Updated on 2025/03/14
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Updated on 2025/03/14
Plant breeding
Genetics
Genetic diversity
Rice
Others / Others / Plant genetics and breeding
Environmental Science/Agriculture Science / Science in plant genetics and breeding
Utilization of DNA markers in rice
イネの収量性に関与する形質の遺伝解析
名古屋大学大学院生命農学研究科准教授
2008.3
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Country：Japan
九州大学大学院農学研究院生物資源開発管理学部門助教
2007.4
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Country：Japan
九州大学大学院農学研究院生物資源開発管理学部門助手
2003.4
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Country：Japan
九州大学大学院農学研究院助手
2000.4
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Country：Japan
九州大学農学部助手
1999.4
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Country：Japan
Kyushu University Graduate School, Division of Agriculture
1995.4 - 1999.3
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Country： Japan
Kyushu University Graduate School, Division of Agriculture
1993.4 - 1995.3
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Country： Japan
Kyushu University Faculty of Agriculture Department of Agriculture
1989.4 - 1993.3
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Country： Japan
Japanese Society of Breeding
Development of an Aus-Derived Nested Association Mapping (Aus-NAM) Population in Rice Reviewed Open Access
Justine K. Kitony, Hidehiko Sunohara, Mikako Tasaki, Jun-Ichi Mori, Akihisa Shimazu, Vincent P. Reyes, Hideshi Yasui, Yoshiyuki Yamagata, Atsushi Yoshimura, Masanori Yamasaki, Shunsaku Nishiuchi, Kazuyuki Doi
Plants Vol. 10 ( 6 ) page： 1255 - 1255 2021.6
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Language：English Publishing type：Research paper (scientific journal) Publisher：MDPI AG
A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study (GWAS). Ehd1 was detected in all the seven families and all the methods. On the other hand, Hd1 and Ghd7 were detected in some families, and joint QTL mapping and GWAS-based methods resulted in weaker and uncertain peaks. Overall, the high allelic variations in aus-NAM provide a valuable genetic resource for the rice community.
Leaf Na+ effects and multi-trait GWAS point to salt exclusion as the key mechanism for reproductive stage salinity tolerance in rice.
de Ocampo MP, Tam BP, Egdane JA, Chebotarov D, Doi K, Yamauchi A, Ismail AM, Henry A, Mitsuya S
Annals of botany 2024.12
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Detection of QTLs regulating the second internode length in rice dwarf mutant <i>d1</i> Open Access
Ha Quynh T., Moe Sandar, Reyes Vincent Pamugas, Doi Kazuyuki, Miura Kotaro, Mizushima Mio, Maeno Akiteru, Tsuda Katsutoshi, Nagai Keisuke, Ashikari Motoyuki
Breeding Science Vol. 74 ( 5 ) page： 443 - 453 2024.12
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Language：English Publishing type：Research paper (scientific journal) Publisher：Japanese Society of Breeding
<p>Stem length is a crucial agronomic trait in rice breeding. The short stature of rice dwarf mutants is caused by shortening of internodes, resulting in five distinct internode elongation patterns: dn, dm, d6, nl and sh. Several genetic studies have been conducted; however, the genetic mechanisms underlying these internode elongation patterns remain unclear. In this study, we examined two Daikoku dwarf (<i>d1</i>) mutants, T65(<i>d1-1</i>) and Kin(<i>d1-7</i>), which display contrasting internode elongation phenotypes. Anatomical observation revealed that T65(<i>d1-1</i>) exhibits a dm-type internode elongation pattern due to the lack of the second internode counted from the top, while Kin(<i>d1-7</i>) shows a dn-type pattern with a relatively elongated second internode. To identify the genetic factors influencing these phenotypes, we conducted a quantitative trait locus (QTL) analysis using two F<sub>2</sub> populations derived from reciprocal crosses between them. The QTL analysis showed that the second internode length is regulated by three QTLs on chromosomes 4, 5, and 6. Epistatic effects were observed through the analysis of F<sub>3</sub> progenies, indicating that the combination of Kin(<i>d1-7</i>) alleles at these QTLs is associated with an increased second internode length. Furthermore, specific combinations of alleles result in varying degrees of elongation in the second internode, significantly impacting the internode elongation pattern. These findings contribute to a deeper understanding of the genetic factors influencing the internode elongation patterns in rice.</p>
DOI： 10.1270/jsbbs.24036
Evaluation of Grain-Filling-Related Traits Using Taichung 65 x DV85 Chromosome Segment Substitution Lines (TD-CSSLs) of Rice. Reviewed Open Access
Mabreja AD, Reyes VP, Soe TK, Shimakawa K, Makihara D, Nishiuchi S, Doi K
Plants (Basel, Switzerland) Vol. 13 ( 2 ) 2024.1
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Language：English Publisher：Plants
Grain yield of rice consists of sink capacity and grain filling. There are some genes known to contribute to sink capacity, but few genes associated with grain filling are known. We conducted a genetic analysis on yield-related traits by using a chromosome segment substitution line population that have introgression from DV85, an aus variety of rice, in the background of T65, a japonica variety. Refined whole-genome genotypes of the 43 TD-CSSLs were obtained by genotyping-by-sequencing. The effects of previously detected quantitative trait loci (QTLs), qNSC1 and qNSC2, were confirmed by the amount of non-structural carbohydrate (NSC) at 5 days after heading (DAH). The CSSL for qSWTR11, the QTL for decrease in shoot weight during the maturity stage, showed the highest NSC at 5 DAH and lowest at 35 DAH. The brown rice yield of these lines were not stably significant. Most of the sink-related traits correlated between the 2 tested years, but most of the grain-filling traits did not show correlation between the 2 years. Correlation analysis revealed that the sink capacity is stable and primarily determines the yield, and grain filling is more affected by the environment. In addition, biomass production before heading and during the maturity stage contributes to higher yield in TD-CSSLs, and the amount of translocation of stem reserve does not affect much to the yield. We conclude that higher NSC at the heading stage and rapid decrease in shoot biomass during the maturity stage did not directly contribute to the yield formation in the japonica genetic background.
Contribution of genes related to grain number (<i>Gn1a</i> and <i>WFP</i>) introgressed into NERICA 1 to grain yield under tropical highland conditions in central Kenya Reviewed Open Access
Mayumi Kikuta, Daniel Makori Menge, Emily Waringa Gichuhi, Hiroaki Samejima, Rena Tomita, John Munji Kimani, Ruth Nzisa Musila, Kazuyuki Doi, Motoyuki Ashikari, Rosalyn Angeles-Shim, Kshirod Kumar Jena, Daigo Makihara
Plant Production Science Vol. 26 ( 3 ) page： 309 - 319 2023.7
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Language：English Publishing type：Research paper (scientific journal) Publisher：Informa UK Limited
Tomita R, Reyes VP, Fukuta Y, Gichuhi EW, Kikuta M, Menge DM, Doi K, Makihara D
Plants (Basel, Switzerland) Vol. 12 ( 4 ) 2023.2
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Language：English Publisher：Plants
In Kenya’s rice-growing areas, Basmati varieties have been produced in monoculture since the late 1980s. This has resulted in the breakdown of the resistance (R) gene-mediated response of the local Basmati varieties to blast disease caused by Pyricularia oryzae. To improve blast resistance in Kenyan Basmati varieties, continuous identification of R genes and suitable breeding materials for Basmati are necessary. Longistaminata chromosome segment introgression lines (LCSILs) with the Kernel Basmati genetic background, developed using a rice line called potential low-input adaptable-1 (pLIA-1) derived from a cross between Taichung 65 (T65) (a rice variety in the Japonica Group) and O. longistaminata, are expected to contain useful blast R genes derived from O. longistaminata or T65. In this study, we investigated the genetic variation of blast R genes in LCSILs and their parents by using a new international differential system for designating blast races based on the gene-for-gene theory and molecular characterization using single nucleotide polymorphism (SNP) markers. LCSILs and their parents were classified into three groups—A, B1, and B2—based on reaction patterns to the standard differential blast isolates (SDBIs). Group A, including pLIA-1, showed the highest resistance in all groups, followed by groups B1 and B2. Kernel Basmati in group B1 was considered to possess Pik-p or Pi7(t), Pi19(t), and other unknown R genes. In addition to these R genes, LCSIL 6, 12, 27, 28, and 40, in group A, were determined to possess one of Pish, Piz-t, or both genes that confer resistance to the Kenyan blast races. These lines can be used for efficiently pyramiding blast R genes in the local Basmati varieties.
Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review. Reviewed Open Access
Reyes VP, Kitony JK, Nishiuchi S, Makihara D, Doi K
Life (Basel, Switzerland) Vol. 12 ( 11 ) page： 1752 2022.11
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Language：English Publishing type：Research paper (scientific journal) Publisher：Life
Molecular markers play a crucial role in the improvement of rice. To benefit from these markers, genotyping is carried out to identify the differences at a specific position in the genome of individuals. The advances in sequencing technologies have led to the development of different genotyping techniques such as genotyping-by-sequencing. Unlike PCR-fragment-based genotyping, genotyping-by-sequencing has enabled the parallel sequencing and genotyping of hundreds of samples in a single run, making it more cost-effective. Currently, GBS is being used in several pre-breeding programs of rice to identify beneficial genes and QTL from different rice genetic resources. In this review, we present the current advances in the utilization of genotyping-by-sequencing for the development of rice pre-breeding materials and the improvement of existing rice cultivars. The challenges and perspectives of using this approach are also highlighted.
DOI： 10.3390/life12111752
Estimating yield-related traits using UAV-derived multispectral images to improve rice grain yield prediction Reviewed Open Access
1. Bascon, M.V., T. Nakata, S. Shibata, I. Takata, N. Kobayashi, Y. Kato, S. Inoue, K. Doi, J. Murase and S. Nishiuchi
Agriculture Vol. 12 ( 8 ) page： 1141 2022.8
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.3390/agriculture12081141
A novel combination of genes causing temperature sensitive hybrid weakness in rice Reviewed
2. Than Kutay Soe, M. Kunieda, H. Sunohara, Y. Inukai, V.P. Reyes, S. Nishiuchi and K. Doi
Front. Plant Sci. Vol. 13 page： 908000 2022.5
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal)
QTL analysis for sodium removal ability in rice leaf sheaths under salinity using an IR-44595/318 F2 population Reviewed International coauthorship Open Access
I. Goto, S. Neang, R. Kuroki, V.P. Reyes, K. Doi, N.S. Skoulding, M. Taniguchi, A. Yamauchi and S. Mitsuya
Frontiers in Plant Science Vol. 13 page： 1002605 2022
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Marker-Assisted Introgression and Stacking of Major QTLs Controlling Grain Number (Gn1a) and Number of Primary Branching (WFP) to NERICA Cultivars Reviewed International coauthorship Open Access
Vincent P. Reyes, Rosalyn B. Angeles-Shim, Merlyn S. Mendioro, Ma. Carmina C. Manuel, Ruby S. Lapis, Junghyun Shim, Hidehiko Sunohara, Shunsaku Nishiuchi, Mayumi Kikuta, Daigo Makihara, Kshirod K. Jena, Motoyuki Ashikari, Kazuyuki Doi
Plants Vol. 10 ( 5 ) page： 844 - 844 2021.4
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Language：English Publishing type：Research paper (scientific journal) Publisher：MDPI AG
The era of the green revolution has significantly improved rice yield productivity. However, with the growing population and decreasing arable land, rice scientists must find new ways to improve rice productivity. Although hundreds of rice yield-related QTLs were already mapped and some of them were cloned, only a few were utilized for actual systematic introgression breeding programs. In this study, the major yield QTLs Grain Number 1a (Gn1a) and Wealthy Farmer’s Panicle (WFP) were introgressed and stacked in selected NERICA cultivars by marker-assisted backcross breeding (MABB). The DNA markers RM3360, RM3452, and RM5493 were used for foreground selection. At BC3F4 and BC3F5 generation, a combination of marker-assisted selection and phenotypic evaluation were carried out to select lines with target alleles and traits. Further, genotyping-by-sequencing (GBS) was conducted to validate the introgression and determine the recurrent parent genome recovery (RPGR) of the selected lines. The Gn1a and/or WFP introgression lines showed significantly higher numbers of spikelets per panicle and primary branching compared to the recurrent parents. In addition, lines with Gn1a and/or WFP alleles were comparatively similar to the recurrent parents (RP) in most yield-related traits. This study demonstrates the success of utilizing yield QTLs and marker-assisted selection to develop and improve rice cultivars.
Diverse panicle architecture results from various combinations of Prl5/GA20ox4 and Pbl6/APO1 alleles Reviewed Open Access
Ayumi Agata, Koki Ando, Sadayuki Ota, Mikiko Kojima, Yumiko Takebayashi, Sayaka Takehara, Kazuyuki Doi, Miyako Ueguchi-Tanaka, Takamasa Suzuki, Hitoshi Sakakibara, Makoto Matsuoka, Motoyuki Ashikari, Yoshiaki Inukai, Hidemi Kitano, Tokunori Hobo
Communications Biology Vol. 3 ( 1 ) page： 302 2020.6
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Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC
DOI： 10.1038/s42003-020-1036-8
Other Link： http://www.nature.com/articles/s42003-020-1036-8
Evaluation of backcrossed pyramiding lines of the yield-related gene and the bacterial leaf blight resistant genes Invited Reviewed
J. Intl. Cooper. Agric. Dev. 2020.3
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Angeles-Shim R.B., Reyes V.P., del Valle M.M., Lapis R.S., Shim J., Sunohara H., Jena K.K., Ashikari M., Doi K.
Rice Science Vol. 27 ( 2 ) page： 113 - 123 2020.3
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Publisher：Rice Science
The quantitative resistance gene pi21 from Sensho was introgressed to an indica breeding line IR63307-4B-13-2, a pyramiding line IRBB4/5/13/21, and a tropical japonica line Kinandang Patong by marker-assisted backcrossing. A total of 192 improved lines at the BC4F3 and BC4F4 generations were developed and confirmed to have the gene introgression via genotyping using a pi21-specific InDel marker. Thirteen randomly selected improved lines, representing all the three genetic backgrounds, demonstrated resistance against leaf blast composites in the field and a broader spectrum resistance against individual isolates compared to the recurrent parents in the glasshouse. Specifically, the tested lines exhibited pi21-acquired resistance against 11 leaf blast isolates that elicited susceptible reactions from the recurrent parents. All the tested lines maintained a comparative heading date, and similar or improved panicle length, number of primary branches per panicle and number of total grains per panicle relative to the recurrent parents. The physical grain characteristics of the recurrent parents were also maintained in the 13 lines tested, although variability in the amylose content and chalkiness degree was observed. The successful marker-assisted introgression of pi21 in diverse genetic backgrounds and the resulting broader spectrum resistance of improved lines against leaf blast indicate the potential of pi21 for deployment in cultivars grown across other rice growing regions in Asia.
Mitsukazu Sakata, Noriko Takano-Kai, Yuta Miyazaki, Hiroyuki Kanamori, Jianzhong Wu, Takashi Matsumoto, Kazuyuki Doi, Hideshi Yasui, Atsushi Yoshimura, Yoshiyuki Yamagata
Frontiers in Plant Science Vol. 11 page： 632420 2020
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Language：English Publishing type：Research paper (scientific journal) Publisher：Frontiers Media SA
Postzygotic reproductive isolation maintains species integrity and uniformity and contributes to speciation by restricting the free gene flow between divergent species. In this study we identify causal genes of two Mendelian factors <italic>S22A</italic> and <italic>S22B</italic> on rice chromosome 2 inducing F<sub>1</sub> pollen sterility in hybrids between <italic>Oryza sativa</italic> japonica-type cultivar Taichung 65 (T65) and a wild relative of rice species <italic>Oryza glumaepatula</italic>. The causal gene of <italic>S22B</italic> in T65 encodes a protein containing DUF1668 and gametophytically expressed in the anthers, designated <italic>S22B_j</italic>. The <italic>O. glumaepatula</italic> allele <italic>S22B-g</italic>, allelic to <italic>S22B_j</italic>, possesses three non-synonymous substitutions and a 2-bp deletion, leading to a frameshifted translation at the S22B C-terminal region. Transcription level of <italic>S22B-j</italic> and/or <italic>S22B_g</italic> did not solely determine the fertility of pollen grains by genotypes at <italic>S22B</italic>. Western blotting of S22B found that one major band with approximately 46 kDa appeared only at the mature stage and was reduced on semi-sterile heterozygotes at <italic>S22B</italic>, implying that the 46 kDa band may associated in hybrid sterility. In addition, causal genes of <italic>S22A</italic> in T65 were found to be <italic>S22A_j1</italic> and <italic>S22A_j3</italic> encoding DUF1668-containing protein. The allele of a wild rice species <italic>Oryza meridionalis</italic> Ng at <italic>S22B</italic>, designated <italic>S22B_m</italic>, is a loss-of-function allele probably due to large deletion of the gene lacking DUF1668 domain and evolved from the different lineage of <italic>O. glumaepatula</italic>. Phylogenetic analysis of DUF1668 suggested that many gene duplications occurred before the divergence of current crops in Poaceae, and loss-of-function mutations of DUF1668-containing genes represent the candidate causal genetic events contributing to hybrid incompatibilities. The duplicated DUF1668-domain gene may provide genetic potential to induce hybrid incompatibility by consequent mutations after divergence.
Shuto Yamada, Yusuke Kurokawa, Keisuke Nagai, Rosalyn B Angeles-Shim, Hideshi Yasui, Naruto Furuya, Atsushi Yoshimura, Kazuyuki Doi, Motoyuki Ashikari, Hidehiko Sunohara
J Internatio. Coop. Agri. Dev. Vol. 18 ( 18 ) page： 18 - 28 2020
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Growth and Yield in Near-isogenic Lines of NERICA1 Introgressed with <i>Gn1a</i> and <i>WFP</i> under Different Fertilization Conditions in Kenya
Kikuta Mayumi, Menge Daniel M., Gichuhi Emily W., Samejima Hiroaki, Kimani John M., Ashikari Motoyuki, Doi Kazuyuki, Makihara Daigo
Abstracts of Meeting of the CSSJ Vol. 248 ( 0 ) page： 99 - 99 2019.9
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Phung Huan Danh, Sugiura Daisuke, Sunohara Hidehiko, Makihara Daigo, Kondo Motohiko, Nishiuchi Shunsaku, Doi Kazuyuki
Breeding Science Vol. 69 ( 2 ) page： 289 - 296 2019.6
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Language：English Publishing type：Research paper (scientific journal) Publisher：Japanese Society of Breeding
<p>Problems with carbon assimilate translocation from source organs to sink (grains) during ripening cause yield losses in rice (<i>Oryza sativa</i> L.), especially in high-sink-capacity varieties. We conducted a genetic analysis of traits related to such translocation by using recombinant inbred lines. Shoot weight (SW) of T65, a <i>japonica</i> parent, was retained from heading to late maturity, whereas that of DV85, an <i>aus</i> parent, was greater than that of T65 at 5 days after heading (DAH) and then decreased until 20 DAH. This difference was observed clearly under standard-fertilizer but not low-fertilizer conditions. Non-structural carbohydrate (NSC) contents in the parents showed a tendency similar to that for SW. QTL analysis revealed pleiotropic QTLs on chromosomes 5 and 10, probably by associations with heading date QTLs. A QTL associated with harvest index and NSC at 5 DAH was detected on chromosome 1. By considering the temporal changes of the traits, we found a QTL for decrease in SW on chromosome 11; the DV85 allele of this QTL facilitated assimilate translocation and suppressed biomass growth. A suggestive QTL for NSC decrease was located on chromosome 2. These QTLs could represent potential targets for controlling carbon assimilate translocation in breeding programs.</p>
DOI： 10.1270/jsbbs.18203
Effect of GN1a and WFP Introgression on the Yield and Yield Components in Two Rice Varieties in Kenya
Menge Daniel Makori, Kikuta Mayumi, Samejima Hiroaki, Gichuhi Emily W, Kimani John M, Ashikari Motoyuki, Angeles-Shim Rosalyn, Sunohara Hidehiko, Jena Kshirod K, Yamauchi Akira, Doi Kazuyuki, Makihara Daigo
Abstracts of Meeting of the CSSJ Vol. 247 ( 0 ) page： 110 2019
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Marker-assisted Introgression of the Quantitative Resistance Gene pi21 Confers Broad Spectrum Resistance of Rice to Blast Reviewed
Rosalyn B ANGELES-SHIM, Vincent P REYES, Marilyn M del VALLE, Ruby S LAPIS, Junghyun SHIM, Hidehiko SUNOHARA, Kshirod K JENA, Motoyuki ASHIKARI, Kazuyuki DOI
Rice Science Vol. 26 2019
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Language：English Publishing type：Research paper (scientific journal)
Development of rice breeding and cultivation technology tailored for Kenya's environment
Daigo Makihara, John Kimani, Hiroaki Samejima, Mayumi Kikuta, Daniel Menge, Kazuyuki Doi, Yoshiaki Inukai, Masahiko Maekawa, Tsugiyuki Masunaga, Yuka Sasaki, Keisuke Katsura, Hidemi Kitano, Shiro Mitsuya, Mana Kano-Nakata, Cornelius Wainaina, Emily Gichuhi, Symon Njinju, Sammy Kagito, Rahab Magoti, Caroline Kundu, Akira Yamauchi
Crop Production under Stressful Conditions: Application of Cutting-edge Science and Technology in Developing Countries page： 27 - 47 2018.8
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Matsukawa M, Tasaki M, Doi K, Ito K, Kawakita K, Tanaka T
Bulletin of entomological research Vol. 108 ( 4 ) page： 471 - 478 2018.8
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Cornelius Mbathi Wainaina, Daigo Makihara, Mitsuru Nakamura, Akihiro Ikeda, Taro Suzuki, Yuko Mizukami, Toshihiro Nonoyama, Kazuyuki Doi, Mayumi Kikuta, Hiroaki Samejima, Daniel Makori Menge, Akira Yamauchi, Akira Yamauchi, John Munji Kimani, Yoshiaki Inukai
Plant Production Science Vol. 21 ( 2 ) page： 132 - 143 2018
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Language：English Publishing type：Research paper (scientific journal) Publisher：TAYLOR & FRANCIS LTD
In Africa, cold temperatures occur in the highlands of East and Southern Africa and in some areas of the Sahel region of West Africa leading to substantial rice yield losses. Cold tolerance (CT) at booting stage on basis of spikelet fertility after cold water irrigation was evaluated using F-2 population derived from a cross between temperate japonica, Hananomai, and tropical japonica, WAB56-104. Two Quantitative trait loci (QTLs) for CT were detected on chromosome 8 and 10 with enhanced effects on the trait coming from Hananomai and WAB56-104 allele, respectively. The QTLs explained 30% and 33% of phenotypic variation in spikelet fertility, respectively. CT was negatively correlated with panicle number (r = -0.35, p < 0.01) and positively correlated with panicle weight (r = 0.61, p < 0.001). Selected BC1F4 and BC1F5 genotypes having homozygous alleles for both CT QTLs exhibited higher spikelet fertility under cold stress. The identified QTLs will be useful in the development of cold-tolerant varieties for production in high altitude areas through marker-assisted selection.
Owusu-Nketia Stella, Inukai Yoshiaki, Ohashi Satomi, Rodriguez Suralta Roel, Doi Kazuyuki, Mitsuya Shiro, Kano-Nakata Mana, Manito Niones Jonathan, Dinh Thi Ngoc Nguyen, Takuya Kabuki, Makihara Daigo, Yamauchi Akira
PLANT PRODUCTION SCIENCE Vol. 21 ( 2 ) page： 106-122 - 122 2018
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Language：English Publishing type：Research paper (scientific journal) Publisher：TAYLOR & FRANCIS LTD
In rainfed lowland rice ecosystem, rice plants are often exposed to alternating recurrences of waterlogging and drought due to erratic rainfall. Such soil moisture fluctuation (SMF) which is completely different from simple or progressive drought could be stressful for plant growth, thereby causing reduction in yield. Root plasticity is one of the key traits that play important roles for plant adaptation under such conditions. This study aimed to evaluate root plasticity expression and its functional roles in dry matter production and yield under SMF using Nipponbare, KDML 105 and three backcross inbred lines (BILs) and to identify QTL(s) associated with root traits in response to SMF at two growth stages using Nipponbare/KDML105 F-2 plants. A BIL, G3-3 showed higher shoot dry matter production and yield than Nipponbare due to its greater ability to maintain stomatal conductance concomitant with greater root system development caused by promoted production of nodal and lateral roots under SMF. QTLs were identified for total nodal root length, total lateral root length, total root length, number of nodal roots, and branching index under SMF at vegetative and reproductive stages. The QTLs detected at vegetative and reproductive stages were different. We discuss here that relationship between root system of G3-3 and the detected QTLs. Therefore, G3-3 and the identified QTLs could be useful genetic materials in breeding program for improving the adaptation of rice plants in target rainfed lowland areas.
Duplication and Loss of Function of Genes Encoding RNA Polymerase III Subunit C4 Causes Hybrid Incompatibility in Rice Reviewed Open Access
Giao Ngoc Nguyen, Yoshiyuki Yamagata, Yuko Shigematsu, Miyako Watanabe, Yuta Miyazaki, Kazuyuki Doi, Kosuke Tashiro, Satoru Kuhara, Hiroyuki Kanamori, Jianzhong Wu, Takashi Matsumoto, Hideshi Yasui, Atsushi Yoshimura
G3-GENES GENOMES GENETICS Vol. 7 ( 8 ) page： 2565 - 2575 2017.8
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Language：English Publishing type：Research paper (scientific journal) Publisher：GENETICS SOCIETY AMERICA
Reproductive barriers are commonly observed in both animals and plants, in which they maintain species integrity and contribute to speciation. This report shows that a combination of loss-offunction alleles at two duplicated loci, DUPLICATED GAMETOPHYTIC STERILITY 1 (DGS1) on chromosome 4 and DGS2 on chromosome 7, causes pollen sterility in hybrid progeny derived from an interspecific cross between cultivated rice, Oryza sativa, and an Asian annual wild rice, O. nivara. Male gametes carrying the DGS1 allele from O. nivara (DGS1-nivaras) and the DGS2 allele from O. sativa (DGS2-T65s) were sterile, but female gametes carrying the same genotype were fertile. We isolated the causal gene, which encodes a protein homologous to DNA-dependent RNA polymerase (RNAP) III subunit C4 (RPC4). RPC4 facilitates the transcription of 5S rRNAs and tRNAs. The loss-of-function alleles at DGS1-nivaras and DGS2-T65s were caused by weak or nonexpression of RPC4 and an absence of RPC4, respectively. Phylogenetic analysis demonstrated that gene duplication of RPC4 at DGS1 and DGS2 was a recent event that occurred after divergence of the ancestral population of Oryza from other Poaceae or during diversification of AA-genome species.
Adapting Genotyping-by-Sequencing for Rice F2 Populations Reviewed Open Access
Tomoyuki Furuta, Motoyuki Ashikari, Kshirod K. Jena, Kazuyuki Doi, Stefan Reuscher
G3-GENES GENOMES GENETICS Vol. 7 ( 3 ) page： 881 - 893 2017.3
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Language：English Publishing type：Research paper (scientific journal) Publisher：GENETICS SOCIETY AMERICA
Rapid and cost-effective genotyping of large mapping populations can be achieved by sequencing a reduced representation of the genome of every individual in a given population, and using that information to generate genetic markers. A customized genotyping-by-sequencing (GBS) pipeline was developed to genotype a rice F2 population from a cross of Oryza sativa ssp. japonica cv. Nipponbare and the African wild rice species O. longistaminata. While most GBS pipelines aim to analyze mainly homozygous populations, we attempted to genotype a highly heterozygous F2 population. We show how species- and population-specific improvements of established protocols can drastically increase sample throughput and genotype quality. Using as few as 50,000 reads for some individuals (134,000 reads on average), we were able to generate up to 8154 informative SNP markers in 1081 F2 individuals. Additionally, the effects of enzyme choice, read coverage, and data postprocessing are evaluated. Using GBS-derived markers, we were able to assemble a genetic map of 1536cM. To demonstrate the usefulness of our GBS pipeline, we determined quantitative trait loci (QTL) for the number of tillers. We were able to map four QTL to chromosomes 1, 3, 4, and 8, and partially confirm their effects using introgression lines. We provide an example of how to successfully use GBS with heterozygous F2 populations. By using the comparatively low-cost MiSeq platform, we show that the GBS method is flexible and cost-effective, even for smaller laboratories.
A single base change explains the independent origin of and selection for the nonshattering gene in African rice domestication Reviewed Open Access
Khin Thanda Win, Yoshiyuki Yamagata, Kazuyuki Doi, Kazuhiro Uyama, Yasuko Nagai, Yosuke Toda, Takahiro Kani, Motoyuki Ashikari, Hideshi Yasui, Atsushi Yoshimura
NEW PHYTOLOGIST Vol. 213 ( 4 ) page： 1925 - 1935 2017.3
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Language：English Publishing type：Research paper (scientific journal) Publisher：WILEY
Reduced seed shattering was a critical evolutionary step in crop domestication. Two cultivated rice species, Oryza sativa and Oryza glaberrima, were independently domesticated from the wild species Oryza rufipogon in Asia and Oryza barthii in Africa, respectively. A single nucleotide polymorphism (SNP) in the c gene, which encodes a trihelix transcription factor, causes nonshattering in O. sativa. However, the genetic mechanism of nonshattering in O. glaberrima is poorly understood.
We conducted an association analysis for the coding sequences of SH3/SH4 in AA-genome rice species and the mutation suggested to cause nonshattering was demonstrated to do so using a positional-cloning approach in the O. sativa genetic background.
We found that the loss of seed shattering in O. glaberrima was caused by an SNP resulting in a truncated SH3/SH4 protein. This mutation appears to be endemic and to have spread in the African gene pool by hybridization with some O. barthii accessions. We showed that interaction between the O. sativa and O. glaberrima domestication alleles of SH3 in heterozygotes induces a 'throwback' seed-shattering phenotype similar to that in the wild species.
Identification of the causative SNP provides new insights into the molecular basis of seed shattering in crops and may facilitate investigation of the history of African rice domestication.
DOI： 10.1111/nph.14290
Identification of QTLs for yield-related traits in RILs derived from the cross between pLIA-1 carrying Oryza longistaminata chromosome segments and Norin 18 in rice Reviewed
Gichuhi, E., E. Himi, H. Takahashi, S. Zhu, K. Doi, K. Tsugane and M. Maekawa
Breed Sci. Vol. 66 page： 720-733 2016.12
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Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice Reviewed
Bessho-Uehara, K., D.R. Wang, T. Furuta, A. Minami, K. Nagai, R. Gamuyao, K. Asano, R.B. Angeles-Shim, Y. Shimizu, M. Ayano, N. Komeda, K. Doi, K. Miura, Y. Toda, T. Kinoshita, S. Okuda, T. Higashiyama, M. Nomoto, Y. Tada, H. Shinohara, Y. Matsubayashi, A. Greenberg, J. Wu, H. Yasui, A. Yoshimura, H. Mori, S.R. McCouch and M. Ashikari
Proc. Natl. Acad. Sci. USA Vol. 113 page： 8969-8974 2016.8
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Construction of a versatile SNP array for pyramiding useful genes of rice Invited Reviewed
Yusuke Kurokawa, Tomonori Noda, Yoshiyuki Yamagata, Rosalyn Angeles-Shim, Hidehiko Sunohara, Kanako Uehara, Tomoyuki Furuta, Keisuke Nagai, Kshirod Kumar Jena, Hideshi Yasui, Atsushi Yoshimura Motoyuki Ashikari , Kazuyuki Doi
Plant Science 2015.9
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Sakata, M., Y. Yamagata, K. Doi and A. Yoshimura
Breeding Science Vol. 64 ( 4 ) page： 309-320 2014.12
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Hybrid incompatibility plays an important role in establishment of post-zygotic reproductive isolation. To unveil genetic basis of hybrid incompatibilities between diverged species of genus Oryza AA genome species, we conducted genetic dissection of hybrid sterility loci, S22(t), which had been identified in backcross progeny derived from Oryza sativa ssp. japonica (recurrent parent) and South American wild rice O. glumaepatula near the end of the short arm of chromosome 2. The S22(t) region was found to be composed of two loci, designated S22A and S22B, that independently induce F1 pollen sterility. Pollen grains containing either of the sterile alleles (S22A-glums or S22B-glums) were sterile if produced on a heterozygous plant. No transmission of the S22A-glums allele via pollen was observed, whereas a low frequency of transmission of S22B-glums was observed. Cytological analysis showed that the sterile pollen grains caused by S22A could reach the bicellular or tricellular stage, and the nearly-sterile pollen grains caused by S22B could reach the tricellular stage. Our genetic analysis showed repulsion linkage effect is possible to induce strong reproductive barrier by high pollen sterility based on recombination value and transmission ratio of hybrid sterility gene to the progeny was influenced by frequency of competitors on fertilization
Validation of QTLs for eating quality of japonica rice `Koshihikari' using backcross inbred lines Reviewed
1. Wada, T., H. Yasui, T. Inoue, M. Tsubone, T. Ogata, K. Doi, A. Yoshimura and Y. Matsue
Plant Prod. Sci. Vol. 16 page： 131-140 2013.3
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Multiple and independent origins of short seeded alleles of GS3 in rice Reviewed
Takano-Kai, N., H. Jiang, A. Powell, S. McCouch, I. Takamure, N. Furuya, K. Doi and A. Yoshimura
Breeding Science Vol. 63 page： 77-85 2013.3
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Molecular mapping of two loci conferring F1 pollen sterility in inter- and intraspecific crosses of rice Reviewed
Win, K.T., Kubo, T., Miyazaki, Y., Doi, K., Yasui, H., Yamagata, Y. and Yoshimura, A.
Genes Genomes and Genomics Vol. 6 page： 16-21 2012
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GS3 participates in stigma exsertion as well as seed length in rice Reviewed
Takano-Kai, N., Doi, K. and Yoshimura A
Breed Sci Vol. 61 page： 244-250 2011.9
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Independent evolution of a new allele of F1 pollen sterility gene S27 encoding mitochondrial ribosomal protein L27 in Oryza nivara Reviewed
4. K.T. Win, Y. Yamagata, Y. Miyazaki, K. Doi, H. Yasui and A. Yoshimura
Theor. Appl. Genet. Vol. 122 ( 2 ) page： 385-394 2011.2
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Artificial selection for a green revolution gene during japonica rice domestication Reviewed
1. K. Asano, M. Yamasaki, S. Takuno, K. Miura, S. Katagiri, T. Ito, K. Doi, J. Wu, K. Ebana, T. Matsumoto, H. Innan, H. Kitano, M. Ashikari and M. Matsuoka
Proc Natl Acad Sci USA. 2011
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Introgression lines of rice (Oryza sativa L.) carrying a donor genome from the wild species, O. glumaepatula Steud. and O. meridionalis Ng. Reviewed
2. A. Yoshimura, H. Nagayama, Sobrizal, T. Kurakazu, P.L. Sanchez, K. Doi, Y. Yamagata and H. Yasui
Breed. Sci. Vol. 60 page： 597-603 2010
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Analysis of rice panicle traits and detection of QTLs using an image analyzing method Reviewed
M. Ikeda, Y. Hirose, T. Takashi, Y. Shibata, T. Yamamura, T. Komura, K. Doi, M. Ashikari, M. Matsuoka and H. Kitano
Breed. Sci. Vol. 60 page： 55-64 2010
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Mitochondrial gene in the nuclear genome induces reproductive barrier in rice Reviewed
Y. Yamagata, E. Yamamoto, K. Aya, K.T. Win, K. Doi, Sobrizal, T. Ito, H. Kanamori, J. Wu, T. Matsumoto, M. Matsuoka, M. Ashikari, A. Yoshimura
Proc. Natl. Acad. Sci. U.S.A. Vol. 107 page： 1494-1499 2010
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A major QTL for resistance to green rice leafhopper (Nephotettix cincticeps Uhler) derived from African rice (Oryza glaberrima Steud.) Reviewed
3. D. Fujita, K. Doi, A. Yoshimura and H. Yasui
Breed. Sci. Vol. 60 page： 336-341 2010
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Evolutionary history of GS3, a gene conferring grain length in rice Reviewed
Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch S.
Genetics Vol. 182 page： 1323-34 2009.8
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Multiple alleles at Early flowering 1 locus making variation in the basic vegetative growth period in rice (Oryza sativa L.) Reviewed
H. Saito, Q. Yuan, Y. Okumoto, K. Doi, A. Yoshimura, H. Inoue, M. Teraishi, T. Tsukiyama, T. Tanisaka
Theor. Apple. Genet. Vol. 119 page： 315-323 2009
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Identification of two loci causing F1 pollen sterility in inter- and intraspecific crosses of rice Reviewed
K.T. Win, T. Kubo, Y. Miyazaki, K. Doi, Y. Yamagata and A. Yoshimura
Breed. Sci. Vol. 59 page： 411-418 2009
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*Mapping of QTLs for floating ability in rice. Reviewed
R. Kawano, K. Doi, H. Yasui, T. Mochizuki and A. Yoshimura
Breed. Sci. Vol. 58 page： 47-53 2008
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*Identification of mutants for abnormal pollen development in rice. Reviewed
Y. Yamagata, K. Doi, H. Yasui and A. Yoshimura
Breed. Sci. Vol. 57 page： 331-337 2007
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QTL analysis of F1 pollen sterility observed in hybrids between Oryza sativa and O. rufipogon. Reviewed
Y. Miyazaki, H. Nagayama A, K. Doi and A. Yoshimura
Rice Genetics Newsletter Vol. 23 page： 39-41 2007
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Identification of a new allele of F1 pollen sterility gene, S21, detected from the hybrid between Oryza sativa and O. rufipogon. Reviewed
Y. Miyazaki, K. Doi, H. Yasui and A. Yoshimura
Rice Genetics Newsletter Vol. 23 page： 36-38 2007
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Genetic Diversity of Myanmar rice cultivars detected by DNA markers. Reviewed
Ohm Mar Saw, K. Doi, Khin Aye, K. Irie and A. Yoshimura
J. Fac. Agr. Kyushu Univ. Vol. 51 page： 181-187 2006
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*Molecular mapping of a novel gene, Grh5, conferring resistance to green rice leafhopper (Nephotettix cincticeps Uhler) in rice, Oryza sativa L. Reviewed
Fujita, D., K. Doi, A. Yoshimura and H. Yasui
Theor. Appl. Genet. Vol. 113 page： 567-73 2006
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Introgression of a resistance gene for green rice leafhopper from Oryza nivara into cultivated rice, Oryza sativa L. Reviewed
Fujita, D., K. Doi, A. Yoshimura and H. Yasui
Rice Genetics Newsletter Vol. 21 page： 64-66 2004
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Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Reviewed
Doi, K., T. Izawa, T. Fuse, U. Yanmanouchi, T. Kubo, Z. Shimatani, M. Yano and A. Yoshimura
Genes Dev. Vol. 18 page： 926-936 2004
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Genetic diversity of Myanmar rice cultivars detected by DNA markers. Reviewed
Ohm Mar Saw, K. Doi, Khin Aye, K. Irie and A. Yoshimura
Rice Genetics Newsletter Vol. 20 page： 14-16 2003
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Identification of new alleles of awnness genes, An7 and An8, in rice using Oryza glumaepatula introgression lines. Reviewed
Matsushita, S., P. L. Sanchez, Sobrizal, K. Doi and A. Yoshimura
Rice Genetics Newsletter Vol. 20 page： 19-20 2003
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Mapping of a new resistance gene for green rice leafhopper introgressed from Oryza rufipogon Griff. into cultivated rice, Oryza sativa L. Reviewed
Fujita, D., K. Doi, A. Yoshimura and H. Yasui
Rice Genetics Newsletter Vol. 20 page： 79-80 2003
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QTL analysis for floating ability in rice. Reviewed
Kawano, R., T. Mochizuki, H. Yasui, K. Doi and A. Yoshimura
Rice Genetics Newsletter Vol. 20 page： 74-77 2003
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Mapping of genes for awn in rice using Oryza meridionalis introgression lines. Reviewed
Matsushita, S., T. Kurakazu, Sobrizal, K. Doi and A. Yoshimura
Rice Genetics Newsletter Vol. 20 page： 17-18 2003
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Sh3, a gene for seed shattering, commonly found in African in wild rices. Reviewed
Nagai, Y. S., P. L. Sanchez, T. Kurakazu, K. Doi and A. Yoshimura
Rice Genetics Newsletter Vol. 19 page： 74-76 2002
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Genetic differentiation for nuclear, mitochondorial and chloroplast genomes in common wild rice (Oryza sativa L.). Reviewed
Sun, C. Q., X. K. Wang, A. Yoshimura and K. Doi
Theor. Appl. Genet. Vol. 104 page： 1335-1345 2002
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Reciprocal chromosome segment substitution series derived from Japonica and Indica cross of rice (Oryza sativa L.). Reviewed
Kubo, T., Y. Aida, K. Nakamura, H. Tsunematsu, K. Doi and A. Yoshimura
Breed. Sci. Vol. 52 page： 319-325 2002
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A seed shattering gene, Sh3, and its inhibitor gene found in an African cultivated rice, Oryza glaberrima Steud. Reviewed
Nagai, Y. S., K. Doi and A. Yoshimura
Rice Genetics Newsletter Vol. 19 page： 76-77 2002
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Oryza meridionalis chromosomal segment introgression lines in cultivated rice, O. sativa L. Reviewed
Kurakazu, T., Sobrizal, K. Ikeda, P. L. Sanchez, K. Doi, E. R. Angeles, G. S. Khush and A. Yoshimura
Rice Genetics Newsletter Vol. 18 page： 81-82 2001
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RFLP relationships of A-genome species in the genus Oryza. Reviewed
Doi, K., M. Nakano, A. Yoshimura, N. Iwata and D. A. Vaughan
J. Fac. Agr., Kyushu Univ. Vol. 45 page： 83-98 2000
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Development of Oryza glumaepatula introgression lines in rice, Oryza sativa L. Reviewed
Sobrizal, K. Ikeda, P. L. Sanchez, K. Doi, E. R. Angeles, G. S. Khush and A. Yoshimura
Rice Genetics Newsletter Vol. 16 page： 107-108 1999
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RFLP mapping of S20 and S21, loci for F1 pollen sterility found in a cross between Oryza sativa and O. glaberrima. Reviewed
Doi, K., K. Taguchi and A. Yoshimura
Rice Genetics Newsletter Vol. 16 page： 65-68 1999
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RFLP mapping of S19, a gene for F1 pollen sterility found in backcross progeny of Oryza sativa and O. glaberrima. Reviewed
Taguchi, K., K. Doi and A. Yoshimura
Rice Genetics Newsletter Vol. 16 page： 70-71 1999
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RFLP mapping of a gene for heading date in African rice. Reviewed
Doi, K. and A. Yoshimura
Rice Genetics Newsletter Vol. 15 page： 148-149 1998
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RFLP mapping and QTL analysis of heading date and pollen sterility using backcross populations between Oryza sativa L. and O. glaberrima Steud. Reviewed
Doi, K., A. Yoshimura and N. Iwata
Breed. Sci. Vol. 48 page： 395-399 1998
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A new locus affecting high F1 pollen sterility found in backcross progenies of Japonica rice and African rice. Reviewed
Doi, K., K. Taguchi and A. Yoshimura
Rice Genetics Newsletter Vol. 15 page： 146-148 1998
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Development of a series of introgression lines of Japonica in the backgroud of Indica rice. Reviewed
Aida, Y., H. Tsunematsu, K. Doi and A. Yoshimura
Rice Genetics Newsletter Vol. 14 page： 41-43 1997
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The construction of chromosome substitution lines of African rice (Oryza glaberrima Steud.) in the background of Japonica rice (O. sativa L.). Reviewed
Doi, K., N. Iwata and A. Yoshimura
Rice Genetics Newsletter Vol. 14 page： 39-41 1997
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Phylogenetic study of A-genome species of genus Oryza using neclear RFLP. Reviewed
Doi, K., A. Yoshimura, M. Nakano, N. Iwata and D. A. Vaughan
RiceGenetics Newsletter Vol. 12 page： 160-162 1995
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Identification of rice QTL for yield and its application for breeding in Kenya
（ Role： Joint author）
2020.7
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Total pages：5 Responsible for pages：526-530 Language：Japanese Book type：General book, introductory book for general audience
Development of rice promising lines using genomic technology and information in Vietnam
Yoshimura A., Yasui H., Van Cuong P., Ashikari M., Angeres E.E., Van Hoan N., Phuong T.T., Yamagata Y., Hamaoka N., Doi K., Hanh T.T., Van Tan M., Trung N.Q., Iseri N., Ogata K.
Crop Production under Stressful Conditions: Application of Cutting-edge Science and Technology in Developing Countries 2018.8 （ ISBN:9789811073083, 9789811073076 ）
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ゲノム情報を利用したイネの育種
永井啓祐、黒川裕介、土井一行、芦苅基行（ Role： Joint author）
国際農林業協力 2015.3
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Total pages：10 Responsible for pages：10 Language：Japanese Book type：Scholarly book
Genetic variation in rice
Doi K, Yasui H, Yoshimura A.（ Role： Joint author）
Elsevier 2008.4
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Language：English
Completion of the genomic sequencing of rice has enhanced the discovery of new genes. Wild rice relatives are good sources for extending the genetic variation of cultivated rice. Reproductive barriers are commonly found in distant crosses of rice and are attracting attention. The combination of genetic analyses and molecular tools has greatly facilitated the molecular cloning of rice genes based on the classical approach and enabled the tracking of dissemination of the alleles for domestication. Basic information for population genetics study in rice is still being collected and is expected to provide an alternative approach for finding new genes. The wide genetic variation available in wild rice relatives and the combination of various genetic approaches will allow the analysis and understanding of genetic variation at the nucleotide sequence level, as well as the discovery of novel alleles by sequence-based approaches.
イネゲノム配列解読でなにができるのか
（ Role： Contributor）
農山漁村文化協会
Identification of rice QTL for yield and its application for breeding in Kenya
Vol. 4 ( 7 ) page： 526 - 530 2020.7
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Effect of GN1a and WFP Introgression on the Yield and Yield Components in Two Rice Varieties in Kenya
MENGE Daniel M, KIKUTA Mayumi, SAMEJIMA Hiroaki, GICHUHI Emily, KIMANI John M, ASHIKARI Motoyuki, ANGELES‐SHIM Rosalyn, SUNOHARA Hidehiko, JENA Kshirod K, YAMAUCHI Akira, DOI Kazuyuki, MAKIHARA Daigo
日本作物学会講演会要旨集 Vol. 247th page： 110 2019.3
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台中65号とausイネの交雑後代で見出された分離ゆがみの遺伝解析
國枝真依, 春原英彦, 田崎三香子, 西内俊策, 西内俊策, 土井一行
育種学研究 Vol. 20 page： 42 2018.9
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台中65号とLijiangxintuanheigu(LTH)の交雑で見出されたイネの新規F<sub>2</sub>弱勢遺伝子hwj1とhwj2
國枝真依, 鈴木竜, 田崎三香子, 西内俊策, 西内俊策, 土井一行, 春原英彦
育種学研究 Vol. 20 page： 247 2018.3
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穂先の退化を示すイネpanicle tip abortion変異体の解析
春原英彦, 田崎三香子, 西内俊策, 犬飼義明, 土井一行
育種学研究 Vol. 19 page： 199 2017.3
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台中65号とaus型イネの交雑後代で見出された染色体1長腕末端領域の分離ゆがみ
國枝真依, 春原英彦, 島津瑛久, 田崎三香子, 西内俊策, 土井一行
育種学研究 Vol. 19 page： 166 2017.3
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イネ登熟期における物質生産能力に関する遺伝解析
笠原麻由，島川昂大，西内俊策，仲田麻奈，槇原大悟，土井一行
第31回日本育種学会中部地区談話会 2024.12
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Event date： 2024.12
Language：Japanese Presentation type：Poster presentation
Venue：信州大学 Country：Japan
葯形質に着目したイネ耐冷性に関する遺伝解析
菊地由夏，島川昂大，笠原麻由，Ni Ni Min Thu，西内俊策，土井一行
第31回日本育種学会中部地区談話会 2024.12
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Event date： 2024.12
Language：Japanese Presentation type：Poster presentation
Venue：信州大学 Country：Japan
イネ節間伸長においてジベレリン感受性を制御する新規QTLの探索
水嶋澪, 三瓶稜悟, Vincent Reyes, 土井一行, 永井啓祐, 芦苅基行
日本育種学界第146回講演会 2024.9
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Event date： 2024.9
Language：Japanese Presentation type：Oral presentation (general)
Venue：広島大学 Country：Japan
イネ矮小突然変異体 d1を用いた節間伸長パターンを制御する QTL の検出(1)
Sandar Moe, Thi Quynh Ha, V.P. Reyes, 土井 一行, 三浦 孝太郎, 前野 哲輝, 津田 勝利, 永井 啓祐, 芦苅 基行
日本育種学会第145回講演会 2024.3
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Event date： 2024.3
Language：English Presentation type：Oral presentation (general)
Venue：東京大学
Dual-NAM集団を用いた出穂期制御に関わる環境応答性遺伝子の同定
齊藤 大樹，土井 一行，阿部 陽，小川 諭志
日本育種学会第145回講演会 2024.3
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Event date： 2024.3
Language：Japanese Presentation type：Poster presentation
Venue：東京大学
イネ矮小突然変異体 d1を用いた節間伸長パターンを制御する QTL の検出(2)
Thi Quynh H, Sandar Mo, VV.P. Reyes, 土井 一行, 三浦 孝太郎, 前野 哲輝, 津田 勝利, 永井 啓祐, 芦苅 基行
日本育種学会第145回講演会 2024.3
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Event date： 2024.3
Language：English Presentation type：Oral presentation (general)
Venue：東京大学
葯形質に着目したイネ耐冷性の遺伝解析
菊地由夏、松山恵美子、島川昂大、Abebaw D. Mabreja、西内俊策、土井一行
第30回日本育種学会中部地区談話会 2023.12
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Event date： 2023.12
Language：Japanese Presentation type：Poster presentation
Venue：名古屋大学
葯形質に着目したイネ耐冷性の遺伝解析
菊地由夏、松山恵美子、島川昂大、Abebaw D. Mabreja、西内俊策、土井一行
愛知県農学系４機関による研究交流会 2023.12
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Event date： 2023.12
Language：Japanese Presentation type：Poster presentation
Venue：名城大学
FOEAS 圃場を活用したイネの水ストレス適応性評価
野田康貴，松山恵美子，黒木隆一，土井一行， 槇原大悟，山内章，江原宏，仲田(狩野)麻奈
東海作物研究 2023.11
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Event date： 2023.11
Language：Japanese Presentation type：Oral presentation (general)
Venue：東海作物研究
イネ染色体部分置換系統（TD-CSSLs）利用による登熟関連形質の評価
A. Mabreja、V. Reyes、西内俊策、土井一行
日本育種学会第144回講演会 2023.9 日本育種学会
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Event date： 2023.9
Language：English Presentation type：Poster presentation
Venue：神戸大学
葯関連形質に着目したイネ耐冷性QTLの探索
黒木隆一，V.P. Reyes，A.D. Mabreja，西内俊策，槇原大悟、土井一行
日本育種学会第143回講演会 2023.3
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Event date： 2023.3
Language：Japanese Presentation type：Oral presentation (general)
Venue：静岡大学 Country：Japan
陸稲の水不足ストレスへの反応に関与するQTLの探索
松山恵美子，仲田麻奈，犬飼義明，黒木隆一，西内俊策，槇原大悟, 土井一行
日本育種学会第143回講演会 2023.3
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Event date： 2023.3
Language：Japanese Presentation type：Oral presentation (general)
Venue：静岡大学 Country：Japan
熱乾燥したイネの葉からの DNA 抽出
熱乾燥したイネの葉からの DNA 抽出
2022年度愛知県農学系4機関による研究交流会 2022.12
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Event date： 2022.12
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
水不足ストレスに対するイネの根系の可塑性の遺伝解析
松山恵美子，仲田麻奈，犬飼義明，黒木隆一，西内俊策，伊藤幸司, 伊藤晃, 槇原大悟, 土井一行
2022年度愛知県農学系4機関による研究交流会 2022.12
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Event date： 2022.12
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
黒木隆一，V.P. Reyes，A.D. Mabreja，西内俊策，土井一行
バスマティイネの耐冷性改善のための遺伝解析
第28回育種学会中部地区談話会 2022.11
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Event date： 2022.11
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
松山恵美子，黒木隆一，西内俊策，土井一行
乾燥ストレスに対するイネの根の可塑性の遺伝解析
第28回育種学会中部地区談話会 2022.11
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Event date： 2022.11
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
UAV 空撮画像と物体検出技術を用いたイネ漏生地図の作成
柴田 悟志 , 土井 一行 , 西内 俊策
柴田 悟志 , 土井 一行 , 西内 俊策 2022.9
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Event date： 2022.9
Language：Japanese Presentation type：Oral presentation (general)
Venue：帯広畜産大学 Country：Japan
イネにおいて温度感受性雑種弱性を引き起こす新たな遺伝子組み合わせ
Than Kutay Soe，國枝 真依，春原 英彦，犬飼 義明，V.P. Reyes，西内 俊策，土井 一行
日本育種学会第142回講演会 2022.9
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Event date： 2022.9
Language：English Presentation type：Poster presentation
Venue：帯広畜産大学 Country：Japan
バスマティイネの耐冷性改善のための遺伝解析
黒木隆一・V.P. Reyes・A.D. Mabreja・西内俊策・土井一行
日本育種学会第141回講演会 2022.3.22 日本育種学会
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Event date： 2022.3
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
バスマティイネの耐冷性改善のための遺伝解析
黒木隆一・V.P. Reyes・A.D. Mabreja・西内俊策・土井一行
愛知県農学系４機関による研究交流会 2021.12.17 名古屋大学・愛知県農業総合試験場
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Event date： 2021.12
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
乾燥ストレスに対するイネの根の可塑性の遺伝解析
松山恵美子・黒木隆一・西内俊策・土井一行
愛知県農学系４機関による研究交流会 2021.12.17 名古屋大学・愛知県農業総合試験場
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Event date： 2021.12
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
バスマティイネの耐冷性改善のための遺伝解析
黒木隆一・V.P. Reyes・A.D. Mabreja・西内俊策・土井一行
第 28 回育種学会中部地区談話会 2021.11.13 日本育種学会
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Event date： 2021.11
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
乾燥ストレスに対するイネの根の可塑性の遺伝解析
松山恵美子・黒木隆一・西内俊策・土井一行
第 28 回育種学会中部地区談話会 2021.11.13 日本育種学会
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Event date： 2021.11
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
イネの配偶体型花粉不稔遺伝子gps7, gps12, gps14のマッピング
渡辺美弥子、山形悦透、土井一行、安井秀、吉村淳
日本育種学会第114会講演会
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Event date： 2008.10
Language：Japanese Presentation type：Oral presentation (general)
Country：Japan
イネのF1花粉不稔遺伝子S22における新たな対立遺伝子
日本育種学会第113回講演会
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Event date： 2008.3
Language：Japanese Presentation type：Oral presentation (general)
Country：Japan
高精度連鎖解析によるイネのF1花粉不稔遺伝子S22領域のダイセクション
阪田光和、土井一行、山形悦透、ソブリザール、吉村淳
日本育種学会第113会講演会
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Event date： 2008.3
Language：Japanese Presentation type：Oral presentation (general)
Country：Japan
ゲノム情報を利用した高バイオマスイネ作出に関する遺伝育種学的研究
2009.4 - 2012.3
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高バイオマスイネの作成を試みる
アフリカイネ由来の一年生遺伝子による転流能の強化
2012.4 - 2015.3
科学研究費補助金 基盤研究(B)
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Authorship：Principal investigator
・アフリカイネ（Oryza glaberrima Steud.）由来の一年生遺伝子（qRA8）を単離し、イネが一年生/多年生の変異を示す原因を分子レベルで明らかにする。
・qRA8遺伝子を手がかりに、イネの一年生化にともなう光合成産物の配分の変化を解析し、それを制御することで、イネの多収化を試みる。
Grant number：24K01733 2024.4 - 2028.3
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
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Authorship：Coinvestigator(s)
Strengthening rice ripening ability through a multifaceted approach
Grant number：22H02310 2022.4 - 2026.3
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
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Authorship：Principal investigator
Grant amount：\16900000 （ Direct Cost: \13000000 、 Indirect Cost：\3900000 ）
Strengthening rice ripening ability through a multifaceted approach
Grant number：23K23576 2022.4 - 2026.3
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
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Authorship：Principal investigator
Grant amount：\16900000 （ Direct Cost: \13000000 、 Indirect Cost：\3900000 ）
Grant number：22H02325 2022.4 - 2025.3
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
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Authorship：Coinvestigator(s)
Grant number：23K23590 2022.4 - 2025.3
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
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Authorship：Coinvestigator(s)
Grant number：21K05522 2021.4 - 2024.3
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
SAITO HIROKI
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Authorship：Coinvestigator(s) Grant type：Competitive
NAM populations (T65_NAM and HT_NAM), which are derived from the cross between 'Taichung 65' or 'Hitomebore' as a common parent and various varieties, were grown in four environments (Iwate Biotechnology Science Center, Iwate Prefecture; Togo experimental Field of Nagoya University, Aichi Prefecture; and Ishigaki island, Okinawa Prefecture, Spring-Summer season and Summer-Autumn season). A total of 11 populations (1,693 lines), were grown and GWAS were conducted for days to heading (DTH) and environmental responsiveness (Photoperiod sensitivity and Temperature sensitivity). The results showed that for DTH in each cropping season, 16-45 significant SNPs were detected, locating on chromosomes 2, 3, 4, 5, 6, 7, 10 and 12. For environmental responsiveness, 1-30 significant SNPs were detected, locating on chromosomes 3, 5, 6, 7 and 10.
出穂期の人為制御による熱帯アジアで多発するイネ高温不稔障害の回避
Grant number：20KK0138 2020.10 - 2025.3
日本学術振興会 科学研究費助成事業 国際共同研究加速基金(国際共同研究強化(B))
犬飼 義明, 黒川 裕介, 土井 一行
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Authorship：Coinvestigator(s)
異常高温がイネの出穂時に重なることで受精に支障が生じ、収量が大幅に低下する。我々は、栽培時の水管理の違いにより、出穂時期を変動できる遺伝系統の選抜に成功した。本系統を利用すれば、高温のピークと出穂時期の重なりを回避できる新品種・栽培技術の開発が期待できる。イネは短日植物であり、花芽形成の誘導を通した出穂期の決定は日長の違いに大きく影響を受ける。そこで本研究課題では、厳しい高温不稔が多発する熱帯アジアのうち、緯度の違いにより日長が大いに異なる3ヶ国を対象国に選定した。これらの海外共同研究者と共に、異常高温に耐えるのではなく、それを回避できるイネ系統の育成とその水管理栽培技術の確立を目指す。
異常高温がイネの出穂時に重なることで不稔が生じ、深刻な収量の低下が誘発されるため、アジア各国の研究者が高温不稔耐性に関わる有用形質の解明に取り組んでいる。一方、さらなる温暖化に備え、高温のピークと出穂時期の重なりを回避できる新技術の開発も必要不可欠である。本年度は昨年度に引き続き、節水栽培下（間断灌漑下）にて出穂期が変動する系統の選抜、および出穂変動のメカニズムを調査した。
昨年度に引き続き、NAM集団（約1000系統）を材料に解析を行いを間断灌漑下にて育成し、出穂期を調査した。その結果、節水栽培下での開花遅延に関する合計 14 個の QTL を検出した。 非機能的 Ehd1 対立遺伝子を持つ遺伝子型は、機能的 Ehd1 グループと比較して、出穂遅延に対してより高い相加効果を示し、開花遅延 が Ehd1 遺伝子の効果によって大きく影響される傾向が認められた。 したがって、Ehd1 の非機能的対立遺伝子と、間断灌漑下での出穂遅延に関わるQTL との組合せが、本研究が目指す育種目標に有用であると考えられた。 2 つ以上の QTL が検出された系統では、平均 7.3 日の出穂遅延が認められた。 この遅延は、個々の QTL 効果と比較して大きく、さらなる各QTL の積み重ねが出穂遅延日数の拡大を導くものと期待された。
現在、世代促進が年3回行えるフィリピンにて交配することで、これまでに検出した出穂遅延に関わる各QTLを複数保有する系統群の作出を進めている。次年度はこれらの材料を用いて間断灌漑下にて栽培し、各QTLの蓄積効果を解析する予定である。
研究当初の渡航制限のため、web上での打合せを通じて材料の輸出入や現地での圃場栽培試験を慎重に進めてきた。しかし、適切な時期におけるデータの取得や遺伝子解析のためのDNA/RNA抽出を目的としたサンプリングが困難な場合が生じ、研究計画の遂行が大きく遅れていた。一方、昨年度からは徐々に回復してきており、適切なデータの取得やサンプリングが可能となってきている。そのため、遅れを少しずつ取りもどすことができつつあり、「やや遅れている」と判断した。
現在、世代促進が年3回行えるフィリピンにて交配することで、これまでに検出した出穂遅延に関わる各QTLを複数保有する系統群の作出を進めている。次年度はこれらの材料を用いて間断灌漑下にて栽培し、各QTLの蓄積効果を解析する。その際、乾燥ストレスの強度や時期の異なる落水処理を行い、出穂遅延能や他の農業形質を精査することで、これらの育成・選抜系統の有用性を評価するとともに、その能力を十分に発揮できる水管理技術を確立する。
Grant number：20H02887 2020.4 - 2023.3
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
MURASE Jun
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Authorship：Coinvestigator(s)
We have developed a nucleic acid extraction and purification method for high-throughput molecular analysis of microbial communities inhabiting plant roots. We clarified the composition and structure of the root microbial communities of 120 paddy rice varieties cultivated under fertilized and non-fertilized conditions. We analyzed the relationship between the root microbiome and the rice genotypes and phenotypes governed by fertilization conditions. Genome-wide association analysis was used to extract candidate rice genes that regulate root microbial communities. The importance of rice genotype, phenotype, and soil type on the composition of root microbial communities was comparatively analyzed. We quantified the nitrogen-fixing activity and nitrogen-fixing genes of root microorganisms. We found that rice cultivars with high fertilization efficiency showed a less intensified decrease in nitrogen-fixing activity and specific nitrogen-fixing genes due to fertilization.
Grant number：18H02187 2018.4 - 2021.3
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
Makihara Daigo
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Authorship：Coinvestigator(s)
Longistaminata Chromosome Segment Introduced Lines (LCSILs), in which chromosome segments from the African wild rice longistaminata were introduced into a cultivated rice variety, were genotyped using next-generation sequencers. Then, their blast resistance, salt tolerance, and cold tolerance were evaluated. The large variation in blast resistance among the lines was attributed to the introduction of chromosome segments of pLIA-1, the donor parent for the longistaminata genes. Positions of pLIA-1 chromosome substitution in the selected salt-tolerant lines did not match the known salt-tolerant QTL. The LCSILs were shown to be useful as breeding material for blast resistance and salt tolerance.
イネ配偶体型花粉不稔遺伝子の単離
2007
科学研究費補助金 特定領域研究，課題番号：19043013
土井 一行
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Authorship：Principal investigator
植物寄生性センチュウ防除剤
澤 進一郎、春原英彦、佐藤 豊、土井一行
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Application no：特願2021-024793 Date applied：2021.2
植物の開花時期を促進するEhd1遺伝子およびその利用
矢野昌裕，布施拓市，山内歌子，吉村淳，土井一行
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Application no：特願2002-153807 Date applied：2004.5
資源生物科学実験実習
2024
生命農学序説
2024
生命農学本論
2024
海外実地研修
2024
海外学生受入研修
2024
資源生物科学専門講義
2024
専門セミナー
2024
博士論文研究
2024
卒業論文研究
2024
国際農学演習
2024
修士論文研究
2024
修士論文研究
2023
国際農学演習
2023
植物分子育種学特論
2023
卒業論文研究
2023
博士論文研究
2023
専門セミナー
2023
資源生物科学専門講義
2023
海外実地研修
2023
海外学生受入研修
2023
生命農学本論
2023
生命農学序説
2023
資源生物科学実験実習
2023
生命農学序説
2022
資源生物科学実験実習
2022
博士論文研究
2022
専門セミナー
2021
卒業論文研究
2021
植物分子育種学特論
2021
博士論文研究
2021
資源生物科学専門講義
2021
海外実地研修
2021
海外学生受入研修
2021
資源生物科学実験実習
2021
生命農学本論
2021
博士論文研究
2020
Basics of Bioagricultural Sciences
2020
Principles of Bioagricultural Sciences
2020
生命農学本論
2020
海外学生受入研修
2020
海外実地研修
2020
資源生物科学専門講義
2020
資源生物科学実験実習
2020
専門セミナー
2020
卒業論文研究
2020
海外学生受入研修
2020
Laboratory in Biology
2011
Laboratory in Biology
2011
職場体験
Role(s)：Lecturer, Demonstrator
春木中学校 2024.11
東郷フィールド講演会
Role(s)：Organizing member
東郷フィールド 2024.10
附属学校の支援（東郷フィールド見学）
Role(s)：Lecturer, Organizing member
東郷フィールド 2024.10
ふれあい教室
Role(s)：Organizing member, Demonstrator
2024.10
東郷フィールド講演会
Role(s)：Organizing member
東郷フィールド 2024.8
JICAアフリカ稲作研修
Role(s)：Lecturer, Informant, Organizing member
JICA・JISNAS（名古屋大学） JICAアフリカ稲作研修 2024.6 - 2024.8
東郷フィールド講演会
Role(s)：Organizing member
東郷フィールド 2022.10
附属学校の支援（東郷フィールド見学）
Role(s)：Lecturer, Organizing member
東郷フィールド 2022.10
ふれあい教室
Role(s)：Organizing member, Demonstrator
2022.10
JICAアフリカ稲作研修
Role(s)：Lecturer, Informant, Organizing member
JICA・JISNAS（名古屋大学） JICAアフリカ稲作研修 2022.9
東郷フィールド講演会
Role(s)：Organizing member
東郷フィールド・東郷町 東郷フィールド講演会 2022.7
Rice breeding workshop
Role(s)：Lecturer, Informant, Organizing member
農学国際教育研究センター Rice breeding workshop 2022.3
職場体験
Role(s)：Organizing member
2021.11
東郷フィールド講演会
Role(s)：Organizing member
東郷フィールド 2021.10
附属学校の支援（東郷フィールド見学）
Role(s)：Lecturer, Organizing member
東郷フィールド 2021.10
JICAアフリカ稲作研修
Role(s)：Lecturer, Informant, Organizing member
JICA・JISNAS（名古屋大学） JICAアフリカ稲作研修 2021.10 - 2021.11
ふれあい教室
Role(s)：Organizing member, Demonstrator
2021.10
東郷フィールド講演会
Role(s)：Organizing member
東郷フィールド・東郷町 東郷フィールド講演会 2021.7
東郷フィールド見学会
Role(s)：Organizing member
東郷フィールド・東郷町 東郷フィールド講演会 2021.7
東郷フィールドでの活動（農場講演会・見学会）実施
Role(s)：Organizing member, Demonstrator
名古屋大学東郷フィールド 2020.10
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