Using transcriptomics to understand the wheat genome

Wheat (Triticum aestivum L.) is one of the most important food crops in the world, and transcriptomics studies of this crop promise to reveal the expression dynamics of genes that control many agriculturally important traits. In this review of wheat transcriptomics research, the current status of transcriptome surveying technology is presented, with particular emphasis on breakthrough techniques that will promote rapid progress in understanding the wheat genome. Microarrays have now become routine in wheat research, and the 55K Affymetrix Wheat GeneChip has enabled the generation of numerous high-quality datasets. In fact, the broad range of gene expression datasets provides future opportunities for integrating these data in a systematic approach that may reveal gene coexpression networks that underlie important traits. Wheat microarrays have also recently been used in other valuable approaches, including simultaneous transcriptome and genome profiling through single-feature polymorphism markers, the mapping of translocation breakpoints, and surveying of antisense transcription. The future use of wheat microarrays for gene expression measurement may be challenged by new sequencing-based transcriptomics techniques. These new techniques are presented, and the application of sequencing-by-synthesis as a future area of wheat transcriptomics research is highlighted. However, the yet to be fully sequenced polyploid wheat genome poses problems for some of these technologies when attempting to annotate and assign short-sequence tags. For this reason, the Roche 454 technology is considered the best option for future progress because of its longer sequence reads that can be more easily annotated, as well as its unbiased potential for covering the entire wheat transcriptome.