研究者詳細 - 山本　敏央

論文 - 山本　敏央

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Genetic background influences mineral accumulation in rice straw and grains under different soil pH conditions 査読

Toshio Yamamoto, Kazunari Kashihara, Tomoyuki Furuta, Qian Zhang, En Yu, Jian Feng Ma

Scientific Reports 14 ( 1 ) 2024年7月

担当区分：筆頭著者,　責任著者記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Springer Science and Business Media LLC

Abstract

Mineral element accumulation in plants is influenced by soil conditions and varietal factors. We investigated the dynamic accumulation of 12 elements in straw at the flowering stage and in grains at the mature stage in eight rice varieties with different genetic backgrounds (Japonica, Indica, and admixture) and flowering times (early, middle, and late) grown in soil with various pH levels. In straw, Cd, As, Mn, Zn, Ca, Mg, and Cu accumulation was influenced by both soil pH and varietal factors, whereas P, Mo, and K accumulation was influenced by pH, and Fe and Ni accumulation was affected by varietal factors. In grains, Cd, As, Mn, Cu, Ni, Mo, Ca, and Mg accumulation was influenced by both pH and varietal factors, whereas Zn, Fe, and P accumulation was affected by varietal factors, and K accumulation was not altered. Only As, Mn, Ca and Mg showed similar trends in the straw and grains, whereas the pH responses of Zn, P, K, and Ni differed between them. pH and flowering time had synergistic effects on Cd, Zn, and Mn in straw and on Cd, Ni, Mo, and Mn in grains. Soil pH is a major factor influencing mineral uptake in rice straw and grains, and genetic factors, flowering stage factors, and their interaction with soil pH contribute in a combined manner.

DOI： 10.1038/s41598-024-66036-7

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その他リンク： https://www.nature.com/articles/s41598-024-66036-7

MCPtaggR: R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison 査読

Tomoyuki Furuta, Toshio Yamamoto

DNA Research 31 ( 1 ) 2023年12月

掲載種別：研究論文（学術雑誌）出版者・発行元：Oxford University Press (OUP)

Abstract

Reduced representation sequencing (RRS) offers cost-effective, high-throughput genotyping platforms such as genotyping-by-sequencing (GBS). RRS reads are typically mapped onto a reference genome. However, mapping reads harbouring mismatches against the reference can potentially result in mismapping and biased mapping, leading to the detection of error-prone markers that provide incorrect genotype information. We established a genotype-calling pipeline named mappable collinear polymorphic tag genotyping (MCPtagg) to achieve accurate genotyping by eliminating error-prone markers. MCPtagg was designed for the RRS-based genotyping of a population derived from a biparental cross. The MCPtagg pipeline filters out error-prone markers prior to genotype calling based on marker collinearity information obtained by comparing the genome sequences of the parents of a population to be genotyped. A performance evaluation on real GBS data from a rice F2 population confirmed its effectiveness. Furthermore, our performance test using a genome assembly that was obtained by genome sequence polishing on an available genome assembly suggests that our pipeline performs well with converted genomes, rather than necessitating de novo assembly. This demonstrates its flexibility and scalability. The R package, MCPtaggR, was developed to provide functions for the pipeline and is available at https://github.com/tomoyukif/MCPtaggR.

DOI： 10.1093/dnares/dsad027

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その他リンク： https://academic.oup.com/dnaresearch/article-pdf/31/1/dsad027/56260214/dsad027.pdf

複数水稲品種の遺伝背景における出穂期の準同質遺伝子系統群の作出と遺伝効果の差異査読

堀清純, 高松光生, 細井淳, 津金胤昭, 林玲子, 渡邉学, 水林達実, 安藤露, 正村純彦, 向井喜之, 山内歌子, 山本敏央

育種学研究 25 ( 2 ) 123 - 139 2023年12月

A cell wall–localized cytokinin/purine riboside nucleosidase is involved in apoplastic cytokinin metabolism in Oryza sativa 査読

Mikiko Kojima, Nobue Makita, Kazuki Miyata, Mika Yoshino, Akira Iwase, Miwa Ohashi, Alicia Surjana, Toru Kudo, Noriko Takeda-Kamiya, Kiminori Toyooka, Akio Miyao, Hirohiko Hirochika, Tsuyu Ando, Ayahiko Shomura, Masahiro Yano, Toshio Yamamoto, Tokunori Hobo, Hitoshi Sakakibara

Proceedings of the National Academy of Sciences 120 ( 36 ) 2023年8月

記述言語：英語掲載種別：研究論文（学術雑誌）出版者・発行元：Proceedings of the National Academy of Sciences

In the final step of cytokinin biosynthesis, the main pathway is the elimination of a ribose-phosphate moiety from the cytokinin nucleotide precursor by phosphoribohydrolase, an enzyme encoded by a gene named LONELY GUY (LOG). This reaction accounts for most of the cytokinin supply needed for regulating plant growth and development. In contrast, the LOG-independent pathway, in which dephosphorylation and deribosylation sequentially occur, is also thought to play a role in cytokinin biosynthesis, but the gene entity and physiological contribution have been elusive. In this study, we profiled the phytohormone content of chromosome segment substitution lines of Oryza sativa and searched for genes affecting the endogenous levels of cytokinin ribosides by quantitative trait loci analysis. Our approach identified a gene encoding an enzyme that catalyzes the deribosylation of cytokinin nucleoside precursors and other purine nucleosides. The cytokinin/purine riboside nucleosidase 1 (CPN1) we identified is a cell wall–localized protein. Loss-of-function mutations ( cpn1 ) were created by inserting a Tos17 -retrotransposon that altered the cytokinin composition in seedling shoots and leaf apoplastic fluid. The cpn1 mutation also abolished cytokinin riboside nucleosidase activity in leaf extracts and attenuated the trans -zeatin riboside-responsive expression of cytokinin marker genes. Grain yield of the mutants declined due to altered panicle morphology under field-grown conditions. These results suggest that the cell wall–localized LOG-independent cytokinin activating pathway catalyzed by CPN1 plays a role in cytokinin control of rice growth. Our finding broadens our spatial perspective of the cytokinin metabolic system.

DOI： 10.1073/pnas.2217708120

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Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice 査読

Kazufumi Nagata, Yasunori Nonoue, Kazuki Matsubara, Ritsuko Mizobuchi, Nozomi Ono, Taeko Shibaya, Kaworu Ebana, Eri Ogiso-Tanaka, Takanari Tanabata, Kazuhiko Sugimoto, Fumio Taguchi-Shiobara, Jun-ichi Yonemaru, Yusaku Uga, Atsunori Fukuda, Tadamasa Ueda, Shin-ichi Yamamoto, Utako Yamanouchi, Toshiyuki Takai, Takashi Ikka, Katsuhiko Kondo, Tomoki Hoshino, Eiji Yamamoto, Shunsuke Adachi, Jian Sun, Noriyuki Kuya, Yuka Kitomi, Ken Iijima, Hideki Nagasaki, Ayahiko Shomura, Tatsumi Mizubayashi, Noriyuki Kitazawa, Kiyosumi Hori, Tsuyu Ando, Toshio Yamamoto, Shuichi Fukuoka, Masahiro Yano

Breeding Science 73 ( 3 ) 332 - 342 2023年7月

GBScleanR: robust genotyping error correction using a hidden Markov model with error pattern recognition. 査読国際誌

Tomoyuki Furuta, Toshio Yamamoto, Motoyuki Ashikari

Genetics 224 ( 2 ) 2023年5月

記述言語：英語掲載種別：研究論文（学術雑誌）

Reduced-representation sequencing (RRS) provides cost-effective and time-saving genotyping platforms. Despite the outstanding advantage of RRS in throughput, the obtained genotype data usually contain a large number of errors. Several error correction methods employing the hidden Markov model (HMM) have been developed to overcome these issues. These methods assume that markers have a uniform error rate with no bias in the allele read ratio. However, bias does occur because of uneven amplification of genomic fragments and read mismapping. In this paper, we introduce an error correction tool, GBScleanR, which enables robust and precise error correction for noisy RRS-based genotype data by incorporating marker-specific error rates into the HMM. The results indicate that GBScleanR improves the accuracy by more than 25 percentage points at maximum compared to the existing tools in simulation data sets and achieves the most reliable genotype estimation in real data even with error-prone markers.

DOI： 10.1093/genetics/iyad055

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Alleles of high-yielding indica rice that improve root hydraulic conductance also increase flag leaf photosynthesis, biomass, and grain production of japonica rice in the paddy field 査読

Masahiro Yamashita, Chikako Ootsuka, Hikaru Kubota, Shunsuke Adachi, Takuya Yamaguchi, Kazumasa Murata, Toshio Yamamoto, Tadamasa Ueda, Taiichiro Ookawa, Tadashi Hirasawa

Field Crops Research 289 108725 - 108725 2022年12月

Genetic Background Negates Improvements in Rice Flour Characteristics and Food Processing Properties Caused by a Mutant Allele of the PDIL1-1 Seed Storage Protein Gene. 査読国際誌

Kiyosumi Hori, Tomoya Okunishi, Kenji Nakamura, Ken Iijima, Masahiro Hagimoto, Katsuyuki Hayakawa, Koka Shu, Takashi Ikka, Hiroto Yamashita, Masanori Yamasaki, Yoshinobu Takeuchi, Shota Koyama, Yoshimasa Tsujii, Toshiaki Kayano, Takuro Ishii, Toshihiro Kumamaru, Yasushi Kawagoe, Toshio Yamamoto

Rice (New York, N.Y.) 15 ( 1 ) 13 - 13 2022年3月

担当区分：最終著者記述言語：英語掲載種別：研究論文（学術雑誌）

Phenotypic differences among breeding lines that introduce the same superior gene allele can be a barrier to effective development of cultivars with desirable traits in some crop species. For example, a deficient mutation of the Protein Disulfide Isomerase Like 1-1 (PDIL1-1) gene can cause accumulation of glutelin seed storage protein precursors in rice endosperm, and improves rice flour characteristics and food processing properties. However, the gene must be expressed to be useful. A deficient mutant allele of PDIL1-1 was introduced into two rice cultivars with different genetic backgrounds (Koshihikari and Oonari). The grain components, agronomic traits, and rice flour and food processing properties of the resulting lines were evaluated. The two breeding lines had similar seed storage protein accumulation, amylose content, and low-molecular-weight metabolites. However, only the Koshihikari breeding line had high flour quality and was highly suitable for rice bread, noodles, and sponge cake, evidence of the formation of high-molecular-weight protein complexes in the endosperm. Transcriptome analysis revealed that mRNA levels of fourteen PDI, Ero1, and BiP genes were increased in the Koshihikari breeding line, whereas this change was not observed in the Oonari breeding line. We elucidated part of the molecular basis of the phenotypic differences between two breeding lines possessing the same mutant allele in different genetic backgrounds. The results suggest that certain genetic backgrounds can negate the beneficial effect of the PDIL1-1 mutant allele. Better understanding of the molecular basis for such interactions may accelerate future breeding of novel rice cultivars to meet the strong demand for gluten-free foods.

DOI： 10.1186/s12284-022-00560-w

PubMed

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iTRAQ-Based Proteomics Investigation of Critical Response Proteins in Embryo and Coleoptile During Rice Anaerobic Germination 査読国際共著

Zhang Guangchen, Liu Zimeng, Liu Youhong, Kuya Noriyuki, Hua Yuchen, Shi Hongru, Zhao Weilin, Han Yuqing, Yamamoto Toshio, Chen Wenfu, Sun Jian

Rice Science 28 ( 4 ) 391 - 401 2021年7月

日本のイネ品種を背景とした準同質遺伝子系統の比較栽培による収量関連 9 対立遺伝子の遺伝的効果査読

上田忠正, 石丸健, 後藤明俊, 一家崇志, 近藤勝彦, 松原一樹, 林武司, 山本敏央, 田中淳一

育種学研究 23 ( 1 ) 16 - 27 2021年6月

記述言語：日本語掲載種別：研究論文（学術雑誌）出版者・発行元：日本育種学会

<p>イネでは，毎年多くの収量関連遺伝子単離の論文が公表されるが，実際の育種に応用されているものは必ずしも多くない．そこで，日本のイネ品種を遺伝的背景とした収量に関連する9の対立遺伝子について，準同質遺伝子系統を収集・作出し，背景品種との比較試験を実施した．粗玄米重の増加が確認されたものは「コシヒカリ」の遺伝的背景にqCTd11^Takanari，SD1^DGWG，TGW6^KasalathとSD1^DGWGの2つの対立遺伝子を導入した系統および「あきだわら」の遺伝的背景にDEP1^Ballilaを導入した系統であった．これらの対立遺伝子やQTLは，遺伝的背景が日本の品種の場合でも収量を向上させるポテンシャルが期待できる．一方で，「コシヒカリ」の遺伝的背景にqLIA3^Takanari，GPS^Takanari，GS3^Oochikara，GW2^BG1およびGN1A^Takanariを導入した系統では粗玄米重の増加が確認できなかった．これらの対立遺伝子やQTLは，単独ではその効果が小さかったり，シンク容量が大きくなりすぎてソース能が不十分である等の可能性が示唆された．また，「コシヒカリ」を遺伝的背景とした複数の準同質遺伝子系統を用いた試験では，穂重と穂数の負の相関が検出された．これは，シンク容量の増加が期待されたGW2^BG1およびGS3^Oochikara（粒大の増加）やGN1A^Takanari（粒数の増加）の多収化の効果が確認できなかった主要な要因と推察された．シンク容量の増加だけでは多収化は達成できず，qCTd11^Takanariのように単位葉面積あたりの光合成能力の向上に繋がる対立遺伝子や，sd1^DGWGやDEP1^Ballilaなどのような群落構造を大きく変化させる対立遺伝子を組合せて利用するなど，ソース能の向上と並行して取組む必要があると考察された．</p>

DOI： 10.1270/jsbbr.20j21

CiNii Article

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Quantitative trait loci for leaf inclination angle in rice detected using reciprocal mapping populations 査読国際共著

Nan Su San, Kazuya Soda, Yosuke Ootsuki, Masahiro Yamashita, Ryoji Karimata, Kasumi Suzuki, Shunsuke Adachi, Toshio Yamamoto, Takanari Tanabata, Tadamasa Ueda, Taiichiro Ookawa, Tadashi Hirasawa

Field Crops Research 266 108128 - 108128 2021年6月

Diploid Male Gametes Circumvent Hybrid Sterility Between Asian and African Rice Species 査読

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 2020年11月

Semi-dwarf 1 (sd1) gene enhances light penetration into the canopy through regulating leaf inclination angle in rice 査読国際共著

Nan Su San, Kasumi Suzuki, Kazuya Soda, Shunsuke Adachi, Hiroyuki Kasahara, Toshio Yamamoto, Takashi Ikka, Katsuhiko Kondo, Utako Yamanouchi, Kazuhiko Sugimoto, Yoshiaki Nagamura, Tadashi Hirasawa, Taiichiro Ookawa

Field Crops Research 246 107694 - 107694 2020年2月

Genetic determination for source capacity to support breeding of high-yielding rice (Oryza sativa) 査読国際共著

Adachi, S, Ohkubo, S, San, N.S, Yamamoto, T

Molecular Breeding 40 ( 20 ) 2020年

Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game. 査読国際共著国際誌

Jian Sun, Dianrong Ma, Liang Tang, Minghui Zhao, Guangchen Zhang, Wenjia Wang, Jiayu Song, Xiang Li, Zimeng Liu, Wenxing Zhang, Quan Xu, Yuncheng Zhou, Jianzhong Wu, Toshio Yamamoto, Fei Dai, Yan Lei, Song Li, Gang Zhou, Hongkun Zheng, Zhengjin Xu, Wenfu Chen

Molecular plant 12 ( 5 ) 632 - 647 2019年5月

Surveillance of panicle positions by unmanned aerial vehicle to reveal morphological features of rice. 査読国際誌

Daisuke Ogawa, Toshihiro Sakamoto, Hiroshi Tsunematsu, Toshio Yamamoto, Noriko Kanno, Yasunori Nonoue, Jun-Ichi Yonemaru

PLOS ONE 14 ( 10 ) e0224386 2019年

Novel method for evaluation of anaerobic germination in rice and its application to diverse genetic collections 査読国際共著

Kuya, N, Sun, J, Iijima, K, Venuprasad, R, Yamamoto, T

Breeding Science 69 ( 4 ) 633 - 639 2019年

Genetic architecture of leaf photosynthesis in rice revealed by different types of reciprocal mapping populations 査読国際共著

Adachi, S, Yamamoto, T, Nakae, T, Yamashita, M, Uchida, M, Karimata, R, Ichihara, N, Soda, K, Ochiai, T, Ao, R, Otsuka, C, Nakano, R, Takai, T, Ikka, T, Kondo, K, Ueda, T, Ookawa, T, Hirasawa, T, Lawson, T

Journal of Experimental Botany 70 ( 19 ) 5131 - 5144 2019年

Next generation long-culm rice with superior lodging resistance and high grain yield, Monster Rice 1 査読国際共著

Nomura, T, Arakawa, N, Yamamoto, T, Ueda, T, Adachi, S, Yonemaru, J.-I, Abe, A, Takagi, H, Yokoyama, T, Ookawa, T

PLoS ONE 14 ( 8 ) e0221424 2019年

Identification of quantitative trait loci for breaking and bending types lodging resistance in rice, using recombinant inbred lines derived from Koshihikari and a strong culm variety, Leaf Star 査読国際共著

Samadi, A.F, Suzuki, H, Ueda, T, Yamamoto, T, Adachi, S, Ookawa, T

Plant Growth Regulation 89 ( 1 ) 83 - 98 2019年

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