Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of developing starchy endosperm of Triticum aestivum at five stages during grain fill

ABSTRACT: Transcriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.

ORGANISM(S): Triticum aestivum

SUBMITTER: Rowan Mitchell

PROVIDER: E-MTAB-861 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome.

Pellny Till K TK Lovegrove Alison A Freeman Jackie J Tosi Paola P Love Christopher G CG Knox J Paul JP Shewry Peter R PR Mitchell Rowan A C RA

Plant physiology 20111128 2

The transcriptome of the developing starchy endosperm of hexaploid wheat (Triticum aestivum) was determined using RNA-Seq isolated at five stages during grain fill. This resource represents an excellent way to identify candidate genes responsible for the starchy endosperm cell wall, which is dominated by arabinoxylan (AX), accounting for 70% of the cell wall polysaccharides, with 20% (1,3;1,4)-β-d-glucan, 7% glucomannan, and 4% cellulose. A complete inventory of transcripts of 124 glycosyltransf ...[more]

PMID: 22123899

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Project description:Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chromosome pairing is restricted to homologous chromosomes despite the presence of homoeologues in the nucleus. The importance of wheat as a crop and the extensive use of wild wheat relatives in breeding programs has prompted many years of cytogenetic and genetic research to develop an understanding of the control of chromosome pairing and recombination. The rapid advance of biochemical and molecular information on meiosis in model organisms such as yeast provides new opportunities to investigate the molecular basis of chromosome pairing control in wheat. However, building the link between the model and wheat requires points of data contact. We report here a large-scale transcriptomics study using the Affymetrix wheat GeneChipÂ® aimed at providing this link between wheat and model systems and at identifying early meiotic genes. Analysis of the microarray data identified 1,350 transcripts temporally-regulated during the early stages of meiosis. Expression profiles with annotated transcript functions including chromatin condensation, synaptonemal complex formation,recombination and fertility were identified. From the 1,350 transcripts, 30 displayed at least an eight-fold expression change between and including pre-meiosis and telophase II, with more than 50% of these having no similarities to known sequences in NCBI and TIGR databases. This resource is now available to support research into the molecular basis of pairing and recombination control in the complex polyploid, wheat. Experiment Overall Design: The seven stages collected were pre-meiosis (PM), leptotene to pachytene (LP), diplotene to anaphase I (DA), telophase I to telophase II (TT), tetrads (T), immature pollen (IP) and mature anthers (MAN). Immediately after determining the stage, the remaining two anthers from the floret were placed into liquid nitrogen. After collecting at least 25 staged anthers for each time point from several biological samples, anthers from the respective stages were pooled. Leaf material used in this study was collected from glasshouse-grown plants (six weeks) and total RNA isolated using TrizolÂ® (Gibco BRL, Australia) according to the manufacturerâs protocol. Experiment Overall Design: Twenty micrograms of aRNA of from each of the seven samples were fragmented for hybridization to each microarray. In total three technical replicates were conducted for each of the seven stages examined. Affymetrix GeneChipÂ® Wheat Genome Arrays were used for all samples. The arrays were hybridized and processed according to the manufacturerâs specifications. Experiment Overall Design: Normalization of the microarray data was conducted using RMA. The software package Acuity 4 (Molecular Devices, CA, USA) was then used to analyze the microarray data.

Dataset Information

RNA-seq of developing starchy endosperm of Triticum aestivum at five stages during grain fill

Publications

Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome.

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