Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/101046
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Type: Journal article
Title: The dynamics of transcript abundance during cellularization of developing barley endosperm
Author: Zhang, R.
Tucker, M.
Burton, R.
Shirley, N.
Little, A.
Morris, J.
Milne, L.
Houston, K.
Hedley, P.
Waugh, R.
Fincher, G.
Citation: Plant Physiology, 2016; 170(3):1549-1565
Publisher: American Society of Plant Physiologists
Issue Date: 2016
ISSN: 0032-0889
1532-2548
Statement of
Responsibility: 
Runxuan Zhang, Matthew R. Tucker, Rachel A Burton, Neil J. Shirley, Alan Little, Jenny Morris, Linda Milne, Kelly Houston, Pete E. Hedley, Robbie Waugh, and Geoffrey B. Fincher
Abstract: Within the cereal grain, the endosperm and its nutrient reserves are critical for successful germination and in the context of grain utilization. The identification of molecular determinants of early endosperm development, particularly regulators of cell division and cell wall deposition, would help predict end-use properties such as yield, quality, and nutritional value. Custom microarray data have been generated using RNA isolated from developing barley grain endosperm 3 d to 8 d after pollination (DAP). Comparisons of transcript abundance over time revealed 47 gene expression modules that can be clustered into 10 broad groups. Superimposing these modules upon cytological data allowed patterns of transcript abundance to be linked with key stages of early grain development. Here, attention was focused on how the datasets could be mined to explore and define the processes of cell wall biosynthesis, remodeling, and degradation. Using a combination of spatial molecular network and gene ontology enrichment analyses, it is shown that genes involved in cell wall metabolism are found in multiple modules, but cluster into two main groups that exhibit peak expression at 3 DAP to 4 DAP and 5 DAP to 8 DAP. The presence of transcription factor genes in these modules allowed candidate genes for the control of wall metabolism during early barley grain development to be identified. The data are publicly available through a dedicated web interface (https://ics.hutton.ac.uk/barseed/), where they can be used to interrogate co- and differential expression for any other genes, groups of genes, or transcription factors expressed during early endosperm development.
Keywords: Cell Wall; Hordeum; Plant Proteins; Oligonucleotide Array Sequence Analysis; Cluster Analysis; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Time Factors; Gene Regulatory Networks; Pollination; Endosperm; Gene Ontology; Edible Grain
Rights: © 2016 American Society of Plant Biologists. All Rights Reserved.
RMID: 0030041435
DOI: 10.1104/pp.15.01690
Appears in Collections:Agriculture, Food and Wine publications

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