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Preface: advances in DNA sequencing accelerating plant biotechnology

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The last 5 years have seen a revolution in next-generation DNA sequencing, with plant researchers readily adopting the technology 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 identification (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 varieties 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 genome has been addressed by the establishment of a consortium approach to data generation. As an alternative to whole-genome 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 chickpea transcriptome. Complexity reduction through sequence capture is becoming increasingly common, especially for highly complex genomes, and here, Bundock et al. (2012) and Winfield 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 differentially expressed genes from the aleurone and starchy endosperm of the developing wheat seed using Illumina transcriptome sequencing. Reid et al. (2012) also applied Illumina transcriptome sequencing to dissect the molecular responses occurring during autoregulation of nodulation in soybean, identifying a new candidate gene and factors contributing to systemic regulation 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.

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