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RNAseq of developmental sequence of wheat starchy endosperm

ABSTRACT: RNAseq of developmental sequence of wheat starchy endosperm

PROVIDER: PRJEB34678 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3568570.fastq.gz	Fastqsanger.gz
	ERR3568571.fastq.gz	Fastqsanger.gz
	ERR3568572.fastq.gz	Fastqsanger.gz
	ERR3568563.fastq.gz	Fastqsanger.gz
	ERR3568573.fastq.gz	Fastqsanger.gz

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RNAseq of developmental sequence of wheat starchy endosperm

Project description:Manually dissected samples of central starchy endosperm tissue at different ages of wheat grain

2019-11-01 | E-MTAB-8397 | biostudies-arrayexpress

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Analysis of the protein distribution within the wheat endosperm

Project description:Starchy endosperm proteins determine wheat quality and exhibit, besides a quantitative protein gradient, a qualitative protein gradient from the outer to inner starchy endosperm. The goal was to investigate the relative differences in protein composition between the aleurone, sub-aleurone and inner endosperm. Using laser microdissection followed by nanoLC-MS/MS, an innovative method combining a high spatial specificity and analytical selectivity in sample-limited situations, 780 proteins were detected and classified by function. Relatively more gluten proteins were detected in the sub-aleurone compared to inner endosperm. Gluten composition-wise, the sub-aleurone is relatively more enriched in ω-gliadins, but impoverished in LMW-GS and γ-gliadins. While a basic set of albumins and globulins is detected across the entire endosperm, some proteins, like puroindoline-B, display an increasing (or decreasing) gradient. Histological origin and relative positioning of the endosperm cells are hypothesized to drive the protein gradient. Knowledge on this gradient provides major opportunities for the wheat manufacturing industry.

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Gene expression in the developing aleurone and starchy endosperm of wheat

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.

2012-08-15 | GSE38344 | GEO

Transcription profiling of wheat B102,1-1 line endosperm at 14 dpa and leaf at 8 dpg of the transgenic line

Project description:The high molecular weight (HMW) subunits of wheat glutenin are synthesised only in the starchy endosperm tissue of the developing wheat grain. To place the differences observed between the endosperms of the transgenic and non-transgenic lines in a wider developmental context, the transcriptomes of endosperm at 14 dpa and leaf at 8 dpg of the transgenic line B102,1-1 were also compared.The experiment was performed with three biological replicates and hybridisations were performed in reverse dye labelling.

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Project description:Transcriptional profiling of developing rice endosperm at seven days after flowering comparing aleurone layers with central starchy endosperm. Cereal productivity is dependent on the accumulation of storage compounds in the endosperm, a nutritive tissue that is composed of aleurone cells in the outermost regions and starchy endosperm in the inner region. The transcriptional analyses provides clues to the molecular basis for different metabolic pathways in response to the spatial and nutritional differences between rice aleurone cells and starchy endosperm.

2012-11-27 | GSE42489 | GEO

Transcription profiling of wheat GF-transgenic-B102,1-1 vs control-L88-31 lines endosperm tissue (14 and 28 days post anthesis-dpa) and in leaf tissue (8 days post germination ?dpg)

Project description:The high molecular weight (HMW) subunits of wheat glutenin are synthesised only in the starchy endosperm tissue of the developing wheat grain. We studied the effect of introducing transgenes on the global gene expression profiles of selected transgenic wheat lines, particularly during wheat seed development. For these particular set of experiments a direct comparison between the hexaploid bread transgenic line B102,1-1 (Rooke, L., Steele, S.H., Barcelo, P.,Shewry, P.R. & Lazzeri,P. Transgene inheritance, segregation and expression in bread wheat. Euphytica 129, 301-309 (2003)) and it background, non transformed L88-31 wheat line (Lawrence,G.J., Macritchie, F. & Wrigley, C.W. Dough and baking quality of wheat lines in glutenin subunits controlled by Glu-A1, Glu-B1 and Glu-D1 loci. J. Cereal. Sci. 7,109-112 (1988)) was performed. Transcriptome comparison analysis was performed in endosperm tissue (14 and 28 days post anthesis-dpa) and in leaf tissue (8 days post germination ?dpg). The transcriptome comparisons analysis was performed using three biological replicates (i.e. per line/tissue /developmental stage selected). Hybridisations were performed in reverse dye labelling.

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Transcription profiling of wheat GF- TRANS_B102,1-1 vs Conv.bred_L88-18 transgenic lines endosperm tissue (14 and 28 days post anthesis-dpa) and in leaf tissue (8 days post germination ?dpg)

Project description:The high molecular weight (HMW) subunits of wheat glutenin are synthesised only in the starchy endosperm tissue of the developing wheat grain. We compared the expressed genomes of the transgenic wheat line B102,1-1 (Rooke et al. Transgene inheritance, segregation and expression in bread wheat. Euphytica 129, 301-309 (2003)). Both lines were shown to express the HMW-GS Ax1 gene (Halford, N.G. et al. Analysis of HMW glutenin subunits encoded bychromosome 1A of bread wheat (Triticum aestivum L.) indicates quantitative effects on grain quality. Theor Appl Genet 83, 373-378 (1992).) to the expressed genome of conventionally bred wheat line L88-18 (Lawrence et al. Dough and baking quality of wheat lines in glutenin subunits controlled by Glu-A1, Glu-B1 and Glu-D1 loci. J. Cereal. Sci. 7,109-112 (1988)) which results in the same effects on traits. Transcriptomes comparison analysis was performed in endosperm tissue (14 and 28 days post anthesis-dpa) and in leaf tissue (8 days post germination dpg), respectively. Each of the transcriptome comparisons was performed using three biological replicates (i.e. per line/tissue /developmental stage selected). Hybridisations were performed in reverse dye labelling.Exceptionally, biological replica 2 was only performed for B102,1-1 (green)/L88-18 (red) labelling and not swap

2005-10-05 | E-MEXP-309 | biostudies-arrayexpress

Transcriptome analyses of different region tissue of wheat grain endosperm

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