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

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


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 


  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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