Elucidation of genome-wide gene regulatory networks underlying the heterosis in Sorghum seed production.

• Project/Area Number: 17H01457
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Science in genetics and breeding
• Research Institution: The University of Tokyo
• Principal Investigator: TSUTSUMI NOBUHIRO 東京大学, 大学院農学生命科学研究科(農学部), 教授 (00202185)
• Project Period (FY): 2017-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥40,950,000 (Direct Cost: ¥31,500,000、Indirect Cost: ¥9,450,000); Fiscal Year 2019: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000); Fiscal Year 2018: ¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000); Fiscal Year 2017: ¥13,780,000 (Direct Cost: ¥10,600,000、Indirect Cost: ¥3,180,000)
• Keywords: ソルガム / 子実収量 / 穂構造 / 小穂構造 / 種子構造 / GWA解析 / QTL解析 / 雑種強勢 / GWA・QTL解析 / 育種学

Outline of Final Research Achievements

The use of heterosis is effective in improving grain yield in sorghum, as in other cereals. The identification of the genome-wide gene regulatory networks underlying the spikelet- and grain-related traits is very important for the rapid and efficient development of high yielding grain sorghum varieties via the use of heterosis. However, in sorghum, which has a short history of modern breeding, these networks have remained largely unknown. In this study, we have developed the cross populations and the genome data for accurate genetic analysis of spikelet- and grain-related traits in sorghum, and succeeded in comprehensively identifying the genetic loci that regulate these traits.

Academic Significance and Societal Importance of the Research Achievements

近年，気候変動に起因する穀倉地帯の干ばつは深刻な問題であり，栽培に多量の水を消費するトウモロコシの代替作物として，優れた乾燥耐性を備えるソルガムが注目されつつあります．さらに，小麦食に起因した健康リスクを忌避する消費嗜好の拡大は，ソルガムの消費需要を今後飛躍的に高めることが予想され，生産量の増大を支える多収品種の開発が急務です．本研究の成果は，子実型ソルガムの飛躍的増産を可能にする多収性F1品種の迅速かつ効率的な育種システムの設計に，大きく寄与する知見です．また，ソルガムを含むイネ科作物の子実収量を規定する遺伝機構の多様性や共通性の理解に向けて，高い価値を持つものと考えられます．

Research Products

• [Journal Article] FMT, a protein that affects mitochondrial distribution, interacts with translation-related proteins in Arabidopsis thaliana (2021)
  • Author(s): Ayabe Hiroki、Kawai Narumi、Shibamura Mitsuhiro、Fukao Yoichiro、Fujimoto Masaru、Tsutsumi Nobuhiro、Arimura Shin-ichi
  • Journal Title: Plant Cell Reports Volume: 40 Issue: 2 Pages: 327-337
  • DOI: 10.1007/s00299-020-02634-9
  • Peer Reviewed
• [Journal Article] Dissecting the Genetic Architecture of Biofuel-related Traits in a Sorghum Breeding Population (2020)
  • Author(s): Ishimori M, Takanashi H, Hamazaki K, Atagi Y, Kajiya-Kanegae H, Fujimoto M, Yoneda J, Tokunaga T, Tsutsumi N, Iwata H
  • Journal Title: G3 Volume: 10 Issue: 12 Pages: 4565-4577
  • DOI: 10.1534/g3.120.401582
  • Peer Reviewed / Open Access
• [Journal Article] Targeted gene disruption of ATP synthases 6-1 and 6-2 in the mitochondrial genome of Arabidopsis thaliana by mitoTALENs (2020)
  • Author(s): Arimura S, Ayabe H, Sugaya H, Okuno M, Tamura Y, Tsuruta Y, Watari Y, Yanase S, Yamauchi T, Itoh T, Toyoda A, Takanashi H, Tsutsumi N
  • Journal Title: Plant J Volume: 104 Pages: 1459-1471
  • Peer Reviewed
• [Journal Article] Impacts of dominance effects on genomic prediction of sorghum hybrid performance. (2020)
  • Author(s): Ishimori M, Hattori T, Yamazaki K, Takanashi H, Fujimoto M, Kajiya-Kanegae H, Yoneda J, Tokunaga T, Fujiwara T, Tsutsumi N, Iwata H
  • Journal Title: Breed Sci. Volume: 70 Pages: 605-616
  • NAID: 130007962583
  • Peer Reviewed
• [Journal Article] Longin R-SNARE is retrieved from the plasma membrane by ANTH domain-containing proteins in Arabidopsis (2020)
  • Author(s): Fujimoto Masaru、Ebine Kazuo、Nishimura Kohji、Tsutsumi Nobuhiro、Ueda Takashi
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 117 Issue: 40 Pages: 25150-25158
  • DOI: 10.1073/pnas.2011152117
  • Peer Reviewed / Open Access
• [Journal Article] RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG. (2020)
  • Author(s): Kajiya-Kanegae H, Takanashi H, Fujimoto M, Ishimori M, Ohnishi N, Wacera W F, Omollo EA, Kobayashi M, Yano K, Nakano M, Kozuka T, Kusaba M, Iwata H, Tsutsumi N, Sakamoto W
  • Journal Title: Plant Cell Physiol. Volume: 61 Issue: 7 Pages: 1262-1272
  • DOI: 10.1093/pcp/pcaa056
  • Peer Reviewed / Open Access
• [Journal Article] A Role for Auxin in Ethylene-Dependent Inducible Aerenchyma Formation in Rice Roots (2020)
  • Author(s): Yamauchi T, Tanaka A, Tsutsumi N, Inukai Y, Nakazono M
  • Journal Title: Plants (Basel) Volume: 9 Issue: 5 Pages: 610-610
  • DOI: 10.3390/plants9050610
  • Peer Reviewed
• [Journal Article] Distance-to-Time Conversion Using Gompertz Model Reveals Age-Dependent Aerenchyma Formation in Rice Roots (2020)
  • Author(s): Yamauchi T, Nakazono M, Inukai Y, Tsutsumi N.
  • Journal Title: Plant Physiol. Volume: 183 Issue: 4 Pages: 1424-1427
  • DOI: 10.1104/pp.20.00321
  • Peer Reviewed
• [Journal Article] Effect of salt tolerance on biomass production in a large population of sorghum accessions (2020)
  • Author(s): Yamazaki Kiyoshi、Ishimori Motoyuki、Kajiya-Kanegae Hiromi、Takanashi Hideki、Fujimoto Masaru、Yoneda Jun-ichi、Yano Kentaro、Koshiba Taichi、Tanaka Ryokei、Iwata Hiroyoshi、Tokunaga Tsuyoshi、Tsutsumi Nobuhiro、Fujiwara Toru
  • Journal Title: Breeding Science Volume: 70 Issue: 2 Pages: 167-175
  • DOI: 10.1270/jsbbs.19009
  • NAID: 130007833812
  • ISSN: 1344-7610, 1347-3735
  • Peer Reviewed / Open Access
• [Journal Article] Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology (2019)
  • Author(s): Sakamoto Lisa、Kajiya-Kanegae Hiromi、Noshita Koji、Takanashi Hideki、Kobayashi Masaaki、Kudo Toru、Yano Kentaro、Tokunaga Tsuyoshi、Tsutsumi Nobuhiro、Iwata Hiroyoshi
  • Journal Title: PLOS ONE Volume: 14 Issue: 11 Pages: e0224695-e0224695
  • DOI: 10.1371/journal.pone.0224695
  • Peer Reviewed / Open Access
• [Journal Article] Comparison and Characterization of Mutations Induced by Gamma-Ray and Carbon-Ion Irradiation in Rice (Oryza sativa L.) Using Whole-Genome Resequencing (2019)
  • Author(s): Li F, Shimizu A, Nishio T, Tsutsumi N, Kato H.
  • Journal Title: G3 (Genes, Genomes, Genetics) Volume: 9 Issue: 11 Pages: 3743-3751
  • DOI: 10.1534/g3.119.400555
  • Peer Reviewed / Open Access
• [Journal Article] Fine control of aerenchyma and lateral root development through AUX/IAA- and ARF-dependent auxin signaling. (2019)
  • Author(s): Yamauchi T, Tanaka A, Inahashi H, Nishizawa NK, Tsutsumi N, Inukai Y, Nakazono M.
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 116 Issue: 41 Pages: 20770-20775
  • DOI: 10.1073/pnas.1907181116
  • Peer Reviewed / Open Access
• [Journal Article] Curing cytoplasmic male sterility via TALEN- mediated mitochondrial genome editing (2019)
  • Author(s): Tomohiko Kazama 1*, Miki Okuno2, Yuta Watari3, Shungo Yanase3, Chie Koizuka4, Yu Tsuruta3, Hajime Sugaya3, Atsushi Toyoda 5, Takehiko Itoh2, Nobuhiro Tsutsumi3, Kinya Toriyama1, Nobuya Koizuka 4* and Shin-ichi Arimura 3,6*
  • Journal Title: Nature Plants Volume: 5 Issue: 7 Pages: 722-730
  • DOI: 10.1038/s41477-019-0459-z
  • Peer Reviewed / Open Access
• [Journal Article] Molecular mechanisms for pith cell death of sorghum stems (2019)
  • Author(s): 藤本 優, 米丸 淳一, 堤 伸浩
  • Journal Title: Regulation of Plant Growth & Development Volume: 54 Issue: 1 Pages: 66-70
  • DOI: 10.18978/jscrp.54.1_66
  • NAID: 130007668424
  • ISSN: 1346-5406, 2189-6305
• [Journal Article] ソルガムの茎糖液含量を規定する遺伝子 (2019)
  • Author(s): 藤本 優，佐塚隆志，米丸淳一，堤 伸浩
  • Journal Title: バイオサイエンスとインダストリー Volume: 77 Pages: 112-115
  • NAID: 40021840498
• [Journal Article] Root Cortex Provides a Venue for Gas-Space Formation and Is Essential for Plant Adaptation to Waterlogging (2019)
  • Author(s): Yamauchi T, Abe F, Tsutsumi N, Nakazono M
  • Journal Title: Frontiers in Plant Science Volume: 10 Pages: 259-259
  • DOI: 10.3389/fpls.2019.00259
  • Peer Reviewed
• [Journal Article] The mitochondrial genome of an asymmetrically cell-fused rapeseed, <i>Brassica napus</i>, containing a radish-derived cytoplasmic male sterility-associated gene (2018)
  • Author(s): Arimura Shin-ichi、Yanase Shungo、Tsutsumi Nobuhiro、Koizuka Nobuya
  • Journal Title: Genes & Genetic Systems Volume: 93 Issue: 4 Pages: 143-148
  • DOI: 10.1266/ggs.18-00005
  • NAID: 130007503896
  • ISSN: 1341-7568, 1880-5779
  • Year and Date: 2018-08-01
  • Peer Reviewed / Open Access
• [Journal Article] Transcriptional switch for programmed cell death in pith parenchyma of sorghum stems. (2018)
  • Author(s): Fujimoto M, Sazuka T, Oda Y, Kawahigashi H, Wu J, Takanashi H, Ohnishi T, Yoneda JI, Ishimori M, Kajiya-Kanegae H, Hibara KI, Ishizuna F, Ebine K, Ueda T, Tokunaga T, Iwata H, Matsumoto T, Kasuga S, Yonemaru JI, Tsutsumi N
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America Volume: 115 Issue: 37
  • DOI: 10.1073/pnas.1807501115
  • Peer Reviewed / Open Access
• [Journal Article] miRNAs control HAM1 functions at the single-cell-layer level and are essential for normal embryogenesis in Arabidopsis (2018)
  • Author(s): Hideki Takanashi, Hikari Sumiyoshi, Mirai Mogi, Yoshikazu Hayashi, Takayuki Ohnishi, Nobuhiro Tsutsumi
  • Journal Title: Plant Molecular Biology Volume: - Issue: 6 Pages: 627-640
  • DOI: 10.1007/s11103-018-0719-8
  • Peer Reviewed
• [Journal Article] Cold Treatment Induces Transient Mitochondrial Fragmentation in Arabidopsis thaliana in a Way that Requires DRP3A but not ELM1 or an ELM1-Like Homologue, ELM2 (2017)
  • Author(s): Arimura SI, Kurisu R, Sugaya H, Kadoya N, Tsutsumi N
  • Journal Title: International Journal of Molecular Sciences Volume: 18 Issue: 10 Pages: 2161-2161
  • DOI: 10.3390/ijms18102161
  • Peer Reviewed / Open Access
• [Journal Article] Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data (2017)
  • Author(s): Kobayashi Masaaki、Ohyanagi Hajime、Takanashi Hideki、Asano Satomi、Kudo Toru、Kajiya-Kanegae Hiromi、Nagano Atsushi J.、Tainaka Hitoshi、Tokunaga Tsuyoshi、Sazuka Takashi、Iwata Hiroyoshi、Tsutsumi Nobuhiro、Yano Kentaro
  • Journal Title: DNA Research Volume: 24 Issue: 4 Pages: 397-405
  • DOI: 10.1093/dnares/dsx012
  • Peer Reviewed / Open Access
• [Journal Article] DRP3 and ELM1 are required for mitochondrial fission in the liverwort Marchantia polymorpha (2017)
  • Author(s): Nagaoka Nagisa、Yamashita Akihiro、Kurisu Rina、Watari Yuta、Ishizuna Fumiko、Tsutsumi Nobuhissro、Ishizaki Kimitsune、Kohchi Takayuki、Arimura Shin-ichi
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 4600-4600
  • DOI: 10.1038/s41598-017-04886-0
  • NAID: 120006366789
  • Peer Reviewed / Open Access
• [Journal Article] An NADPH oxidase RBOH functions in rice roots during lysigenous aerenchyma formation under oxygen-deficient conditions. (2017)
  • Author(s): Yamauchi, T., Yoshioka, M., Fukazawa, A., Mori, H., Nishizawa, N.K., Tsutsumi, N., Yoshioka, H. and Nakazono, M.
  • Journal Title: The Plant Cell Volume: 印刷中 Issue: 4 Pages: 775-790
  • DOI: 10.1105/tpc.16.00976
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Presentation] 遺伝子型×環境交互作用モデルによるソルガムのゲノミック予測 (2020)
  • Author(s): 石森元幸, 山﨑清志, 高梨秀樹, 鐘ヶ江弘 美, 藤本優, 米田淳一, 徳永毅, 藤原徹, 堤伸浩, 岩田洋佳
  • Organizer: 日本育種学会・第137回講演会
• [Presentation] 植物ミトコンドリアゲノム編集の試み: mitoTALENによるシロイヌナズナNAD7遺伝子の破壊 (2020)
  • Author(s): 綾部弘基, 日高朋美, 田村美子, 堤伸浩, 有村慎一
  • Organizer: 日本育種学会・第137回講演会
• [Presentation] パーティクルガンを用いたミトコンドリアゲノムへの外来遺伝子導入の試み (2020)
  • Author(s): 中里一星，肥塚信也，堤伸浩，有村慎一
  • Organizer: 日本育種学会・第137回講演会
• [Presentation] たかきびRILのイオノームを用いたソルガム種子の元素含量に関するQTL解析 (2020)
  • Author(s): ワセラフィオナ，藤原徹 ，山崎清志，高梨秀樹，堤伸浩，鐘ヶ江弘美，坂本亘
  • Organizer: 日本育種学会・第137回講演会
• [Presentation] mitoTALEN によるミトコンドリアゲノム編集：シロイヌナズナ ATP6-1・ATP6-2 遺伝子の冗長性の解析 (2019)
  • Author(s): 鶴田遊, 菅谷元, 柳瀬俊吾, 亘悠太, 堤伸浩, 有村慎一
  • Organizer: 日本育種学会・第136回講演会
• [Presentation] mitoTALENによるシロイヌナズナミトコンドリアゲノムNAD7の標的遺伝子破壊 (2019)
  • Author(s): 綾部弘基，日高朋美，田村美子，堤伸浩，有村慎一
  • Organizer: 日本育種学会・第136回講演会
• [Presentation] 遺伝子型×年次交互作用モデルによるソルガムのゲノムワイド関連解析 (2019)
  • Author(s): 石森 元幸, 高梨 秀樹, 藤本 優, 鐘ヶ江 弘美, 米田 淳一, 徳永 毅, 堤 伸浩, 岩田 洋佳
  • Organizer: 日本育種学会第135回講演会
• [Presentation] 多様な土壌水分環境に適応的なイネ科植物の根の解剖学的形質のモデル化 (2019)
  • Author(s): 山内 卓樹, 中園 幹生, 堤 伸浩
  • Organizer: 日本育種学会第135回講演会
• [Presentation] ピーカン遺伝資源のもつ可食部形態の多様性を画像とゲノムデータをもとに解析する (2019)
  • Author(s): 千々谷 涼介，坂本 莉沙，石森 元幸，高梨 秀樹，Kimberly Cervantes，永野 惇，鐘ケ江 弘美，L.J. Grauke，堤 伸浩，Jennifer J. Randall，岩田 洋佳
  • Organizer: 日本育種学会第135回講演会
• [Presentation] ソルガム毛状突起の先端構造に関する遺伝子座の探索 (2018)
  • Author(s): 三輪幸哉，七条光年，高梨秀樹，藤本優，鐘ケ江弘美，石森元幸，矢野健太郎，山崎清志，藤原徹，米田淳一，徳永毅，石綱史子，小童谷利恵，大西紀和，坂本亘，岩田洋佳，堤伸浩
  • Organizer: 日本育種学会第133回講演会
• [Presentation] ソルガム未熟胚の培養応答性に関するGWA 解析およびQTL 解析 (2018)
  • Author(s): 西村明日香，七条光年，三輪幸哉，高梨秀樹，藤本優，鐘ヶ江弘美，小林正明，矢野健太郎，小柴太一，徳永毅，岩田洋佳，坂本亘，堤伸浩ソルガム未熟胚の培養応答性に関するGWA 解析およびQTL 解析
  • Organizer: 日本育種学会第133回講演会
• [Presentation] 全ゲノムSNP を用いたGWAS におけるSNP-set 解析の可能性 (2018)
  • Author(s): 石森元幸, 鐘ケ江弘美, 山﨑清志, 高梨秀樹, 藤本優, 米田淳一, 徳永毅, 藤原徹,堤伸浩, 岩田洋佳
  • Organizer: 日本育種学会第133回講演会
• [Presentation] 輪郭形状のゲノミック予測のための定量化手法の比較 (2018)
  • Author(s): 坂本 莉沙，鐘ケ江弘美，野下浩司，石森元幸，小林正明，藤本 優，高梨 秀樹，永野 惇，佐塚隆志，矢野 健太郎，徳永 毅，堤 伸浩，岩田 洋佳
  • Organizer: 日本育種学会第133回講演会
• [Presentation] 高速ジェノタイピングによるテーラーメード育種 (2018)
  • Author(s): 堤伸浩
  • Organizer: 日本育種学会第134回講演会・ワークショップ植物科学は農業生産へいかに貢献するか～植物科学のこれから～
  • Invited
• [Presentation] Phenomics に適したQTL 解析手法の提案：ソルガムRIL 集団の葉形態を例に (2018)
  • Author(s): 坂本 莉沙, 藤本 優, 高梨 秀樹, 鐘ケ江 弘美, 野下 浩司, 小林 正明, 矢野 健太郎, 小童谷 利恵, 大西 紀和, 堤 伸浩, 坂本 亘, 岩田 洋佳
  • Organizer: 日本育種学会第134回講演会
• [Presentation] Large scale analysis of elemental composition in sorghum (2018)
  • Author(s): Yamasaki, K., Fujimoto, M., Yoneda, J., Koshiba, T., Ishimori, M., Takanashi, H., Kajiya-Kanegae, H., Iwata, H., Tsutsumi, N., Tokunaga, T., Fujiwara, T
  • Organizer: Sorghum in the 21st Century, Cape Town, South Africa
• [Presentation] Genome-Wide association studies and genomic prediction with 3,000 biomass sorghum plants (2018)
  • Author(s): Ishimori, M., Takanashi, H., Fujimoto, M., Kajiya-Kanegae, H., Yoneda, J., Yano, K., Tokunaga, T., Tsutsumi, N., Iwata, H
  • Organizer: Sorghum in the 21st Century, Cape Town, South Africa
• [Presentation] Mapping of QTLs associated with awn length in sorghum (2018)
  • Author(s): Takanashi, H., Kajiya-Kanegae H., Ishimori, M., Yano, K., Ohnishi, N., Fujiwara, T., Iwata, H., Sakamoto, W., Tsutsumi, N
  • Organizer: Sorghum in the 21st Century, Cape Town, South Africa
• [Presentation] ソルガム不稔小穂の発達度合に関するGWA 解析 (2017)
  • Author(s): 七条光年, 高梨秀樹, 藤本優, 鐘ケ江弘美, 石森元幸, 小林正明, 矢野健太郎, 山崎清志, 藤原徹, 米田淳一, 徳永毅, 岩田洋佳, 堤伸浩
  • Organizer: 日本育種学会第132回講演会
• [Presentation] ソルガム苞穎毛の先端構造に関する遺伝子座の探索 (2017)
  • Author(s): 三輪幸哉, 七条光年, 高梨秀樹, 藤本優, 鐘ケ江弘美, 石森元幸, 小林正明, 矢野健太郎, 山崎清志, 藤原徹, 米田淳一, 徳永毅, 小童谷利恵, 大西紀和, 坂本亘, 岩田洋佳, 堤伸浩
  • Organizer: 日本育種学会第132回講演会
• [Presentation] QTL解析に価値ある画像解析：ソルガムRIL集団の葉形態を例に (2017)
  • Author(s): 坂本莉沙,藤本優,高梨秀樹,鐘ケ江弘美,野下浩司,小林正明,矢野健太郎,七条光年,小童谷利恵,大西紀和,堤伸浩,坂本亘,岩田洋佳
  • Organizer: 日本育種学会第132回講演会
• [Presentation] ソルガム RIL 集団を用いた塩・浸透圧ストレス耐性に関する QTL 解析 (2017)
  • Author(s): 山内卓樹，高梨秀樹，藤本優，鐘ケ江弘美，石森元幸，小林正明，矢野健太郎，小童谷利恵，大西紀和，岩田洋佳，坂本亘，堤伸浩
  • Organizer: 日本育種学会第132回講演会
• [Remarks] 世界初の植物ミトコンドリアのゲノム編集に成功
  • URL: https://www.a.u-tokyo.ac.jp/topics/topics_20190709-1.html
• [Remarks] イネの水田での生育を支える通気組織形成の仕組みを解明
  • URL: https://www.a.u-tokyo.ac.jp/topics/topics_20190924-1.html
• [Remarks] ソルガムにおける乾汁性決定遺伝子の発見～糖やエタノールの生産性向上に関わる100年来の謎を解明～
  • URL: https://www.a.u-tokyo.ac.jp/topics/2018/20180828-1.html