Next-Generation Breeding of Rice by Whole-Genome Approaches

  • Akira Abe
  • Hiroki Takagi
  • Hiroki Yaegashi
  • Satoshi Natsume
  • Hiroe Utsushi
  • Muluneh Tamiru
  • Ryohei Terauchi
Chapter

Abstract

Owing to recent developments in DNA sequencing technologies, whole-genome analysis of crop species has become a routine procedure. In order to improve local rice cultivars adapted to northern Japan, we are applying whole-genome analysis to identify and utilize useful alleles for crossbreeding. Here we show that large-scale generation of genetic resources combined with whole-genome analyses including MutMap and QTL-seq provides a powerful platform for the application of “next-generation breeding” in rice.

Keywords

Whole-genome sequencing (WGS) Mutant Recombinant inbred lines (RILs) MutMap QTL-seq 

Notes

Acknowledgments

This study was supported by the grant from “Science and technology research promotion program for agriculture, forestry, fisheries and food industry.” We extend our gratitude to Dr. S. kuroda for a general support and Prof. T. Sasaki and Prof. M. Ashikari for improvement of the manuscript.

References

  1. Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H et al (2012) Genome sequencing reveals agronomically important loci in rice using MutMap. Nat Biotechnol 30:174–178CrossRefPubMedGoogle Scholar
  2. Fekih R, Takagi H, Tamiru M, Abe A, Natsume S et al (2013) MutMap+: genetic mapping and mutant identification without crossing in rice. PLoS One 10:e68529CrossRefGoogle Scholar
  3. Goff SA, Ricker D, Lan T-H, Presting G, Wang R et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100CrossRefPubMedGoogle Scholar
  4. IRGSP (2005) The map based sequence of the rice genome. Nature 436:793–800CrossRefGoogle Scholar
  5. Rakshit S, Kanzaki H, Matsumura H, Rakhist A, Fujibe H et al (2010) Use of TILLING for reverse and forward genetics of rice. In: Kahl G, Meksem K (eds) The handbook of plant mutation screening. Wiley-VCH, WeinheimGoogle Scholar
  6. Takagi H, Uemura A, Yaegashi H, Tamiru M, Abe A et al (2013a) MutMap-gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii. New Phytol 200:276–283Google Scholar
  7. Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S et al (2013b) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183Google Scholar
  8. Takagi H, Tamiru M, Abe A, Yoshida K, Uemura A et al (2015) MutMap accelerates breeding of a salt-tolerant rice cultivar. Nat Biotechnol 33:445–449CrossRefPubMedGoogle Scholar
  9. Till BJ, Stevene HR, Greene EA, Comodo CA, Enns LC et al (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res 13:524–530CrossRefPubMedPubMedCentralGoogle Scholar
  10. Varshney R, Terauchi R, McCouch S (2014) Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol 12(6):e1001883.  https://doi.org/10.1371/journal.pbio.1001883 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Yu J, Hu S, Wang J, Wong GKS, Li S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92CrossRefPubMedGoogle Scholar
  12. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Akira Abe
    • 1
  • Hiroki Takagi
    • 1
    • 2
  • Hiroki Yaegashi
    • 1
  • Satoshi Natsume
    • 1
  • Hiroe Utsushi
    • 1
  • Muluneh Tamiru
    • 1
  • Ryohei Terauchi
    • 1
    • 3
  1. 1.Iwate Biotechnology Research CenterKitakamiJapan
  2. 2.Division of Bioproduction ScienceIshikawa Prefectural UniversityNonoichiJapan
  3. 3.Graduate School of AgricultureKyoto UniversityKyotoJapan

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