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Dynamic transcription of all genes in Triticum urartu endosperms throughout grain-filling stages

ABSTRACT: Endosperms (with the embryo, aleurone, seed coat, and pericarp removed) at 5, 10, 15, 20, and 25 DPAs of the T. urartu accession PI 428198 were used for RNA-Seq analysis. Each sample had three independent biological replicates. The total RNA of endosperms was isolated and a library with an insert length of ~350 bp was sequenced using the Illumina HiSeq 2000 (San Diego, CA, USA). An integrated reference sequence of T. urartu PI 428198 was prepared by combining the annotated gene set (ftp://ftp.ensemblgenomes.org/pub/plants/release3 9/fasta/triticum_urartu) with cloned low-molecule-weight glutenin subunit genes and gliadin genes after gene redundancy removal. The relative transcript abundance of seed storage protein genes and the 41,507 predicted genes from genome sequences were calculated using the unique aligned reads as the expected number of fragments per kilobase of the transcript sequence per million base pairs sequenced (FPKM).

ORGANISM(S): Triticum urartu

PROVIDER: GSE165862 | GEO | 2021/02/01

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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Dynamic transcription of all genes in Triticum urartu endosperms throughout grain-filling stages

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