Dataset Information

Cell walls and the developmental anatomy of the Brachypodium distachyon stem internode.

ABSTRACT: While many aspects of plant cell wall polymer structure are known, their spatial and temporal distribution within the stem are not well understood. Here, we studied vascular system and fiber development, which has implication for both biofuel feedstock conversion efficiency and crop yield. The subject of this study, Brachypodium distachyon, has emerged as a grass model for food and energy crop research. Here, we conducted our investigation using B. distachyon by applying various histological approaches and Fourier transform infrared spectroscopy to the stem internode from three key developmental stages. While vascular bundle size and number did not change over time, the size of the interfascicular region increased dramatically, as did cell wall thickness. We also describe internal stem internode anatomy and demonstrate that lignin deposition continues after crystalline cellulose and xylan accumulation ceases. The vascular bundle anatomy of B. distachyon appears to be highly similar to domesticated grasses. While the arrangement of bundles within the stem is highly variable across grasses, B. distachyon appears to be a suitable model for the rind of large C4 grass crops. A better understanding of growth and various anatomical and cell wall features of B. distachyon will further our understanding of plant biomass accumulation processes.

SUBMITTER: Matos DA

PROVIDER: S-EPMC3836760 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Cell walls and the developmental anatomy of the Brachypodium distachyon stem internode.

Matos Dominick A DA Whitney Ian P IP Harrington Michael J MJ Hazen Samuel P SP

PloS one 20131121 11

While many aspects of plant cell wall polymer structure are known, their spatial and temporal distribution within the stem are not well understood. Here, we studied vascular system and fiber development, which has implication for both biofuel feedstock conversion efficiency and crop yield. The subject of this study, Brachypodium distachyon, has emerged as a grass model for food and energy crop research. Here, we conducted our investigation using B. distachyon by applying various histological app ...[more]

PMID: 24278300

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Project description:BackgroundA complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement.ResultsWe have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors.ConclusionsThe description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors.

Dataset Information

Cell walls and the developmental anatomy of the Brachypodium distachyon stem internode.

Publications

Cell walls and the developmental anatomy of the Brachypodium distachyon stem internode.

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