Submitted to: CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: December 10, 2008
Publication Date: December 10, 2008
Citation: Coram, T., Brown Guedira, G.L., Chen, X. 2008. Using Transcriptomics to Understand the Wheat Genome. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources.3:083. Interpretive Summary: In this review, we researched the literature to present the current state of knowledge regarding gene expression studies, or transcriptomics, in wheat. We focused on the varying use of microarrays for studying gene expression, as well as generating molecular markers and analyzing antisense transcription. The current repository of microarray data for wheat transcriptomics presents an opportunity for applying a systematic approach to identify gene networks that underlie important traits. We also focused on novel technologies and techniques including sequence-by-synthesis approaches that represent true open systems for surveying gene expression on a large scale. We also discuss the limitations of wheat transcriptomics, mainly brought about by a lack of genome sequence and its polyploid genome. Finally, we conclude with the prospects for future research and advancement in this field, and recommend strategies for maximizing resources.
Technical Abstract: 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 transclocation 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.