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Mapping translocation breakpoints using a wheat microarray

ABSTRACT: Five RNA samples were used. The RNA source material was from wheat cytogenetic stocks from Dr. Adam Lukaszewski, University of California, Riverside. The lines used for this study are Pavon, Pavon Dt1BL, 1RS.1BL, 1B+5 and T-1 wheat samples. whole seedling minus starchy endosperm. Equal portions of RNA from unstressed and 48 hr drought-stressed seedling were combined to make one RNA sample. The person who produced the RNA was Prasanna R. Bhat in the TJ Close lab at University of California, Riverside. Everything downstream of RNA production was done at the UC Irvine DNA and Protein Microarray Facility (Denis Heck, manager) by Sriti Misra. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Prasanna Bhat. The equivalent experiment is TA10 at PLEXdb.]

ORGANISM(S): Triticum aestivum

PROVIDER: GSE31754 | GEO | 2011/08/31

SECONDARY ACCESSION(S): PRJNA145335

REPOSITORIES: GEO

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Project description:This reports the transcript profiling of the aleurone and starchy endosperm layers of wheat seed over 3 time points critical in the development of the aleurone layer. Wheat is a critical food source globally. The aleurone layer develops from the starchy endosperm and is a concentrated source of vitamins and minerals, essential for the germination of the plant embryo. However the molecular mechanisms behind the development of this layer remain poorly understood. Here we present the first direct systematic comparison of the transcriptomes of the aleurone and starchy endosperm tissues of the wheat seed (Triticum aestivum) at time points critical to the development of the aleurone layer of 6, 9 and 14 days post anthesis. Gene expression patterns reflect the changing role of these tissues in seed development. Illumina sequencing gave 25 to 55 million sequence reads per tissue, of the trimmed reads, 70 – 81% mapped to reference expressed sequence transcripts. To quantify transcript abundance, RNA-Seq normalisation was performed to generate RPKM values, these were used in comparative analyses between the tissues at each time point using Kals Z-test. Sequences with significantly different RPKM values were categorised on the basis of tissue and time point expression and functionally annotated using standardised gene ontology vocabularies, revealing two very distinct tissues. In conclusion we show the relationships between and the fundamental biological reprogramming of the two major biologically and economically significant tissues of the wheat seed over time. Understanding these changes in gene expression profiles is essential to mining the potential these tissues hold for human nutrition and contributing to foundational and systems biology of this important crop. Examines the transcript profile of aleurone and starchy endoperm tissues at 6,9 and 14DPA. A minimum of 5 individual seeds from 3 separate spikes from three individual plants were pooled for each tissue preparation.

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Mapping translocation breakpoints using a wheat microarray

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