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      Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots

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          Abstract

          Background

          There have been few studies on the partial defoliation response of grass. It has been unclear how partial defoliation may affect roots at the levels of nutrient accumulation and transcriptional regulation. Hereby we report a comprehensive investigation on molecular impacts of partial defoliation by using a model grass species, Brachypodium distachyon.

          Results

          Our Inductively Coupled Plasma Mass Spectrometry analyses of B. distachyon revealed shoot- and root-specific accumulation patterns of a group of macronutrients including potassium (K), Phosphorus (P), Calcium (Ca), Magnesium (Mg), and micronutrients including Sodium (Na), iron (Fe), and Manganese (Mn). Meanwhile, our genome-wide profiling of gene expression patterns depicts transcriptional impacts on B. distachyon roots by cutting the aerial portion. The RNAseq analyses identified a total of 1,268 differentially expressed genes in B. distachyon with partial defoliation treatment. Our comprehensive analyses by means of multiple approaches, including Gene Ontology, InterPro and Pfam protein classification, KEGG pathways, and Plant TFDB, jointly highlight the involvement of hormone-mediated wounding response, primary and secondary metabolites, and ion homeostasis, in B. distachyon after the partial defoliation treatment. In addition, evidence is provided that roots respond to partial defoliation by modifying nutrient uptake and rhizosphere acidification rate, indicating that an alteration of the root/soil interaction occurs in response to this practice.

          Conclusions

          This study reveals how partial defoliation alters ion accumulation levels in shoots and roots, as well as partial defoliation-induced transcriptional reprogramming on a whole-genome scale, thereby providing insight into the molecular mechanisms underlying the recovery process of grass after partial defoliation.

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          Most cited references59

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Transcriptional profiling reveals novel interactions between wounding, pathogen, abiotic stress, and hormonal responses in Arabidopsis.

            Mechanical wounding not only damages plant tissues, but also provides pathways for pathogen invasion. To understand plant responses to wounding at a genomic level, we have surveyed the transcriptional response of 8,200 genes in Arabidopsis plants. Approximately 8% of these genes were altered by wounding at steady-state mRNA levels. Studies of expression patterns of these genes provide new information on the interactions between wounding and other signals, including pathogen attack, abiotic stress factors, and plant hormones. For example, a number of wound-responsive genes encode proteins involved in pathogen response. These include signaling molecules for the pathogen resistance pathway and enzymes required for cell wall modification and secondary metabolism. Many osmotic stress- and heat shock-regulated genes were highly responsive to wounding. Although a number of genes involved in ethylene, jasmonic acid, and abscisic acid pathways were activated, many in auxin responses were suppressed by wounding. These results further dissected the nature of mechanical wounding as a stress signal and identified new genes that may play a role in wounding and other signal transduction pathways.
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              Brachypodium distachyon. A new model system for functional genomics in grasses.

              A new model for grass functional genomics is described based on Brachypodium distachyon, which in the evolution of the Pooideae diverged just prior to the clade of "core pooid" genera that contain the majority of important temperate cereals and forage grasses. Diploid ecotypes of B. distachyon (2n = 10) have five easily distinguishable chromosomes that display high levels of chiasma formation at meiosis. The B. distachyon nuclear genome was indistinguishable in size from that of Arabidopsis, making it the simplest genome described in grasses to date. B. distachyon is a self-fertile, inbreeding annual with a life cycle of less than 4 months. These features, coupled with its small size (approximately 20 cm at maturity), lack of seed-head shatter, and undemanding growth requirements should make it amenable to high-throughput genetics and mutant screens. Immature embryos exhibited a high capacity for plant regeneration via somatic embryogenesis. Regenerated plants display very low levels of albinism and have normal fertility. A simple transformation system has been developed based on microprojectile bombardment of embryogenic callus and hygromycin selection. Selected B. distachyon ecotypes were resistant to all tested cereal-adapted Blumeria graminis species and cereal brown rusts (Puccinia reconditia). In contrast, different ecotypes displayed resistance or disease symptoms following challenge with the rice blast pathogen (Magnaporthe grisea) and wheat/barley yellow stripe rusts (Puccinia striformis). Despite its small stature, B. distachyon has large seeds that should prove useful for studies on grain filling. Such biological characteristics represent important traits for study in temperate cereals.
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                Author and article information

                Contributors
                Journal
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ
                PeerJ Inc. (San Diego, USA )
                2167-8359
                13 June 2019
                2019
                : 7
                : e7102
                Affiliations
                [1 ]Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden , Shanghai, China
                [2 ]Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences , Shanghai, China
                [3 ]Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences , Shanghai, China
                [4 ]College of Life Sciences, Shanghai Normal University , Shanghai, China
                [5 ]Center for Agroforestry Mega Data Science and FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University , Fuzhou, Fujian, China
                Author information
                http://orcid.org/0000-0002-0757-9217
                http://orcid.org/0000-0002-3982-9858
                Article
                7102
                10.7717/peerj.7102
                6571136
                0e4049d3-47b4-404c-b8c9-e1dfaae08d89
                © 2019 Wang et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

                History
                : 17 January 2019
                : 7 May 2019
                Funding
                Funded by: Shanghai Landscaping Administrative Bureau
                Award ID: G182405 and G192412
                This work was funded by grants from the Shanghai Landscaping Administrative Bureau (Grant Nos. G182405 and G192412). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Bioinformatics
                Genomics
                Molecular Biology
                Plant Science

                brachypodium distachyon,transcriptome,defoliation,grass,nutrition

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