Doctor of Philosophy in Agricultural Science, Hokkaido University

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

Life Science, Developmental biology

Life Science, Plant molecular biology and physiology

Life Science, Genetics

Life Science, Morphology and anatomical structure

Apr. 2026, 日本育種学会, 優秀発表賞
ダイズの莢形成における細胞分裂の制御：組織成長率との相関および位置による効果
曵地 究;三浦 誠一朗;徳山 芳樹;小出 陽平

Nov. 2025, 日本育種学会, 優秀発表賞
イネ捻れ葉変異体における葉身の左右非対称性と器官間物理的相互作用による捻れ発生メカニズム
曵地 究, 岡田 脩平, 徳山 芳樹, 三浦 誠一郎, 田口 みなみ, 貴島 祐治, 高牟禮 逸郎, 小出 陽平

Mar. 2024, 日本育種学会, 石原（志方）守一奨学金
イネ捻れ葉変異体における捻れ形成原理の解明と原因変異の遺伝解析

Mar. 2023, 日本育種学会, 優秀発表賞
イネ捻れ葉変異体における捻れ形成原理の解明と原因変異の遺伝解析
曵地 究, 岡田 脩平, 徳山 芳樹, 高牟禮 逸郎, 貴島 祐治, 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.), 19, 1, 13, 13, 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.

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
New Phytologist, Sep. 2025
Scientific journal

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, May 2024
English, 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, Jan. 2024
English, Scientific journal

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, 01 Jul. 2021
English, Scientific journal, Abstract
Three-dimensional plant shapes are influenced by their phyllotaxy, which plays a significant role in their environmental adaptation. Grasses with distichous phyllotaxy have linearly aligned culms and usually have vertical fan-like shapes. Counterintuitively, some distichous phyllotaxy grasses have radial shapes. Here, we investigate the organ-level mechanism underlying radial shape development in the distichous phyllotactic wild rice species (Oryza rufipogon). Detailed time-course phenotyping and three-dimensional micro-computed tomography showed that changes in the elevation angle in the main culm and azimuth angle in the primary tillers contribute to radial shape development. To infer the mechanical basis of the shape change, we simulated the movements of culms controlled by different kinematic factors. The computational models predicted that the combination of movements, including that controlled by negative gravitropism, produces the overall radial shape. This prediction was experimentally assessed. The analysis using a near-isogenic line of the gene, PROG1 for prostrate growth and the gravitropic mutant (lazy1) showed an association between genes and our model parameters. Our findings provide a simple, yet substantial, kinematic model for how the shape in distichous phyllotaxy plants changes as part of their adaptation to the surrounding environment.

Genetic Mapping of the Gamete Eliminator Locus, S2, 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, 20 Mar. 2021
English, Scientific journal, Hybrid sterility is a reproductive barrier that prevents gene flow between species. In Oryza species, some hybrid sterility loci, which are classified as gamete eliminators, cause pollen and seed sterility and sex-independent transmission ratio distortion (siTRD) in hybrids. However, the molecular basis of siTRD has not been fully characterized because of lacking information on causative genes. Here, we analyze one of the hybrid sterility loci, S2, which was reported more than forty years ago but has not been located on rice chromosomes. Hybrids between African rice (Oryza glaberrima) and a near-isogenic line that possesses introgressed chromosomal segments from Asian rice (Oryza sativa) showed sterility and siTRD, which confirms the presence of the S2 locus. Genome-wide SNP marker survey revealed that the near-isogenic line has an introgression on chromosome 4. Further substitution mapping located the S2 locus between 22.60 Mb and 23.54 Mb on this chromosome. Significant TRD in this chromosomal region was also observed in a calli population derived from cultured anther in hybrids of another cross combination of African and Asian rice species. This indicates that the pollen abortion caused by the S2 locus occurs before callus induction in anther culture. It also suggests the wide existence of the S2-mediated siTRD in this interspecific cross combination. Chromosomal location of the S2 locus will be valuable for identifying causative genes and for understanding of the molecular basis of siTRD.

Left-right asymmetry-driven physical interaction causes twisting in rice (Oryza sativa) leaves
曵地究; 岡田脩平; 徳山芳樹; 三浦誠一郎; 田口みなみ; 貴島祐治; 高牟禮逸郎; 小出陽平, 育種学研究, 27, 2025

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

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

イネの生育予測モデルに基づいた品種組み合わせ 最適化アルゴリズムの構築
渡邉 真悠; 曵地 究; 小出 陽平; 棟朝 雅晴
22 Mar. 2026, Oral presentation

ダイズの莢形成における細胞分裂の制御：組織成長率との相関および位置による効果
曵地究; 三浦誠一朗; 徳山芳樹; 小出陽平
日本育種学会第149回講演会, 22 Mar. 2026, Oral presentation

葉身の左右非対称性が引き起こす器官間物理的相互作用を介した捻れについて
曵地究; 岡田脩平; 徳山芳樹; 三浦誠一朗; 田口みなみ; 貴島祐治; 高牟禮逸朗; 小出陽平
国立遺伝学研究所研究集会「イネ分子遺伝学の跳躍」, 19 Dec. 2025, Oral presentation

葉身の左右非対称性が引き起こす器官間物理的相互作用を介した捻れについて
曵地究; 岡田脩平; 徳山芳樹; 三浦誠一朗; 田口みなみ; 貴島祐治; 高牟禮逸朗; 小出陽平
第３回北海道バイオ"Mix-up", 29 Sep. 2025, Oral presentation

イネ捻れ葉変異体における葉身の左右非対称性と器官間物理的相互作用による捻れ発生メカニズム
曵地究; 岡田脩平; 徳山芳樹; 三浦誠一朗; 田口みなみ; 貴島祐治; 高牟禮逸朗; 小出陽平
日本育種学会第148回講演会, 11 Sep. 2025, Oral presentation

イネ捻れ葉変異体における捻れ形成原理の解明と原因変異の遺伝解析
曵地究; 岡田脩平; 徳山芳樹; 高牟禮逸朗; 貴島祐治; 小出陽平
日本育種学会第143回講演会, 18 Mar. 2023, Oral presentation

マイクロ CT を用いたイネ捻れ葉変異体の表現型解析
岡田脩平; 曵地究; 徳山芳樹; 小出陽平; 貴島祐治; 高牟禮逸朗
日本育種学会・日本作物学会北海道談話会 年次講演会, 03 Dec. 2022, Oral presentation

フォトグラメトリを利用した野生イネ草姿の3次元解析
徳山芳樹; 串田栞; 曵地究; 貴島祐治; 小出陽平
日本育種学会第142回講演会, 23 Sep. 2022, Oral presentation

ダイズの莢における形態形成モデル
曵地究; 徳山芳樹; ドュイヤンティ マリア ステファニ; 小出陽平
日本育種学会第139回講演会, 19 Mar. 2021, Oral presentation

Mar. 2021 - Present
日本育種学会

Apr. 2023 - Mar. 2026
北海道大学EXEX博士人材フェローシップ 採択