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研究者情報

マスター

アカウント（マスター）

  • 氏名

    小出　陽平(コイデ　ヨウヘイ), コイデ　ヨウヘイ

所属（マスター）

  • 農学研究院　基盤研究部門　応用生命科学分野

所属（マスター）

  • 農学研究院　基盤研究部門　応用生命科学分野

独自項目

syllabus

  • 2021, 生物学概論, Introduction to Biolgy, 学士課程, 農学部, 基礎生物学，作物学，生理・組織細胞学，形態学，系統学・分類学，遺伝学，生態学・行動学，分子生物学、畜産学
  • 2021, 植物育種学Ⅰ, Plant Breeding I, 学士課程, 農学部, 植物，育種，遺伝，変異，ゲノム，形質，自殖性，他殖性
  • 2021, 応用生命科学概論, Introduction to Applied Biosciences, 学士課程, 農学部, 応用生命科学，植物育種学，遺伝子制御学，応用分子昆虫学，分子生物学，分子酵素学，生態化学生物学，分子環境生物学，生物情報分子解析学，ゲノム生化学
  • 2021, 植物育種学Ⅱ, Plant Breeding II, 学士課程, 農学部, 植物、育種、遺伝、形質、ゲノム
  • 2021, 応用生命科学演習Ⅰ, Seminar in Applied Bioscience Ⅰ, 学士課程, 農学部, 応用生命科学，分子生物学，応用分子昆虫学，分子酵素学，遺伝子制御学，生態化学生物学，植物育種学，分子環境生物科学，生物情報分子解析学，ゲノム生化学
  • 2021, 生物学実験, Laboratory Work on Biology, 学士課程, 農学部, 顕微鏡操作，形態，組織，染色体，無菌飼育，遺伝子分析

researchmap

プロフィール情報

学位

  • 博士（農学）（北海道大学）

プロフィール情報

  • 姓

    小出, コイデ

  • 名

    陽平, ヨウヘイ

  • ID各種

    201301062956609018

業績リスト

研究キーワード

  • アフリカイネ   雑種不稔   イネ   

研究分野

  • 環境・農学 / 遺伝育種科学

経歴

  • 2017年07月 - 2018年03月 ジョンイネスセンター Visiting Collaborator
  • 2013年04月 - 2016年03月 京都大学白眉センター 特定助教
  • 2010年04月 - 2013年03月 国際農林水産業研究センター 日本学術振興会PD
  • 2008年04月 - 2010年03月 国際稲研究所 Visiting Research Fellow

受賞

  • 2019年03月 日本育種学会奨励賞
     
    受賞者: 小出 陽平
  • 2018年11月 第17回日本農学進歩賞
     
    受賞者: 小出 陽平
  • 2018年09月 第134回講演会日本育種学会優秀発表賞
     
    受賞者: 小出 陽平

論文

  • Daichi Kuniyoshi, Megumi Ishihara, Koichi Yamamori, Yohei Koide, Yuji Kishima
    Genetics 2024年06月28日 
    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.
  • 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年05月17日 [査読有り]
     
    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.
  • Yoshiki Tokuyama, Miku Omachi, Shiori Kushida, Kiwamu Hikichi, Shuhei Okada, Kazumitsu Onishi, Takashige Ishii, Yuji Kishima, Yohei Koide
    Planta 259 1 19 - 19 2023年12月12日 [査読有り]
     
    PROG1 is necessary but insufficient for the main culm inclination while TAC1 partially takes part in it, and both genes promote tiller inclination in Asian wild rice. Asian wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), has a prostrate architecture, with tillers branching from near the ground. The main culm of each plant grows upward and then tilts during the vegetative stage. Genes controlling tiller angle have been reported; however, their genetic contributions to the culm movement have not been quantified. Here, we quantified their genetic contributions to angular kinematics in the main culm and tillers. For the main culm inclination, one major QTL surrounding the PROG1 region was found. In cultivated rice, tillers firstly inclined and lately rose, while it kept inclining in wild rice. It was suggested that PROG1 affected the tiller elevation angle in the later kinematics, whereas TAC1 was weakly associated with the tiller angle in the whole vegetative stage. Micro-computed tomography (micro-CT) suggested that these angular changes are produced by the bending of culm bases. Because near-isogenic lines (NILs) of wild rice-type Prog1 and Tac1 alleles in the genetic background of cultivated rice did not show the prostrate architecture, the involvement of another gene(s) for inclination of the main culm was suggested. Our findings will not only contribute to the understanding of the morphological transition during domestication but also be used in plant breeding to precisely reproduce the ideal plant architecture by combining the effects of multiple genes.
  • 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年12月 [査読有り]
     
    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.
  • 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年 [査読有り]
     
    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.
  • 石川 亮, 山形 悦透, 小出 陽平, 石井 尊生, 石川 隆二, 秋本 正博, 津田 勝利, 藤田 大輔
    育種学研究 advpub 日本育種学会 2023年
  • 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年12月18日 [査読有り]
     
    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.
  • Shasha Wang, Yohei Koide, Yuji Kishima
    Genes & genetic systems 97 4 177 - 184 2022年12月17日 [査読有り]
     
    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.
  • Yoshimichi Fukuta, Yohei Koide, Nobuya Kobayashi, Hiroshi Kato, Hiroki Saito, Mary Jeanie Telebanco‐Yanoria, Leodegario A. Ebron, Doris Mercado‐Escueta, Hiroshi Tsunematsu, Ikuo Ando, Daisuke Fujita, Mitsuhiro Obara, Asami Tomita, Nagao Hayashi, Tokio Imbe
    Plant Breeding 141 5 609 - 620 2022年10月 [査読有り]
  • Yoshimichi Fukuta, Mary Jeanie Telebanco-Yanoria, Yohei Koide, Hiroki Saito, Nobuya Kobayashi, Mitsuhiro Obara, Seiji Yanagihara
    Field Crops Research 282 108506 - 108506 2022年06月 [査読有り]
  • Daisuke Fujita, Analiza G. Tagle, Yohei Koide, Eliza V. Simon, Yoshimichi Fukuta, Tsutomu Ishimaru, Nobuya Kobayashi
    Euphytica 218 5 2022年05月 [査読有り]
  • Elias G. Balimponya, Maria S. Dwiyanti, Toshiaki Ito, Shuntaro Sakaguchi, Koichi Yamamori, Yoshitaka Kanaoka, Yohei Koide, Yoshifumi Nagayoshi, Yuji Kishima
    Breeding Science 2022年 [査読有り]
  • Zin Mar Myint, Yohei Koide
    Frontiers in plant science 13 898206 - 898206 2022年 [査読有り]
     
    Hybrid sterility genes define species identities, setting reproductive barriers between distantly related Oryza relatives. They induce allelic-specific selective gametic abnormalities by killing pollens, embryo sacs, or both, and thus resulting in the male specific transmission ratio distortion (mTRD), female specific transmission ratio distortion (f TRD), and/or sex-independent transmission ratio distortion (siTRD) in hybrids. Although more than 50 hybrid sterility genes have been reported, comprehensive analysis on the distributional pattern of TRD systems in Oryza species is limited. In this review, we surveyed the TRD systems and the underlying possible mechanisms in these species. In rice, pollen killers which cause mTRD are often observed in higher frequency than egg killers and gamete eliminators, which are factors affecting f TRD and siTRD, respectively. Due to the rather massive population of pollen grains, their reduction in the number caused by hybrid sterility possesses a smaller selective disadvantage to the hybrid individuals, in contrast to female gamete abortion. The pattern of TRD distribution displays less abundancy in siTRD. It suggests that fixation of siTRD might require a certain time rather than single sex-specific factors. The presence of linked sterility factors worked for mTRD and f TRD, and strength of their linkage in chromosomal regions might determine the type of sterility and TRD. The study of TRD systems has a potential to reveal the relationships between selfish genes and their functions for reproductive isolation.
  • Yohei Koide, Kazuki Matsubara, Dayun Tao, Kenneth L McNally
    Frontiers in plant science 13 974613 - 974613 2022年
  • Koichi Yamamori, Kei Ogasawara, Seiya Ishiguro, Yohei Koide, Itsuro Takamure, Kaien Fujino, Yutaka Sato, Yuji Kishima
    Annals of botany 128 5 559 - 575 2021年07月07日 [査読有り]
     
    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.
  • Yoshiki Tokuyama, Yohei Koide, Kazumitsu Onishi, Kiwamu Hikichi, Miku Omachi, Itsuro Takamure, Yuji Kishima
    in silico Plants 3 2 2021年07月01日 [査読有り]
     
    Abstract 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.
  • Myint Zin Mar, Yohei Koide, Mei Ogata, Daichi Kuniyoshi, Yoshiki Tokuyama, Kiwamu Hikichi, Mitsuhiro Obara, Yuji Kishima
    AGRICULTURE-BASEL 11 3 2021年03月 [査読有り]
     
    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.
  • Dayun Tao, Kenneth L McNally, Yohei Koide, Kazuki Matsubara
    Frontiers in plant science 12 699761 - 699761 2021年
  • Yohei Koide, Daichi Kuniyoshi, Yuji Kishima
    FRONTIERS IN PLANT SCIENCE 11 2020年08月 [査読有り]
     
    Ploidy manipulation is an efficient technique for the development of novel phenotypes in plant breeding. However, in rice (Oryza sativaL.), 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.
  • Yohei Koide
    Molecular plant 2020年02月24日 [査読有り][招待有り]
  • 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年 [査読有り]
     
    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.
  • Birendra Bahadur Rana, Misa Kamimukai, Mukunda Bhattarai, Yohei Koide, Masayuki Murai
    Hereditas 156 2019年12月18日 [査読有り][通常論文]
     
    © 2019 The Author(s). Background: Heading time is an important trait for regional and seasonal adaptabilities in rice, and is controlled by genetic factors in relation with environmental factors, mainly day length and temperature. The following genes controlling heading were examined for their responses to six different environmental conditions involving different day lengths using five early near-isogenic lines (NILs) of T65-R and three late NILs of T65wx: two earliness genes, Ef1 and Efx controlling basic vegetative phase (BVG), and m-Ef1, the enhancer to the former gene; and two lateness genes, Se1-pat(t) and se-pat controlling photo-sensitivity and BVG, respectively. T65-R and T65-T were different accessions of Taichung 65. T65wx is a NIL of T65-T carrying wx. Results: The five early NILs of T65-R were in the order of ER50 (Ef1, Efx, m-Ef1) < ER40 (Ef1, m-Ef1) ≤ ER20 (Ef1, Efx) < ER1 (Ef1) ≤ ER21 (Efx) < T65-R regarding days to heading (DTH) under two spring-sowing and one summer-sowing paddy field (PF) conditions. The three late NILs of T65wx were in the order of LF3 (Se1-pat(t)) ≤ LF2 (Se1-pat(t), se-pat) ≤ T65wx < LF1 (se-pat) under two short-day conditions (10-h photoperiod condition with artificial-light and natural short-day condition from autumn to winter). The NILs and T65wx were in the order of T65wx < LF3 < LF1 < LF2 under the two spring-sowing PF (long day) conditions. T65-R (Ac-ef1) was 2.8 or 5.1 days earlier in DTH than T65-T (ac-ef1) under the two spring-sowing PF conditions. However, T65-R was 19 and 10 days earlier than T65-T under the two short-day conditions. Conclusions: Earliness gene(s) and their combinations reduced DTH regardless of photoperiod lengths. Se1-pat(t) increased DTH under long-day conditions but decreased it under short-day conditions, while se-pat elongated DTH under both short-day and long-day conditions indicating that se-pat is responsible for BVG. The se-pat increased DTH by adding its effect over that of Se1-pat(t) under long-day conditions. However, this increasing effect of DTH by se-pat was almost completely masked when it coexisted with Se1-pat(t) under the short-day conditions. Notably, the response of Ac-ef1 to day length was found to delay heading under the short-day conditions.
  • Nguyen Thanh Tam, Dwiyanti, Maria Stefanie, Koide, Yohei, Nagano, Atsushi J., Ky, Huynh, Huynh Quang Tin, Nguyen Loc Hien, Le Viet Dung, Kishima, Yuji
    PLANT GENOME 12 3 2019年11月 [査読有り][通常論文]
     
    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, pi-value is commonly used. We think that whole genome distribution of pi-values representing the nucleotide diversity of each population can be used to characterize local populations. Our simple profiling using low pi-value genomic regions was able to reveal regional characteristics of rice genomes and should be useful for identifying local rice populations.
  • Lee KJI, Bushell C, Koide Y, Fozard JA, Piao C, Yu M, Newman J, Whitewoods C, Avondo J, Kennaway R, Marée AFM, Cui M, Coen E
    PLoS biology 17 10 e3000427  2019年10月 [査読有り][通常論文]
  • Koide Y, Sakaguchi S, Uchiyama T, Ota Y, Tezuka A, Nagano AJ, Ishiguro S, Takamure I, Kishima Y
    G3 (Bethesda, Md.) 9 5 1655 - 1662 2019年03月 [査読有り][通常論文]
     
    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.
  • 小出 陽平
    育種学研究 日本育種学会 2019年 [査読無し][通常論文]
  • Yohei Koide, Atsushi Ogino, Takanori Yoshikawa, Yuki Kitashima, Nozomi Saito, Yoshitaka Kanaoka, Kazumitsu Onishi, Yoshihiro Yoshitake, Takuji Tsukiyama, Hiroki Saito, Masayoshi Teraishi, Yoshiyuki Yamagata, Aiko Uemura, Hiroki Takagi, Yoriko Hayashi, Tomoko Abe, Yoshimichi Fukuta, Yutaka Okumoto, Akira Kanazawa
    Proceedings of the National Academy of Sciences of the United States of America 115 9 E1995 - E1962 2018年02月27日 [査読有り][通常論文]
     
    Understanding the genetic basis of reproductive barriers between species has been a central issue in evolutionary biology. The S1 locus in rice causes hybrid sterility and is a major reproductive barrier between two rice species, Oryza sativa and Oryza glaberrima. The O. glaberrima-derived allele (denoted S1g) on the S1 locus causes preferential abortion of gametes with its allelic alternative (denoted S1s) in S1g/S1s heterozygotes. Here, we used mutagenesis and screening of fertile hybrid plants to isolate a mutant with an allele, S1mut, which does not confer sterility in the S1mut/S1g and S1mut/S1s hybrids. We found that the causal mutation of the S1mut allele was a deletion in the peptidase-coding gene (denoted “SSP”) in the S1 locus of O. glaberrima. No orthologous genes of SSP were found in the O. sativa genome. Transformation experiments indicated that the introduction of SSP in carriers of the S1s allele did not induce sterility. In S1mut/S1s heterozygotes, the insertion of SSP led to sterility, suggesting that SSP complemented the loss of the functional phenotype of the mutant and that multiple factors are involved in the phenomenon. The polymorphisms caused by the lineage-specific acquisition or loss of the SSP gene were implicated in the generation of hybrid sterility. Our results demonstrated that artificial disruption of a single gene for the reproductive barrier creates a “neutral” allele, which facilitates interspecific hybridization for breeding programs.
  • Daisuke Fujita, Yohei Koide, Nobuya Kobayashi
    Japan Agricultural Research Quarterly 52 2 91 - 103 2018年 [査読無し][通常論文]
     
    To enhance the yield potential of rice by improving plant type, we have developed introgression lines (ILs: BC3-derived lines) with the genetic background of the elite indica variety IR64. A total of 334 ILs derived from crosses between IR64 as the recurrent parent and 10 donor parents (nine new-planttype lines IR65600-87-2-2-3, IR65598-112-2, IR65564-2-2-3, IR69093-41-2-3-2, IR69125-25-3-1-1, IR66215-44-2-3, IR68522-10-2-2, IR71195-AC1 and IR66750-6-2-1, and one Japanese high-yielding cultivar, 'Hoshiaoba') have been developed by recurrent backcross breeding. The agronomic traits of the 334 ILs were evaluated in the experimental field of the International Rice Research Institute from 2005 to 2007, and their genotypes were determined using SSR markers. Several agronomic traits (days to heading, leaf length and width, culm and panicle length, number of panicles, total spikelet number per panicle, and 100-grain weight) were dissected genetically by QTL analysis using hybrid populations derived from crosses between IR64 and ILs with unique traits. More than 30 QTLs were detected and their effects were confirmed by developing and evaluating near-isogenic lines (NILs). These ILs and NILs are useful for both breeding and further genetic dissection of agronomic traits across various environments.
  • Yohei Koide, Mitsuhiro Obara, Seiji Yanagihara, Yoshimichi Fukuta
    Japan Agricultural Research Quarterly 52 1 29 - 37 2018年 [査読有り][通常論文]
     
    New Rice for Africa (NERICA) varieties have been developed by inter-specific crossings to produce rice suitable for the harsh environments in Africa. The basic idea of NERICA was to combine the most useful characteristics of an African species (Oryza glaberrima) and an Asian species (Oryza sativa). However, the genetic basis of the agronomic characteristics of NERICA varieties remains unknown. In a previous study, we detected QTLs for days to heading (DTH) by using a segregating population derived from a cross between NERICA10 and its parent variety of O. sativa (WAB56- 104). In the present study, we evaluated the agronomic traits of the same population and found positive correlations between DTH and culm length, culm and leaf weight, and flag leaf length. Negative correlations were found between DTH and panicle weight (PW), and between the ratio of panicle weight per culm and leaf weight. In the QTL analysis, a total of 33 SSR markers showed significant association with more than one trait and some markers were associated with more than two traits, suggesting the presence of a QTL with pleiotropic effects on multiple traits or a cluster of QTLs controlling different traits. QTLs on chromosome 8 conferred shorter DTH and larger PW in NERICA10 than WAB56-104. This QTL might explain the negative correlation between DTH and PW in the population. This information on the QTLs of agronomic traits will be useful for improving NERICA varieties adapted to low-yielding environments in Africa.
  • Kanaoka Y, Kuniyoshi D, Inada E, Koide Y, Okamoto Y, Yasui H, Kishima Y
    Plant methods 14 102  2018年 [査読有り][通常論文]
     
    BackgroundTo 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.ResultsMicrospores 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.ConclusionsWe 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.
  • Kazuhiro Sasaki, Daisuke Fujita, Yohei Koide, Patrick D. Lumanglas, Ritchel B. Gannaban, Analiza G. Tagle, Mitsuhiro Obara, Yoshimichi Fukuta, Nobuya Kobayashi, Tsutomu Ishimaru
    JOURNAL OF EXPERIMENTAL BOTANY 68 11 2693 - 2702 2017年05月 [査読有り][通常論文]
     
    Total spikelet number per panicle (TSN) is one of the determinants of grain productivity in rice (Oryza sativa L.). In this study, we attempted to detect quantitative trait loci (QTLs) for TSN in the introgression lines with high TSN, derived from the cross of Indica Group variety IR 64 with new plant type lines. Two QTLs were detected on the long arm of chromosome 12: qTSN12.1 in the BC4F2 population of YTH63/IR 64 and qTSN12.2 in the BC4F3 population of YTH83/IR 64. TSN of the main tiller was significantly higher in near-isogenic lines (NILs) for qTSN12.1 (IR 64-NIL1; 188.6) and for qTSN12.2 (IR 64-NIL12; 199.4) than in IR 64 (141.2), owing to a significant increase in both primary and secondary branch numbers. These results suggest the critical function of these QTLs in the promotion of rachis branching at the panicle formation stage. Fine mapping of qTSN12.2 revealed six candidate genes in a 92-kb region of the Nipponbare reference genome sequence between flanking markers RM28746 and RM28753. Detailed phenotyping of agronomic traits of IR 64-NIL12 carrying qTSN12.2 showed drastic changes in plant architecture: this line had lower panicle number, longer culm, and longer and wider leaves compared with IR 64. Percentage of fertility and 1000-grain weight tended to be greater, and grain yield per square meter was also greater in IR 64-NIL12 than in IR 64. The newly identified QTLs will be useful for genetic improvement of the yield potential of Indica Group varieties. The markers tightly linked to qTSN12.2 are available for marker-assisted breeding.
  • Eri Ogiso-Tanaka, Tsuyoshi Tanaka, Keisuke Tanaka, Yasunori Nonoue, Takuji Sasaki, Erina Fushimi, Yohei Koide, Yutaka Okumoto, Masahiro Yano, Hiroki Saito
    Breeding Science 2017年03月04日 [査読有り][通常論文]
  • Theophile Odjo, Yohei Koide, Drissa Silue, Seiji Yanagihara, Takashi Kumashiro, Yoshimichi Fukuta
    Breeding Science 67 5 500 - 508 2017年 [査読有り][通常論文]
     
    The genetic variation in resistance to blast (Pyricularia oryzae Cavara) in 195 rice accessions comprising 3 species of the AA genome complex (Asian rice [Oryza sativa L.], African rice [Oryza glaberrima Steud.] and wild rice [Oryza barthii]) was investigated based on their patterns of reaction to standard differential blast isolates (SDBIs) and SSR marker polymorphism data. Cluster analysis of the polymorphism data of 61 SSR markers identified 3 major clusters: cluster A (mainly Japonica Group or upland accessions), cluster B (mainly Indica Group or lowland accessions) and cluster C (O. glaberrima and O. barthii). The accessions were classified again into 3 resistance groups based on reactions to SDBIs: group Ia (susceptible), group Ib (middle resis-tance) and group II (high resistance). Group Ia included only a few differential varieties, susceptible controls and the Japonica Group cultivar Nipponbare. Accessions in clusters A and B included all 3 resistance groups and showed a wide variation in blast resistance, but cluster C contained only group Ib. These results demonstrated that variations in Asian rice (O. sativa) accessions in West Africa were skewed toward high resistance and that variations in O. glaberrima and O. barthii were limited and lower than the Asian rice accessions.
  • Chhourn Orn, Rieko Shishido, Masahiro Akimoto, Ryo Ishikawa, Than Myint Htun, Ken-Ichi Nonomura, Yohei Koide, Men Sarom, Seng Vang, Sakhan Sophany, Ouk Makara, Takashige Ishii
    BREEDING SCIENCE 65 5 430 - 437 2015年12月 [査読有り][通常論文]
     
    A total of 448 samples in five natural populations of wild rice (Oryza rufipogon) were collected in Cambodia. They were examined using 12 SSR and two chloroplast markers to evaluate the degree of variation among populations and the genetic structure within populations. In the two annual populations, the number of plants with homozygous alleles at all 12 SSR loci were high (66.3% and 79.5%), suggesting that these plants propagate mainly through self-pollination. In the three perennial populations, no individuals had all homozygous genotypes, but redundant genotypes resulted from clonal propagation were observed. Percentages of the redundant genotypes were highly varied (3.6%, 29.2% and 86.0%). This may be due to the different stable levels of environmental conditions. As for chloroplast genome, most of the wild plants showed the same chloroplast types as most Indica-type cultivars have. However, plants with different chloroplast types were maintained, even in the same population. In tropical Asian countries, many wild rice populations were observed under similar ecological conditions examined in this study. Therefore, the present results concerning population structure will be important to further elucidate genetic features of wild rice, and will also give strong clues to utilize and conserve wild natural genetic resources.
  • Yohei Koide, Akiko Kawasaki-Tanaka, Theophile Odjo, Mitsuhiro Obara, Seiji Yanagihara, Yoshimichi Fukuta
    EUPHYTICA 203 1 153 - 164 2015年05月 [査読有り][通常論文]
     
    To produce rice varieties adaptable to unfavorable environments in Africa, New Rice for Africa (NERICA) varieties have been developed by inter-specific crossings. The basic idea of NERICA was to combine the useful characteristics of the African rice species Oryza glaberrima and an Asian rice species, Oryza sativa. However, the genetic basis of the agronomic characteristics of NERICA varieties is not fully understood. We performed a QTL analysis to examine the genetic basis of days to heading (DTH) in an upland variety, NERICA10. We found that NERICA10 had weaker photoperiod sensitivity (PS) and shorter DTH under long day-length conditions than its parental varieties. We then examined QTLs controlling DTH under natural long-day-length conditions by using segregating populations. We found three QTLs for DTH, on chromosomes 4, 6, and 8. Among them, qDTH8.1, located on chromosome 8, had the strongest effect. By comparing nucleotide sequences, we found that NERICA10 had a loss of the functional allele of DTH8, which was located in the candidate region of qDTH8.1. These results suggested that loss of function of DTH8 is the causal factor of weakened PS in NERICA10. The information on these QTLs will be useful for improving rice varieties for better adaption to African conditions.
  • Yoshimichi Fukuta, Ikumi Koga, Tochi Ung, Khay Sathya, Akiko Kawasaki-Tanaka, Yohei Koide, Nobuya Kobayashi, Mitsuhiro Obara, Hun Yadana, Nagao Hayashi
    JARQ-JAPAN AGRICULTURAL RESEARCH QUARTERLY 48 2 155 - 166 2014年04月 [査読有り][通常論文]
     
    The evaluation of a total of 122 blast (Pyricularia oryzae Cavara) isolates collected from the Tonle Sap and Mekong river regions of Cambodia revealed wide variation. Using a new designation system, the blast isolates were categorized into 92 races based on the reaction patterns of rice (Oryza sativa L.) differential varieties (DVs) harboring 23 resistance genes and of 1 susceptible cultivar, Lijiangxintuanheigu (LTH). Cluster analysis was used to classify the blast isolates into 3 groups - I, IIa, and IIb - using data from these reaction patterns of the DVs and LTH. We used the classifications established under the new designation system, alongside cluster analysis and the geographical distribution of blast isolates, to investigate the diversity and differentiation of blast races in the Tonle Sap and Mekong river regions. The distributions of the blast races differed between the 2 regions, although blast isolates of group IIa were distributed commonly in both regions and groups I and IIb occurred at higher frequencies in the Tonle Sap region rather than the Mekong region. The blast isolates in groups I and IIb were also less diverse than those in group IIa. Accordingly, Group II blast isolates overall were distributed in both regions with high diversity, but some modified blast isolates were additionally distributed in the Tonle Sap region. We also investigated the pathogenicities of blast isolates from wild rice (Oryza rufipogon Griff) weeds neighboring the cultivated rice, and discuss the relationship between these isolates and those from cultivated rice.
  • 小出 陽平
    作物研究 59 59 67 - 71 近畿作物・育種研究会 2014年 [査読無し][通常論文]
     
    高等生物は突然変異により生じる新たな遺伝子セットを遺伝的組換えにより再編成することで膨大な遺伝的多様性を生み出し,変動する環境に適応している.したがって,作物の遺伝的多様性を支える生物資源を有効に利用することが,変動する地球環境に対応した農業を推進する上で重要となると考えられる.本稿では生物資源利用の一例として,イネの種間交雑により作出されたNew Rice for Africa (NERICA)を取り上げ,NERICAが持つ遠縁種由来の有用遺伝子や潜在的な不良遺伝子の解析について紹介する.
  • Daisuke Fujita, Kurniawan Rudi Trijatmiko, Analiza Grubanzo Tagle, Maria Veronica Sapasap, Yohei Koide, Kazuhiro Sasaki, Nikolaos Tsakirpaloglou, Ritchel Bueno Gannaban, Takeshi Nishimura, Seiji Yanagihara, Yoshimichi Fukuta, Tomokazu Koshiba, Inez Hortense Slamet-Loedin, Tsutomu Ishimaru, Nobuya Kobayashi
    Proceedings of the National Academy of Sciences of the United States of America 110 51 20431 - 20436 2013年12月17日 [査読有り][通常論文]
     
    Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13-36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica- growing regions such as South and Southeast Asia.
  • Yohei Koide, Mary Jeanie Telebanco-Yanoria, Yoshimichi Fukuta, Nobuya Kobayashi
    MOLECULAR BREEDING 32 2 241 - 252 2013年08月 [査読有り][通常論文]
     
    The use of broad-spectrum R genes is an effective way to achieve durable resistance against rice blast (Magnaporthe oryzae Couch, anamorph: Pyricularia oryzae Cavara) in rice (Oryza sativa L.). We previously surveyed the diversity of blast resistance in 948 rice varieties and found a Myanmar rice landrace, Haoru (International Rice Research Institute genebank acc. no. IRGC33090), with broad-spectrum resistance against the standard differential blast isolates. Here, we examined the genetic basis of Haoru's broad-spectrum resistance by using the standard blast differential system consisting of the standard isolates and differential varieties. For genetic analysis, we used a BC1F1 population and BC1F2 lines derived from crosses of Haoru with a susceptible variety, US-2. Co-segregation analysis of the reaction pattern in the BC1F1 population against the 20 standard isolates suggested that Haoru harbors three R genes. By using bulk-segregant and linkage analysis, we mapped two of the three R genes on chromosomes 12 and 6, and designated them as Pi58(t) and Pi59(t), respectively. Pi58(t) and Pi59(t) were differentiated from other reported R genes using the standard differential system. The estimated resistance spectrum of Pi58(t) corresponded with that of Haoru, suggesting that Pi58(t) is primarily responsible for Haoru's broad-spectrum resistance. In addition, Pi59(t) and the third gene were also proven to be new and useful genetic resources for studying and improving blast resistance in rice.
  • Yohei Koide, Daisuke Fujita, Analiza G. Tagle, Kazuhiro Sasaki, Tsutomu Ishimaru, Yoshimichi Fukuta, Nobuya Kobayashi
    EUPHYTICA 192 1 97 - 106 2013年07月 [査読有り][通常論文]
     
    Total spikelet number per panicle (TSN) is thought to be one of the most important agronomic traits associated with grain production in rice (Oryza sativa L.). We previously reported the development of 334 introgression lines (ILs) with variations in agronomic traits in the genetic background of indica rice variety IR64. Among these, an IL derived from high-yielding rice variety Hoshiaoba showed significantly higher TSN than IR64. We therefore have conducted a quantitative trait locus (QTL) analysis for TSN in an F-2 population of IL x IR64 to ascertain the genetic basis for the high TSN of the IL. The analysis revealed the presence of a QTL for TSN on chromosome 7, where several QTLs for grain number have been previously reported. We developed a near-isogenic line (NIL) for this QTL by using DNA marker-assisted selection and characterized its effect. The NIL showed significantly higher TSN than IR64. These results suggest that the QTL and the NIL will be useful materials in breeding programs aimed at increasing TSN.
  • Yohei Koide, Juan Pariasca Tanaka, Terry Rose, Ayumi Fukuo, Kunihiko Konisho, Seiji Yanagihara, Yoshimichi Fukuta, Matthias Wissuwa
    PLANT BREEDING 132 3 259 - 265 2013年06月 [査読有り][通常論文]
     
    Phosphorous (P) deficiency is a major yield limiting factor in rice (Oryza sativa L.) production. The interspecific New Rice for Africa (NERICA) varieties combine general stress tolerance from African cultivated rice (Oryza glaberrima Steud) with characteristics associated with high yield from O.sativa. However, little is known about their ability to tolerate P deficiency. Here, we examined the variation for tolerance to P deficiency among the 18 upland NERICAs and their parents in multi-year field experiments. The good performance under P deficiency of the O.glaberrima parent CG 14 and some NERICAs suggested that these tolerant NERICAs contain loci associated with P deficiency tolerance inherited from CG 14. Additionally, four QTL clusters for P deficiency tolerance were detected on chromosomes 4, 6 and 11 using F3 lines derived from the cross between the P deficiency tolerant variety NERICA10 and a Japonica-type sensitive variety Hitomebore'. These QTLs represent the first step in identifying stress tolerance genes from O.glaberrima that could subsequently be used to enhance P deficiency tolerance in O.sativa.
  • KOBAYASHI NOBUYA, TELEBANCO-YANORIA MARY JEANIE, FUKUTA YOSHIMICHI, KOIDE YOHEI, KATO HIROSHI, IMBE TOKIO
    Annu Rep Jpn Int Res Cent Agric Sci 2010 20 - 21 2012年03月30日 [査読無し][通常論文]
  • Y. Koide, Y. Shinya, M. Ikenaga, N. Sawamura, K. Matsubara, K. Onishi, A. Kanazawa, Y. Sano
    HEREDITY 108 3 242 - 247 2012年03月 [査読有り][通常論文]
     
    Transmission ratio distortion (TRD), in which one allele is transmitted more frequently than the opposite allele, is presumed to act as a driving force in the emergence of a reproductive barrier. TRD acting in a sex-specific manner has been frequently observed in interspecific and intraspecific hybrids across a broad range of organisms. In contrast, sex-independent TRD (SITRD), which results from preferential transmission of one of the two alleles in the heterozygote through both sexes, has been detected in only a few plant species. We previously reported an S-6 locus-mediated SITRD, in which the S-6 allele from an Asian wild rice strain (Oryza rufipogon) was transmitted more frequently than the S-6(a) allele from an Asian cultivated rice strain (O. sativa) through both male and female gametes in heterozygous plants. Here, we report on the effect of a difference in genetic background on S-6 locus-mediated SITRD, based on the analysis using near-isogenic lines and the original wild strain as a parental strain for crossing. We found that the degree of TRD through the male gametes varied depending on the genetic background of the female (pistil) plants. Despite the occurrence of TRD through both male and female gametes, abnormality was detected in ovules, but not in pollen grains, in the heterozygote. These results suggest the involvement of unlinked modifiers and developmentally distinct, sex-specific genetic mechanisms in S-6 locus-mediated SITRD, raising the possibility that SITRD driven by a single locus may be affected by multiple genetic factors harbored in natural populations. Heredity (2012) 108, 242-247; doi:10.1038/hdy.2011.64; published online 27 July 2011
  • Yohei Koide, Mary Jeanie Telebanco-Yanoria, Daisuke Fujita, Analiza G. Tagle, Yoshimichi Fukuta, Nobuya Kobayashi
    MOLECULAR BREEDING 28 3 359 - 366 2011年10月 [査読有り][通常論文]
     
    An introgression line (INL) for a major rice blast resistance gene, Pia, was developed, with the genetic background of a blast susceptible variety, US-2. The reaction pattern of the INL was characterized by using 20 standard blast isolates from the Philippines. The introgression of the Pia gene was confirmed by DNA markers on the short arm of chromosome 11 where Pia was previously mapped. A genome-wide DNA marker survey revealed that most of the chromosomal regions were US-2 type. By using an F2 population derived from a cross between the INL and US-2, the chromosomal location of the Pia locus was mapped between RM26281 and RM3701. For fine mapping of the Pia locus, five additional markers were developed based on the genomic sequence of the corresponding region of a japonica-type variety, Nipponbare. The candidate region of Pia was delimited between two DNA markers, RM26281 and 82N19365, corresponding to a 140 kb region on the Nipponbare genome sequence. We obtained three DNA markers within this region. The developed INL, information on the map position of Pia, and DNA markers developed in the candidate region of the Pia locus are useful tools for blast resistance studies and a marker-aided breeding strategy.
  • Yohei Koide, Leodegario A. Ebron, Hiroshi Kato, Hiroshi Tsunematsu, Mary Jeanie Telebanco-Yanoria, Nobuya Kobayashi, Masao Yokoo, Sachio Maruyama, Tokio Imbe, Yoshimichi Fukuta
    FIELD CROPS RESEARCH 123 1 19 - 27 2011年07月 [査読有り][通常論文]
     
    A set of near-isogenic lines for blast resistance genes was developed by using an Indica-type elite rice variety, IR49830-7-1-2-2, suitable for the rainfed lowland conditions in the tropics, as a genetic background. Initially, we revealed that IR49830-7-1-2-2 harbors five blast resistance genes - Pia, Pib, Pik-s, Pita, and Pi11(t) - by using a differential system involving 19 selected standard blast isolates from the Philippines. Based on this result, we developed nine near-isogenic lines (NILs) targeting eight resistance genes - Pik, Pi7(t), Pi3, Pi5, Pita-2, Piz-5, Pish, and Pi9 - by recurrent backcrossing. The introgression of each resistance gene in the NILs was confirmed by reaction patterns to the blast isolates, allelism tests, and DNA marker analysis. In addition, a genome-wide DNA marker survey revealed that most of the chromosome regions in each NIL were of the IR49830-7-1-2-2 type. The agricultural characteristics of most of the developed NILs were al most the same as those of IR49830-7-1-2-2. Moreover, with one exception, they showed submergence tolerance similar to IR49830-7-1-2-2. The developed NILs could be used as a multiline variety suitable for the rainfed lowland in the tropics. (C) 2011 Elsevier By. All rights reserved.
  • Mary Jeanie Telebanco-Yanoria, Yohei Koide, Yoshimichi Fukuta, Tokio Imbe, Hiroshi Tsunematsu, Hiroshi Kato, Leodegario A. Ebron, Thi Minh Nguyet Nguyen, Nobuya Kobayashi
    MOLECULAR BREEDING 27 3 357 - 373 2011年03月 [査読有り][通常論文]
     
    Twenty-seven near-isogenic lines (NILs) with the genetic background of a blast-susceptible variety, CO 39, were developed by repeated backcrossing as a first set of a large number of differential varieties (DVs) with Indica-type genetic background. The NILs included 14 resistance genes-Pish, Pib, Piz-5, Piz-t, Pi5(t), Pik-s, Pik, Pik-h, Pik-m, Pik-p, Pi1, Pi7(t), Pita, and Pita-2-derived from 26 donor varieties. The reaction patterns of NILs against 20 standard isolates from the Philippines were similar to those of blast monogenic lines with the same resistance gene, except for those against two isolates that are avirulent to Pia in the genetic background of CO 39. A genome-wide DNA marker survey revealed that chromosome segments were introgressed in the regions where each resistance gene was previously mapped and most of the other chromosome regions in each NIL were CO 39 type. Segregation analysis of resistance and co-segregation analysis between resistance and DNA markers using F3 populations derived from the crosses between each NIL and the recurrent parent, CO 39, revealed a single-gene control of resistance and association between resistance and target introgressed segments. The morphological characters of each NIL were almost the same as those of the recurrent parent except for some lines, suggesting that these NILs can be used even under tropical conditions where Japonica-type DVs are not suitable for cropping. Thus, these NILs are useful not only as genetic tools for blast resistance study but also as sources of genes for breeding of Indica-type rice varieties.
  • Yohei Koide, Mary Jeanie Telebanco-Yanoria, Fe Dela Pena, Yoshimichi Fukuta, Nobuya Kobayashi
    JOURNAL OF PHYTOPATHOLOGY 159 2 85 - 93 2011年02月 [査読有り][通常論文]
     
    To facilitate resistance gene characterization in the present study, the pathogenicities of newly collected blast isolates from rice fields in the Philippines were characterized using international blast differential varieties consisting of 31 monogenic lines that target 24 resistance genes. To classify and designate the blast isolates, we used a new international blast designation system, which has been proposed as a suitable naming system for comparing blast races among different studies. A total of 23 rice blast isolates collected from the Philippines were classified into 16 pathotypes, which showed reaction patterns different from those seen in the standard isolates. Among the blast pathotypes, 11 had differentiating ability for four Pik alleles (Pik, Pik-m, Pik-h, and Pik-p) and Pi1, whereas the standard blast isolates from the Philippines were not able to differentiate these genes. In addition, several blast isolates were avirulent to IRBLt-K59, IRBL19-A, and Lijiangxintuanheigu, although the standard differential blast isolates were virulent to these lines. Moreover, two blast isolates were virulent to a monogenic line, IRBL9-W, which harbours Pi9 and was resistant to all standard differential blast isolates. By using the isolates avirulent to IRBL19-A, Pi19(t) was successfully mapped in the centromeric region on chromosome 12 with simple sequence repeat markers RM27937 and RM1337. These markers are useful for marker-assisted Pi19(t) introgression worldwide.
  • Mary Jeanie Telebanco-Yanoria, Yohei Koide, Yoshimichi Fukuta, Tokio Imbe, Hiroshi Kato, Hiroshi Tsunematsu, Nobuya Kobayashi
    BREEDING SCIENCE 60 5 629 - 638 2010年12月 [査読有り][通常論文]
     
    Twenty near-isogenic lines (NILs) of rice (Oryza sativa L.) containing 11 blast resistance genes (Pib, Piz-5, Pi9, Pi3, Pia, Pik-s, Pik, Pik-h, Pi7(t), Pita and Pita-2) were developed by recurrent backcrossing of 19 donor varieties to a susceptible Japonica-type variety, Lijiangxintuanheigu (LTH). The resistant plants were selected in each backcross generation using a specific avirulent blast isolate for each targeted resistance gene. The NILs showed similar reaction patterns to those of the corresponding resistance-containing monogenic lines (MLs) when challenged with 20 standard blast isolates from the Philippines, suggesting that the target resistance genes were successfully introduced. The introgression of the targeted resistance genes was further confirmed by SSR markers that were located within the chromosome regions where the resistance genes had previously been mapped. Genome surveys using SSR markers showed that the NILs had genetic compositions more similar to that of the recurrent parent LTH than did the MLs, which had been derived using fewer backcrosses to LTH. The morphological characteristics of each NIL were generally similar to those of LTH. These NILs, with the genetic background of a Japonica-type variety, are expected to be valuable genetic tools for research and breeding programs for blast resistance.
  • Y. Koide, A. Kawasaki, M. J. Telebanco-Yanoria, A. Hairmansis, N. T. M. Nguyet, J. Bigirimana, D. Fujita, N. Kobayashi, Y. Fukuta
    PLANT BREEDING 129 6 670 - 675 2010年12月 [査読有り][通常論文]
     
    P>Gene pyramiding is considered one of the most effective strategies for achieving durable resistance against blast disease (Magnaporthe oryzae B. Couch) in rice (Oryza sativa L.), although few studies have evaluated the combining effect of the resistance genes. We report the development of pyramided lines with two major blast resistance genes, Pish and Pib, and the evaluation of the combining effect of them. The two genes pyramided lines were selected from the progenies of a cross between one near isogenic line (NIL), which harbours Pish, and another NIL, which harbours Pib, in the genetic background of blast susceptible variety, CO 39. The presence of the resistance genes was confirmed by DNA markers linked to them. To obtain DNA markers for Pish, we genetically mapped the Pish locus. We confirmed the additive effect of Pish and Pib in the pyramided lines by their reaction patterns to blast isolates, suggesting the potential availabilities of the combinations of these genes. In addition, we provide DNA markers linked to Pish for marker aided selection in rice blast resistance breeding.
  • Varying patterns of blast (Magnaporthe grisea (Hebert) Barr.) resistance in rice (Oryza sativa L.) varieties in water-saving production system
    Y. Koide, M. J. Telebanco-Yanoria, Y. Fukuta, N. Kobayashi
    International Rice Research Notes, 35 2010年 [査読有り][通常論文]
  • Yohei Koide, Nobuya Kobayashi, Donghe Xu, Yoshimichi Fukuta
    JARQ-JAPAN AGRICULTURAL RESEARCH QUARTERLY 43 4 255 - 280 2009年10月 [査読有り][通常論文]
     
    Blast is a serious disease caused by a fungal pathogen Pyricularia oryzae Cavara of rice (Oryza sativa L.). The use of resistant varieties is considered one of the most efficient ways of crop protection from the disease. In addition to a large amount of information accumulated during the long history of genetic studies on resistance to rice blast, recent progress in rice genomics has enabled us to use DNA markers for breeding the resistant varieties by marker assisted selection (MAS). In this report, we summarize the reported rice blast resistance genes and their selection markers to encourage further utilization for breeding. First, we assemble the information about the reported genes with regard to their number, chromosomal locations, patterns of resistance, donor strains, and molecular characterization of the cloned genes by reviewing the literature. In addition, we present some remaining issues about the nomenclature system and identification of the resistance genes. Then, we provide the first assembled list of the reported DNA markers for blast resistance genes, including the sequences of the primer pairs, genetic distances from the resistance genes, and cross combinations of the parental strains used to detect the polymorphisms. This information will help rice breeders to improve the resistance to rice blast by MAS.
  • KOIDE YOHEI, KOBAYASHI NOBUYA, XU DONGHE, FUKUTA YOSHIMICHI
    JIRCAS Working Rep 63 95 - 122 2009年03月31日 [査読無し][通常論文]
  • Yohei Koide, Mitsunobu Ikenaga, Yuhei Shinya, Kazuki Matsubara, Yoshio Sano
    EUPHYTICA 164 3 753 - 760 2008年12月 [査読有り][通常論文]
     
    Cross-incompatibility caused by endosperm abortion was found in advanced generations of backcrossing between the Asian wild (W593) and cultivated (T65wx) rice strains. The near isogenic line, T65WxS(6) (W593), carrying a segment of chromosome 6 from W593 showed a low seed setting when pollinated with pollen grains of T65wx in spite of the fact that the reciprocal cross gave a high seed setting. The unidirectional or asymmetric crossing barrier was previously explained by an interaction between Cif and cim, both of which acted sporophytically, resulting in the cross-incompatibility reactions in the female (CIF) and male (CIM), respectively. In the genetic model, endosperm abortion is induced only when CIF gametes are fertilized with CIM gametes. This predicted that the double homozygote for Cif and cim might be self-incompatible since the plant expresses both CIF and CIM simultaneously. However, we failed to obtain such a self-incompatible plant by transferring Cif into a cim plant. The present results showed that CIF is controlled not only by Cif but also by an additional gene(s) loosely linked with it. We propose here that Cif(1) (formerly named as Cif) and Cif(2) determine CIF. In addition, Cif(2) and Cim were not separated due to restriction of recombination, which might explain why it is difficult to obtain a self-incompatible rice plant expressing both CIF and CIM.
  • Yohei Koide, Mitsunobu Ikenaga, Noriko Sawamura, Daisuke Nishimoto, Kazuki Matsubara, Kazumitsu Onishi, Akira Kanazawa, Yoshio Sano
    GENETICS 180 1 409 - 420 2008年09月 [査読有り][通常論文]
     
    Transmission ratio distortion (TRD) is frequently observed in inter-and intraspecific hybrids of plants, leading to a violation of Mendelian inheritance. Sex-independent TRD (siTRD) was detected in a hybrid between Asian cultivated rice and its wild ancestor. Here we examined how siTRD is controlled by the S-6 locus via a mechanism in which the S-6 allele acts as a gamete eliminator, and both the male and female gametes possessing the opposite allele (S-6(a)) are aborted only in heterozygotes (S-6/S-6(a)). Fine mapping revealed that the S-6 locus is located neaar the centromere of chromosome 6. Tescross experiments using near-isogenic lines (NILs) carrying either the S-6 or S-6(a) alleles revealed that Asian rice strains frequently harbor an additional allele (S-6(n)) the presence of which, in heterozygotic states (S-6/S-6(n) and S-6(a)/S-6(n)), does not result in siTRD. A prominent reduction in the nucleotide diversity of S-6 or S-6(a) carries relative to that of S-6(n) carries was detected in the chromosomal region. These results suggest that the two incompatible alleles (S-6/S-6(a)) arose independently from S-6(n) and established genetically discontinuous relationships between limited constituents of the Asian rice population.
  • Yohei Koide, Kazumitsu Onishi, Daisuke Nishimoto, Akhil Ranjan Baruah, Akira Kanazawa, Yoshio Sano
    NEW PHYTOLOGIST 179 3 888 - 900 2008年 [査読有り][通常論文]
     
    A sex-independent transmission ratio distortion (siTRD) system detected in the interspecific cross in rice was analyzed in order to understand its significance in reproductive barriers. The S(1) gene, derived from African rice Oryza glaberrima, induced preferential abortion of both male and female gametes possessing its allelic alternative (S(1)(a)), from Asian rice O. sativa, only in the heterozygote. The siTRD was characterized by resolving it into mTRD and fTRD occurring through male and female gametes, respectively, cytological analysis of gametophyte development, and mapping of the S(1) locus using near-isogenic lines. The allelic distribution of the S(1) locus in Asian and African rice species complexes was also analyzed. The siTRD system involved at least two components affecting male and female gametogeneses, respectively, including a modifier(s) that enhances fTRD. The chromosomal location of the major component causing the mTRD was delimited within an approx. 40 kb region. The S(1) locus induced hybrid sterility in any pairwise combination between Asian and African rice species complexes. The allelic state of the S(1) locus has diverged between Asian and African rice species complexes, suggesting that the TRD system has a significant role in the reproductive barriers in rice.
  • Yohei Koide, Kazumitsu Onishi, Akira Kanazawa, Yoshio Sano
    Biotechnology in Agriculture and Forestry 62 247 - 259 2008年 [査読有り][通常論文]
     
    One of the central issues of evolutionary biology is the origin of the species, although the definition of species is an endlessly debated issue (Coyne and Orr 2004). According to the biological species concept (BSC), a species is a group of an actually or potentially interbreeding natural population, which is reproductively isolated from other such groups (Mayr 1942). No concept of speciation could be complete without a genetic interpretation of the rise of isolating mechanisms. Fitness reduction can range from maladaptation to inviability or sterility. The loci that underlie such reduction in fitness might be considered ‘speciation genes’, which are important in driving the nascent species to become independent genetic entities (Wu and Ting 2004). Therefore, we can analyze the genetic basis of speciation as a more tractable problem by focusing on the genetic basis for reproductive isolation. Recent work on reproductive isolation in Drosophila has advanced our understanding of many fundamental questions about speciation (see review in Coyne and Orr 2004). The BSC can be favorably adopted regarding domesticated plants, and the concept of gene pools based on the degree of their sexual affinities is useful for their classification (Harlan 1975). Any good species are by no means completely isolated. Wild and cultivated complexes in crops are taxonomically distinct but phylogenetically conspecific. Their genetic differentiation is maintained through disruptive selection associated with habitat adaptation, indicating that domestication proceeds at the intra-specific level under human influence.
  • 堀米 綾子, 西本 大祐, 小出 陽平, 大西 一光, 長野 宏則, 貴島 祐治, 佐野 芳雄
    日本育種学会・日本作物学会北海道談話会会報 44 3 - 4 日本作物学会 2003年12月

MISC

共同研究・競争的資金等の研究課題

  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2021年04月 -2025年03月 
    代表者 : 小出 陽平, 山形 悦透, 石川 亮, 藤田 大輔
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2021年07月 -2024年03月 
    代表者 : 小出 陽平
     
    作物の器官の形を自在に操ることは、遺伝育種学や作物学において、未だ達成されていない未解決の問題である。しかしながら、個々の細胞の成長と、多細胞からなる器官の複雑な立体構造形成がどのように関与しているのかは明らかではなく、そのため、器官形状の自在な制御は未だ困難である。さらに、植物の立体形状は遺伝子と環境の双方によって複合的にコントロールされており、従来の遺伝学のみでは立体構造形成の原理をとらえることは困難である。本研究では、イネのコメの形を決定する頴花の形状をモデルケースとし、物理ベースの数理モデリングにより、器官の立体構造の形成原理を解明する。コメは世界の主要な食料の一つであり、その形は食味や収量性だけでなく、食文化などとも関連する重要な形質である。そのため、コメの形状を予測・操作できる技術はイネの品種改良や、食糧生産の安定化にとって重要であると考えられる。 そのために、まず、単一の遺伝子型かつ単一の環境下において、イネの頴花発生過程をシミュレートする物理ベースのモデルを構築する。発生過程にあるイネ頴花を、実体顕微鏡および共焦点レーザー顕微鏡により時系列的に解析し、立体構造の変形過程を、器官を形成する部位毎の生長率として定量する。定量データをもとに、最終的な形状を記述できるモデルを構築し、検証を行う。 さらに、遺伝子型情報とモデルパラメータの関係性を明らかにするために、ゲノム情報が既知のイネ品種を多数利用し、発生過程にあるイネ頴花の立体構造の変形過程を実体顕微鏡と共焦点レーザー顕微鏡を用いて解析する。
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2019年04月 -2023年03月 
    代表者 : 貴島 祐治, 山本 敏央, 長岐 清孝, 小出 陽平, 金 鍾明
     
    本研究は、１）小胞子から個体分化を誘導するメカニズム、２）イネ小胞子から効率的に個体を再生するシステムの構築、３）イネ種間雑種の葯培養個体で誘導される倍数性の発生メカニズムの解明、４）イネ種間雑種の葯培養個体によって雑種不稔性を回避する遺伝機構の解析、５）葯培養個体から生じた倍数体種間雑種による新しい育種材料の開発、の5つの問題から構成されている。2020年度は主に２）と４）について進展があった。２）について本研究では、葯から抽出した小胞子を直接培養することによって効率的に植物体再生を行うことが可能かどうかをキタアケを用いて行った。培地を検討するため、葯より抽出した小胞子に対してN6液体培地とすべての成分を10倍希釈した1/10 N6液体培地を用いて培養を行った。興味深いことに希釈培地でもカルス形成が確認された。誘導されたカルスに対して再分化処理を行い、1/10 N6液体培地に由来するカルスにおいても植物体が再生された。カルス形成率に着目すると培地の濃度によるカルス形成率への影響はなかった。しかし、培養過程にある小胞子生存率は1/10 N6培地中で大きく低下することが確認された。このことから、希釈培地では、カルス形成に関与しない小胞子が死滅したことが考えられる。両培地において葯に由来するカルスは、360葯から280個以上誘導された。これらカルスの再分化実験では、1/10 N6培地に由来するカルスは、N6液体培地に由来するカルスの再分化率を大きく上回った（1/10 N6液体培地:21%、N6液体培地12%）。さらに再分化後の馴化段階での枯死率も1/10 N6培地に由来の個体が低く安定的だった（1/10N6液体培地: 6%、 N6液体培地:22%）。したがって、カルス誘導培地の違いにより、再分化の効率が異なることが示された。
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2019年04月 -2022年03月 
    代表者 : 吉川 貴徳, 門田 有希, 小出 陽平, 寺石 政義, 奥本 裕
     
    本研究は、イネjaponica品種とindica品種間において栄養成長期間のjuvenile-adult相転換期の分化に関与する遺伝的要因を同定し、生育相転換が農業形質に及ぼす効果の解明を試みた。主たる成果は、１）qJA1、qJA2の原因遺伝子を同定し、トランスクリプトームにおいて関連する経路を見出した。２）qJA1、qJA2のjaponicaアリルが高緯度地域での栽培に適する可能性を見出した。３）生育環境が相転換に及ぼす影響を明らかにした。４）生育ステージの進行に伴っていもち病に対する防御応答機構が変化することを見出した。
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2018年04月 -2022年03月 
    代表者 : 小出 陽平
     
    日本人の主食であるイネは2倍体の植物である。一方、コルヒチン等の化学物質の処理により、染色体の数を倍に増やした4倍体のイネを作ることが可能である。この研究では、将来的に4倍体のイネを品種改良に利用することを目的として、遺伝的多様性の幅を広げるための研究を行った。4倍体では、2倍体と比べて、雑種を作った際の種子稔性が向上することが示唆されていたが、本研究では、4倍体雑種における種子低稔性以外の栄養成長期の発育異常が見いだされ、新たな育種障壁となることが考えられた。
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2016年07月 -2020年03月 
    代表者 : 藤田 大輔, 山形 悦透, 石川 亮, 小出 陽平
     
    本研究は、（課題１）として、国際稲研究所で維持されているアフリカイネO. glaberrima 150 系統に関して、次世代シークエンサーにより、全ゲノム領域の解読を行い、多数のSNP情報を検出した。（課題２）として、アフリカイネ150系統の生物的ストレス・収量関連形質の特性評価を行った。課題１で得られたSNP情報を用いてゲノムワイド関連解析により、これらの形質に関して関連する遺伝子座を複数検出した。 （課題３）として、次世代植物資源を作出するために、インド型品種Peikuの不稔緩和系統とO. glaberrimaを交雑し、複数の交雑組み合わせにおいてBC1F1種子を得た。
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2014年04月 -2019年03月 
    代表者 : 奥本 裕, 寺石 政義, 吉川 貴徳, 築山 拓司, 齊藤 大樹, 小出 陽平
     
    イネ品種銀坊主のゲノム内で高い転移活性を示す非自律性転移因子mPingを利用した新たな育種法の開発に繋がる以下の点を明らかにした。１）銀坊主集団より選抜したストレス耐性系統には特異的なmPing挿入があり、耐性獲得は挿入下流の遺伝子にストレス応答性が付与されことによると推察された。２）銀坊主の細粒突然変異系統Rurm1遺伝子内に挿入されたmPingの切出しに伴って分離する復帰型個体の中には旺盛な生育を示す生育強勢個体も分離する。この生育強勢個体は極めて多数の新規mPing挿入が生じており、mPing挿入に関してヘテロ箇所がゲノム内に多数生じることが生育強勢個体分離の原因と推察された。
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2014年04月 -2017年03月 
    代表者 : 石井 尊生, 宍戸 理恵子, 石川 亮, 野々村 賢一, 小出 陽平
     
    野生イネ（Oryza rufipogon）の遺伝学的および生態学的特性を把握するため、熱帯アジアのベトナム、カンボジア、ミヤンマーに調査地を設定し、まず野生イネ自生集団における遺伝的多様性についてDNAレベルで調査を行った。その結果、1年生と多年生の集団構造は繁殖様式と周囲の環境条件により変動することが明らかになった。次に、野生イネと栽培イネの間の遺伝子流動を栽培化形質に関するDNAマーカーを用いて調査したところ、両者間の遺伝子流動は熱帯アジアで普通に起こるものであり、その頻度は生育環境に大きく依存していることが示唆された。
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2014年04月 -2016年03月 
    代表者 : 小出 陽平
     
    イネの種間雑種で見いだされた顕著な雑種強勢を利用するためには、障壁となる雑種不稔の誘導機構の解明が必要である。アジア栽培イネO.sativaとアフリカ栽培イネO.glaberrimaの種間交雑で種子不稔を引き起こす遺伝的要因の一つとして、第6染色体上に存在するS1領域が知られている。本研究ではこれまでに得られている雑種不稔の変異体を利用し、S1の原因遺伝子の解析を行った。まず、RNA-seqにより、変異周辺の遺伝子構造を明らかにし、候補遺伝子を特定した。次に形質転換により候補遺伝子を導入し、雑種不稔性が相補できることを明らかにした。
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2013年08月 -2015年03月 
    代表者 : 小出 陽平
     
    本研究ではイネの種間雑種で見いだされた顕著な雑種強勢を利用するため、障壁となる現象「雑種不稔」の克服を目指している。アジア栽培イネO.sativaとアフリカ栽培イネO.glaberrimaの種間交雑では得られた雑種は種子不稔を示す。これまでにイネの種間雑種において種子不稔を引き起こす遺伝的要因の一つとして、S1遺伝子が報告されている。S1はヘテロ接合の状態で特異的に作用し、花粉および種子の退化を引き起こす。S1はイネ第6染色体上にマッピングされているが、原因となる遺伝子の同定はできていない。そこで本研究では、S1に着目し、遺伝子機能欠損変異体を単離する。得られた変異体を利用してS1の原因遺伝子の特定を行う。変異体の作出には重イオンビームを用いる。通常、突然変異処理を行うと多くの遺伝子が影響を受けるため、種子稔性が低下した個体が頻繁に生じる。一方、重イオンビームはその軌跡に沿って半径数nm程度の範囲に広がるDNA二本鎖を電離作用により切断するため、切断箇所以外の遺伝子が影響を受けるリスクが低いと考えられている。そのため、本研究においてS1遺伝子のみを欠損させ、種子稔性が上昇する個体をスクリーニングするために適した変異処理であると考えられる。 本年度はS1遺伝子をヘテロ接合で持つ種子を交配により作出し、得られた交配後の種子に重イオンビーム（炭素イオン照射 150Gy LET30）を照射した。重イオンビーム処理後、圃場に植物体を移植し、種子稔性が高い個体を選抜した。選抜した個体はS1遺伝子が欠損した個体である可能性が高い。そこですでに報告されているS1遺伝子候補領域をシークエンスし、変異が生じている箇所を特定した。
  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2010年 -2012年 
    代表者 : 小出 陽平
     
    本研究の目的はNERICAに存在するアフリカ栽培イネ由来の有用遺伝子およびアジア栽培イネ由来の収量性関連遺伝子の座乗染色体領域を明らかにし、遺伝子の選抜に利用可能なDNAマーカーを作出すること、およびNERICAが潜在的に持つアジア栽培イネ・アフリカ栽培イネ間の雑種不稔遺伝子(不良形質)の座乗位置を決定し、遺伝障壁克服のための方策を検討することである。本年度はNERICAにアジア栽培イネを交雑して作成された雑種集団を用い、複数の形質に関してQTL解析およびQTL領域の詳細な絞り込みを行った。 1)昨年度までにリン酸欠乏圃場条件下における分げつ数の低下を指標とし、リン酸欠乏耐性に関する複数のQTLを検出した。これらのQTLはアフリカ栽培イネに由来する対立遺伝子がリン酸欠乏耐性を増加させる効果があったことから、NERICAが持つアフリカ栽培イネ由来の有用遺伝子の一つであると考えられた。本年度はこれらの結果をまとめ、公表した。 2)また、同様の集団を用いて到穂日数に関するQTL解析を行ったところ、複数のQTLが存在し、そのうちの一つはすでに報告のあるイネの出穂期関連遺伝子の座乗領域に存在することが明らかとなった。そこで本年度は、当該遺伝子の塩基配列解析を行った。その結果、検出したQTL領域に存在する出穂期関連遺伝子において、NERICAが塩基変異を持つことを明らかにした。 3)同様に雑種不稔性に関与する解析を行ったところ、複数のQTLが検出され、QTLの一つは上述のリン酸欠乏耐性に関与するQTLと連鎖していることを明らかにした。 4)さらに日本、フィリピン、アフリカから得られたいもち病菌系を用いてNERICAのいもち病抵抗性に関与する染色体領域の解析を行った。その結果、NERICAのいもち病抵抗性にも、複数の遺伝子が関与していることを明らかにした。

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