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Identification of hybrid vigor related loci in Brassica

Research Project

Project/Area Number 15H05614
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Horticultural science
Research InstitutionKobe University

Principal Investigator

FUJIMOTO RYO  神戸大学, 農学研究科, 准教授 (60620375)

Research Collaborator KAJI makoto  
KAWANABE takahiro  
ITABASHI etsuko  
TAKUNO shohei  
SHIMIZU motoki  
SEKI motoaki  
Project Period (FY) 2015-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥23,790,000 (Direct Cost: ¥18,300,000、Indirect Cost: ¥5,490,000)
Fiscal Year 2018: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2017: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Fiscal Year 2016: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
Fiscal Year 2015: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Keywords雑種強勢 / ヘテロシス / エピジェネティクス / エピゲノム / トランスクリプトーム / アブラナ科 / QTL / DNAメチル化 / 園芸学 / 育種学 / 遺伝学 / 植物 / ヘテローシス
Outline of Final Research Achievements

To elucidate the molecular mechanism of hybrid vigor in Chinese cabbage (Brassica rapa L. var. pekinensis), we performed genetic, epigenome, and transcriptome analyses. We showed that genetic distance of parental lines was not associated with the level of hybrid vigor. QTLs of leaf area at 14 days after sowing or yield were identified. We characterized the epigenetic states such as DNA methylation or histone modification at the whole genome level in the F1 hybrid and its parental lines. We identified differentially expressed genes between parents and their F1 hybrid by RNA sequencing, and chloroplast-targeted genes tended to be upregulated in F1 hybrid compared to the parental lines at 2 days after sowing.

Academic Significance and Societal Importance of the Research Achievements

両親系統間の遺伝距離と雑種強勢の関連性については様々な植物種で議論されているが、少なくとも本研究によりハクサイでは、両親系統間の遺伝距離を指標に雑種強勢の発現を予測できないことを示した。これにより、雑種強勢は、ある特定領域のヘテロ接合性が重要であると予想される。本研究により、雑種強勢が見られる形質について複数のQTLを同定した。今後、これらの領域について更なる解析を進めることで、雑種強勢に重要な遺伝子領域の同定へと繋がれば、DNAマーカー等により両親系統の選抜や両親系統の組合せ能力検定にかかるコストと労力の軽減が期待され、その社会的な意義は大きいと考える。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (44 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (4 results) Journal Article (15 results) (of which Int'l Joint Research: 9 results,  Peer Reviewed: 13 results,  Open Access: 12 results,  Acknowledgement Compliant: 1 results) Presentation (25 results) (of which Int'l Joint Research: 6 results,  Invited: 2 results)

  • [Int'l Joint Research] CSIRO(オーストラリア)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] CSIRO(オーストラリア)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] CSIRO(Australia)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] CSIRO(Australia)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of a commercial F<sub>1</sub> hybrid cultivar of Chinese cabbage2018

    • Author(s)
      Shea DJ, Shimizu M, Itabashi E, Miyaji N, Miyazaki J, Osabe K, Kaji M, Okazaki K, Fujimoto R.
    • Journal Title

      Breeding Science

      Volume: 68 Issue: 3 Pages: 375-380

    • DOI

      10.1270/jsbbs.17124

    • NAID

      130007430198

    • ISSN
      1344-7610, 1347-3735
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.2018

    • Author(s)
      Takahashi Satoshi、Osabe Kenji、Fukushima Naoki、Takuno Shohei、Miyaji Naomi、Shimizu Motoki、Takasaki-Yasuda Takeshi、Suzuki Yutaka、Dennis Elizabeth S、Seki Motoaki、Fujimoto Ryo
    • Journal Title

      DNA Research

      Volume: 25 Issue: 5 Pages: 511-520

    • DOI

      10.1093/dnares/dsy021

    • NAID

      120006552896

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems.2018

    • Author(s)
      Fujimoto R, Uezono K, Ishikura S, Osabe K, Peacock WJ, Dennis ES.
    • Journal Title

      Breeding Science

      Volume: 68 Pages: 145-158

    • NAID

      130006743989

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Hybrid Vigor: Importance of Epigenetic Processes and Consequences for Breeding2018

    • Author(s)
      Miyaji N, Fujimoto R
    • Journal Title

      Advances in Botanical Research

      Volume: 88 Pages: 247-275

    • DOI

      10.1016/bs.abr.2018.10.001

    • ISBN
      9780128154038
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of DNA methylated regions by using methylated DNA immunoprecipitation sequencing in Brassica rapa2018

    • Author(s)
      Takahashi Satoshi、Fukushima Naoki、Osabe Kenji、Itabashi Etsuko、Shimizu Motoki、Miyaji Naomi、Takasaki-Yasuda Takeshi、Suzuki Yutaka、Seki Motoaki、Fujimoto Ryo
    • Journal Title

      Crop and Pasture Science

      Volume: 69 Issue: 1 Pages: 107-107

    • DOI

      10.1071/cp17394

    • NAID

      120006727813

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems2018

    • Author(s)
      Ryo Fujimoto, Kosuke Uezono, Sonoko Ishikura, Kenji Osabe, W. James Peacock, Elizabeth S. Dennis
    • Journal Title

      Breeding Science

      Volume: ahead of print

    • NAID

      130006743989

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Epigenetic regulation of agronomical traits in Brassicaceae2017

    • Author(s)
      Itabashi Etsuko、Osabe Kenji、Fujimoto Ryo、Kakizaki Tomohiro
    • Journal Title

      Plant Cell Reports

      Volume: 37 Issue: 1 Pages: 87-101

    • DOI

      10.1007/s00299-017-2223-z

    • NAID

      120006546777

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Towards network construction between basic and applied researchers in Brassicaceae2017

    • Author(s)
      Yamamoto Masaya、Fujii Sota、Kakizaki Tomohiro、Fujimoto Ryo、Hikosaka Kouki、Hatakeyama Katsunori、Ito Hidetaka、Okazaki Keiichi
    • Journal Title

      Breeding Research

      Volume: 19 Issue: 1 Pages: 21-29

    • DOI

      10.1270/jsbbr.19.21

    • NAID

      130006832290

    • ISSN
      1344-7629, 1348-1290
    • Related Report
      2017 Annual Research Report
    • Open Access
  • [Journal Article] Research on genome diversity and hybrid vigour in Brassicaceae2017

    • Author(s)
      Fujimoto Ryo
    • Journal Title

      Breeding Research

      Volume: 19 Issue: 3 Pages: 116-123

    • DOI

      10.1270/jsbbr.19.116

    • NAID

      130006106487

    • ISSN
      1344-7629, 1348-1290
    • Related Report
      2017 Annual Research Report
    • Open Access
  • [Journal Article] Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in <i>Brassica rapa</i> L.2016

    • Author(s)
      Kawanabe, T., Osabe, K., Itabash, E., Okazaki, K., Dennis, E.S., and Fujimoto, R.
    • Journal Title

      Genes & Genetic Systems

      Volume: 91 Issue: 1 Pages: 1-10

    • DOI

      10.1266/ggs.15-00058

    • NAID

      130005165461

    • ISSN
      1341-7568, 1880-5779
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Role of DNA methylation in hybrid vigor in Arabidopsis thaliana2016

    • Author(s)
      Kawanabe, T., Ishikura, S., Miyaji, N., Sasaki, T., Wu, L., Itabash, E., Takada, S., Shimizu, M., Takasaki-Yasuda, T., Osabe, K., Peacock, W.J., Dennis, E.S., and Fujimoto, R.
    • Journal Title

      Proceedings of the National Academy of Sciences of the United States of America

      Volume: 113 Issue: 43

    • DOI

      10.1073/pnas.1613372113

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The importance of reproductive barriers and the effect of allopolyploidization on crop breeding2016

    • Author(s)
      Tonosaki, K., Osabe, K., Kawanabe, T., and Fujimoto, R.
    • Journal Title

      Breeding Science

      Volume: 66 Issue: 3 Pages: 333-349

    • DOI

      10.1270/jsbbs.15114

    • NAID

      130005160897

    • ISSN
      1344-7610, 1347-3735
    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage2016

    • Author(s)
      Saeki N, Kawanabe T, Ying H, Shimizu M, Kojima M, Abe H, Okazaki K, Kaji M, Taylor JM, Sakakibara H, Peacock WJ, Dennis ES, Fujimoto R.
    • Journal Title

      BMC Plant Biology

      Volume: 16 Issue: 1 Pages: 45-45

    • DOI

      10.1186/s12870-016-0734-3

    • NAID

      120005714785

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Development of primer sets that can verify the enrichment of histone modifications, and their application to examining the vernalization mediated chromatin changes in Brassica rapa L.2016

    • Author(s)
      Kawanabe T, Osabe K, Itabashi E, Okazaki K, Dennis ES, Fujimoto R
    • Journal Title

      Genes & Genetics Systems

      Volume: in press

    • NAID

      130005165461

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genetic distance of inbred lines of Chinese cabbage and its relationship to heterosis2016

    • Author(s)
      Kawamura K, Kawanabe T, Shimizu M, Nagano AJ, Saeki N, Okazaki K, Kaji M, Dennis ES, Osabe K, Fujimoto R
    • Journal Title

      Plant Gene

      Volume: 5 Pages: 1-7

    • DOI

      10.1016/j.plgene.2015.10.003

    • NAID

      120005743235

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] ハクサイ初期生育期における子葉および本葉サイズ関連遺伝子の探索2018

    • Author(s)
      上園 倖輔; シェア ダニエル; 清水 元樹; 板橋 悦子; ハサン メエラジ; 岡崎 桂一; 安田 (高崎) 剛志; 藤本 龍
    • Organizer
      日本育種学会第134回講演会
    • Related Report
      2018 Annual Research Report
  • [Presentation] アブラナ科野菜における雑種強勢研究の動向2018

    • Author(s)
      藤本 龍
    • Organizer
      平成30年度野菜花き課題別研究会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] ハクサイにおける全ゲノムメチル化解析2018

    • Author(s)
      藤本 龍; 高橋 聡史; 鈴木 穣; 関 原明; 安田 剛志
    • Organizer
      園芸学会平成31年度春季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Brassica rapaにおけるメチローム解析2018

    • Author(s)
      高橋 聡史;長部 謙二;宮路 直実;鈴木 穣;関 原明;藤本 龍
    • Organizer
      日本育種学会第134回講演会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Characterization of epigenetic states in Brassica rapa L.2018

    • Author(s)
      Ryo Fujimoto; Ayasha Akter; Satoshi Takahashi; Takeshi Takasaki-Yasuda; Yutaka Suzuki; Elizabeth S. Dennis; Motoaki Seki
    • Organizer
      Brassica 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Characterization of histone H3 lysine 27 tri-methylation in Brassica rapa L.2018

    • Author(s)
      Ryo Fujimoto; Ayasha Akter; Satoshi Takahashi; Namiko Nishida; Takashi Takasaki-Yasuda; Yutaka Suzuki; Motoaki Seki; Elizabeth S. Dennis
    • Organizer
      The 25th International Congress on Sexual Plant Reproduction
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] DDM1 has an important function on heterosis in Arabidopsis thaliana2018

    • Author(s)
      Naomi Miyaji; Etsuko Itabashi; Takeshi Takasaki-Yasuda; W. James Peacock; Elizabeth S. Dennis; Ryo Fujimoto
    • Organizer
      The 25th International Congress on Sexual Plant Reproduction
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Distribution of histone H3 lysine 27 trimethylation in different tissues of Brassica rapa2018

    • Author(s)
      アクタ アヤシャ; 宮路 直実; 安田 剛志; 藤本 龍
    • Organizer
      園芸学会平成31年度春季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] ハクサイ市販品種'W77'の両親系統間リシークエンスによる片親特異的遺伝子変異の同定2018

    • Author(s)
      上園 倖輔; Shea Daniel; 清水 元樹; 板橋 悦子; 宮路 直美; 岡崎 桂一; 安田 (高崎) 剛志; 藤本 龍
    • Organizer
      園芸学会平成30年度春季大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] アブラナ科植物におけるゲノム多様性および雑種強勢に関する研究2017

    • Author(s)
      藤本龍
    • Organizer
      日本育種学会第131回講演会
    • Place of Presentation
      名古屋大学
    • Year and Date
      2017-03-29
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] DDM1 is required for a full level of heterosis in Arabidopsis thaliana.2017

    • Author(s)
      Naomi Miyaji; Sonoko Ishikura; Satoko Takada; Takeshi Takasaki-Yasuda; W. James Peacock; Elizabeth S. Dennis; Ryo Fujimoto
    • Organizer
      Plant Biology 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] MeDIP-seqによるハクサイ系統間のDNAメチル化比較解析2017

    • Author(s)
      藤本 龍; 高橋 聡史; 鈴木 穣; 関 原明; 安田 剛志
    • Organizer
      園芸学会平成29年度秋季大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] ハクサイ市販品種'W77'における初期生育の雑種強勢関連領域の同定にむけて2017

    • Author(s)
      譚 永; 上園 倖輔; 板橋 悦子; 安田 (高崎) 剛志; 藤本 龍
    • Organizer
      平成29年度園芸学会近畿支部滋賀大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] ハクサイ市販品種'W77'の両親系統のリシークエンスによるゲノム構造の系統間比較2017

    • Author(s)
      上園 倖輔; Shea Daniel; 清水 元樹; 板橋 悦子; 譚 永; 宮路 直美; 岡崎 桂一; 安田 (高崎) 剛志; 藤本 龍
    • Organizer
      平成29年度園芸学会近畿支部滋賀大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Re-sequencing and SNP analysis of the parental lines of a commercial F1 hybrid cultivar of Chinese cabbage2017

    • Author(s)
      Daniel Shea; Motoki Shimizu; Etsuko Itabashi; Naomi Miyaji; Makoto Kaji; Keiichi Okazaki; Ryo Fujimoto
    • Organizer
      日本育種学会第132回講演会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Characterization of early developmental and yield heterosis in Chinese cabbage2016

    • Author(s)
      Fujimoto, R., Shimizu, M., Miyaji, N., Takada, S., Fukushima, N., Kaji, M., Peacock W.J., and Dennis, E.S.
    • Organizer
      Brassica 2016
    • Place of Presentation
      Melbourne, Australia
    • Year and Date
      2016-10-03
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Genome-wide analysis of DNA methylation in Chinese cabbage2016

    • Author(s)
      Fukushima, N., Takahashi, S., Itabashi, E., Shimizu, M., Osabe, K., Yasuda, T., Suzuki, Y., Seki, M., Dennis, E.S., and Fujimoto, R.
    • Organizer
      Brassica 2016
    • Place of Presentation
      Melbourne, Australia
    • Year and Date
      2016-10-03
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] シロイヌナズナの雑種強勢に関与する遺伝子領域の探索2016

    • Author(s)
      宮路直実、石倉園子、高田紗都子、板橋悦子、安田剛志、藤本龍
    • Organizer
      日本育種学会第130回講演会
    • Place of Presentation
      鳥取大学
    • Year and Date
      2016-09-24
    • Related Report
      2016 Annual Research Report
  • [Presentation] クロマチンリモデリング因子DDM1によるエピジェネティックな制御がシロイヌナズナのヘテローシスに及ぼす影響2016

    • Author(s)
      石倉園子、宮路直実、板橋悦子、高田紗都子、高橋聡史、清水元樹、安田剛志、関原明、藤本龍
    • Organizer
      日本育種学会第130回講演会
    • Place of Presentation
      鳥取大学
    • Year and Date
      2016-09-24
    • Related Report
      2016 Annual Research Report
  • [Presentation] ハクサイにおけるメチローム解析2016

    • Author(s)
      福島尚樹、高橋聡史、板橋悦子、清水元樹、安田剛志、鈴木穣、関原明、藤本龍
    • Organizer
      日本育種学会第130回講演会
    • Place of Presentation
      鳥取大学
    • Year and Date
      2016-09-24
    • Related Report
      2016 Annual Research Report
  • [Presentation] ハクサイにおけるエピゲノム解析2016

    • Author(s)
      藤本龍、高橋聡史、板橋悦子、鈴木穣、関原明
    • Organizer
      日本育種学会第130回講演会
    • Place of Presentation
      鳥取大学
    • Year and Date
      2016-09-24
    • Related Report
      2016 Annual Research Report
  • [Presentation] Whole genome bisulfite sequencingによるハクサイのDNAメチル化領域の探索2016

    • Author(s)
      福島尚樹、高橋聡史、板橋悦子、清水元樹、安田剛志、鈴木穣、関原明、藤本龍
    • Organizer
      園芸学会平成28年度秋季大会
    • Place of Presentation
      名城大学
    • Year and Date
      2016-09-10
    • Related Report
      2016 Annual Research Report
  • [Presentation] ハクサイにおけるヒストンメチル化抗体を用いたクロマチン免疫沈降法のポジティブ/ネガティブコントロールプライマーの作製2015

    • Author(s)
      藤本 龍 , 川辺 隆大, 板橋 悦子, 安田 剛志, 岡崎 桂一
    • Organizer
      園芸学会平成27年度秋季大会
    • Place of Presentation
      徳島大学 (徳島県・徳島市)
    • Year and Date
      2015-09-26
    • Related Report
      2015 Annual Research Report
  • [Presentation] アブラナ科の雑種強勢の分子機構の解明を目指した後成遺伝学的なアプローチ2015

    • Author(s)
      藤本 龍, 川辺 隆大
    • Organizer
      日本遺伝学会第87大会
    • Place of Presentation
      東北大学 (宮城県・仙台市)
    • Year and Date
      2015-09-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] ハクサイにおいて、両親系統間の遺伝距離から雑種強勢を予測できるか?2015

    • Author(s)
      川村 和隆, 佐伯 なつみ, 今野 周平, 永野 敦, 本庄 三恵, 八杉 公基, 工藤 洋, 安田 剛志, 加治 誠, 岡崎 桂一, 藤本 龍
    • Organizer
      日本育種学会第128回講演会
    • Place of Presentation
      新潟大学 (新潟県・新潟市)
    • Year and Date
      2015-09-11
    • Related Report
      2015 Annual Research Report

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Published: 2015-04-16   Modified: 2022-09-27  

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