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.
Florian Jupe, Xinwei Chen, and Walter Verweij contributed equally to this manuscript.
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References
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 20:317–332
Schulze-Lefert P, Panstruga R (2011) A molecular evolutionary concept connecting nonhost resistance, pathogen host range, and pathogen speciation. Trends Plant Sci 16: 117–125
Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–195
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 13:75
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 76:530–544
Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641
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 27:182–189
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 30:693–700
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
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 155:645–655
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 156:240–253
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Jupe, F., Chen, X., Verweij, W., Witek, K., Jones, J.D.G., Hein, I. (2014). Genomic DNA Library Preparation for Resistance Gene Enrichment and Sequencing (RenSeq) in Plants. In: Birch, P., Jones, J., Bos, J. (eds) Plant-Pathogen Interactions. Methods in Molecular Biology, vol 1127. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-986-4_22
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DOI: https://doi.org/10.1007/978-1-62703-986-4_22
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