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Genomic DNA Library Preparation for Resistance Gene Enrichment and Sequencing (RenSeq) in Plants

  • Florian Jupe
  • Xinwei Chen
  • Walter Verweij
  • Kamel Witek
  • Jonathan D. G. Jones
  • Ingo Hein
Part of the Methods in Molecular Biology book series (MIMB, volume 1127)

Abstract

Enrichment of genomic DNA for genes of interest prior to high-throughput sequencing offers an efficient and cost-effective approach to reduce genome complexity. Target enrichment typically yields higher read-depth for selected genes and is therefore suitable for determination of sequence polymorphisms and enables multiplexing of samples. Target enrichment also provides a means to annotate specific gene families within the sequenced organisms without the requirements for gene models. Here we describe enrichment procedures for NB-LRR-type plant resistance genes that can, for example, be used to establish the NB-LRR gene complements of individual plants and to map resistances more rapidly using a bulked segregant analysis.

Key words

Agilent SureSelect Target enrichment High-throughput sequencing NB-LRR genes 

References

  1. 1.
    Meyers BC, Dickerman AW, Michelmore RW, Sivaramakrishnan S, Sobral BW, Young ND (1999) Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J 20:317–332PubMedCrossRefGoogle Scholar
  2. 2.
    Schulze-Lefert P, Panstruga R (2011) A molecular evolutionary concept connecting nonhost resistance, pathogen host range, and pathogen speciation. Trends Plant Sci 16: 117–125PubMedCrossRefGoogle Scholar
  3. 3.
    Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195CrossRefGoogle Scholar
  4. 4.
    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 13:75PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Jupe F, Witek K, Verweij W, Sliwka J, Pritchard L, Etherington GJ, Maclean D, Cock PJ, Leggett RM, Bryan GJ, Cardle L, Hein I, Jones JD (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant J 76:530–544Google Scholar
  6. 6.
    Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641CrossRefGoogle Scholar
  7. 7.
    Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27:182–189PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Adam MP (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30:693–700PubMedCentralPubMedCrossRefGoogle Scholar
  9. 9.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  10. 10.
    Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, Stupar RM (2011) The composition and origins of genomic variation among individuals of the soybean Reference Cultivar Williams 82. Plant Physiol 155:645–655PubMedCentralPubMedCrossRefGoogle Scholar
  11. 11.
    Bolon YT, Haunm WJ, Xum WW, Grant D, Stacey MG, Nelson RT, Gerhardt DJ, Jeddeloh JA, Stacey G, Muehlbauer GJ, Orf JH, Naeve SL, Stupar RM, Vance CP (2011) Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiol 156:240–253PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, New York 2014

Authors and Affiliations

  1. 1.The Sainsbury LaboratoryNorwich Research ParkNorwichUK
  2. 2.CMS and Dundee Effector ConsortiumThe James Hutton InstituteInvergowrie DundeeUK
  3. 3.The Genome Analysis CentreNorwichUK

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