Molecular Breeding

, 36:59 | Cite as

Genetic analysis of NEKODE1 gene involved in panicle branching of foxtail millet, Setaria italica (L.) P. Beauv., and mapping by using QTL-seq

  • Hisato Masumoto
  • Hiroki Takagi
  • Yohei Mukainari
  • Ryohei Terauchi
  • Kenji FukunagaEmail author


We carried out genetic analysis and mapping of a gene for the tip-branched panicle (Nekode or Neko-ashi in Japanese) in foxtail millet. We revealed that this trait is controlled by a single dominant gene by using two F2 populations and designated the gene as NEKODE1. By using an F2 population between closely related Taiwanese landraces with a new method based on next-generation sequencing (NGS), QTL-seq, we successfully and rapidly mapped the responsible gene (NEKODE1) on chromosome 9. We also mapped the gene by using SSR markers to verify that this gene is located at the position on chromosome 9, suggested by QTL-seq, and we obtained SSR markers closely linked to the gene and found several candidate genes for this trait in a foxtail millet genome sequence database. The use of a foxtail millet genome sequence and NGS enables rapid mapping of a gene(s) by using a segregation population derived from a cross even between closely related foxtail millet landraces.


Genome sequence Linkage map QTL-seq Setaria italica SSR (simple sequence repeat) markers Tip-branched panicles 



This work was partly supported by PUH Research Grant Program (advanced research A) of Prefectural University of Hiroshima to KF and Grant-in-Aid for Scientific Research (C) from Japan Society for the Promotion of Science (JSPS) to KF (No. 25450501).

Supplementary material

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Supplementary material 1 (XLSX 10 kb)
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Supplementary material 2 (XLSX 16 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Hisato Masumoto
    • 1
  • Hiroki Takagi
    • 2
  • Yohei Mukainari
    • 1
  • Ryohei Terauchi
    • 2
  • Kenji Fukunaga
    • 1
    Email author
  1. 1.Faculty of Life and Environmental SciencesPrefectural University of HiroshimaShobaraJapan
  2. 2.Iwate Biotechnology CenterKitakamiJapan

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