title: The Dynamics of Transcript Abundance during Cellularization of Developing Barley Endosperm.
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.
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.).
authors.forename: Runxuan
authors.initials: R
authors.lastname: Zhang
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.).
authors.forename: Matthew R
authors.identifier: http://orcid.org/0000-0003-4661-6700
authors.initials: MR
authors.lastname: Tucker
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.).
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Burton
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.).
authors.forename: Neil J
authors.initials: NJ
authors.lastname: Shirley
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.).
authors.forename: Alan
authors.initials: A
authors.lastname: Little
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.).
authors.forename: Jenny
authors.initials: J
authors.lastname: Morris
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.).
authors.forename: Linda
authors.initials: L
authors.lastname: Milne
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.).
authors.forename: Kelly
authors.identifier: http://orcid.org/0000-0003-2136-245X
authors.initials: K
authors.lastname: Houston
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.).
authors.forename: Pete E
authors.identifier: http://orcid.org/0000-0003-0866-324X
authors.initials: PE
authors.lastname: Hedley
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.).
authors.forename: Robbie
authors.identifier: http://orcid.org/0000-0003-1045-3065
authors.initials: R
authors.lastname: Waugh
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom (R.Z., L.M., K.H., P.E.H., R.W.); Australian Research Council Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia (M.R.T., R.A.B., N.J.S., A.L., G.B.F.); and Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 4HN, United Kingdom (R.W.) geoff.fincher@adelaide.edu.au.
authors.forename: Geoffrey B
authors.identifier: http://orcid.org/0000-0003-4703-3494
authors.initials: GB
authors.lastname: Fincher
mesh_terms: D002473:Cell Wall / Q000235:genetics / Q000378:metabolism; D016000:Cluster Analysis; D002523:Edible Grain / Q000166:cytology / Q000196:embryology / Q000235:genetics; D056625:Endosperm / Q000166:cytology / Q000196:embryology / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D001467:Hordeum / Q000166:cytology / Q000196:embryology / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D054817:Pollination / Q000235:genetics; D013997:Time Factors
chemical_list: D010940:Plant Proteins