Identification of hybrid vigor related loci in Brassica

• Project/Area Number: 15H05614
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Horticultural science
• Research Institution: Kobe 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: ¥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。

Research Products

• [Int'l Joint Research] CSIRO(オーストラリア)
• [Int'l Joint Research] CSIRO(オーストラリア)
• [Int'l Joint Research] CSIRO(Australia)
• [Int'l Joint Research] CSIRO(Australia)
• [Journal Article] Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of a commercial F₁ hybrid cultivar of Chinese cabbage (2018)
  • 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
  • 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
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Hybrid Vigor: Importance of Epigenetic Processes and Consequences for Breeding (2018)
  • 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
  • Peer Reviewed
• [Journal Article] Identification of DNA methylated regions by using methylated DNA immunoprecipitation sequencing in Brassica rapa (2018)
  • 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
  • Peer Reviewed
• [Journal Article] Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems (2018)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Epigenetic regulation of agronomical traits in Brassicaceae (2017)
  • 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
  • Peer Reviewed
• [Journal Article] Towards network construction between basic and applied researchers in Brassicaceae (2017)
  • 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
  • Open Access
• [Journal Article] Research on genome diversity and hybrid vigour in Brassicaceae (2017)
  • 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
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Role of DNA methylation in hybrid vigor in Arabidopsis thaliana (2016)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] The importance of reproductive barriers and the effect of allopolyploidization on crop breeding (2016)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage (2016)
  • 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
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Genetic distance of inbred lines of Chinese cabbage and its relationship to heterosis (2016)
  • 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
  • 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
• [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
  • 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
• [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
• [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
  • 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
  • Int'l Joint Research
• [Presentation] DDM1 has an important function on heterosis in Arabidopsis thaliana (2018)
  • 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
  • Int'l Joint Research
• [Presentation] Distribution of histone H3 lysine 27 trimethylation in different tissues of Brassica rapa (2018)
  • 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
• [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
• [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
  • 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
  • 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
• [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
• [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
• [Presentation] Re-sequencing and SNP analysis of the parental lines of a commercial F1 hybrid cultivar of Chinese cabbage (2017)
  • 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
• [Presentation] Characterization of early developmental and yield heterosis in Chinese cabbage (2016)
  • 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
  • Int'l Joint Research
• [Presentation] Genome-wide analysis of DNA methylation in Chinese cabbage (2016)
  • 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
  • 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
• [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
• [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
• [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
• [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
• [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
• [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
• [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