Researcher basic information

• 博士（農学）, 北海道大学

• https://researchmap.jp/yoheikoide?lang=en

• https://jglobal.jst.go.jp/detail?JGLOBAL_ID=201301062956609018

• 201301062956609018

• Oryza glaberrima
• Hybrid sterility
• Rice

• Environmental Science/Agriculture Science, Science in plant genetics and breeding

• Bachelor's degree program, School of Agriculture
• Master's degree program, Graduate School of Agriculture
• Doctoral (PhD) degree program, Graduate School of Agriculture

Research activity information

• Mar. 2019, 日本育種学会奨励賞
  小出 陽平
• Nov. 2018, 第17回日本農学進歩賞
  小出 陽平
• Sep. 2018, 第134回講演会日本育種学会優秀発表賞
  小出 陽平

• Independent Origin of Phenol Non-responsive Phenotype Caused By Phr1 Variation During Domestication of Asian and African Rice.
  Thet Htar San; Kokoro Iguchi; Daichi Ujiie; Shuhei Okada; Intan Widia Santika; Kiwamu Hikichi; Yoshiyuki Yamagata; Daisuke Fujita; Maria Stefanie Dwiyanti; Yuji Kishima; Yohei Koide
  Rice (New York, N.Y.), 22 Jan. 2026, [International Magazine]
  English, Scientific journal, Phenol color reaction has been used to distinguish between two subspecies of Asian rice (Oryza sativa), indica and japonica. The trait is controlled by one single Phr1 gene, which encodes a PPO enzyme that catalyzes the oxidation of phenolic compounds into brown or black pigments upon contact to phenol solution. In O. sativa, ssp. indica responds to phenol chemical assay by altering the rice hull color to black, whereas ssp. japonica remains unaffected due to mutations that render the gene non-functional. Although the different characteristics between subspecies in Asian rice is well known, there is no information about the variation of this trait in African rice, Oryza glaberrima, which was originated and domesticated independently of Asian rice. In this study, we found both phenol negative and positive lines in O. glaberrima and its wild ancestor O. barthii and detected the responsible non-functional mutation (1-bp deletion) in the exon 1 of the Phr1 gene. Geographical distribution of its haplotype suggested that this mutation originated in O. barthii in Mali and was later inherited by O. glaberrima. The predominance of the non-functional Phr1 alleles in O. glaberrima lines and the occurrence of the identical haplotypes in negative group of both O. barthii and O. glaberrima suggest that the negative phenol reaction was favored during domestication and breeding selection. The presence of a selection event is also supported by low nucleotide diversity of Phr1 locus. However, genetic diversity of Phr1 persists in African rice germplasm, as the functional alleles are still present in O. glaberrima. We also compared the nucleotide diversity of Phr1 in African rice with that in Asian rice and found that their origins of the phenol responsive phenotype are independent. These findings expand the current understanding of African rice domestication and offer the valuable molecular marker for improved rice breeding.
• Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.
  Elias George Balimponya; Maria Stefanie Dwiyanti; Koichi Yamamori; Shuntaro Sakaguchi; Yoshitaka Kanaoka; Yohei Koide; Yuji Kishima
  Plant methods, 21, 1, 125, 125, 03 Oct. 2025, [International Magazine]
  English, Scientific journal, BACKGROUND: The use of Illumina sequencing technologies has enabled the identification and removal of mutations in various plant species. However, the Illumina sequencing method requires a considerable amount of data to ensure its integrity and quality due to the enormous number of false positives. This study aimed to explore an effective genomic data analysis for the detection of heterozygous variant (HV) in rice varieties. RESULTS: We compared the accuracy of four combinations of mapping tools and variant calling pipelines and selected BWA-MEM2 with GATK4.3 HaplotypeCaller. To detect heterozygous de novo polymorphisms such as HVs in the three different rice varieties (Nipponbare, Kitaake, and Hinohikari), we adopted the following cost-saving procedures; secondary references were created in Nipponbare and Kitaake, and generation-based comparison was performed in Hinohikari. The similar HVs were estimated by the three varieties to range from 2.55814 × 10-8 to 4.41860 × 10-8, with an average of 3.10278 × 10-8 per nucleotide in a single rice plant, a rate consistent with observations in other organisms. Of 107 HVs identified in all eight plant samples, nine were found to be non-synonymous, resulting in an average of one non-synonymous HV per plant in a single generation. CONCLUSIONS: We have developed a methodology for the detection of true positive HVs within Illumina sequencing techniques. This system removed false positive HVs, allowing for the estimation of true positive HVs and, consequently, the estimation of the mutation rate. The study outlines a clear, step-by-step procedure that can be employed to detect true HVs in different organisms.
• Left-right asymmetry causes twisting in rice (Oryza sativa) leaves via physical interaction between organs.
  Kiwamu Hikichi; Shuhei Okada; Yoshiki Tokuyama; Seiichiro Miura; Minami Taguchi; Yuji Kishima; Itsuro Takamure; Yohei Koide
  The New phytologist, 15 Jul. 2025, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
  English, Scientific journal, Shape of plant organs is constrained by other organs within the same plant, yet these constraints remain under-reported. In grasses, new leaves typically develop inside the space formed by the older leaf, which imposes spatial restrictions on the developing leaf. This study focused on the rice (Oryza sativa) mutant, DSK115, which exhibits twisted leaf blades to understand how constraints affect leaf development. We quantified 3D shapes of twisted and nontwisted leaves developing inside the cylindrical space formed by the older leaf sheath by micro X-ray computed tomography (micro-CT). We also used computational modelling for qualifying leaf phenotype. CT scanning showed physical contact between the inner and outer edges of a leaf blade due to left-right asymmetry in leaf width, and physical inhibition of leaf growth due to reduced space within the enclosing leaf sheath. The simulation models demonstrated these factors could produce a twisted structure like DSK115. The study revealed the twisting of leaf blades is consistent with a mechanical explanation by physical contact between the inner and outer edges of a leaf blade and physical inhibition of leaf growth.
• The attraction of Oryza, II
  小出陽平; 藤田大輔; 石川亮; 山形悦透; 塩野克宏; 清水元樹; 殿崎薫; 吉川貴徳
  育種学研究, 27, 1, 2025, [Lead author, Corresponding author]
• 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, 28 Jun. 2024, [Peer-reviewed], [International Magazine]
  English, Scientific journal, 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.
• 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, 17 May 2024, [Peer-reviewed], [Lead author, Corresponding author], [International Magazine]
  English, Scientific journal, 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.
• GRAS-Di analysis on recombinant inbred lines derived from the cross between Asian cultivated and wild rice species suitable for agronomic evaluation in high-latitude areas
  Yohei Koide; Yoshiki Tokuyama; Miku Omachi; Shiori Kushida; Shuhei Okada; Minami Taguchi; Zin Mar Myint; Thet Hter San; Yuji Kishima; Kazumitsu Onishi
  Genetic Resources and Crop Evolution, 2024, [Peer-reviewed], [Lead author, Corresponding author]
  Scientific journal
• 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, 19, 19, Springer Science and Business Media LLC, 12 Dec. 2023, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
  English, Scientific journal, 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.
• 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, Dec. 2023, [Peer-reviewed], [International Magazine]
  English, Scientific journal, 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, [Peer-reviewed], [International Magazine]
  English, Scientific journal, 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.
• The attraction of genus Oryza
  Ishikawa Ryo; Yamagata Yoshiyuki; Koide Yohei; Ishii Takashige; Ishikawa Ryuji; Akimoto Masahiro; Tsuda Katsutoshi; Fujita Daisuke
  Breeding Research, advpub, Japanese Society of Breeding, 2023
  Japanese
• 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, 18 Dec. 2022, [Peer-reviewed], [International Magazine]
  English, Scientific journal, 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.
• How to establish a mutually beneficial relationship between a transposon and its host: lessons from Tam3 in Antirrhinum.
  Shasha Wang; Yohei Koide; Yuji Kishima
  Genes & genetic systems, 97, 4, 177, 184, 17 Dec. 2022, [Peer-reviewed], [Domestic magazines]
  English, Scientific journal, 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.
• Lines for blast resistance genes with genetic background of Indica Group rice as international differential variety set
  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, Wiley, Oct. 2022, [Peer-reviewed], [Lead author]
  Scientific journal
• Near-isogenic lines for resistance to blast disease, in the genetic background of the Indica Group rice (Oryza sativa L.) cultivar IR64
  Yoshimichi Fukuta; Mary Jeanie Telebanco-Yanoria; Yohei Koide; Hiroki Saito; Nobuya Kobayashi; Mitsuhiro Obara; Seiji Yanagihara
  Field Crops Research, 282, 108506, 108506, Elsevier BV, Jun. 2022, [Peer-reviewed]
  Scientific journal
• Characterization of QTLs for grain weight from New Plant Type rice cultivars through the development of near-isogenic lines with an IR 64 background
  Daisuke Fujita; Analiza G. Tagle; Yohei Koide; Eliza V. Simon; Yoshimichi Fukuta; Tsutomu Ishimaru; Nobuya Kobayashi
  Euphytica, 218, 5, Springer Science and Business Media LLC, May 2022, [Peer-reviewed]
  Scientific journal
• Seed management using NGS technology to rapidly eliminate a deleterious allele from rice breeder seeds
  Elias G. Balimponya; Maria S. Dwiyanti; Toshiaki Ito; Shuntaro Sakaguchi; Koichi Yamamori; Yoshitaka Kanaoka; Yohei Koide; Yoshifumi Nagayoshi; Yuji Kishima
  Breeding Science, Japanese Society of Breeding, 2022, [Peer-reviewed]
  Scientific journal
• Influence of Gender Bias on Distribution of Hybrid Sterility in Rice.
  Zin Mar Myint; Yohei Koide
  Frontiers in plant science, 13, 898206, 898206, 2022, [Peer-reviewed], [Last author, Corresponding author], [International Magazine]
  English, Scientific journal, 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.
• Editorial: Reproductive Barriers and Gene Introgression in Rice Species, Volume II.
  Yohei Koide; Kazuki Matsubara; Dayun Tao; Kenneth L McNally
  Frontiers in plant science, 13, 974613, 974613, Frontiers Media SA, 2022, [Lead author, Corresponding author], [International Magazine]
  English, Scientific journal
• 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, 07 Jul. 2021, [Peer-reviewed], [International Magazine]
  English, Scientific journal, 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
  Yoshiki Tokuyama; Yohei Koide; Kazumitsu Onishi; Kiwamu Hikichi; Miku Omachi; Itsuro Takamure; Yuji Kishima
  in silico Plants, 3, 2, Oxford University Press ({OUP}), 01 Jul. 2021, [Peer-reviewed], [Corresponding author]
  Scientific journal,
  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, Mar. 2021, [Peer-reviewed], [Corresponding author]
  English, Scientific journal
• Editorial: Reproductive Barriers and Gene Introgression in Rice Species.
  Dayun Tao; Kenneth L McNally; Yohei Koide; Kazuki Matsubara
  Frontiers in plant science, 12, 699761, 699761, 2021, [Corresponding author], [International Magazine]
  English
• Fertile Tetraploids: New Resources for Future Rice Breeding?
  Yohei Koide; Daichi Kuniyoshi; Yuji Kishima
  FRONTIERS IN PLANT SCIENCE, 11, Aug. 2020, [Peer-reviewed], [Lead author, Corresponding author]
  English
• Evolution of the "Neutral": Diverse Forms of Wide-Compatibility Haplotypes at the Locus for Reproductive Isolation.
  Yohei Koide
  Molecular plant, 24 Feb. 2020, [Peer-reviewed], [Invited], [Lead author, Last author, Corresponding author], [International Magazine]
  English
• 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, [Peer-reviewed], [International Magazine]
  English, Scientific journal, 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.
• Responses of earliness and lateness genes for heading to different photoperiods, and specific response of a gene or a pair of genes to short day length in rice
  Birendra Bahadur Rana; Misa Kamimukai; Mukunda Bhattarai; Yohei Koide; Masayuki Murai
  Hereditas, 156, 18 Dec. 2019, [Peer-reviewed]
• Profiling SNP and Nucleotide Diversity to Characterize Mekong Delta Rice Landraces in Southeast Asian Populations
  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, Nov. 2019, [Peer-reviewed]
  English, Scientific journal
• Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism.
  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, Oct. 2019, [Peer-reviewed], [Lead author]
• Genetic Properties Responsible for the Transgressive Segregation of Days to Heading in Rice.
  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, Mar. 2019, [Peer-reviewed], [Lead author], [International Magazine]
  English, Scientific journal, 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.
• Genetic and breeding studies on overcoming reproductive isolation barrier in inter-specific hybrids of rice
  Koide Yohei
  Breeding Research, 日本育種学会, 2019, [Lead author, Last author, Corresponding author]
  Japanese
• Lineage-specific gene acquisition or loss is involved in interspecific hybrid sterility in rice
  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, 27 Feb. 2018, [Peer-reviewed], [Lead author, Corresponding author]
  Scientific journal
• Genetic dissection of agronomic traits in introgression lines and improvement of an elite indica rice variety
  Daisuke Fujita; Yohei Koide; Nobuya Kobayashi
  Japan Agricultural Research Quarterly, 52, 2, 91, 103, Japan International Research Center for Agricultural Sciences, 2018
  English
• Identification of QTLs for agronomic characteristics in an upland New Rice for Africa (NERICA) variety
  Yohei Koide; Mitsuhiro Obara; Seiji Yanagihara; Yoshimichi Fukuta
  Japan Agricultural Research Quarterly, 52, 1, 29, 37, Japan International Research Center for Agricultural Sciences, 2018, [Peer-reviewed], [Lead author]
  English, Scientific journal
• Anther culture in rice proportionally rescues microspores according to gametophytic gene effect and enhances genetic study of hybrid sterility.
  Kanaoka Y; Kuniyoshi D; Inada E; Koide Y; Okamoto Y; Yasui H; Kishima Y
  Plant methods, 14, 102, 2018, [Peer-reviewed]
  English, Scientific journal
• Fine mapping of a quantitative trait locus for spikelet number per panicle in a new plant type rice and evaluation of a near-isogenic line for grain productivity
  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, May 2017, [Peer-reviewed]
  English, Scientific journal
• Detection of novel QTLs qDTH4.5 and qDTH6.3, which confer late heading under short-day conditions, by SSR marker-based and QTL-seq analysis
  Eri Ogiso-Tanaka; Tsuyoshi Tanaka; Keisuke Tanaka; Yasunori Nonoue; Takuji Sasaki; Erina Fushimi; Yohei Koide; Yutaka Okumoto; Masahiro Yano; Hiroki Saito
  Breeding Science, 04 Mar. 2017, [Peer-reviewed]
  English, Scientific journal
• Genetic variation in blast resistance in rice germplasm from West Africa
  Theophile Odjo; Yohei Koide; Drissa Silue; Seiji Yanagihara; Takashi Kumashiro; Yoshimichi Fukuta
  Breeding Science, 67, 5, 500, 508, Japanese Society of Breeding, 2017, [Peer-reviewed]
  English, Scientific journal
• Evaluation of genetic variation among wild rice populations in Cambodia
  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, Dec. 2015, [Peer-reviewed]
  English, Scientific journal
• Identification of QTLs and candidate genes for days to heading in an upland New Rice for Africa (NERICA) variety
  Yohei Koide; Akiko Kawasaki-Tanaka; Theophile Odjo; Mitsuhiro Obara; Seiji Yanagihara; Yoshimichi Fukuta
  EUPHYTICA, 203, 1, 153, 164, May 2015, [Peer-reviewed], [Lead author]
  English, Scientific journal
• Pathogenicity of Rice Blast (Pyricularia oryzae Cavara) Isolates from Cambodia
  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, Apr. 2014, [Peer-reviewed]
  English, Scientific journal
• The use of distantly related rice species for breeding of environmental stress tolerance : an example of genetic analysis of NERICA(Proceedings of the 41th Symposium)
  Koide Yohei
  Journal of crop research, 59, 59, 67, 71, 近畿作物・育種研究会, 2014, [Lead author]
  Japanese, Higher organisms adapt in changing environments by reorganizing a new set of genes through genetic recombination and producing a large amount of genetic variation. Therefore, the efficient use of biological resources underlying the genetic variation of crops is important for achieving the sustainable agriculture under global climate change. Here, I present an overview of the genetic studies on New Rice for Africa (NERICA) that was developed by interspecific crossings in rice, and review our recent analysis about useful and potentially useless genes introgressed from a distantly related species into NERICA.
• NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars
  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, 17 Dec. 2013, [Peer-reviewed]
  English, Scientific journal
• Detection of novel blast resistance genes, Pi58(t) and Pi59(t), in a Myanmar rice landrace based on a standard differential system
  Yohei Koide; Mary Jeanie Telebanco-Yanoria; Yoshimichi Fukuta; Nobuya Kobayashi
  MOLECULAR BREEDING, 32, 2, 241, 252, Aug. 2013, [Peer-reviewed], [Lead author]
  English, Scientific journal
• QTL for spikelet number from a high-yielding rice variety, Hoshiaoba, detected in an introgression line with the genetic background of an indica rice variety, IR64
  Yohei Koide; Daisuke Fujita; Analiza G. Tagle; Kazuhiro Sasaki; Tsutomu Ishimaru; Yoshimichi Fukuta; Nobuya Kobayashi
  EUPHYTICA, 192, 1, 97, 106, Jul. 2013, [Peer-reviewed], [Lead author]
  English, Scientific journal
• QTLs for phosphorus deficiency tolerance detected in upland NERICA varieties
  Yohei Koide; Juan Pariasca Tanaka; Terry Rose; Ayumi Fukuo; Kunihiko Konisho; Seiji Yanagihara; Yoshimichi Fukuta; Matthias Wissuwa
  PLANT BREEDING, 132, 3, 259, 265, Jun. 2013, [Peer-reviewed], [Lead author]
  English, Scientific journal
• Near isogenic lines of rice for blast resistance genes as differential varieties
  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, 30 Mar. 2012
  English
• Complex genetic nature of sex-independent transmission ratio distortion in Asian rice species: the involvement of unlinked modifiers and sex-specific mechanisms
  Y. Koide; Y. Shinya; M. Ikenaga; N. Sawamura; K. Matsubara; K. Onishi; A. Kanazawa; Y. Sano
  HEREDITY, 108, 3, 242, 247, Mar. 2012, [Peer-reviewed], [Lead author, Corresponding author]
  English, Scientific journal
• Fine mapping and identification of tightly linked DNA markers of blast resistance gene Pia by using an introgression line
  Yohei Koide; Mary Jeanie Telebanco-Yanoria; Daisuke Fujita; Analiza G. Tagle; Yoshimichi Fukuta; Nobuya Kobayashi
  MOLECULAR BREEDING, 28, 3, 359, 366, Oct. 2011, [Peer-reviewed], [Lead author]
  English, Scientific journal
• A set of near-isogenic lines for blast resistance genes with an Indica-type rainfed lowland elite rice (Oryza sativa L.) genetic background
  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, Jul. 2011, [Peer-reviewed], [Lead author]
  English, Scientific journal
• A set of near-isogenic lines of Indica-type rice variety CO 39 as differential varieties for blast resistance
  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, Mar. 2011, [Peer-reviewed], [Lead author]
  English, Scientific journal
• Characterization of Rice Blast Isolates by the Differential System and their Application for Mapping a Resistance Gene, Pi19(t)
  Yohei Koide; Mary Jeanie Telebanco-Yanoria; Fe Dela Pena; Yoshimichi Fukuta; Nobuya Kobayashi
  JOURNAL OF PHYTOPATHOLOGY, 159, 2, 85, 93, Feb. 2011, [Peer-reviewed], [Lead author]
  English, Scientific journal
• Development of near-isogenic lines of Japonica-type rice variety Lijiangxintuanheigu as differentials for blast resistance
  Mary Jeanie Telebanco-Yanoria; Yohei Koide; Yoshimichi Fukuta; Tokio Imbe; Hiroshi Kato; Hiroshi Tsunematsu; Nobuya Kobayashi
  BREEDING SCIENCE, 60, 5, 629, 638, Dec. 2010, [Peer-reviewed]
  English, Scientific journal
• Development of pyramided lines with two resistance genes, Pish and Pib, for blast disease (Magnaporthe oryzae B. Couch) in rice (Oryza sativa L.)
  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, Dec. 2010, [Peer-reviewed], [Lead author]
  English, Scientific journal
• 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, [Peer-reviewed], [Lead author]
  English
• Resistance Genes and Selection DNA Markers for Blast Disease in Rice (Oryza sativa L.)
  Yohei Koide; Nobuya Kobayashi; Donghe Xu; Yoshimichi Fukuta
  JARQ-JAPAN AGRICULTURAL RESEARCH QUARTERLY, 43, 4, 255, 280, Oct. 2009, [Peer-reviewed], [Lead author]
  English
• Blast resistance genes and their selection markers in rice (Oryza sativa L.)
  KOIDE Yohei; KOBAYASHI Nobuya; XU Donghe; FUKUTA Yoshimichi
  JIRCAS Working Rep, 63, 95, 122, 31 Mar. 2009, [Lead author]
  English
• Two loosely linked genes controlling the female specificity for cross-incompatibility in rice
  Yohei Koide; Mitsunobu Ikenaga; Yuhei Shinya; Kazuki Matsubara; Yoshio Sano
  EUPHYTICA, 164, 3, 753, 760, Dec. 2008, [Peer-reviewed], [Lead author, Corresponding author]
  English, Scientific journal
• The evolution of sex-independent transmission ratio distortion involving multiple allelic interactions at a single locus in rice
  Yohei Koide; Mitsunobu Ikenaga; Noriko Sawamura; Daisuke Nishimoto; Kazuki Matsubara; Kazumitsu Onishi; Akira Kanazawa; Yoshio Sano
  GENETICS, 180, 1, 409, 420, Sep. 2008, [Peer-reviewed], [Lead author, Corresponding author]
  English, Scientific journal
• Sex-independent transmission ratio distortion system responsible for reproductive barriers between Asian and African rice species
  Yohei Koide; Kazumitsu Onishi; Daisuke Nishimoto; Akhil Ranjan Baruah; Akira Kanazawa; Yoshio Sano
  NEW PHYTOLOGIST, 179, 3, 888, 900, 2008, [Peer-reviewed], [Lead author]
  English, Scientific journal
• Genetics of speciation in rice
  Yohei Koide; Kazumitsu Onishi; Akira Kanazawa; Yoshio Sano
  Biotechnology in Agriculture and Forestry, 62, 247, 259, Springer International Publishing, 2008, [Peer-reviewed], [Lead author]
  English, In book
• 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, 44, 3, 4, The Crop Science Society of Japan, Dec. 2003
  Japanese

• Identification of hybrid sterility gene S13 detected in African wild rice, Oryza longistaminata
  高西若菜; MAR MYINT Z.; 貴島祐治; 金澤章; 小出陽平, 育種学研究, 26, 2024
• Identification of the causative gene for the hybrid sterility and its application to the breeding in rice (Oryza sativa)
  MAR Myint Zin; 小出陽平, 飯島藤十郎記念食品科学振興財団年報, 39, 2024
• Three dimensional live imaging analysis of cellular growth dynamics in the grass leaf primordium
  徳山芳樹; 田口みなみ; KELLY-BELLOW Robert; SMITH Richard S.; 貴島祐治; 小出陽平, 育種学研究, 26, 2024
• Fertility-related QTL and segregation distortion in tetraploid rice
  蒲池行美; 岡田脩平; 片岡成海; MYINT Z.; 貴島祐治; 小出陽平, 育種学研究, 26, 2024
• Analysis of 3D growth pattern in primordia of rice husk
  三浦誠一朗; 徳山芳樹; 田口みなみ; 貴島祐治; 小出陽平, 育種学研究, 26, 2024
• Wild and cultivated allele effects at PROG1 and TAC1 loci for plant architecture in rice
  後迫萌々花; 徳山芳樹; 小出陽平; 石井尊生, 育種学研究, 26, 2024
• Time-series analysis of kinematics of the main culm and tillers in wild rice in micro-gravity condition
  串田栞理; 徳山芳樹; 石井尊生; 貴島祐治; 小出陽平, 育種学研究, 26, 2024
• Three-dimensional cellular growth dynamics in the whole tissue of rice leaf primordium
  田口みなみ; 徳山芳樹; Kelly-Bellow Robert; SMITH Richard S.; 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), 65, 2024
• Fine-mapping of hybrid sterility gene S2 locus between Asian rice and Africa rice species
  CHOI KWAN; ZIN Mar Myint; 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), 65, 2024
• Analysis of twisting formation principle in rice twisted leaf mutant and its genetic analysis
  曵地究; 岡田脩平; 徳山芳樹; 高牟禮逸郎; 貴島祐治; 小出陽平, 育種学研究, 25, 2023
• Estimation of a novel locus associated with seed-shattering degree in African cultivated rice, Oryza glaberrima
  山崎美樹; 前田安紗実; LIM Sathya; 石井尊生; 山形悦透; 小出陽平; 藤田大輔; 石川亮, 育種学研究, 25, 2023
• Single-cell growth analysis of rice leaf primordium by 3D timelapse scanning
  徳山芳樹; KELLY-BELLOW Robert; SMITH Richard S.; 小出陽平, 育種学研究, 25, 2023
• QTL analysis using segregation population of autotetraploid rice
  岡田脩平; 蒲池行美; MYINT Zin Mar; 貴島祐治; 小出陽平, 育種学研究, 25, 2023
• Detection of meiotic abnormality in interspecific hybrids between Asian and African rice species by immunostaining method
  石原萌; 國吉大地; 小出陽平; 長岐清孝; 貴島祐治, 育種学研究, 24, 2022
• Control of heading dates by low-temperature and its relationship with photosensitive genes
  高鳥将希; 坂口俊太郎; 小出陽平; 藤野賢治; 貴島祐治, 育種学研究, 24, 2022
• Variation of seed-shattering degree in African cultivated rice, Oryza glaberrima
  山崎美樹; 前田安紗実; LIM Sathya; 石井尊生; 山形悦透; 小出陽平; 藤田大輔; 石川亮, 育種学研究, 24, 2022
• Time-series 3D analysis of tiller rotation around the apical-basal axis in wild rice
  串田栞理; 徳山芳樹; 貴島祐治; 小出陽平, 育種学研究, 24, 2022
• 3D analysis of wild rice architecture using photogrammetry
  徳山芳樹; 串田栞理; 曳地究; 貴島祐治; 小出陽平, 育種学研究, 24, 2022
• Phenotipic analysis of twisted leaf mutatant using micro CT
  岡田脩平; 曵地究; 徳山芳樹; 小出陽平; 貴島祐治; 高牟禮逸郎, 日本育種学会・日本作物学会北海道談話会会報(Web), 63, 2022
• 雑種強勢を示すF1イネのマルチオミクス解析
  保坂碧; 保坂碧; 木田春菜; 小出陽平; 辻寛之; 辻寛之, 日本植物学会大会研究発表記録(CD-ROM), 86th, 2022
• Genome-wide association study for heading date using panel of African rice (Oryza glaberrima Steud.)
  平尾愛喜; 藤田大輔; 石川亮; 小出陽平; 安井秀; 山形悦透, 育種学研究, 23, 2021
• アフリカ栽培イネの種皮成分に関するゲノムワイド関連解析
  小出 陽平, 報告書 / エリザベス・アーノルド富士財団 [編], 214, 221, 2021
  エリザベス・アーノルド富士財団, Japanese
• 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, 62, 42, 43, 2021
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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, 62, 46, 47, 2021
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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, 62, 40, 41, 2021
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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, 62, 44, 45, 2021
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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, 62, 38, 39, 2021
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• Morphogenesis modeling of seed pods of soybean
  曳地究; 徳山芳樹; DWIYANTI M.; 小出陽平, 育種学研究, 23, 2021
• 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
• 野生イネにおける放射状草姿の形成機構
  徳山芳樹; 小出陽平, 日本植物学会大会研究発表記録(CD-ROM), 84th, 2020
• 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, 61, 60, 61, 2020
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, English
• 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, 61, 58, 59, 2020
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, English
• Computational modeling of radial plant type forming in wild rice
  徳山芳樹; 大西一光; 小出陽平, 育種学研究, 22, 2020
• Simulating rice domestication using tissue-level growth modeling
  小出陽平, 育種学研究, 22, 2020
• Genetic analysis of the mutant showing zebra chlorosis and tillering dwarf in rice
  池田慧; GARCON J.; 永井麻美子; 川島拓也; 伊藤豪志; 小出陽平; 高牟禮逸朗, 育種学研究, 22, 2020
• 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
• Evaluation of genetic diversity by resequencing of a diversity panel of African rice (Oryza glaberrima)
  平尾愛喜; 藤田大輔; 石川亮; 小出陽平; 安井秀; 山形悦透, 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
• 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
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• Genetic analysis of spikelet mutants for morphogenesis in rice (Focused on sterile lemmas and rudimentary glumes)
  Nagai M; Garcon J E; Ikeda S; Kiode Y; Takamure I, Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, 60, 0, 46, 47, 2019
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• Tiller angle dynamics of wild and cultivated rice
  Tokuyama Y; Onishi K; Koide Y, Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, 60, 0, 80, 80, 2019
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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, 22 Sep. 2018
  Japanese
• 熱帯アジアにおける栽培イネから野生イネへの遺伝子流動について
  谷尾侑香; ORN Chhourn; 秋本正博; 宍戸理恵子; HTUN Than Myint; PHAN Phuong; Dang Thai; 野々村賢一; 小出陽平; 石川亮; 石井尊生, 育種学研究, 20, 131, 22 Sep. 2018
  Japanese
• イネ雑種不稔遺伝子S1の中立対立遺伝子作出と原因遺伝子の特定
  小出陽平; 荻野篤史; 吉川貴徳; 吉川貴徳; 北嶋ゆき; 齋藤希; 金岡義高; 大西一光; 吉竹良洋; 築山拓司; 齊藤大樹; 齊藤大樹; 寺石政義; 山形悦透; 植村亜衣子; 高木宏樹; 林依子; 阿部知子; 福田善通; 奥本裕; 金澤章, 育種学研究, 20, 41, 22 Sep. 2018
  Japanese
• 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, 25 Mar. 2018
  Japanese
• 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
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• Molecular evolutionaly analysis on interspecific hybrid sterility locus in rice
  Kitashima Y; Saito N; Koide Y, Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, 59, 0, 10, 11, 2018
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• Genetic analysis of the early heading gene derived from rice variety Reimei.
  Ikeda S; Kawahara C; Garcon JE; Nagano H; Koide Y; Bahadur RB; Murai M; Takamure I, Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, 59, 0, 14, 15, 2018
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• The rice interspecific hybrid sterility gene S2 is located on chromosome 4
  Ogata M; Koide Y, Report of the Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, 59, 0, 8, 9, 2018
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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, 07 Oct. 2017
  Japanese
• 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, 07 Oct. 2017
  Japanese
• Genetic analysis of transgressive segregation for early heading trait derived from rice varieties in Hokkaido
  坂口俊太郎; 内山尭; 太田雄也; 手塚あゆみ; 永野惇; 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, 0, 14‐15(J‐STAGE), 15, 2017
  Hokkaido Branch, the Japanese Society of Breeding and Hokkaido Branch, the Crop Science Society of Japan, Japanese
• 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
  Japanese
• 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
  Japanese
• 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
  Japanese
• 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
  Japanese
• Mapping of a quantitative trait locus for spikelet number per panicle, qTSN12.2, and its impact on grain productivity
  Sasaki Kazuhiro; Fujita Daisuke; Koide Yohei; D. Lumanglas Patrick; B. Gannaban Ritchel; G. Tagle Analiza; Fukuta Yoshimichi; Kobayashi Nobuya; Ishimaru Tsutomu, Abstracts of Meeting of the CSSJ, 244, 0, 44, 44, 2017
  CROP SCIENCE SOCIETY OF JAPAN, Japanese
• 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, 24 Sep. 2016
  Japanese
• 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, 24 Sep. 2016
  Japanese
• イネ群落形成パターンに対する出穂期突然変異遺伝子の効果
  伏見栄利奈; 齊藤大樹; 小出陽平; 小出陽平; GUO W; 二宮正士; 谷坂隆俊; 谷坂隆俊; 奥本裕, 育種学研究, 18, 126, 21 Mar. 2016
  Japanese
• Development of a high-throughput method for examining the intra-genic recombination frequency in Wx locus in rice using an image analysis
  Uenoyama Anan; Koide Yohei; Tsukiyama Takuji; Teraishi Masayoshi; Okumoto Yutaka, Journal of Crop Research, 61, 0, 45, 49, 2016
  Plant breeding is to select agronomically valuable genotypes from a diverse set of gene combinations established through hybridizations and subsequent genetic recombinations. Therefore, it is important for the breeding science to understand how to control the recombination frequency. In the present study, we developed a new high-throughput method for analyzing the recombination frequency within wx locus in rice using an image processing software(ImageJ) and analyzed the effect of a retrotransposon(RT) on the recombination frequency around it. To develop the method, we used two near-isogenic rice lines, T65wx and 73wx1. These lines have different mutations on Wx gene, which controls starch synthesis in rice. Although these two lines produce only wx type pollen, F₁ plants developed from a cross between them produce Wx type pollen in a low frequency because of an intra-genic recombination between the two mutations on Wx locus. Therefore, it is possible to analyze the recombination frequency from a frequency of Wx type pollen. In this study, we used an image processing techniques for counting the total number of pollen grains. This enabled us to count the number of pollen grains more efficiently and precisely. By using the method described in this report, we also examined the effect of RT-insertion and found that an RT insertion on Wx gene reduces the intra-genic recombination frequency around the insertion., The Society of Crop Science and Breeding in Kinki, Japan, Japanese
• 重イオンビーム照射によるイネ生殖隔離障壁打破への取り組み
  小出陽平; 小出陽平; 築山拓司; 寺石政義; 奥本裕; 阿部知子, 変異創成によるグリーンイノベーションの未来-花・食・エネルギー 理研シンポジウム 仁科加速器研究センター応用研究開発室品種改良ユーザー会報告書2015 平成28年, 2, 2016
  Japanese
• 野生イネOryza australiensis由来のいもち病抵抗性遺伝子Pi40(t)は栽培イネOryza sativaのPiz‐tと同一である
  橋本沙也加; TELEBANCO‐YANORIA Mary Jeanie; JENA Kshirod.K; 小林伸哉; 小出陽平; 藤田泰成; 福田善通, 育種学研究, 17, 25, 21 Mar. 2015
  Japanese
• インド型イネ品種の籾収量を増加させる遺伝子SPIKE
  小林伸哉; 藤田大輔; TAGLE Analiza G; 小出陽平; 佐々木和浩; GANNABAN Ritchel B; 柳原誠司; 福田善通; 石丸努, 育種学研究, 16, 65, 21 Mar. 2014
  Japanese
• IRRI育成New Plant Typeイネ品種由来の粒数増加に関するQTLの検出と評価
  藤田大輔; TAGLE Analiza G; GANNABAN Ritchel B; 小出陽平; 福田善通; 小林伸哉, 育種学研究, 13, 313, 29 Mar. 2011
  Japanese
• Development of near-isogenic lines of Japonica-type rice variety Lijiangxintuanheigu as differentials for blast resistance
  Mary Jeanie Telebanco-Yanoria; Yohei Koide; Yoshimichi Fukuta; Tokio Imbe; Hiroshi Kato; Hiroshi Tsunematsu; Nobuya Kobayashi, BREEDING SCIENCE, 60, 5, 629, 638, Dec. 2010
  English
• インド型イネ品種IR64染色体断片導入系統を用いた粒重に関するQTLの検出と準同質遺伝子系統の作出
  藤田大輔; TAGLE Analiza G; 小出陽平; 福田善通; 小林伸哉, 育種学研究, 12, 287, 24 Sep. 2010
  Japanese
• 染色体導入系統で検出した多収性イネ品種ホシアオバ由来の一穂籾数に関与するQTL
  小出陽平; 藤田大輔; TAGLE Analiza; TELEBANCO‐YANORIA Mary Jeanie; 福田善通; 小林伸哉, 育種学研究, 12, 310, 26 Mar. 2010
  Japanese
• 判別品種としてのUS‐2準同質遺伝子系統群のいもち病抵抗性評価
  川崎顕子; TELEBANKO‐YANORIA Mary Jeanie; 小出陽平; 小林伸哉; 林長生; SANTOSO S; PHETMANYSENG; Xangsayasane; JENNIFER T.Niones; HA Thi Thu Pham; 福田善通, 育種学研究, 12, 252, 26 Mar. 2010
  Japanese
• インド型イネ品種IR64を遺伝的背景とする出穂および一穂籾数の準同質遺伝子系統の作出
  小林伸哉; 藤田大輔; TAGLE Analiza G; TELEBANCO‐YANORIA Mary Jeanie; 小出陽平; 福田善通, 育種学研究, 12, 321, 26 Mar. 2010
  Japanese
• A role of the centromere region of chromosome 6 in the cross-incompatibility between rice species
  Shinya Y; Koide Y; Matsubara K; Ikenaga M; Sano Y, 日本育種学会・日本作物学会北海道談話会会報, 50, 31, 32, Dec. 2009
  The Crop Science Society of Japan, Japanese
• Polymorphisms of genes in the S1 locus which induces reproductive barrier between Asian and African rice species
  Ogino A; Koide Y; Onishi K; Kanazawa A; Sano Y, 日本育種学会・日本作物学会北海道談話会会報, 50, 33, 34, Dec. 2009
  The Crop Science Society of Japan, Japanese
• イネの遠縁種間交雑で雑種不稔を導く遺伝子座S13における中立的な新規対立遺伝子S13ⁿのfine mapping
  池ケ谷智仁; 小出陽平; 佐野芳雄; 金澤章, 育種学研究, 11, 256, 25 Sep. 2009
  Japanese
• アジア‐アフリカイネ間の生殖的隔離に寄与するS₁遺伝子座における遺伝子多型
  荻野篤史; 小出陽平; 大西一光; 金澤章; 佐野芳雄, 育種学研究, 11, 255, 25 Sep. 2009
  Japanese
• フィリピン産標準判別いもち病菌菌系に対して広い抵抗性スペクトラムを示す新規抵抗性遺伝子の同定
  小出陽平; TELEBANKO‐YANORIA Mary Jeanie; 福田善通; 小林伸哉, 育種学研究, 11, 39, 25 Sep. 2009
  Japanese
• Polymorphisms and expression of genes in the candidate region of S_1, a gene responsible for hybrid sterility between Asian and African rice species
  Ogino A; Koide Y; Onishi K; Nishimoto D; Baruah Akhil Ranjan; Horigome A; Kanazawa A; Sano Y, 日本育種学会・日本作物学会北海道談話会会報, 49, 9, 10, Dec. 2008
  The Crop Science Society of Japan, Japanese
• A sterility between rice species S_<13^n>, a novel allele at the S_<13> locus that induces hybrid sterility between rice species
  Ikegaya T; Koide Y; Sano Y; Kanazawa, 日本育種学会・日本作物学会北海道談話会会報, 49, 7, 8, Dec. 2008
  The Crop Science Society of Japan, Japanese
• Genetic complexity of the female reaction in cross incompatibility between wild and caltivated rice
  Shinya Y; Koide Y; Matsubara K; Ikenaga M; Sano Y, 日本育種学会・日本作物学会北海道談話会会報, 49, 5, 6, Dec. 2008
  The Crop Science Society of Japan, Japanese
• Hybrid male sterility induced by S13 found in a distantly related rice species
  Yohei Koide; Tomohito Ikegaya; Daisuke Nishimoto; Akira Kanazawa; Yoshio Sano, GENES & GENETIC SYSTEMS, 82, 6, 522, 522, Dec. 2007
  English, Summary international conference
• Comparative genetic studies of hybrid sterility on chromosome 6 in rice
  Koide Y; Sinya Y; Onishi K; Kanazawa A; Sano Y, 日本育種学会・日本作物学会北海道談話会会報, 48, 11, 12, Dec. 2007
  The Crop Science Society of Japan, Japanese
• Polymorphisms in the candidate gene region of S13, a pollen killer detected by a cross between distantly related rice species
  Ikegaya T; Koide Y; Sano Y; Kanazawa A, 日本育種学会・日本作物学会北海道談話会会報, 48, 13, 14, Dec. 2007
  The Crop Science Society of Japan, Japanese
• イネ遠縁種間交雑において雄性配偶子致死を誘導する遺伝子S13の解析
  小出陽平; 池ケ谷智仁; 西本大祐; 金澤章; 佐野芳雄, 日本遺伝学会大会プログラム・予稿集, 79th, 91, 07 Sep. 2007
  Japanese
• Comparative genetics of a hybrid sterility gene found between O.sativa and O.longistaminata
  Takasuke Taneichi; Yohei Koide, GENES & GENETIC SYSTEMS, 81, 6, 445, 445, Dec. 2006
  English, Summary international conference
• Genetic dissection of pollen killer found in Oryza longistaminata
  Taneichi T; Koide Y; Kanazawa A; Sano Y, 日本育種学会・日本作物学会北海道談話会会報, 47, 21, 22, Dec. 2006
  The Crop Science Society of Japan, Japanese
• Hybrid sterility gene S13 found in a distantly related rice species, O-longistaminata
  TANEICHI TAKASUKE; KOIDE YOHEI; NISHIMOTO DAISUKE; SANO YOSHIO, GENES & GENETIC SYSTEMS, 80, 6, 477, 477, Dec. 2005
  English, Summary international conference
• Genes responsible for reproductive isolation found near the centromere region of chromosome 6 in rice
  Ikenaga M; Koide Y; Matsubara K; Sano Y, 日本育種学会・日本作物学会北海道談話会会報, 44, 1, 2, Dec. 2003
  日本作物学会, Japanese
• Changes in recombination frequency under different genetic backgrounds in rice
  Koide Y; Nishimoto D; Onishi K; Nagano H; Sano Y, 日本育種学会・日本作物学会北海道談話会会報, 43, 13, 14, Nov. 2002
  日本作物学会, Japanese

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• 植物の地下部バイオマスが増大する機構の研究
  科学研究費助成事業
  27 Jun. 2025 - 31 Mar. 2028
  久保 友彦; 黒田 洋輔; 北崎 一義; 小出 陽平
  日本学術振興会, 挑戦的研究(萌芽), 北海道大学, 25K22354
• アフリカのイネジーンプールに潜在する有用遺伝子の計画的利用に向けた種間雑種戦略
  科学研究費助成事業
  01 Apr. 2021 - 31 Mar. 2025
  小出 陽平; 山形 悦透; 石川 亮; 藤田 大輔
  将来の食糧安定生産のため、利用可能な遺伝子プールを拡大することは、育種学の使命の一つである。アフリカ栽培・野生イネは、膨大な遺伝変異を有するが、有用遺伝子探索がほとんど行われていない未利用遺伝資源である。本研究では、ゲノム情報を利用した効率的な遺伝子探索システムをアフリカイネに適用し、初期生育や耐虫性などの有用形質に関わる遺伝子の迅速な単離を行う。また、雑種不稔性を回避する種間橋渡し系統を確立し、異種遺伝子の利用を促進するとともに、未解明である種間雑種強勢の遺伝基盤を明らかにし、種間雑種の新しい活用法を構築する。
  これまでに、主に、独自のアフリカ栽培イネ集団をもちいたゲノム解析を行い、データを参照配列である日本晴にマッピングした際に得られるSNP情報に基づくゲノムワイド関連解析実験系を構築した。この実験系を用いることで様々な形質に関してゲノムワイド関連解析を行うことが可能となった。さらに、SNP情報より、アフリカ栽培イネを複数の分集団に区分し、各分集団ごとの系統の特徴化を進めた。また、アフリカ栽培イネが持つ遺伝子の単離を迅速に行うために、分集団ごとに系統を選抜し、これら系統の交配による組換え自殖系統群作出を行った。当該年度においては、F3世代まで世代促進を進めた。さらに、アフリカイネが持つ初期生育性や耐虫性など、特徴的な表現型の予備的解析を行った。その結果、初期生育の旺盛さに関与すると考えられる第2葉と第3葉の葉身長にアフリカ栽培イネ内で表現型多型があることが示された。ゲノムワイド関連解析を行ったところ、第2葉葉身長および第3葉葉身長と有意に関連のある染色体領域が明らかとなった。また、複数の種間雑種不稔遺伝子について、遺伝子同定に向けた準備を行うとともに、ゲノム編集による遺伝子ノックアウトの実験系の構築を進めた。
  日本学術振興会, 基盤研究(B), 北海道大学, 23K21183
• アフリカのイネジーンプールに潜在する有用遺伝子の計画的利用に向けた種間雑種戦略
  科学研究費助成事業
  01 Apr. 2021 - 31 Mar. 2025
  小出 陽平; 山形 悦透; 石川 亮; 藤田 大輔
  日本学術振興会, 基盤研究(B), 北海道大学, 21H02160
• 器官成長モデリングによる作物の3D構造形成の原理解明と予測技術の開発
  科学研究費助成事業
  09 Jul. 2021 - 31 Mar. 2024
  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, 挑戦的研究(萌芽), 北海道大学, 21K19101
• 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
  科学研究費助成事業
  01 Apr. 2019 - 31 Mar. 2023
  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, 基盤研究(A), 北海道大学, 19H00937
• Identification and utilization of QTLs for the regulation of rice juvenile-adult phase transition
  Grants-in-Aid for Scientific Research
  01 Apr. 2019 - 31 Mar. 2022
  Yoshikawa Takanori
  In the present study, we identified the genetic factors involved in the differentiation of juvenile-adult phase transition during vegetative growth between rice japonica and indica varieties, and attempted to elucidate the effect of phase transition on agricultural traits. The main results were 1) identification of the causal genes for qJA1 and qJA2, and finding related pathways in the transcriptome. 2) We found that the japonica alleles of qJA1 and qJA2 may be suitable for cultivation in high latitude areas. 3) The effect of the growing environment on the phase transition was clarified. 4) It was found that the defense response mechanism against blast disease changes as the progresses of growing stage.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Kyoto University, 19H02929
• Understanding of genetic basis on differences in sterility in hybrids of diploid and tetraploid rice
  Grants-in-Aid for Scientific Research
  01 Apr. 2018 - 31 Mar. 2022
  Koide Yohei
  Rice, the staple food of the Japanese, is a diploid plant. On the other hand, it is possible to produce tetraploid rice, in which the number of chromosomes is doubled, by treatment with chemical substances such as colchicine. Although it has been suggested that tetraploid rice plants have higher seed fertility when hybridized compared to diploid rice plants, this study found abnormal vegetative growth other than low seed fertility in tetraploid hybrids, which may be a new breeding barrier.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, 18K05565
• Improvement of sustainability for crop production and development of next-generation plant resource through gene circulation between relative species
  Grants-in-Aid for Scientific Research
  19 Jul. 2016 - 31 Mar. 2020
  FUJITA DAIUSKE
  In this study, there are three parts. (1) The whole genome sequence of 150 accessions of African rice (Oryza glaberrima) that is maintained in genetic resource center of International Rice Research Institute had been conducted through next-generation sequencer. A lot of SNPs are detected through whole genome sequence data. (2) The biotic stress and yield related traits on 150 accessions of African rice were characterized. The multiple gene loci for these characteristics were detected by Genome-wide association study based on SNP information. (3) To develop next generation plant resource, BC1F1 seeds from multiple cross combinations between indica rice line with mitigating sterility and African rice were developed.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Saga University, 16KT0034
• Rice breeding strategy with the use of active transposable elements
  Grants-in-Aid for Scientific Research
  01 Apr. 2014 - 31 Mar. 2019
  OKUMOTO Yutaka
  Non-autonomous transposable element mPing is actively transposing in the genome of rice variety Gimbozu. To reveal the usage of mPing as a tool to develop novel breeding strategy, we analyzed the novel traits closely related to the mPing transposition. At first, several stress tolerant plants could be selected from Gimbozu population. In addition, a novel mPing insertion specifically observed in a tolerant line causes the activation of the downstream gene under the stress condition. Secondary, slender-glume mutant line (IM294) derived from Gimbozu is frequently reverted to a normal-glume plant as the result of excision of mPing inserted at the Rurm1 gene. Among the reverse mutants, a few plants (VGI: Vigorously growing IM294) which exceptionally exhibited the vigorous growth are segregating. All the VGI plants harbor large number of newly inserted mPing. Induction of tentative heterozygosity caused by the newly inserted mPing elements may trigger the vigorous growth.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (A), Kyoto University, 26252002
• Clarification of gene flow between wild and cultivated rice in tropical Asian countries
  Grants-in-Aid for Scientific Research
  01 Apr. 2014 - 31 Mar. 2017
  ISHII TAKASHIGE; Nguyen Thi Lang; Phuong Dang Thai Phan; Ouk Makara; Tin Htut; Than Myint Htun
  In order to figure out the nature of Asian wild rice, Oryza rufipogon, natural wild populations were investigated in three tropical Asian countries, Vietnam, Cambodia and Myanmar. Based on the genetic variation among wild populations using molecular markers, genetic population structures of annual and perennial wild rice were found to vary according to the propagation manners and environmental conditions. Gene flow between wild and cultivated rice was detected using molecular markers on domestication traits. It suggests that frequency of the gene flow is mainly due to the plant distribution conditions.
  Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Kobe University, 26304020
• Genetic studies on the S1 gene, which induces sterility in heterozygotes in rice
  Grants-in-Aid for Scientific Research
  01 Apr. 2014 - 31 Mar. 2016
  Koide Yohei
  To utilize the inter-specific hybrid vigor, it is necessary to understand the genetic mechanisms inducing hybrid sterility, which is a major obstacle for using hybrids in rice. Previous studies showed that the S1 chromosomal region causes seed sterility in hybrids between African rice species, O. glaberrima and Asian rice species, O. sativa. In this study, I used a mutant for hybrid sterility induced by the S1 chromosomal region. By using RNA-seq analysis, I identified one candidate gene carrying the mutation. I revealed that hybrid sterility phenotype is complemented by transformation of the candidate gene into the mutant.
  Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), Kyoto University, 26850003
• イネ種間雑種強勢の実用化に向けた雑種不稔遺伝子S1の単離と変異体作出
  科学研究費助成事業
  30 Aug. 2013 - 31 Mar. 2015
  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, 研究活動スタート支援, 京都大学, 25892014
• アフリカでの高生産性イネ育種のためのNERICA遺伝子構成解明と選抜マーカー開発
  科学研究費助成事業
  2010 - 2012
  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。
  日本学術振興会, 特別研究員奨励費, 独立行政法人国際農林水産業研究センター, 10J06429