Identification of genes for sex ratio in bittetr gourd

• Project/Area Number: 17K07601
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Science in genetics and breeding
• Research Institution: Shinshu University
• Principal Investigator: Matsumura Hideo 信州大学, 学術研究院総合人間科学系, 准教授 (40390885)
• Project Period (FY): 2017-04-01 – 2020-03-31
• Project Status: Completed (Fiscal Year 2019)
• Budget Amount: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2019: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: ニガウリ / 性決定 / 雌雄比率 / ゲノム / QTL / 栽培化 / リシークエンス / 全ゲノム配列 / 次世代シークエンス解析 / 雌花率 / 雌雄同株異花 / RAD-seq / 植物 / 育種学

Outline of Final Research Achievements

For identifying genes and gene networks for sex determination in bitter gourd (Momordica charantia), QTL mapping of F2 population was carried out using genome-wide RAD-seq markers. Three loci were detected as QTLs for female flower frequency and the most effective locus was presumed to be a gynoecious locus. Another QTL in LG5 was focused and several candidate genes in this region, showing non-synonymous change in their sequences between parents, were found. Additionally, bitter gourd reference genome sequence was re-constructed by de novo assembling of PacBio long reads. Consequently, pseudomolecule, comprising 11 chromosomes, could be developed. Resequencing analysis of 60 varieties and read mapping against this pseudomolecule demonstrated unique region with low Fst between wild and cultivar groups, which corresponds to female flower frequency QTL.

Academic Significance and Societal Importance of the Research Achievements

本成果はニガウリの果実生産性に直接影響する雌性花率のQTLおよびそのマーカーを見出すことができたため、今後のニガウリ育種の効率化に大きく貢献が期待できる。またニガウリにおいて染色体レベルの全ゲノム配列を構築できたことから、他の形質に関する遺伝子、マーカーの同定にも寄与する。さらにニガウリ野生系統と栽培品種群における雌性花率QTL領域の解析から、さらにその栽培化や進化における意義の一部を見出すことができた。

Research Products

• [Int'l Joint Research] 台湾大学/World Vegetable Center(その他の国・地域)
• [Int'l Joint Research] Taiwan University(その他の国・地域 台湾)
• [Journal Article] Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of non-classic domestication (2020)
  • Author(s): Hideo Matsumura, Min-Chien Hsiao, Ya-Ping Lin, Atsushi Toyoda, Naoki Taniai4 Kazuhiko Tarora, Naoya Urasaki, Shashi S. Anand, Narinder P. S. Dhillon, Roland Schafleitner, Cheng-Ruei Lee
  • Journal Title: Proceedings of the National Academy of Science USA Volume: -
  • Peer Reviewed / Int'l Joint Research
• [Presentation] ニガウリにおける Long Readデータによるゲノム配列の構築と系統間の多型解析 (2020)
  • Author(s): 松村 英生, Min-Chien Hsiao, 豊田 敦, 太郎良 和彦, 谷合 直樹, 宮城 徳道, 浦崎 直也, Shashi Anand, Narinder Dhillon, Roland Schafleitner, Cheng-Ruei Lee
  • Organizer: 日本育種学会
• [Presentation] Draft Genome Sequence of Bitter Gourd (Momordica charantia) as Vegetable Crop and Medicinal Plant (2019)
  • Author(s): Hideo Matsumura
  • Organizer: Plant&Animal Genome XXVII
  • Int'l Joint Research
• [Presentation] ニガウリにおける染色体レベルの全ゲノム配列情報整備へ向けて (2019)
  • Author(s): 松村英生、太郎良和彦、谷合直樹、宮城徳道、高木宏樹、浦崎直也
  • Organizer: 日本育種学会第135回講演会
• [Presentation] ニガウリ雌性花着花率に関するQTL解析の試み (2017)
  • Author(s): 三宅真佑子、鈴木翔太、福島舞、谷合直樹、宮城徳道、太郎良和彦、浦崎直也、松村英生
  • Organizer: 日本育種学会第132回講演会
• [Book] The Bitter Gourd Genome (2020)
  • Author(s): Chittaranjan Kole, Hideo Matsumura, Tusar Kanti Behera
  • Total Pages: 135
  • Publisher: Springer Narute
  • ISBN: 9783030150624