Skip to main content

Next-Generation Breeding of Rice by Whole-Genome Approaches

  • Chapter
  • First Online:
Rice Genomics, Genetics and Breeding

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 229.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 299.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • 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 30:174–178

    Article  CAS  PubMed  Google Scholar 

  • 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:e68529

    Article  Google Scholar 

  • 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 296:92–100

    Article  CAS  PubMed  Google Scholar 

  • IRGSP (2005) The map based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  • 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, Weinheim

    Google Scholar 

  • 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 200:276–283

    Google Scholar 

  • 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 74:174–183

    Google Scholar 

  • Takagi H, Tamiru M, Abe A, Yoshida K, Uemura A et al (2015) MutMap accelerates breeding of a salt-tolerant rice cultivar. Nat Biotechnol 33:445–449

    Article  CAS  PubMed  Google Scholar 

  • 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 13:524–530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Yu J, Hu S, Wang J, Wong GKS, Li S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92

    Article  CAS  PubMed  Google Scholar 

  • Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551

    Article  PubMed  PubMed Central  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ryohei Terauchi .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Abe, A. et al. (2018). Next-Generation Breeding of Rice by Whole-Genome Approaches. In: Sasaki, T., Ashikari, M. (eds) Rice Genomics, Genetics and Breeding. Springer, Singapore. https://doi.org/10.1007/978-981-10-7461-5_26

Download citation

Publish with us

Policies and ethics