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Whole Genome Sequencing to Identify Genes and QTL in Rice

  • Ryohei TerauchiEmail author
  • Akira Abe
  • Hiroki Takagi
  • Muluneh Tamiru
  • Rym Fekih
  • Satoshi Natsume
  • Hiroki Yaegashi
  • Shunichi Kosugi
  • Hiroyuki Kanzaki
  • Hideo Matsumura
  • Hiromasa Saitoh
  • Kentaro Yoshida
  • Liliana Cano
  • Sophien Kamoun

Abstract

The recent accumulation of whole genome sequences (WGS) in a large number of plant species creates new opportunities to use this information for identifying genes/quantitative trait loci (QTL) and to accelerate crop improvement. To this end, we recently developed the MutMap method (Abe et al., Nat Biotechnol 30:174–178, 2012) and its derivatives MutMap+ (Fekih et al., PLoS One 8(7):e68529, 2013) and MutMap-Gap (Takagi et al., New Phytol 200(1):276–283, 2013a), which take full advantage of WGS to efficiently identify mutant genes from EMS mutagenized plant populations. We also reported QTL-seq (Takagi et al., Plant J 74:174–183, 2013b), a WGS-based method for identification of QTL. We applied these methods to rice for rapid identification and discovery of genes of agronomic importance. In this chapter, we introduce these WGS-based methods, MutMap family and QTL-seq, and provide an overview of the genetic analyses that we expect to accelerate crop improvement in rice and other crop species of economic importance.

Keywords

QTL Mutation MutMap QTL-seq SNP-index Crop WGS NGS Rice 

Notes

Acknowledgements

This study was supported by the Program for Promotion of Basic Research Activities for Innovative Biosciences, the Ministry of Education, Cultures, Sports and Technology, Japan to HK and RT (Grant-in-Aid for Scientific Research on Innovative Areas 23113009) and JSPS KAKENHI to RT (Grant No. 24248004). We thank Shigeru Kuroda for general supports.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Ryohei Terauchi
    • 1
    Email author
  • Akira Abe
    • 1
  • Hiroki Takagi
    • 1
  • Muluneh Tamiru
    • 1
  • Rym Fekih
    • 1
  • Satoshi Natsume
    • 1
  • Hiroki Yaegashi
    • 1
  • Shunichi Kosugi
    • 2
  • Hiroyuki Kanzaki
    • 1
  • Hideo Matsumura
    • 3
  • Hiromasa Saitoh
    • 1
  • Kentaro Yoshida
    • 4
  • Liliana Cano
    • 4
  • Sophien Kamoun
    • 4
  1. 1.Division of Genomics and BreedingIwate Biotechnology Research CenterKitakamiJapan
  2. 2.Kazusa DNA Research InstituteKisarazuJapan
  3. 3.Gene Research CenterShinshu UniversityUedaJapan
  4. 4.The Sainsbury LaboratoryNorwich Research ParkNorwichUK

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