 [Refereed][Not invited]
  
• COMPARATIVE-ANALYSIS OF PETAL PROTEINS IN RED AND WHITE LINES FROM NEAR-ISOGENIC PORTULACA SP JEWEL PLANTS

  Y KISHIMA, C HATADE, M SUIKO, T ADACHI

  EUPHYTICA 61 (1) 67 - 71 0014-2336 1992/04 [Refereed][Not invited]
   

  A couple of near-isogenic lines, JR and JW from Portulaca sp. 'Jewel' has red and white petals respectively. The difference in petal color in the two lines is caused by an alteration of single genetic locus which is involved in the biosynthesis of betalain pigmentation. In order to detect this genetic difference at the polypeptide level, we have now attempted the comparative analysis of petal proteins between JR and JW. The protein profiles of SDS-polyacrylamid gel electrophoresis from three different stages of the developing petals, and the autoradiographic protein profiles of in vivo labeled petals showed that a 27 KD fragment strongly appeared as a characteristic of JR petal fraction. Thus, this fragment can be considered as a candidate for certain polypeptides which is associated with the betalain synthesis pathway functioning in the pigmented petals.
• LIGHT-INDUCIBLE PIGMENTATION IN PORTULACA CALLUS - SELECTION OF A HIGH BETALAIN PRODUCING CELL-LINE

  Y KISHIMA, K NOZAKI, R AKASHI, T ADACHI

  PLANT CELL REPORTS 10 (6-7) 304 - 307 0721-7714 1991/09 [Refereed][Not invited]
   

  We have established a unique betalain pigmentation system in callus cultures that originated from seedlings of Portulaca sp. 'Jewel'. Within three different 'Jewel' lines examined, one line (JR) was clearly superior with regard to callus growth rate and pigment formation. Furthermore, after ten cycles of selection of deeply colored callus patches, the selected clones contained on an average four times the amount of betalain as compared to the non-selected mother line. The colorization was induced by light, but disappeared in the dark. Pigment synthesis was detectable within 30 h after irradiation and showed positive correlation with irradiation periods.
• BETALAIN PIGMENTATION IN PETAL OF PORTULACA IS PRECEDED BY A DRAMATIC TYROSINE ACCUMULATION

  Y KISHIMA, M SUIKO, T ADACHI

  JOURNAL OF PLANT PHYSIOLOGY 137 (4) 505 - 506 0176-1617 1991/02 [Refereed][Not invited]
   

  To study the turnover of two betalain precursors in magenta petals of Portulaca sp. Jewel, we measured the concentrations of tyrosine and DOPA at distinct developmental stages during flower maturation. A striking increase in tyrosine at least 200 times that in leaves and stems was observed to precede betalain synthesis and petal colorization. The concentration of tyrosine diminished rapidly and synchronously with pigment appearance. The concentration of DOPA, on the other hand, did not follow the same kinetics of accumulation and metabolism as tyrosine and betalain but remained relatively steady at a moderate concentration. Our data indicate an important role of tyrosine as a betalain precursor.
• Isolation and macro molecular analysis of chloroplast DNA in common buckwheat.

  Kishima Y, Yabuya T, Adachi T

  Fagopyrum 10 65 - 68 1989 [Refereed][Not invited]
  
• The variation of petal protein among different flower color strains in the genus portulaca

  KISHIMA Y, SUIKOU M, ADACHI T

  Japanese Journal of Breeding 日本育種学会 38 (2) 400 - 401 0536-3683 1988 [Not refereed][Not invited]
  
• Molecular analysis of chloroplast genome diversity among Beta species

  MIKAMI T., KISHIMA Y., KINOSHITA T.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (27) 44 - 44 1987/02
• BETA-CHLOROPLAST GENOMES - ANALYSIS OF FRACTION-I PROTEIN AND CHLOROPLAST DNA VARIATION

  Y KISHIMA, T MIKAMI, A HIRAI, M SUGIURA, T KINOSHITA

  THEORETICAL AND APPLIED GENETICS 73 (3) 330 - 336 0040-5752 1987 [Refereed][Not invited]
  
• Restriction endonuclease mapping of chloroplast DNA in sugar beet

  KISHIMA Y., MIKAMI T., KINOSHITA T.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (26) 28 - 28 1986/02
• UBIQUITY OF THE GENES FOR COMPONENTS OF A NADH DEHYDROGENASE IN HIGHER-PLANT CHLOROPLAST GENOMES

  BY MENG, T MATSUBAYASHI, T WAKASUGI, K SHINOZAKI, M SUGIURA, A HIRAI, T MIKAMI, Y KISHIMA, T KINOSHITA

  PLANT SCIENCE 47 (3) 181 - 184 0168-9452 1986 [Refereed][Not invited]
  
• RESTRICTION FRAGMENT MAP OF SUGAR-BEET (BETA-VULGARIS L) CHLOROPLAST DNA

  Y KISHIMA, T MIKAMI, T HARADA, K SHINOZAKI, M SUGIURA, T KINOSHITA

  PLANT MOLECULAR BIOLOGY 7 (3) 201 - 205 0167-4412 1986 [Refereed][Not invited]
  
• Molecular basis of the genetic diversity among different sources of male sterile cytoplasms in sugar beet.

  MIKAMI T., HARADA T., KISHIMA Y.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (25) 47 - 47 1985/02
• Differentiation of the chloroplast DNA and Fraction 1 protein in the genus Bata.

  KISHIMA Y., MIKAMI T., KINOSHITA T.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (25) 45 - 45 1985/02
• ORGANELLE GENOME DIVERSITY IN SUGAR-BEET WITH NORMAL AND DIFFERENT SOURCES OF MALE STERILE CYTOPLASMS

  T MIKAMI, Y KISHIMA, M SUGIURA, T KINOSHITA

  THEORETICAL AND APPLIED GENETICS 71 (2) 166 - 171 0040-5752 1985 [Refereed][Not invited]
  
• Variation in the chloroplast DNA resriction patterns among the cytoplasms of sugar beet and its related species

  KISHIMA Y., MIKAMI T., KINOSHITA T.

  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan 日本作物学会 (24) 33 - 33 1984/01
• CHLOROPLAST DNA DIVERSITY IN THE CYTOPLASMS OF SUGAR-BEET AND ITS RELATED SPECIES

  T MIKAMI, Y KISHIMA, M SUGIURA, T KINOSHITA

  PLANT SCIENCE LETTERS 36 (3) 231 - 235 0304-4211 1984 [Refereed][Not invited]
  

MISC

• Exploration of introgressed regions between O. sativa ssp. japonica and AA-genome species of the genus Oryza based on comparative genome analysis

  小柳香奈子, 神徳雄太, 貴島祐治  育種学研究  26-  2024
• Genome composition of tetraploid rice plants consisting of Asian and African cultivars

  古田智敬, 長岐清孝, 柏原壱成, 國吉大地, 北島克哉, 小出陽平, 貴島祐治, 山本敏央  育種学研究  23-  2021
• Variation of abnormal anther morphology and its correlation with pollen sterility during chilling stress in rice

  山森晃一, 小笠原慧, 石黒聖也, 小出陽平, 高牟禮逸郎, 佐藤裕, 貴島祐治  育種学研究  23-  2021
• Overcoming the hybrid sterility using the tetraploid hybrid between Oryza sativa and O. glaberrima

  國吉大地, 石原萌, 小出陽平, 貴島祐治  育種学研究  23-  2021
• A2 fusion rice-Fertile interspecific hybrid rice between Asian and African cultivated rice-

  北島克哉, 増田到, 齋藤希, 國吉大地, 金岡義高, 高牟禮逸朗, 高牟禮逸朗, 星野洋一郎, 小出陽平, 貴島祐治  育種学研究  22-  2020
• The screening of genes that show insensitivity to low tempeeature during rice booting stage

  山森晃一, 石黒聖也, 小笠原慧, 小出陽平, 藤野介延, 佐藤裕, 貴島祐治  育種学研究  22-  2020
• A Few Selected Approaches to Increase Genetic Diversity in Rice Breeding

  山本敏央, 古田智敬, 小川大輔, 米丸淳一, 國吉大地, 貴島祐治  作物研究  65-  2020
• Evaluation of photoperiod and temperature sensitivity according to growth stage fractions in Hokkaido rice varieties

  Kohno K, Sakaguchi S, Ota Y, Uchiyama T, Koide Y, Takamure I, Kishima Y  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  60-  (0)  38  -39  2019  [Refereed][Not invited]
  
• Reduction of tetraploid rice to diploid through anther culture and its apllication

  Shimazaki Y, Kuniyoshi D, Masuda I, Kanaoka Y, Hoshino Y, Koide Y, Kishima Y  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  60-  (0)  34  -35  2019  [Refereed][Not invited]
  
• Rice tetraploid production by means of anther culture and its application to feed rice

  Hoshi S, Shimazaki Y, Kishima Y, Koide Y, Hoshino Y  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  60-  (0)  36  -37  2019  [Refereed][Not invited]
  
• Genetic analysis of the Old Stabiliser gene that supresses transposition of Tam3 in Antirrhinum majus

  Asano H, Yuasa I, Koide Y, Kishima Y  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  60-  (0)  76  -77  2019  [Refereed][Not invited]
  
• Oryza sativaとO.glaberrima種間雑種の葯培養カルスから推定した減数分裂の異常

  國吉大地, 増田到, 島崎優樹, 金岡義高, 星野洋一郎, 小出陽平, 貴島祐治  育種学研究  20-  40  2018/09/22  [Not refereed][Not invited]
  
• 出穂期が類似する北海道イネ品種間の交雑から生じた超越分離の遺伝的基礎

  太田雄也, 小出陽平, 内山尭, 坂口俊太郎, 手塚あゆみ, 永野惇, 高牟禮逸朗, 貴島祐治  育種学研究  20-  27  2018/03/25  [Not refereed][Not invited]
  
• Speciation of interceller localization mechanism of transposase from Antirrhinum mujus

  Ohigashi T, Zhou H, Yuasa I, Mitsui S, Koide Y, Tsugama D, Fujino K, Kishima Y  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  59-  (0)  2  -3  2018  [Not refereed][Not invited]
  
• Comparative analyses of the function and structure of two Stabiliser genes for transposon Tam3 in Antirrhinum majus using progenies from various cross combinations

  Yuasa I, Hirata M, Zhou H, Makiya K, Ohigashi T, Mitsui S, Koide Y, Kishima Y  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  59-  (0)  4  -5  2018  [Not refereed][Not invited]
  
• The relationship between the copy numbers of endogenous virus segments in rice genome and the symptom of RTBV-infected plants

  Kitajima K, Utu K, Saito N, Koide Y, Kishima Y  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  59-  (0)  12  -13  2018  [Not refereed][Not invited]
  
• アジアイネとアフリカイネを用いた内在性RTBV様(ERTBVL)配列由来siRNAの発現解析

  齋藤希, ENCABO Jaymee, 宇津康太郎, 小出陽平, CHOI Il‐Ryong, 貴島祐治  育種学研究  19-  60  2017/10/07  [Not refereed][Not invited]
  
• アフリカイネとアジアイネの雑種四倍体の作出

  増田到, 金岡義高, 國吉大地, 小出陽平, 高牟禮逸朗, 高牟禮逸朗, 近江戸伸子, 星野洋一郎, 貴島祐治  育種学研究  19-  126  2017/10/07  [Not refereed][Not invited]
  
• Extraction of a single rice pollen and microspore by cell sorter

  島崎優樹, 増田到, 金岡義高, 貴島祐治, 小出陽平  日本育種学会・日本作物学会北海道談話会会報(Web)  58-  10‐11(J‐STAGE)  2017  [Not refereed][Not invited]
  
• Phenotyping and genome-wide transcriptome analysis for F1whose parents have different genetic distance at booting stage in rice

  宇津康太郎, Hu N, 斉藤希, 吉住遥香, 小出陽平, 貴島祐治  日本育種学会・日本作物学会北海道談話会会報(Web)  58-  12‐13(J‐STAGE)  2017  [Not refereed][Not invited]
  
• Characterization of a fertility restorer for CMS found in Japonica rice, Taichung 65

  金岡義高, 山形悦透, Chen S, 菊池駿太, 小出陽平, 安井秀, 吉村淳, 貴島祐治  日本育種学会・日本作物学会北海道談話会会報(Web)  58-  4‐5(J‐STAGE)  2017  [Not refereed][Not invited]
  
• Comparative analyses of anther structure and genome-wide expression at booting stage under low-temperature stress among rice varieties

  山森晃一, 菊池駿太, 石黒聖也, 小笠原慧, 小出陽平, 藤野介延, 佐藤裕, 貴島祐治  日本育種学会・日本作物学会北海道談話会会報(Web)  58-  8‐9(J‐STAGE)  2017  [Not refereed][Not invited]
  
• Genetic analysis of transgressive segregation for early heading trait derived from rice varieties in Hokkaido

  Sakaguchi S, Uchiyama A, Ota Y, Tezuka A, Nagano Z, Koide Y, Kishima Y  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  58-  (0)  14  -15  2017  [Not refereed][Not invited]
  
• Epigenetic-independent regulation of Tam3 in Antirrhinum majus detains transposase to the plasma membrane by targeting its BED-zinc finger domain

  Zhou Hua, Megumi Hirata, Ryo Osawa, Kaien Fujino, Yuji Kishima  GENES & GENETIC SYSTEMS  91-  (6)  359  -359  2016/12  [Not refereed][Not invited]
  
• The analysis of comprehensive transition motion of transposon Tam3 in Nivea locus of Antirrhinum majus

  Kayo Makiya, Izuru Ebinuma, Masahiro Asano, Taichi Tateo, Tomo Kasahara, Yuya Nakayama, Takako Uchiyama, Yuji Kishima  GENES & GENETIC SYSTEMS  91-  (6)  359  -359  2016/12  [Not refereed][Not invited]
  
• Oryza AAゲノム種に散在する化石ウイルスの進化的および機能的役割

  齋藤希, CHEN S, 山田加奈恵, CHOI I, ENCABO J. R, 小出陽平, 貴島祐治  育種学研究  18-  15  2016/09/24  [Not refereed][Not invited]
  
• SNPを利用した北海道イネ品種間交雑に由来する極早生集団の遺伝解析

  内山尭, 小出陽平, 太田雄也, 手塚あゆみ, 永野惇, 貴島祐治  育種学研究  18-  229  2016/09/24  [Not refereed][Not invited]
  
• イネの低温鈍感力強化

  貴島 祐治  グリーンテクノ情報  12-  (1)  2  -5  2016/06
• P4-3-10 イネの塩害に対する生育評価および遺伝学的解析(ポスター,4-3 植物の有害元素,2014年度東京大会)

  清水 克, 石黒 聖也, 渡部 敏裕, 大崎 満, 貴島 祐治  日本土壌肥料学会講演要旨集  (60)  77  -77  2014/09/09
• Toward breeding strategy for rice resistances against insects and viruses in global warming

  KISHIMA Yuji, MATSUMURA Masaya, KIKUCHI Shoshi, ASANO Takayuki, YASUI Hideshi  Breeding Research (in Japanese)  15-  (3)  110  -114  2013/09  [Not refereed][Not invited]
  
• イネゲノムの反復配列に基づく低温鈍感力の解析

  石黒 聖也, 佐藤 裕, 貴島 祐治  日本草地学会誌  (59)  60  -63  2013  [Refereed][Not invited]
  
• Evolutionary Force of AT-rich Repeats to Trap Genomic and Episomal DNAs into the Rice Genome(The Information of Comparative Genome Sequence Reveals Biological Diversity and Phenotypic Expression)

  Koyanagi Kanako O., Li Ruifang, Chen Sunlu, Mizuno Midori, Kishima Yuji  Japanese Journal of Grassland Science  59-  (1)  55  -59  2013  [Refereed][Not invited]
   

  高等植物のゲノムは倍数化や転位因子の影響でそのサイズが大きく，一般にゲノム解読は困難であった。高等植物で最初にゲノムが解読されたのは，シロイヌナズナ(Arabidopsis thaliana)であり(The Arabidopsis Genome Initiative 2000)，次いでイネ(Oryza sativa)のゲノムが解読されたが(Yuら 2002;International Rice Genome Sequencing Project 2005)，いずれもゲノムサイズの小さなモデル植物であった。しかしながらゲノム解読技術の急速な進展を背景に，近年ゲノムサイズの大きな高等植物のゲノム解読の報告が相次いでおり(Schnableら 2009; The International Barley Genome Sequencing Consortium 2012)，今後もモデル植物以外の生物種や，栽培種の野生種のゲノム解読等が期待される。ゲノム解読が進むと，ゲノム中に自身の遺伝情報以外の外来性配列が存在することもわかってきた。例えばイネではパラレトロウイルスであるrice tungro bacilliform virus-like sequencesがゲノム中に発見された(ERTBV，内在性rice tungro bacilliform virus-like sequences)(Kuniiら 2004)。
• イネゲノムのATリピートはウイルス様配列やジャックDNA配列を集積し,進化を促進する

  LIU R, CHEN S, KOYANAGI KANAKO, KISHIMA YUJI  育種学研究  14-  44  2012/09/14  [Not refereed][Not invited]
  
• The integrations of endogenous DNA virus-like sequences and episomal DNAs in the rice genomes

  Liu R, Koyanagi O K, Chen S, Kishima Y  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  53-  (53)  11  -12  2012  [Not refereed][Not invited]
  
• Characterization of microspore through the expression patterns of repetitive sequences in rice

  Yuji Kishima, Seiya Ishiguro, Yuya Ota, Yutaka Sato  GENES & GENETIC SYSTEMS  86-  (6)  379  -379  2011/12  [Not refereed][Not invited]
  
• Control of the nuclear import of Tam3 transposase and identification of the gene associated with the low-temperature-dependent transposition in Antirrhinum

  Tomoko Natsume, Takashi Ogawa, Satomi Hukumoto, Kaien Hujino, Yuji Kishima  GENES & GENETIC SYSTEMS  86-  (6)  421  -421  2011/12  [Not refereed][Not invited]
  
• Structural variation caused by somatic transposition of Tam3 in Antirrhinum majus

  Tomo Kasahara, Masahiro Asano, Yuji Kishima  GENES & GENETIC SYSTEMS  85-  (6)  434  -434  2010/12  [Not refereed][Not invited]
  
• Insertion of transposon Tam3 into promoters induces leaky phenotype in Antirrhinum

  Takako Uchiyama, Kaien Fujin, Yuji Kishima  GENES & GENETIC SYSTEMS  84-  (6)  485  -485  2009/12  [Not refereed][Not invited]
  
• トランスポゾンTam3と宿主の親和的関係 (日本の遺伝学の潮流--日本遺伝学会第78回大会ハイライト) -- (シンポジウム 栽培植物の遺伝的多様性と転移因子の役割)

  貴島 祐治, 橋田 慎之助, 内山 貴子  生物の科学「遺伝」 別冊  (21)  82  -86,39  2007/03
• 植物のゲノムに潜むウイルス : 反復配列に秘められたしなやかでしたたかな植物の防御戦略?

  貴島 祐治  化学と生物  42-  (11)  704  -706  2004/11/25
• MITEトランスポゾンディスプレイによるイネ属AAゲノム種間の効率的多型検出

  高木 恭子, 長野 宏則, 貴島 祐治, 佐野 芳雄  育種学研究  5-  (2)  61  -61  2003/06/01
• Transposon of snapdragon expresses forces for novel gene regulation and chromosome breakage

  Y Kishima  PLANT AND CELL PHYSIOLOGY  44-  S13  -S13  2003  [Not refereed][Not invited]
  
• Chromosome breakage and inheritance of nivea locus associated with Tam3 excision in Antirrhinum majus

  NORO Y., TOZAKI T., HIURA S., MIKAMI T., SANO Y., KISHIMA Y.  育種学研究 = Breeding research  4-  121  -121  2002/08/26
• Transposase of Tam3 in Antirrhinum binding to its termini and inhibition by DNA methylation

  KITAMURA M., HASHIDA S., MIKAMI T., KISHIMA Y.  育種学研究 = Breeding research  4-  120  -120  2002/08/26
• A fine disection of the rice genome based on MITE-Transposon-Display

  KISHIMA Y., TAKAGI K., NAGANO H., SANO Y.  育種学研究 = Breeding research  4-  260  -260  2002/08/26
• Comparative analysis of a hybrid sterility gene(S1) under the different genetic backgrounds of O. sativa.

  NISHIMOTO D., ONISHI K., NAGANO H., KISHIMA Y., SANO Y.  育種学研究 = Breeding research  4-  (1)  252  -252  2002/03/30
• Comparative analysis of Oryza species based on MITE-transposon display

  TAKAGI K., NAGANO H., KISHIMA Y., SANO Y.  育種学研究 = Breeding research  4-  (1)  91  -91  2002/03/30
• Study on transpositional regulation of the plant transposons

  3-  169  -175  2001  [Not refereed][Not invited]
  
• Production of the Antirrhinum lines showing diffrent variegation patterns in the flower ans isolation of the involved genes.

  KISHIMA Y., HIURA S., MIKAMI T.  育種学研究 = Breeding research  2-  (2)  89  -89  2000/09/25
• Rapid nucleotide changes in a 300 bp shortspacer region of epsps-rps40 in the Oryza species

  KOBAYASHI S., KISHIMA Y., SANO Y.  育種学研究 = Breeding research  2-  (2)  96  -96  2000/09/25
• Repetitive sequences surrounding the rice Waxy are mostly present in the Poaceae species.

  NAGANO H., KISHIMA Y., SANO Y.  育種学研究 = Breeding research  2-  (2)  95  -95  2000/09/25
• Analysis of factor(s) involved in thermoregulated-transposotion of Antirrhimum transposon Tam3.

  HASHIDA S., KITAMURA K., MIKAMI T., KISHIMA Y.  育種学研究 = Breeding research  2-  (2)  88  -88  2000/09/25
• Position effect of the transposon Tam3 in the somatic transposition

  KITAMURA K., MIKAMI T., KISHIMA Y.  育種学研究 = Breeding research  2-  (1)  139  -139  2000/04
• Molecular breeding of grain quality in rice.

  SANO YOSHIO, KISHIMA YUJI, ITO KAZUHIKO, HIRANO HIROYUKI  飯島記念食品科学振興財団年報  1997-  240  -243  1999/08  [Not refereed][Not invited]
  
• Molecular Characterization of AT rich minisatellite located downstream of the rice wx gene.

  INUKAI TSUYOSHI, NAGANO HIRONORI, KISHIMA YUJI, SANO YOSHIO  育種学研究  1-  113  1999/04  [Not refereed][Not invited]
  
• The conserved regions among different genomes in rice species may be of functional region

  NAGANO H., KAWASAKI S., YOSHIDA K., KISHIMA Y., SANO Y.  日本分子生物学会年会プログラム・講演要旨集  21-  237  -237  1998/12/01
• Structural characterization based on the physical map of the rice BAC clones and its applications

  KISHIMA Y., SANO Y.  育種学最近の進歩  40-  69  -72  1998/09
• Intragenic recombination at the wx locus in rice.

  INUKAI TSUYOSHI, SAKO AYA, KISHIMA YUJI, SANO YOSHIO  育種学雑誌  48-  15  1998/04  [Not refereed][Not invited]
  
• A fine structural analysis in the wx locus of rice : 1. Construction of an intragenic map by pollen analysis

  Inukai T, Sako A, Kishima Y, Sano Y  Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan  0-  (38)  2  -3  1997/12  [Not refereed][Not invited]
  
• Identification of the transposon Tam3 copies that are immobilized in the chromosome of Antirrhinum majus.

  貴島祐治, 最相大輔, 三上哲夫  育種学雑誌  46-  1996
• TRANSPOSON TAGGING FOR Stabilizer GENE IN Antirrhinum majus

  KISHIMA Y., MARTIN C.  The Japanese journal of genetics  70-  (6)  713  -713  1995/12/01
• Fagopyrum chloroplast genome: construction of physical maps and characterization of unique sequence.

  Aii J, Kishima Y, Adachi T  Current Advances in Buckeat Research  135  -140  1995  [Refereed][Not invited]
  
• Blue-light inducible gene expression for betalain pigmentation in the Portulaca cell line. In

  Adachi T, Kishima Y  Plant Tissue Culture and Gene Manipulation for Breeding and Formation of Phytochemicals, ed. by K. Oono  355  -359  1992  [Refereed][Not invited]
  
• INSERTION DELETION MUTATIONS OCCURRED IN CHLOROPLAST GENOME OF THE SECTION PATELLARES IN THE GENUS BETA

  Y KISHIMA, T MIKAMI, T KINOSHITA  JAPANESE JOURNAL OF GENETICS  62-  (6)  526  -527  1987/12  [Not refereed][Not invited]
  
• Beta属Patellares節植物の葉緑体ゲノムに見出された変異多発域の構造解析．

  貴島 祐治, 三上 哲夫, 木下 俊郎  てん菜研究会報  (29)  22  -28  1987  [Refereed][Not invited]
  
• PHYSICAL MAPPING OF VARIATIONS AMONG CHLOROPLAST GENOMES OF BETA-SPECIES

  Y KISHIMA, T MIKAMI, M SUGIURA, T KINOSHITA  JAPANESE JOURNAL OF GENETICS  61-  (6)  590  -591  1986/12  [Not refereed][Not invited]
  
• Variation in organelle genome organization associated with male sterile cytoplasms in sugar beet.

  Mikami T, Harada T, Kishima Y, Sugihara M, Kinoshita T  Gamma Field Symposia  (25)  131  -149  1986  [Refereed][Not invited]
  
• テンサイ葉緑体ゲノムの構造と遺伝子構成．

  三上 哲夫, 貴島 祐治, 木下 俊郎  てん菜研究会報  (28)  14  -18  1986  [Refereed][Not invited]
  
• Beta属の葉緑体ゲノムにみられる構造変異の機構解析．

  貴島 祐治, 三上 哲夫, 木下 俊郎  てん菜研究会報  (28)  19  -24  1986  [Refereed][Not invited]
  
• PHYSICAL MAP OF CHLOROPLAST DNA IN SUGAR-BEETS

  Y KISHIMA, T MIKAMI, T KINOSHITA  JAPANESE JOURNAL OF GENETICS  60-  (6)  603  -603  1985/12  [Not refereed][Not invited]
  
• テンサイにおける葉緑体DNAライブラリーの作成．

  三上 哲夫, 貴島 祐治, 木下 俊郎  てん菜研究会報  (27)  1  -6  1985  [Refereed][Not invited]
  
• テンサイおよび近縁種に見られる葉緑体DNAとフラクションIタンパクの分化について．

  貴島 祐治, 三上 哲夫, 木下 俊郎  てん菜研究会報  (27)  7  -12  1985  [Refereed][Not invited]
  
• DIFFERENTIATION OF THE CHLOROPLAST GENOME IN THE GENUS-BETA

  Y KISHIMA, T MIKAMI, T KINOSHITA, A HIRAI  JAPANESE JOURNAL OF GENETICS  59-  (6)  629  -629  1984  [Not refereed][Not invited]
  
• ORGANELLE DNA VARIATION AMONG DIFFERENT SOURCES OF MALE STERILE CYTOPLASMS IN SUGAR-BEET

  T MIKAMI, Y KISHIMA, T KINOSHITA  JAPANESE JOURNAL OF GENETICS  59-  (6)  637  -638  1984  [Not refereed][Not invited]
  
• テンサイの異型雄性不稔細胞質間に見出されたミトコンドリアおよび葉緑体DNAの多型性.

  三上 哲夫, 貴島 祐治, 木下 俊郎  てん菜研究会報  (26)  15  -21  1984  [Refereed][Not invited]
  
• テンサイの雄性不稔における復帰型細胞質突然変異の誘発．

  木下 俊郎, 三上 哲夫, 貴島 祐治  てん菜研究会報  (26)  7  -14  1984  [Refereed][Not invited]
  
• テンサイおよび近縁種における葉緑体DNAの分子構造変異．

  貴島 祐治, 三上 哲夫, 木下 俊郎  てん菜研究会報  (26)  1  -6  1984  [Refereed][Not invited]
  

Books etc

• 遺伝学の基礎 第２版

  貴島 祐治 (Contributor)
  朝倉書店 2018/09
• Establishment of endogenous pararetroviruses in the rice genome

  R. Liu, Y. Kishima (Chapter 12 p229-240)
  Elsevier New York 2014/01
• 植物育種学第４版

  吉村 淳, 西尾 剛編 (第２章1.遺伝子と形質発現 4.生殖様式と近交弱性)
  文永堂出版 2012
• 植物の分子育種学

  鈴木 正彦編 (第５章トランスポゾンタギング)
  講談社 2011
• 花色の多様性生む遺伝子

  貴島 祐治 
  日本農業新聞 2007/05
• キンギョソウTam3の多彩な転移コントロール

  内山 貴子, 貴島 祐治 
  実験医学 2007
• トランスポゾンTam3と宿主の親和的関係

  貴島 祐治, 橋田 慎之介, 内山 貴子 
  遺伝 別冊 2007
• Genomics of rice: markers as a tool for breeding. Biotechnology in Agriculture and Forestry

  Kishima Y, Onishi K, Sano Y 
  Biotechnology in Agriculture and Forestry, vol. 55, Molecular Marker Systems,-Verlag Berlin Heidelberg 2004
• 植物のゲノムに潜むウイルス −反復配列に秘められたしなやかでしたたかな植物ゲノム−

  貴島 祐治 
  化学と生物 2004
• 植物色素研究法<植物色素研究会編>

  貴島 祐治, 高田 美和子, 桑原 裕之, 佐野 芳雄 (トランスポゾンを利用した花色関連形質の解析)
  大阪公立大学共同出版会 2004
• 植物トランスポゾンの転移機構に関する分子育種学的研究

  貴島 祐治 (植物トランスポゾンの転移機構に関する分子育種学的研究.)
  育種学研究 2001
• トランスポゾンによるキンギョソウの分子遺伝学

  貴島 祐治 (細胞工学」別冊植物細胞工学シリーズ５「植物のゲノムサイエンス」 p.122-131)
  1996
• 植物のゲノムサイエンス

  貴島 祐治 (トランスポゾンによるキンギョソウの分子遺伝学.)
  細胞工学 別冊植物細胞工学シリーズ５ 1996
• Fagopyrum chloroplast genome: construction of physical maps and characterization of unique sequence.

  Aii J, Kishima Y, Adachi T (Fagopyrum chloroplast genome: construction of physical maps and characterization of unique sequence.)
  Current Advances in Buckeat Research 1995
• Blue-light inducible gene expression for betalain pigmentation in the Portulaca cell line

  Adachi T, Kishima Y 
  In: Plant Tissue Culture and Gene Manipulation for Breeding and Formation of Phytochemicals 1992
• Betalain pigmentation manners in flower petal and callus of Portulaca.

  Kishima Y, Shimaya A, Kuroki M, Iki T, Hirai A, Adachi T 
  Proceeding of International Colloquium of Overcoming Breeding Barriers by Means of Plant Biotechnology in Miyazaki 1991

Presentations

• Rice transposable elements reside in specific methylation emvironments of the genome.  [Not invited]

  The 5th International Symposium of Rice Functional Genomics  2007
• Genetic variation in cultured cells of rice: comparative study of natural variation.  [Not invited]

  The 8th International Congress of Plant Molecular Biology  2006
• 植物ゲノムと寄生配列の相互作用  [Not invited]

  日本育種学会第１１０講演会シンポジウム：植物と寄生者との相互作用：理論と機能から育種学へ  2006
• トランスポゾンTam3と宿主の親和的関係  [Not invited]

  日本遺伝学会第７８回大会シンポジウム：栽培植物の遺伝的多様性と転移因子の役割  2006
• 植物の生殖過程を通じたトランスポゾンの動態とゲノム障壁  [Not invited]

  植物生殖過程におけるゲノム障壁遺伝研ワークショップ  2006
• 非エピジェネティックな植物宿主とトランスポゾンの相互関係  [Not invited]

  神戸大学農学部インターゲノミックスセミナー  2006
• The nivea promoter in Antirrhinum passes by the transposon Tam3 insertion.  [Not invited]

  New Dimensions of RNA in Cellular Functions.  2005
• Temperature-dependent transposition of Tam3 is controlled by the nuclear localization of the transposase.  [Not invited]

  15th Antirrhinum meeting  2005

Research Projects

• サブサハラ・アフリカにおける即時的稲品種育成とその普及に関する実証研究

  日本学術振興会：科学研究費助成事業

  Date (from‐to) : 2021/04 -2024/03 

  Author : 近藤 巧, 松田 浩敬, 貴島 祐治
• イネ小胞子に潜在する個体分化能と倍数化能を活用した育種基盤の新構築

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

  Date (from‐to) : 2019/04 -2023/03 

  Author : 貴島 祐治, 山本 敏央, 長岐 清孝, 小出 陽平, 金 鍾明
• 温暖化により新規発病が危惧されるイネツングロ病の抵抗性機構とイネ品種の抵抗性評価

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

  Date (from‐to) : 2013/04 -2014/03 

  Author : 貴島 祐治
• イネの雑種強勢に関する形質指標とゲノム指標の作成

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

  Date (from‐to) : 2011 -2013 

  Author : 貴島 祐治, 高牟禮 逸朗

   

  イネのヘテロシスに関して形質の指標とゲノム指標の作成を目標に研究を行ってきた。形質指標に関しては、従来行われたイネのF1種子に比べ、交雑組み合わせや系統数を大幅に増やし、日本晴に対して、コシヒカリ、Taichung65 (T65)、キタアケ、黒色稲２号(A58)、インディカ系統のIR36、Kasalath、Peiku (#108)、アジア栽培稲の近縁野生種(O. rufipogon)であるW107、W593、W630、アフリカの栽培稲(O. glaberrima)であるWK18、WK21を交配に用いた。組合せは日本晴を基準親として、他の11系統を対応させ、全て相反交雑をした。これら20組み合わせのF1種子を３反復以上で試験することにより、高い精度でイネにおける全体的なヘテロシスの評価を行った。形質調査には、ヘテロシスが現れやすいと言われているF1種子の形質調査を実施し、胚サイズ、種子重量および発芽能について検討した。胚のサイズには交雑の組合せによってヘテロシスが現れ、母性効果と関連している可能性が指摘できた。イネ属内における種間交雑において、インプリンティングが関与した胚乳の発達不良により種子重量が低下することが示唆できた。発芽後3日間シュート長を測定したところ複数の組合せにおいてヘテロシスが確認でき、特に日本晴を雌親としインディカ系統とO.rufipogonおよびO. glaberrimaを雄親とした組合せでは、2日目から3日目のシュートの成長がヘテロシスに対応していることが分かった。ゲノム指標としては、マイクロアレイ解析を実施し、F1個体の葯の反復配列の発現が親に比べて低下することが判明した。以上の結果は、従来のアプローチでは得られない結果であり、本研究の独自の切り口によって明らかになった。研究開始以前の予想とは異なる結論が得られたことも興味深い。
• Functional analysis on endogenous pararetrovirus in rice genome-relationship with rice tungro disease-

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

  Date (from‐to) : 2010 -2012 

  Author : KISHIMA Yuji, KOYANAGI Kanako, YASUI Hideshi

   

  We have addressed two questions as to endogenous RTBV; theinsertion mechanism of ERTBV into rice genome and the relationship between ERTBVand RTBV resistance. ERTBVs are preferentially present in AT-rich repeats in ricegenome, and we described that AT-rich repeats have integrated chromosomal andepisomal DNAs, which would have been suspended in the nucleus. We also identified atolerance allele against RTBV, qTDR5, located on chromosome 5 by the genetic analysesusing the progenies between an African rice strain Oryza glaberrima WK18 and a japonicarice strain Taichung 65. The region in qTDR5 contains an ERTBV sequence.
• Evaluation of the genome stability in the rice cultivars based on indication of the transposable elements

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

  Date (from‐to) : 2006 -2007 

  Author : KISHIMA Yuji

   

  Recently, active transposable elements have been abundantly found in plants. Thus, our understanding in evolutionary aspects has accumulated information on the genetic variations caused by transposable elements. However, most of these genetic variations have been described on the genome diversity during speciation. This study was focused on the genetic variations within the cultivar of rice. We have circumstantial evidence of the transpositions of the rice transposon, m-Ping, within the premier rice cultivar, Koshihikari, which was established more than 50 years ago and wildly distributed in the whole Japan. The Koshihikari samples were collected from 84 locations from Fukushima to 14 prefectures in the North. A total of 36 polymorphisms were observed in these Koshihikari collections by transposon display using m-Ping primers. Among these collections, four were obviously originated from other than Koshihikari because the other transposons also showed the similar polymorphisms with m-Ping. It was strongly assumed that the other 32 types are the m-Ping transpositions, which occurred after the Koshihikari was bred. The results represent that transpositions of the transposons can readily inherit to the next generation, and the produced genetic variations are maintained in the different populations within the same cultivars.
• Studies on agronomic genes in rice.

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

  Date (from‐to) : 2004 -2006 

  Author : SANO Yoshio, KISHIMA Yuji, TAKMURE Itsuro

   

  The objective of this study is to examine why genetic diversity, especially in agronomic traits, is maintained in crop species. To understand ongoing micro-evolutionary processes, genetic alterations in response to temperature (cold resistance), photoperiod (flowering time) and biotic environments (competition with weeds) were investigated in wild and cultivated rice. The adaptive mechanism in these traits was not well explained by a few major genes, suggesting that epistasis, genotype x environment (GE) interaction and linked genes were involved in addition to genes with a small additive effect. The results showed that the presence of epistasis and GE interaction play a significant role for the maintenance of genetic diversity in rice. Genetic diversity is also affected both by current patterns of micro-evolutionary forces, such as gene flow and selection, and by the phylogenetic history. Genealogies of agronomic genes provided insight into their history. Unexpectedly, "Green Revolution" gene (sd1) preexisted in the wild ancestor, showing that farmers have selected it to obtain a high yield in response to altered practices in agriculture. In contrast, in the case of C, A and wx genes, it was indicated that variants have generated from landraces through natural or artificial selection. These results lead us to consider that each of the genes has a unique history, which might reflect on different patterns of natural and/or artificial selection. It seems that farmers have mined the sd1 allele from the wild population and have maintained it in different landraces, while farmers have selected newly arisen mutations from landraces in the case of C, wx and A genes consciously or unconsciously. Therefore, landraces are also expected to preserve agronomically valuable genes, even if a reduction in nucleotide diversity was caused by the population bottleneck due to domestication.
• イネゲノムに内在するウイルス様配列の耐病性付与機能の検証

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

  Date (from‐to) : 2004 -2005 

  Author : 貴島 祐治

   

  本年度はOryza属AAゲノムにおける内在性イネツングロバシリフォルムウイルス(ERTBV)の存在様式に関して調査を行い、以下の2点についてその結果をまとめることができた。 (1)イネ日本晴ゲノムに散在する6つのERTBV断片をはさむプライマーを設計し、PCRによってAAゲノム種34系統における多型の検出を行った。多型の結果から、日本晴と同一のERTBVの挿入はO.sativaやO.rufipogonに集中していることが判ったが、さらにO.sativa内でさえもこのERTBVの挿入に関して多型を検出することができた。一方、サザンハイブリダイゼーション分析によって、O.longistaminataやO.meridionalisゲノムにおいてもO.sativaやO.rufipogonに次ぐ数のERTBV断片が検出されている。従って、ERTBVのイネゲノムに対する挿入はAAゲノム種が種分化した後に起こったと考えられる。かつてウイルスとして存在していたERTBVは、東南アジア周辺域に分布するRTBVに比べてより広範な領域に分布していた可能性が示唆された。 (2)日本晴ゲノムの配列から、ほぼ全てのERTBV断片の末端にATの単純な反復配列(AT-SSR)が配置されていることが明かとなっている。ERTBVの挿入について多型が生じていた系統を対象として塩基配列の比較解析を行った結果、日本晴ゲノムで同定されたAT-SSRより長い同配列がERTBVの代わりに見出された。従って、ERTBVがイネゲノムのAT-SSRを標的にして挿入することが推定された。このAT-SSRは核マトリクス結合配列(MAR)として機能することが予測され、ERTBVはMARに取り込まれた可能性が高い。
• Identification of plant genome segments that change methylation states and its implication for breeding traits

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

  Date (from‐to) : 2003 -2005 

  Author : KISHIMA Yuji, SANO Yoshio

   

  In plants, phenotypic variations have generally been found to be caused by genetic changes. However, it has recently been shown that phenotypic variations can also be potentially caused by epigenetic changes due to aberrant methylation states. Unlike that in mammalian genomes, DNA methylation in the plant genome was found to be heritably maintained during both meiotic and mitotic phases. Therefore, an altered methylation state in a plant genomic segment might be transmitted and maintained in the progeny. This study consists of two parts to identify presence of genetic segments with variable methylation state and to understand its mechanism. Firstly, we surveyed genomic segments that change methylation state among different nine rice strains including Japonica, Indica and wild rices. Second, we analyzed demethylation process in Antirrhinum transposon Tam3, of which activity is tightly controlled by temperature and appears to be correlated with its methylation state. On the first issue, our results showed that the occurrence of epigenetic (epi)-markers in non-polymorphic fragments appeared to be correlated with the genetic distance between any two of the nine rice strains examined. In contrast, the proportion of epi-markers in the total number of fragments, including polymorphic and non-polymorphic fragments, was constant (2-3%) in all the pairs. We assume that the epigenetic differences in methylation among the rice genomes influence certain phenotypic variations. On the second issue, we found that the methylation level of Tam3 in Antirrhinum is regulated by the Tam3 activity. It is the activity of Tam3, which is dependent on the ability of its transposase to bind DNA, which is affected by growing temperature and the methylation/demethylation of Tam3 is the consequence, not the cause, of transposition.
• イネゲノムに内在するウイルス様断片と耐病性との関係解明

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Priority Areas

  Date (from‐to) : 2003 -2003 

  Author : 貴島 祐治, 佐野 芳雄

   

  イネゲノムからイネツングロ・バシリフォーム・ウイルス(RTBV)と相同性を有するRTBV様配列(ERTBV)を見出した。RTBVは東南アジアを中心にヨコバエを媒介してイネに感染し病害を生じる2本鎖DNAからなるパラレトロウイルスである。イネゲノム内のERTBVは高度に再編成が生じているために,同一構造を有する断片は見出されず,また転写産物も検出されなかった。これらのERTBVをReverse-Transcriptase (RT)遺伝子の塩基配列を基に分類すると,断片は3つに明瞭に分かれ,3グループそれぞれで完全なORFを有する約7.5kbのウイルスゲノムが再現できた(ERTBV-A,-Bおよび-C)。ERTBVの最も長いORFにはRTBVのORF3と同一の機能を持つタンパク質遺伝子が同じ順序でコードされていた。この中にはRTタンパク質およびRibonucleaseHタンパク質などが含まれ,これらのタンパク質に必須のアミノ酸モチーフはRTBVとの間でも高度に保存されていた。以上の状況証拠から,ERTBVはイネの祖先種に感染した(今は存在しないあるいは見つけられていない)2本鎖DNAパラレトロウイルスである可能性が高い。RTBVと接触する可能性のあるOryza属植物からは、接する機会の少ないものより,多くのERTBV断片が検出される傾向にあった。ERTBVはアジアに分布するイネ植物種を中心に検出され,アフリカや南米種のイネ属植物では検出されなかった。従って,ERTBVのイネ属植物ゲノムへの挿入は,Oryza属のアフリカや南米種が分化した後からジャポニカ・インディカ系統に分化する前の期間に起こったと考えられた。ERTBV断片の存在程度は,RTBVに対する罹病性の程度と一致した。また,ERTBVのコピー数に応じてゲノムに存在するERTBVのメチル化程度は強い傾向にあることが判明した。
• 高度反復配列MITEを利用したイネゲノム解析法の開発

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

  Date (from‐to) : 2002 -2003 

  Author : 佐野 芳雄, 貴島 祐治

   

  本研究は、イネゲノム内に高頻度に存在する転移性因子MITE (Miniature Inverted Repeat Transposable Elements)の配列を利用したMITE-Transposon display (MITE-TD)がゲノム解析において有用であることを検証する目的で実施した。本年度は、MITE-TDを用いたイネゲノムの高密度連鎖地図を作成した。北海道在来系統の栽培イネA58とインド由来の野生イネW107の交雑によって得られたRILs(F5)79系統を供試材料としてMITE-TD解析をおこなった。これによって得られたMITE-マーカー152個は既知のPCRマーカー114個に矛盾無く対応し、イネゲノム12染色体連鎖群全域にわたってマップされた。また、アジアイネ16系統に関してMITEマーカーにおけるバンドの有無から不一致度を計算し、染色体領域毎のゲノム分化程度を調査した。その結果、栽培イネと野生イネの間に第4染色体長腕末端に不一致度の高いマーカーが認められた。この領域は、栽培種と野生種間の特性の違いを顕著に現わす脱粒性遺伝子が座乗することが知られている。従って同領域がアジアイネの栽培化過程における非脱粒性の獲得に貢献した可能性は高い。こうした事例からも今後、MITE-TDがイネゲノムの比較解析に有用な手段となることが検証できた。
• Identification of mitochondrial male sterility gene and molecular dissection of pollen abortion sugarbeet

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

  Date (from‐to) : 2001 -2003 

  Author : MIKAMI Tetsuo, KUBO Tomohiko, KISHIMA Yuji

   

  We determined the complete nucleotide sequence of the mtDNA from cytoplasmic male sterile sugarbeet (cv.TK81-MS), with the expectation that the data will aid in identifying genes responsible for male sterility. The entire genome comprises 501020 bp. Although the mitochondrial genome of TK81-MS is 130kb larger than the normal fertile mtDNA (TK81-O), there is no difference in the content of identified genes between the two mitochondrial genomes. Most of the additional sequences in TK81-MS mtDNA are composed of sequence duplications and increased intergenic regions of unknown origin. In an attempt to identify the TK81-MS-specific ORF(open reading frame) involved in male sterility, we found that atp6 gene from TK81-MS has a 387-codon presequence which shows no similarity to the presequence of either TK81-O atp6, or any other sequences of TK81-O mtDNA. The TK81-MS atp6 presequence is actually transcribed and translated in the mitochondrion, resulting in the expression of a 35-kDa protein. The variant 35-kDa protein was revealed to be characteristic of the male-sterile mitochondria and to accumulate in flower buds. This study is the first to describe that the atp6 presequence is actually translated in mitochondria and causally related with the male sterility phenotype.
• Positional cloning of fertility restorer genes in sugarbeet and its appliation to molecular breeding

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

  Date (from‐to) : 2000 -2003 

  Author : MIKAMI Tetsuo, TANAKA Masakatsu, KISHIMA Yuji, KUBO Tomohiko, IKEGUCHI Syoujiro

   

  Sugarbeet plants containing the Owenmitochondria encoding cytoplasmic male sterility are fertile if they carry two dominant nuclear restorer genes (RfX and RfZ). In order to understand the molecular mechanism of fertility restoration mediated by RfX and RfZ, we decided to clone RfX using a positional cloning strategy. Bulked segregant analysis was utilized to identify RAPD and AFLP markers linked to the RfX locus. Out of 812 RADP markers examined, the closest marker was observed to be located 5.7cM away from RfX. A total of 2721 AFLP primer combinations were further tested for polymorphisms, which allows the screening of approximately 27000 loci for linkage to RfX. We obtained eight markers tightly linked to the RfX locus which was restricted within 3.4cM by these markers. It should also be mentioned that three AFLP markers co-segregated with the RfX locus. A sugarbeet BAC library (3.4 genome equivalents), with an average insert size of 98kb, was constructed and screened with the linked markers. The target region around RfX comprises approximately 300kb and is covered with a minimum of eight BAC clones. By nucleotide suquencing and RT-PCR analysis, we identified some open reading frames within the 300kb-region, which were observed to be actively transcribed in anther tissues and to have mitochondrial targeting sequences. It thus seems reasonable to consider that one of the reading frames identified here is a good candidate for RfX gene.
• イネゲノムに見出されたツングロウイルスゲノム断片の構造と機能に関する分子的基礎

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Priority Areas

  Date (from‐to) : 2001 -2002 

  Author : 貴島 祐治, 佐野 芳雄

   

  1.イネゲノムに内在するRTBV様配列の構造 イネゲノムのデータベースやライブラリーのスクリーニングから内在するRTBV様配列(ERTBV)を単離し,合計18断片の構造を解析した。これらの断片はRTBVのORF3(最も長いORF)と相同部位を持つ。ERTBVの断片間では高度に再編成が生じていたが,塩基配列のレベルでは全体的に高い相同性(90%以上)を示していた。再編成部位を順々に並べ換えた結果,約7.5kbの環状構造を有する配列が再構築された。 2.ERTBVのウイルス様構造 これら3つのグループごとにコンセンサス配列を選んで塩基配列を組み直すと,3つのグループそれぞれで完全なORFを有する約7.5kbのウイルスゲノムが再現できた。3つグループの配列は似た構造からなるが,塩基レベルでは構造の違いが区別でき,ERTBV-A,-Bおよび-Cとした。ERTBVの最も長いORFにはRTBVのORF3と同一の機能を持つタンパク質遺伝子が同じ順序でコードされていた。ERTBV-A,-BおよびCは過去に存在した2本鎖DNAウイルスで現在のイネの祖先種に感染し,ウイルスの環状配列が,ゲノムへ挿入した時に逆位等の再編成が生じ,現在のERTBV断片が発生したと推定できた。また,RTBVウイルスゲノムは植物ゲノムに比べ,140倍の速さで進化していると推定できた。 3.ERTBVとイネ属植物の種分化 ERTBVの3つのグループそれぞれにジャポニカ系統およびインディカ系統で得られたERTBV断片が存在することから、ERTBVはO. sativaの分化以前に挿入していたと考えて間違いない。また,ハイブリダイゼーション実験からERTBVはアジアに分布するイネ植物種を中心に検出され,アフリカや南米種のイネ属植物では検出されなかった。従って,ERTBVのイネ属植物ゲノムヘの挿入は,Oryza属のアフリカや南米種が分化した後からジャポニカ・インディカ系統に分化する前の期間に起こったと考えられる。
• Comparative genetics of pigmentation patterns due to multiple alleles at the C gene in cultivated rice

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

  Date (from‐to) : 2001 -2002 

  Author : SANO Yoshio, TAKAMURE Itsuro, KISHIMA Yuji

   

  Diverged phenotypes is often detected in domesticated plants despite invariant phenotypes in their wild forms. One of an example in rice is observed in varying degrees of apiculus coloration due to anthocyanin pigmentation which was previously reported to be caused by a series of alleles in the C locus. The present study revealed, based on their comparative map, that a possible candidate of the C gene is the rice homologue (OsCl) of the maize Cl that belongs to the group of R2R3-Myb factors. Two different types of deletions causing a frameshift were detected in the 3rd exon and both the deleted nucleotides were corresponding to the positions of putative base-contacting residues, suggesting that Indica and Japocia types carries mutations of loss of function with their independent origins. In addition, replacement substitutions were frequently detected in OsCl of strains carrying the previously defined C alleles. Molecular population analysis revealed that 17 haplotypes were found in 39 wild and cultivated rice and haplotypes of cultivated forms were mostly included into one of the three distinct groups, showing few shared haplotypes between taxa including Indica an Japonica types. The genealogy of the OsCl gene suggested that allelic diversification causing phenotypic change possibly resulted from mutations in the coding region rather than from recombination between pre-existing alleles. The changes in amino acids might be associated with selective forces that took places in the lineage of O. sativa as supported by a Ka/Ks ratio higher than 1.0, which gives a significant implication on genetic diversity in landraces.
• Molecular basis on the regulation of methylation that controls transposition of the plant transposons

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

  Date (from‐to) : 2001 -2002 

  Author : KISHIMA Yuji

   

  The transposition frequency of Tam3 in Antirrhinum, unlike that of most other cut-and-paste type transposons, is tightly controlled by temperature : Tam3 transposes rarely at 25℃, but much more frequently at 15℃. Here we studied the mechanism of the low-temperature-dependent transposition (LTDT) of Tam3. Our results strongly suggest that LTDT is not likely to be due to either transcriptional regulation or posttranscriptional regulation of the Tam3 Tpase gene. We found that temperature shift induced a remarkable change of the methylation state unique to Tam3 sequences in the genome : higher temperature resulted in hypermethylation, while lower temperature resulted in reduced methylation. The methylation state was reversible within a single generation in response to a temperature shift. Although our data demonstrate a close link between LTDT and the methylation of Tam3, they also suggest that secondary factor(s) other than DNA methylation is involved in repression of Tam3 transposition.
• Molecular analysis of genetic diversity in natural populations of beech species

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

  Date (from‐to) : 1999 -2000 

  Author : MIKAMI Tetsuo, KUBO Tomohiko, KISHIMA Yuji, KOIKE Takayoshi

   

  The amount and distribution of mitochondrial (mt) DNA restriction fragment length polymorphism was determined among individual tree samples of two Japanese beech species, Fagus crenata and F.japonica. Individual plants were collected from 16 F.crenata populations throughout the range of the species, and from three F.japonica populations. We detected enough variation to characterize eleven and three chondriome types in F.crenata and F.japonica, respectively. The grouping of beech chondriome types based upon the cladistic analysis of mtDNA polymorphism allowed us to recognize the apparent geographical patterns of mtDNA diversity : the resulting three main groups occupied distinct geographic areas. This geographic differentiation is likely to reflect the history of the Japanese beech forests after the last glacial period of the Pleistocene. In addition, the mtDNA polymorphism encountered within F.crenata encompassed all the variation observed in F.japonica. Our result suggests the need for re-evaluation of their phylogenetic relationships. MtDNA restriction fragment length polymorphisms were also used to examine cytoplasmic diversity within a relic-like population of F.hayatae, located in northern Taiwan. The analysis failed to reveal any polymorphisms, an observation that suggests cytoplasmic uniformity in the F.hayatae population examined. It is also interesting to note that the chondriome type of our F.hayatae samples is very close to that characteristic of F.crenata populations in the southernmost area of Japan.
• Function of a short spacer between rice EPSP synthase and rps20 genes.

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

  Date (from‐to) : 1999 -2000 

  Author : KISHIMA Yuji

   

  We mapped the fragments with sequence (s) expressed in the rice callus onto a physical map for a 328-kb BAC contig around the rice waxy locus. Among the hybridized fragments, we attempted to characterize strongly hybridized fragments located in a region about 45 kb downstream of waxy. The fragments were found to contain two housekeeping genes encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPs) and ribosomal protein small subunit 20 (rps20). Interestingly, these housekeeping genes are adjoined, with only a 303-bp spacer, and are directed in a tail-to-tail orientation. Nearly-full-length cDNA clones of the two genes were obtained by screening the callus cDNA library. A clone for the EPSPs gene possessed an open reading frame of 1683 bp encoding a deduced 561-amino-acid (aa) polypeptide that is the first expressed gene identified in rice using this method. EPSPs is a key enzynae on the shikimate pathway and is localized in the plastids of higher plants. This enzyme is known to be targeted by glyphosate, which has been employed as a nonselective herbicide. A gene for the rice rps20 peptide had previously been isolated, and our rps2O cDNA clone completely matched the registered sequence for this peptide. Northern blotting analyses were conducted using blots of total RNAs extracted from roots, seedlings, spikelets and anthers of Japonica and Indica rice strains. The 2.2-kb transcript of the EPSPs gene was easily detected in RNA samples from roots, seedlings and spikelets, but not the RNA from anthers. A 0.75-kb rps20 transcript was detected in all the tissues we examined, although the expression in roots from both rice strains was very weak. We have examined an extent of the transcript of either gene. These transcripts proceeded beyond the spacer ; the expression of the other gene might be modified by the antisense RNA from the opposite gene, resulting in double-stranded RNA, which might act as a trigger for RNA degradation in the mechanism called post-transcriptional gene silencing. The short spacer found here is uncommon in the nuclear gene organization in higher plants. This segment may have evolutionary implications about spacer expansion or contraction in the plant nuclear genome, and may play a role in gene regulation caused by the opposite gene transcript.
• Studies on the differentiation of genepools in rice

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

  Date (from‐to) : 1997 -2000 

  Author : SANO Yoshio, KANAZAWA Akira, INUKAI Tsuyoshi, KISHIMA Yuji

   

  Plant breeding is mainly to select favorable gene combinations from naturally occurring variants through hybridization. Since species have the primary genepool which is used as the genetic materials for their adaptation, the differential genepool is closely related with the difficulties in hybridization breeding. The objectives of the present study is to reveal the differentiated genepool among rice taxa and to examine the causal factors. The genic diversity was examined regarding to Wx and C genes controlling amylose content and anthocyanin coloration since these variations are distinct among cultivars than in wild relative regardless of the genetic bottleneck effects during the rice domestication. Sequence data of the Wx gene revealed that at least 5 alleles have been established after the domestication. The alleles resulted from frameshifts and changes in RNA processing and amino acids. The C gene showing allelic diversity in rice cultivars was found to be the homolog of maize cl encoding Myb-like protein. Sequence data showed that the frequency of non-synonymous mutations was high in the C of rice cultivars than the wild progenitor, indicating that such alteration in C might have been positively selected for during the domestication process. The internal barriers were also examined since they act as the mechanism of differentiated genepools. A hybrid sterility gene, S10, was located near wx and the candidate was detected by fine mapping and gene expression. In addition, at least 3 genes on chromosome 6 were found to play a significant role for cross-incompatibity in rice. The results will contribute for their molecular clonning to figure out their molecular evolution during the differentiation of genepools in rice.
• キンギョソウ・トランスポゾンTam3の温度依存性転移機構の分子遺伝学的解析

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

  Date (from‐to) : 1997 -1998 

  Author : 貴島 祐治

   

  キンギョソウの2つの系統HAM2とHAM5はともにCHSをコードする色素合成遺伝子のブロモータにトランスポゾンTam3を配置した対立遺伝子をホモ接合型で有している。Tam3は高温(25℃)に対して低温(15℃)での切り出し頻度が1000倍高い。従って、低温では両者ともに斑入り形質を現す。一方、高温のHAM2は花弁に赤いバックグラウンド色が観察されるが、HAM5は白色花弁である。今回、この高温での花色発現の違いとTam3の温度依存性転移との関連性をCHS遺伝子の発現に着目し調査した。 ノーザンハイブリダイゼーションの結果、HAM2とHAM5の違いはCHS遺伝子の発現量の差によるものであることが判明した。両系統のCHS遺伝子座に挿入したTam3の切り出しの挙動は、ともに低温で著しく活発になるが、高温では抑えられていた。また、CHS対立遺伝子の構造はTam3挿入部位を含め両系統で差は見られなかった。niv遺伝子の転写開始点も両系統とも野生型と同一であった。以上の結果より、HAM2とHAM5の高温での花色形質の違いは、nivの転写活性に依存し、その制御にはトランス因子が関与することが示唆された。 このCHS対立遺伝子のプロモーター活性をトランジェントアッセイにより調査した。CHSプロモーターのTam3挿入部位(転写開始点より71bp上流)より下流の配列だけではniv遺伝子の転写が起こらなかった。CHS遺伝子の転写は、Tam3の2658bpから721bpの間で最も活性化された。一方、721bpから265bpの間にはその活性を下げる領域があり、下げ幅はHAM2に比べHAM5で著しいことがわかった。このことから、当CHS対立遺伝子の転写はプロモーター域に存在するTam3の内部配列がシス因子として機能していると推定された。
• キンギョソウ・トランスポゾンTam3に対する転移抑制遺伝子の機能解析

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

  Date (from‐to) : 1996 -1996 

  Author : 貴島 祐治

   

  本研究では、キンギョソウのトランスポゾンTam3の転移を抑制すると考えられているStabilizer遺伝子の機能について調査した。まず、キンギョソウの斑入花系統(HAM5)よりゲノミックライブラリーを作成し、その中からTam3をプローブに99個のクローンを選抜した。得られたクローンはTam3との相同性を確認後、Tam3トランスポゾンの内部およびその周辺域の構造解析に供試された。各クローンのTam3コピーの比較の結果、Tam3ファミリーには構造的特徴として変異の著しい領域と保存性の高い領域のあることが明らかとなった。変異の著しい領域はTam3の両端に位置し、そこはトランスポゼ-ス結合部位として知られているサブターミナルリピートが含まれる。また、変異領域の範囲はループ形成部位と一致することから、構造変異がループ形成と関連する可能性の高いことが示唆できた。保存性の高い領域はトランスポゼ-スをコードする部位を中心に約2.5kbpの範囲にわたっていた。これらのコピーの中で可動性あるいは非可動性が明確になったものはそれぞれ、7および6コピーで全体の約半数のコピーは染色体に固定され転移活性を失っているもの考えられる。 次に、Stabilizer遺伝子の効果を前述のHAM5系統と遺伝的背景を同じくし、Stabilizer遺伝子を付加したHAM3系統を使って調査した。Stabilizerを有するHAM3系統の花弁では斑の形成が少ないことからこの遺伝子はトランスポゾンの転移を抑える効果をもつとされる。本研究では、先にHAM5より単離したTam3コピーを同様に有するHAM3系統において、各コピーの転移挙動をHAM5と比較した。その結果Stabilizerの効果が認められるコピー(HAM5に対しHAM3ではTam3の転移が検出されない)と効果が認められないコピー(Tam3の転移が検出される)の両方が存在した。従って、Stabilizer遺伝子は選択的にTam3コピーの転移挙動を制御していることが示唆できた。今後、Stabilizerの転移制御とその選択性について詳細な調査を行う必要がある。
• キンギョソウ・トランスポゾンTem3の転移活性が形質変異に及ぼす影響

  日本学術振興会：科学研究費助成事業

  Date (from‐to) : 1995 -1995 

  Author : 貴島 祐治

   

  Nivea^はアントシアン色素生合成の鍵酵素となる遺伝子座Niveaのプロモーター部位にTam3が挿入した対立遺伝子である。このNivea^はTam3の転移によって白花から斑入り花を生じる。この花弁の斑の発生頻度は温度や転移抑制遺伝子の有無などによっても異なってくる。本研究では斑入り花個体(Nivea^)と斑入り抑制個体(Stabilizer/Nivea^)およびwild type系統からゲノミックライブラリーをそれぞれ作成し、各ライブラリーよりTam3コピーの単離を試みた。その結果、今までにTam3に相同な配列を含む合計50個のクローンを精製した。得られたクローンについてはTam3近傍配列をTAIL-PCRによって増幅し、これをプローブに各コピーの転移挙動をRFLPやPCRによって調査した。その結果以下3つの知見を得た。1)Tam3はキンギョソウの染色体に散在している。2)Niveaなどの易変遺伝子座以外の多くのTam3コピーでも転移している。3)いくつかのTam3コピーについては例外的に染色体に固定され転移不能となっている可能性がある。 さらにTam3の転移活性に影響を及ぼす温度や転移抑制遺伝子以外の他の因子の存在についても調査した。同じNivea^を持つ2つの異なる系統HAM2およびHAM5について温度を一定にして斑の発生を観察するとHAM2はHAM5に対して顕著に多くの色素を生じていることが認められた。これはおそらく2系統の遺伝的差異によってTam3の切り出し活性に違いが生じたものと考えられるので両系統のF1種子を採り、これに関わる因子について遺伝学的調査を進めることにしている。
• 配偶体形成におけるキンギョソウ・トランスポゾンの転移機構

  日本学術振興会：科学研究費助成事業

  Date (from‐to) : 1995 -1995 

  Author : 貴島 裕治

   

  本年度は斑入り花個体(Nivea^)と斑入り抑制個体(Stabilizer/Nivea^)およびwild type系統からゲノミックライブラリーをそれぞれ作成し、各ライブラリーよりTam3コピーの単離を試みた。その結果、今までにTam3に相同な配列を含む合計50個のクローンを精製した。得られたクローンについてはTam3近傍配列をTAIL-PCRによって増幅し、これをプローブに各コピーの転移挙動をRFLPやPCRによって調査を進めている。また、配偶体で特異的に切り出されるコピーを特定するためには、各系統の自殖後代が必要なのでそのためのF1種子の採種も行った。一方単離されたクローンを用いて、キンギョソウの異なる系統間で共通したDNA断片に挿入しているTam3コピーの候補を見出した。このようなTam3は何らかの原因で染色体に固定され、転移不能になったと考えられる。現在、その近傍配列の構造解析を進めている。トランスポゾンの配偶子での転移を詳しく調査するためには、体細胞での転移と区別することが重要となる。そこで今年度はNivea^の自殖後代を採取した。本実験はTam3がNivea遺伝子座から切り出される時、体細胞で起こったものが生殖細胞に伝達されると、その自殖後代ではすべて復帰型変異花弁を持つことになる。これに対して、生殖細胞で転移すると一部の個体しか復帰しないことを期待して行ったものである。今後Nivea^後代の花色を観察し、体細胞および配偶体レベルでの転移の頻度を明らかにした上でTam3の転移によって生じた両レベルにおけるNivea遺伝子座の構造変異についても解析を加える予定である。
• Joint Study on Post-Translational Protein Tyrosine Sulfation

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 1994 -1995 

  Author : SUIKO Masahito, LIU Chau-ching, LIU Ming-cheh, ETO Nozomu, NISHIYAMA Kazuo

   

  The sulfation of protein is a post-translational modification by covalent attachment of sulfate. Among a number of possible funcitonal roles that have been proposed, the involvement of tyrosine sulfation in intracellular protein sorting and transport received strong support from our recent finding of Golgi located 175 k Da membrane-bound tyrosine-O-sulfate binding protein from bovine liver.Here we described the bindingproperties fo the tyrosine-O-sulfate (TyrS) receptor. TyrS receptor was highly purified from bovine liver using a combination of TyrS-Affi-gel 10 affinity chromatography, hydroxylapatite chromatography and electroelution. The purified receptor exhibited an apparent molecular weight of 175k Da as determined by SDS-PAGE under reducing conditions. We established mouse monoclonal antibodies reactive to the purified receptor using P3-X63-Ag8-Ul cells as fusion partner cells. Two stable hybridoma clone secreting anti TyrS receptor monoclonal antibodies were obtained (R3-1, R2-4). We analyzed for the binding against TyrS,after solubilization the membrane-bound protein containing TyrS receptor. Trypsin was added to the suspension and the mixture was digested. To examine the ligand binding specificity, the reaction mixtures were incubated with TyrS-Affi-Gel 10.Then we analyzed by SDS-PAGE.It was apparent that three fragments of 65k, 63k and 59k Da have the ability to bind against TyrS. TyrS receptor migrated as double protein bands with apparent molecular weights of ca. 175K upon SDS-PAGE.In order to obtain information concerning the sturctural form of these proteins and three fragments we investigated V8 peptide maps. Partial V8 protease mapping of these TyrS receptor were similar showing the homology. TyrS is a glycoprotein which has N-liked carbohydrate chain. So, TyrS receptor variously trimmed their carbohydrate chains by glycosidase showing the change of reactivity or loss of the ability to bind against TyrS. It is concluded that TyrS receptor is a glycoprotein which is having a molecular weight of 175 K.The N linked carbohydrate residue of this protein is very important in recognition of the TyrS and has a functional contribution in receptor activity.
• Improving genetic resources and food manufacture by biotechnology

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 1992 -1994 

  Author : ADACHI Taiji, BOHANEC Borut, AKASHI Ryo, TAKAKI Hiroshi, SUIKO Masahito, KISHIMA Yuji, YABUYA Tsutomu, NISHIYAMA Kazuo, LUTHER Zulata, JAVORNIK Branka, KREFT Ivan

   

  This project has developed to be held an International Colloquium on "Impact of Plant Biotechnology on Agriculture" in the final year 1994. We have very close collaboration in research work between University of Ljubljana and Miyazaki University under the auspecies of the Ministry of Agriculture and Forestry of the Republic of Slovenia. The fruits of the collaboration are to some extent described in the Proceedings (which is attached in this report). Some one would be very excellent paper, for example the complementary application of conventional but standard breeding techniques and mordern biotechnology tools in buckwheat genetic improvement program in crops, especially in buckwheat appear to be indispensable for the achievement of effective breeding goals. This is evident from the results so far obtaind from studies on dimorphic heterostylism and incompatibility, developmental analysis of embryo abortion, inheritance of some physical traits and interspecific hybridization and cybridization. The theme of this project should be continue in future with another financial help, if possible. I would like to end by thanking colleagues and higher officers which concern this works.
• Genetic variations underlying phenotypic variations in plants

  Date (from‐to) : 1994
• Comparison of agronomic and chemical properties of new variety of autotetraploid buckwheat.

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 1990 -1991 

  Author : ADACHI Taiji, NISHIYAMA Kazuo, MIURA Michio, KISHIMA Yuji, YABUYA Tsutomu

   

  The head investigator and others have developed and released to register the autotetraploid buckwheat variety, 'Miyazaki-ootsubu'. The new variety was adopted to cultivate in the Southwestern Japan, i. e. Miyazaki, Kagoshina and Tokushina prefectures, as a leading variety. The new cultivar was to be settled the agronomic performance and chemical properties. Fatty acids were compared among four varieties and two growing regions. Boron effect on seed fertility was recognized.
• Overcoming Breeding Barriers by Means of Plant Biotechnology

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 1988 -1990 

  Author : ADACHI Taiji, BOHANEC Borut, IKEDA Hajime, TAKAKI Hiroshi, SUIKO Masahito, KISHIMA Yuji, YABUYA Tsutomu, NESKOVIC Miraelina, OSORNIK Boris, BRANKA Javornik, KREFT Ivan

   

  International collaboration between Miyazaki Univ., Faculty of Agric. And University of Ljubljana, Biotechnical Faculty has developed as these faculties became sister schools under the financial support entitled " Overcoming breeding barriers by means of plant biotechnology. Under the following categories some approaches have performed. 1) DNA transfer or genetic engineering, 2) chromosomal engineering for the introduction of alien genes, 3) Cellular handling including somatic fusion, 4) Clonal proliferation at tissue level. Protoplasts were isolated from two apomictic species of Paspalum dilatatum and Panicum maximum. Protoplast division and colony formation were found to be effective. Attempts of protoplast fusion between both species were succeeded to form hybrid callus. Preliminary work has been carried out on the tyrosine sulfation of protein in higher plants using callus. Tyrosylprotein sulfotransferase from the bovine liver Golgi was considered as a guide line for this study. No protein sulfation could be, however, observed in higher plants under the experimental conditions. The chromosome association of amphidiploids of Iris laevigata x I. ensata were analysed and compared with that of the parental species and F_1 hybrids. These interspecific cross-breeding strategy was discussed. To evaluate the yielding ability of buckwheat varieties, selections and crosses a new experimental approach was designed based on a comparison of the expected and actual yields of a certain plot. Haploid plant have been induced by in vitro culture techniques in many species. This methods were applied to buckwheat genetics and breeding studies. Isolation, identification and determination of glucosamine were performed in callus of potato. Accumulation of glucosamine was observed in aged-callus, and was particularly evident in the SDS-insoluble and soluble fractions. It is speculated that in aged-callus, structural components of the cell may be cemented by glucosamine.
• STUDIES ON GENETIC MANIPULATIONS OF FLOWER COLOR USING PLANT PROTOPLASTS.

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 1988 -1989 

  Author : ADACHI Taiji, KISHIMA Yuji

   

  In order to develop genetic manipulations in crops by means of biotechnology, we have to investigate with a model system. Biogenesis of betalain pigments is available not only for a genetical analysis of flower color but also for a biotechnological approach to secondary metabolites in plants. Portulaca is acceptable as an ideal plant which allows 1) genetical analysis, 2) in vitro culture and 3) interesting secondary metabolites. In this project, protoplast isolation was established with some parts of plant in the genus Portulaca. Micro analytical method was developed for testing betalain biogenesis during tissue culture. The actions of four genes were set up in the biosynthetic process of betalains. These genotypes were compared with protein constitutions during developmental stages. Some target proteins were specified, but further analysis and genetic approach for improvement were still remained

Industrial Property Rights

• 特願2010-64232:イネコシヒカリの産地判別用プライマーセット及びイネコシヒカリの産地判別方法  2010年/03/19

  貴島 祐治
• 特開2004-121032:イネの個体識別方法及びトランスポゾンを含む塩基配列  2004/04/22

  貴島 祐治  

  2002-286628
• 核移行に対する阻害活性を有するタンパク質およびこれを用いたタンパク質の核移行制御方法

  2005-046553