Detection of novel loci involved in reduced seed-shattering behaviour in cultivated rice and their application for increasing yield

• Project/Area Number: 18K05594
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 39020:Crop production science-related
• Research Institution: Kobe University
• Principal Investigator: Ryo Ishikawa 神戸大学, 農学研究科, 准教授 (70467687)
• Project Period (FY): 2018-04-01 – 2023-03-31
• Project Status: Completed (Fiscal Year 2022)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2019: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2018: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: seed shattering / domestication / Oryza sativa / Oryza rufipogon / 栽培イネ / 野生イネ / 栽培化 / 脱粒性 / イネ

Outline of Final Research Achievements

During rice domestication, seed-shattering behaviour was supressed, but the loci involved in shattering loss were not fully identified. The objective of this study was to genetically identify novel loci involved in non-seed shattering behaviour of cultivated rice, Oryza sativa, using wild rice O. rufipogon.. We identified qCSS3 (QTL for the Control of Seed Shattering in rice on chromosome 3) using japonica rice Nipponbare and qCSS2/qCSS7 using indica rice IR36. In addition, three novel loci were also identified using AUS type cultivated rice Kasalath.

Academic Significance and Societal Importance of the Research Achievements

栽培イネが持つ非脱粒性に関与した遺伝子座は、2006年に報告されたsh4とqSH1が知られていたが、他の遺伝子座は報告されていなかった。これまでの研究において、既知の脱粒性遺伝子座を栽培イネの染色体断片で置換した野生イネを交雑によって作出し、これと栽培イネを再び交雑することで、既知の遺伝子座が遺伝的に固定した分離集団を作成した。本研究ではこれらの遺伝解析を進め新規の脱粒性遺伝子座の同定とそれらの効果検証に成功した。これら新規遺伝子座の原因変異の同定はイネの栽培化過程の解明に役立つ。また、栽培イネの脱粒程度を遺伝学的に調節する育種にも応用できる可能性が考えられ、イネの収量性の向上が期待される。

Research Products

• [Int'l Joint Research] University College London/Warwick University(英国)
• [Int'l Joint Research] University Collage London/Warwick university(英国)
• [Int'l Joint Research] University Collage London/Warwick University(英国)
• [Int'l Joint Research] University Collage London/Warwick University(英国)
• [Int'l Joint Research] University Collage London/Warwick University(英国)
• [Journal Article] A stepwise route to domesticate rice by controlling seed shattering and panicle shape (2022)
  • Author(s): Ishikawa Ryo、Castillo Cristina Cobo、Htun Than Myint、Numaguchi Koji、Inoue Kazuya、Oka Yumi、Ogasawara Miki、Sugiyama Shohei、Takama Natsumi、Orn Chhourn、Inoue Chizuru、Nonomura Ken-Ichi、Allaby Robin、Fuller Dorian Q.、Ishii Takashige
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 119 Issue: 26
  • DOI: 10.1073/pnas.2121692119
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Genetic evaluation of domestication-related traits in rice: implications for the archaeobotany of rice origins. (2021)
  • Author(s): Ishikawa, R., Castillo, C.C. & Fuller, D.Q
  • Journal Title: Archaeol Anthropol Sci Volume: 12 Issue: 8 Pages: 197-197
  • DOI: 10.1007/s12520-020-01112-3
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Detection of a novel locus involved in non-seed-shattering behaviour of Japonica rice cultivar, Oryzasativa ‘Nipponbare’ (2019)
  • Author(s): Tsujimura Yuki、Sugiyama Shohei、Otsuka Kotaro、Htun Than Myint、Numaguchi Koji、Castillo Cristina、Akagi Takashi、Ishii Takashige、Ishikawa Ryo
  • Journal Title: Theoretical and Applied Genetics Volume: 132 Issue: 9 Pages: 2615-2623
  • DOI: 10.1007/s00122-019-03376-3
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] バイオリソースと育種学のこれからを考える：NBRPリソースの活用事例から (2019)
  • Author(s): 那須田周平、佐藤豊、久野裕、佐藤和広、小松田隆夫、石川亮、橋口正嗣、鈴木章弘、星川健、伊藤瑛海
  • Journal Title: 育種学研究 Volume: 21 Pages: 81-85
  • NAID: 130007664808
• [Presentation] ジャポニカイネ朝日の非脱粒性の遺伝学的解剖 (2023)
  • Author(s): 狩野舞, 辻村雄紀, 石井尊生, 石川亮
  • Organizer: 日本育種学会第143回講演会
• [Presentation] インディカイネ IR36 の非脱粒性に関与する新規遺伝子座の検証 (2022)
  • Author(s): 作田幹樹, 杉山昇平, 辻村雄紀, Htun Than Myint, 井上千鶴, 沼口孝司, 石井尊生, 石川亮
  • Organizer: 日本育種学会第142回講演会
• [Presentation] イネ栽培化における種子脱粒性喪失過程の実験検証 (2022)
  • Author(s): 石川亮, Castillo Cristina Cobo, Htun Than Myint, 沼口孝司, 井上一哉, 岡佑美, 小笠原実希, 杉山 昇平, 高間菜摘, Orn Chhourn, 井上千鶴, 野々村賢一, Allaby Robin, Fuller. Dorian, 石井 尊生
  • Organizer: 日本育種学会第142回講演会
• [Presentation] イネの種子脱粒性喪失に関与した qSH3遺伝子座における変異の役割と多様性 (2022)
  • Author(s): 沼口孝司，Htun Than Myint，岡佑美，小笠原実希，杉山昇平，高間菜摘，Orn Chhourn，井上千鶴，石井尊生，石川亮
  • Organizer: 日本育種学会第142回講演会
• [Presentation] インディカ型栽培イネIR36の非脱粒性に関与する新規遺伝子座の推定 (2019)
  • Author(s): 杉山昇平、辻村雄紀、井上千鶴、Than Myint Htun、沼口孝司、石井尊生、石川亮
  • Organizer: 日本育種学会第136回講演会
• [Presentation] Identifying scratches on chromosomes: an approach to understand the process of rice domestication based on loss of seed shattering (2019)
  • Author(s): Ryo Ishikawa
  • Organizer: 第70回染色体学会年会
  • Invited
• [Presentation] ジャポニカ型栽培イネ（日本晴）の非脱粒性に関与する新規遺伝子座の離層形成への効果 (2018)
  • Author(s): 杉山昇平、辻村雄紀、大塚宏太郎、Than Myint Htun、石井尊生、石川亮
  • Organizer: 日本育種学会第134回講演会