Editorial Preface: advances in DNA sequencing accelerating plant biotechnology The last 5 years have seen a revolution in next-generation DNA sequencing, with plant researchers readily adopting the technol- ogy to decipher the structure and function of plant genomes. This special edition aims to capture the latest developments in plant biotechnology driven by advances in DNA sequencing technology. The use of this technology varies, with applications in genome sequencing (Berkman et al., 2011; Edwards and Batley, 2010), molecular genetic marker discovery (Allen et al., 2011; Imelfort et al., 2009; Kharabian-Masouleh et al., 2011), transcriptomics (Hiremath et al., 2011), candidate gene identifi- cation (Malory et al., 2011) and plant taxonomy (Nock et al., 2011). As an increasing number of reference genomes are being sequenced, next-generation DNA sequencing is increasingly being applied for crop improvement through the discovery of molecular markers associated with agronomic traits. Several papers in this special issue describe SNP discovery in a range of crops following diverse approaches. Subbaiyan et al. (2012) describe the whole-genome re-sequencing of six elite rice varie- ties and the discovery of almost 3 million SNPs as well as more than 300 000 indels. Edwards et al. (2012) describe a similar approach in hexaploid wheat, where the large size of the gen- ome has been addressed by the establishment of a consortium approach to data generation. As an alternative to whole-gen- ome re-sequencing, complexity reduction approaches can reduce costs and allow the targeting of specific regions. The sequencing of amplicons for SNP discovery is demonstrated in B. napus and Eucalyptus by Gholami et al. (2012) and Hendre et al. (2012), respectively, while Hiremath et al. (2012) and Jhanwar et al. (2012) focussed on SNP discovery from the chick- pea transcriptome. Complexity reduction through sequence cap- ture is becoming increasingly common, especially for highly complex genomes, and here, Bundock et al. (2012) and Win- field et al. (2012) describe exome capture and re-sequencing for SNP discovery in sugarcane and wheat, respectively. Gene expression studies have evolved greatly from the days of Northern blots and spotted microarrays. Here, Gillies et al. (2012) describe the identification of several thousand differen- tially expressed genes from the aleurone and starchy endosperm of the developing wheat seed using Illumina transcriptome sequencing. Reid et al. (2012) also applied Illumina transcrip- tome sequencing to dissect the molecular responses occurring during autoregulation of nodulation in soybean, identifying a new candidate gene and factors contributing to systemic regu- lation of nodulation. Using an Illumina whole-genome re-sequencing approach, Tollenaere et al. (2012) have identified a candidate gene for resistance to Leptosphaeria maculans in canola. The increased application of next-generation sequencing in plant biotechnology is demonstrated by the large number of manuscripts submitted to this special issue, and further papers describing SNP discovery from wheat transcriptome data and gene discovery in the Brassicaceae will be published in future issues. As next-generation DNA sequencing continues to develop, we can expect to see many further examples of gene identification and trait association with valuable outcomes, increasing our understanding of plant growth and development and accelerating crop improvement. David Edwards, Robert J. Henry and Keith J. Edwards Editors References Allen, A.M., Barker, G.L.A., Berry, S.T., Coghill, J.A., Gwilliam, R., Kirby, S., Robinson, P., Brenchley, R.C., D’Amore, R., McKenzie, N., Waite, D., Hall, A., Bevan, M., Hall, N. and Edwards, K.J. (2011) Transcript-specific, single- nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol. J. 9, 1086–1099. Berkman, B.J., Skarshewski, A., Lorenc, M.T., Lai, K., Duran, C., Ling, E.Y.S., Stiller, J., Smits, L., Imelfort, M., Manoli, S., McKenzie, M., Kubalakova, M., Simkova, H., Batley, J., Fleury, D., Dolezel, J. and Edwards, D. (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol. J. 9, 768–775. Bundock, P.C., Casu, R.E. and Henry, R.J. (2012) Enrichment of genomic DNA for polymorphism detection in a non-model highly polyploid crop plant. Plant Biotechnol. J. 10, 657–667. Edwards, D. and Batley, J. (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol. J. 7, 1–8. Edwards, D., Wilcox, S., Barrero, R.A., Fleury, D., Cavanagh, C.R., Forrest, K.L., Hayden, M.J., Moolhuijzen, P., Gagnere, G.K., Bellgard, M.I., Lorenc, M.T., Shang, C.A., Baumann, U., Taylor, J.M., Morell, M.K., Langridge, P., Appels, R. and Fitzgerald, A. (2012) Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnol. J. 10, 703–708. Gholami, M., Bekele, W.A., Schondelmaier, J. and Snowdon, R.J. (2012) A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants. Plant Biotechnol. J. 10, 635–645. Gillies, S.A., Futardo, A. and Henry, R.J. (2012) Gene expression in the developing aleurone and starchy endosperm of wheat. Plant Biotechnol. J. 10, 668–679. Hendre, P.S., Kamalakannan, R. and Varghese, M. (2012) High-throughput and parallel SNP discovery in selected candidate genes in Eucalyptus camaldulensis using Illumina NGS platform. Plant Biotechnol. J. 10, 646– 656. Hiremath, P.J., Farmer, A., Cannon, S.B., Woodward, J., Kudapa, H., Tuteja, R., Kumar, A., BhanuPrakash, A., Mulaosmanovic, B., Gujaria, N., Krishnamurthy, L., Gaur, P.M., KaviKishor, P.B., Shah, T., Srinivasan, R., Lohse, M., Xiao, Y., Town, C.D., Cook, D.R., May, G.D. and Varshney, R.K. (2011) Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnol. J. 9, 922–931. Hiremath, P.J., Kumar, A., Penmetsa, V.R., Farmer, A., Schlueter, J.A., Chamarthi, S.K., Whaley, A.M., Carrasquilla-Garcia, N., Gaur, P.M., Upadhyaya, H.D., Kavi Kishor, P.B., Shah, T.M., Cook, D.R. and Varshney, R.K. (2012) Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol. J. 10, 716–732. ª 2012 The Authors Plant Biotechnology Journal ª 2012 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd 621 Plant Biotechnology Journal (2012) 10, pp. 621–622 doi: 10.1111/j.1467-7652.2012.00724.x