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      Comparative proteomic investigation of drought responses in foxtail millet

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          Abstract

          Background

          Foxtail millet ( Setaria italica L. P. Beauv) has been considered as a tractable model crop in recent years due to its short growing cycle, lower amount of repetitive DNA, inbreeding nature, small diploid genome, and outstanding abiotic stress-tolerance characteristics. With modern agriculture facing various adversities, it’s urgent to dissect the mechanisms of how foxtail millet responds and adapts to drought and stress on the proteomic-level.

          Results

          In this research, a total of 2474 differentially expressed proteins were identified by quantitative proteomic analysis after subjecting foxtail millet seedlings to drought conditions. 321 of these 2474 proteins exhibited significant expression changes, including 252 up-regulated proteins and 69 down-regulated proteins. The resulting proteins could then be divided into different categories, such as stress and defense responses, photosynthesis, carbon metabolism, ROS scavenging, protein synthesis, etc., according to Gene Ontology annotation. Proteins implicated in fatty acid and amino acid metabolism, polyamine biosynthesis, hormone metabolism, and cell wall modifications were also identified. These obtained differential proteins and their possible biological functions under drought stress all suggested that various physiological and metabolic processes might function cooperatively to configure a new dynamic homeostasis in organisms. The expression patterns of five drought-responsive proteins were further validated using western blot analysis. The qRT-PCR was also carried out to analyze the transcription levels of 21 differentially expressed proteins. The results showed large inconsistency in the variation between proteins and the corresponding mRNAs, which showed once again that post-transcriptional modification performs crucial roles in regulating gene expression.

          Conclusion

          The results offered a valuable inventory of proteins that may be involved in drought response and adaption, and provided a regulatory network of different metabolic pathways under stress stimulation. This study will illuminate the stress tolerance mechanisms of foxtail millet, and shed some light on crop germplasm breeding and innovation.

          Electronic supplementary material

          The online version of this article (10.1186/s12870-018-1533-9) contains supplementary material, which is available to authorized users.

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          Most cited references 59

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          Salt and drought stress signal transduction in plants.

           Jian Zhu (2001)
          Salt and drought stress signal transduction consists of ionic and osmotic homeostasis signaling pathways, detoxification (i.e., damage control and repair) response pathways, and pathways for growth regulation. The ionic aspect of salt stress is signaled via the SOS pathway where a calcium-responsive SOS3-SOS2 protein kinase complex controls the expression and activity of ion transporters such as SOS1. Osmotic stress activates several protein kinases including mitogen-activated kinases, which may mediate osmotic homeostasis and/or detoxification responses. A number of phospholipid systems are activated by osmotic stress, generating a diverse array of messenger molecules, some of which may function upstream of the osmotic stress-activated protein kinases. Abscisic acid biosynthesis is regulated by osmotic stress at multiple steps. Both ABA-dependent and -independent osmotic stress signaling first modify constitutively expressed transcription factors, leading to the expression of early response transcriptional activators, which then activate downstream stress tolerance effector genes.
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            Reactive Oxygen Species, Oxidative Damage, and Antioxidative Defense Mechanism in Plants under Stressful Conditions

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              Reference genome sequence of the model plant Setaria.

              We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).
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                Author and article information

                Contributors
                jwpan01@126.com
                lizhen1891@126.com
                wangqingguo1963@163.com
                agarrell@boragenbio.com
                jnlium@sina.com
                yguan65@163.com
                Alica.Wenqing@gmail.com
                wheiliu@163.com
                Journal
                BMC Plant Biol
                BMC Plant Biol
                BMC Plant Biology
                BioMed Central (London )
                1471-2229
                29 November 2018
                29 November 2018
                2018
                : 18
                Affiliations
                [1 ]ISNI 0000 0004 0644 6150, GRID grid.452757.6, Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, ; Jinan, 250100 Shandong China
                [2 ]ISNI 0000 0004 0644 6150, GRID grid.452757.6, Crop Research Institute, Shandong Academy of Agricultural Sciences, ; Jinan, 250100 Shandong China
                [3 ]GRID grid.410585.d, College of Life Sciences, , Shandong Normal University, ; Jinan, 250014 Shandong China
                [4 ]ISNI 0000 0004 1796 3356, GRID grid.494558.1, Shandong Agriculture and Engineering University, ; Jinan, 250100 Shandong China
                [5 ]Boragen Inc, Durham, North Carolina 27709 USA
                Article
                1533
                10.1186/s12870-018-1533-9
                6267058
                30497407
                © The Author(s). 2018

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Funding
                Funded by: Shandong Provential Natural Science Foundtion
                Award ID: ZR2016CM23
                Funded by: the Young Talents Training program of Shandong Academy of Agricultural Sciences
                Award ID: 2016-2018
                Award Recipient :
                Funded by: Major in Shandong Province Science and Technology Projects
                Award ID: 2015ZDJS03001-2
                Funded by: the Shandong Key Research and Development Program
                Award ID: 2016ZDJS10A03-05
                Award Recipient :
                Funded by: National Natural Science Foundation of China
                Award ID: 31401310
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2018

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