MutRenSeq: A Method for Rapid Cloning of Plant Disease Resistance Genes

  • Burkhard Steuernagel
  • Kamil Witek
  • Jonathan D. G. Jones
  • Brande B. H. Wulff
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1659)

Abstract

MutRenSeq is a method to clone disease resistance (R) genes in plants. Tips and detailed experimental protocols for the pipeline, including the complexity reduction by R gene targeted enrichment sequencing, and computational analysis based on comparative genomics are provided in this chapter.

Key words

MutRenSeq Gene cloning NB-LRR Resistance gene Target enrichment sequencing 

Notes

Acknowledgements

The authors thank the support by the Gatsby Charitable Foundation, UK, the Two Blades Foundation, USA and the Biotechnology and Biological Sciences Research Council, UK, Grant numbers BB/H019820/1, BB/L009293/1 and BB/L011794/1.

References

  1. 1.
    Dodds PN, Rathjen JP (2010) Plant immunity: towards an integrated view of plant-pathogen interactions. Nat Rev Genet 11:539–548CrossRefPubMedGoogle Scholar
  2. 2.
    Dangl JL, Horvath DM, Staskawicz BJ (2013) Pivoting the plant immune system from dissection to deployment. Science 341:746–751CrossRefPubMedGoogle Scholar
  3. 3.
    Takken FLW, Goverse A (2012) How to build a pathogen detector: structural basis of NB-LRR function. Curr Opin Plant Biol 15:375–384CrossRefPubMedGoogle Scholar
  4. 4.
    Steuernagel B, Periyannan SK, Hernandez-Pinzon I, Witek K, Rouse MN, Yu G, Hatta A, Ayliffe M, Bariana H, Jones JD et al (2016) Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture. Nat Biotechnol 34:652–655CrossRefPubMedGoogle Scholar
  5. 5.
    Jupe F, Chen X, Verweij W, Witek K, Jones JD, Hein I (2014) Genomic DNA library preparation for resistance gene enrichment and sequencing (RenSeq) in plants. Methods Mol Biol 1127:291–303CrossRefPubMedGoogle Scholar
  6. 6.
    Periyannan S, Moore J, Ayliffe M, Bansal U, Wang X, Huang L, Deal K, Luo M, Kong X, Bariana H et al (2013) The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science 341:786–788CrossRefPubMedGoogle Scholar
  7. 7.
    Witek K, Jupe F, Witek AI, Baker D, Clark MD, Jones JDG (2016) Accelerated cloning of a potato late blight-resistance gene using RenSeq and SMRT sequencing. Nat Biotechnol 34:656–660CrossRefPubMedGoogle Scholar
  8. 8.
    Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA (2013) The MaSuRCA genome assembler. Bioinformatics 29:2669–2677CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Li H, Durbin R (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25:1754–1760CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, GPDPS (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Bailey TL, Gribskov M (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14:48–54CrossRefPubMedGoogle Scholar
  12. 12.
    Zhang Z, Schwartz S, Wagner L, Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203–214CrossRefPubMedGoogle Scholar
  13. 13.
    Fiume M, Smith EJ, Brook A, Strbenac D, Turner B, Mezlini AM, Robinson MD, Wodak SJ, Brudno M (2012) Savant genome browser 2: visualization and analysis for population-scale genomics. Nucleic Acids Res 40:W615–W621CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Jupe F, Pritchard L, Etherington GJ, Mackenzie K, Cock PJ, Wright F, Sharma SK, Bolser D, Bryan GJ, Jones JD, Hein I (2012) Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics 13:75CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Burkhard Steuernagel
    • 1
  • Kamil Witek
    • 2
  • Jonathan D. G. Jones
    • 2
  • Brande B. H. Wulff
    • 1
  1. 1.John Innes Centre, Norwich Research ParkNorwichUK
  2. 2.The Sainsbury Laboratory, Norwich Research ParkNorwichUK

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