Wheat is a critical food source globally. Food security is an increasing concern; current production levels are not expected to keep pace with global demand. New technologies have provided a vast array of wheat genetic data; however, best use of this data requires placing it within a framework in which the various genes, pathways and interactions can be examined. Here we present the first systematic comparison of the global transcriptomes of the aleurone and starchy endosperm of the developing wheat seed (Triticum aestivum), at time points critical to the development of the aleurone layer; 6-, 9- and 14-day post-anthesis. Illumina sequencing gave 25—55 million sequence reads per tissue, of the trimmed reads, 70%—81% mapped to reference expressed sequence transcripts. Transcript abundance was analysed by performing RNA-Seq normalization to generate reads per kilobase of exon model per million mapped reads values, and these were used in comparative analyses between the tissues at each time point using Kal’s Z-test. This identified 9414—13 202 highly differentially expressed transcripts that were categorized on the basis of tissue and time point expression and functionally analysed revealing two very distinct tissues. The results demonstrate the fundamental biological reprogramming of the two major biologically and economically significant tissues of the wheat seed over this time course. Understanding these changes in gene expression profiles is essential to mining the potential these tissues hold for human nutrition and contributing to the systems biology of this important crop plant.
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