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      Metabolomics for Plant Improvement: Status and Prospects

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          Abstract

          Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.

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          Most cited references297

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          MS-DIAL: Data Independent MS/MS Deconvolution for Comprehensive Metabolome Analysis

          Data-independent acquisition (DIA) in liquid chromatography tandem mass spectrometry (LC-MS/MS) provides more comprehensive untargeted acquisition of molecular data. Here we provide an open-source software pipeline, MS-DIAL, to demonstrate how DIA improves simultaneous identification and quantification of small molecules by mass spectral deconvolution. For reversed phase LC-MS/MS, our program with an enriched LipidBlast library identified total 1,023 lipid compounds from nine algal strains to highlight their chemotaxonomic relationships.
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            Cytokinin oxidase regulates rice grain production.

            Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.
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              A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening.

              A major component in the regulatory network controlling fruit ripening is likely to be the gene at the tomato Colorless non-ripening (Cnr) locus. The Cnr mutation results in colorless fruits with a substantial loss of cell-to-cell adhesion. The nature of the mutation and the identity of the Cnr gene were previously unknown. Using positional cloning and virus-induced gene silencing, here we demonstrate that an SBP-box (SQUAMOSA promoter binding protein-like) gene resides at the Cnr locus. Furthermore, the Cnr phenotype results from a spontaneous epigenetic change in the SBP-box promoter. The discovery that Cnr is an epimutation was unexpected, as very few spontaneous epimutations have been described in plants. This study demonstrates that an SBP-box gene is critical for normal ripening and highlights the likely importance of epialleles in plant development and the generation of natural variation.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                07 August 2017
                2017
                : 8
                : 1302
                Affiliations
                [1] 1Department of Plant Sciences, University of Hyderabad (UoH) Hyderabad, India
                [2] 2International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
                [3] 3Crop Improvement Division, Indian Institute of Pulses Research (IIPR) Kanpur, India
                [4] 4Department of Botany, Indira Gandhi National Tribal University (IGNTU) Amarkantak, India
                Author notes

                Edited by: Manoj K. Sharma, Jawaharlal Nehru University, India

                Reviewed by: Stefanie Wienkoop, University of Vienna, Austria; Prateek Tripathi, Scripps Research Institute, United States

                This article was submitted to Plant Biotechnology, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2017.01302
                5545584
                28220127
                25df4981-7932-4674-85a2-ef9d088deced
                Copyright © 2017 Kumar, Bohra, Pandey, Pandey and Kumar.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 04 April 2017
                : 11 July 2017
                Page count
                Figures: 2, Tables: 1, Equations: 0, References: 360, Pages: 27, Words: 0
                Categories
                Plant Science
                Review

                Plant science & Botany
                biofortification,crop improvement,metabolomics,phytonutrient,fruit quality
                Plant science & Botany
                biofortification, crop improvement, metabolomics, phytonutrient, fruit quality

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