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      Effects of Arbuscular Mycorrhization on Fruit Quality in Industrialized Tomato Production

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          Abstract

          Industrialized tomato production faces a decrease in flavors and nutritional value due to conventional breeding. Moreover, tomato production heavily relies on nitrogen and phosphate fertilization. Phosphate uptake and improvement of fruit quality by arbuscular mycorrhizal (AM) fungi are well-studied. We addressed the question of whether commercially used tomato cultivars grown in a hydroponic system can be mycorrhizal, leading to improved fruit quality. Tomato plants inoculated with Rhizophagus irregularis were grown under different phosphate concentrations and in substrates used in industrial tomato production. Changes in fruit gene expression and metabolite levels were checked by RNAseq and metabolite determination, respectively. The tests revealed that reduction of phosphate to 80% and use of mixed substrate allow AM establishment without affecting yield. By comparing green fruits from non-mycorrhizal and mycorrhizal plants, differentially expressed genes (DEGs) were found to possibly be involved in processes regulating fruit maturation and nutrition. Red fruits from mycorrhizal plants showed a trend of higher BRIX values and increased levels of carotenoids in comparison to those from non-mycorrhizal plants. Free amino acids exhibited up to four times higher levels in red fruits due to AM, showing the potential of mycorrhization to increase the nutritional value of tomatoes in industrialized production.

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          Differential expression analysis for sequence count data

          High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.
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            The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.

            Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader's ability to evaluate critically the quality of the results presented or to repeat the experiments. The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement. Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.
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              AN EVALUATION OF TECHNIQUES FOR MEASURING VESICULAR ARBUSCULAR MYCORRHIZAL INFECTION IN ROOTS

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                Author and article information

                Journal
                Int J Mol Sci
                Int J Mol Sci
                ijms
                International Journal of Molecular Sciences
                MDPI
                1422-0067
                24 September 2020
                October 2020
                : 21
                : 19
                : 7029
                Affiliations
                [1 ]Leibniz Institute of Plant Biochemistry, Department of Cell and Metabolic Biology, 06120 Halle, Germany; ramona.schubert@ 123456ipb-halle.de (R.S.); stephanie.werner@ 123456julius-kuehn.de (S.W.)
                [2 ]Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, 06484 Quedlinburg, Germany
                [3 ]INOQ GmbH, 29465 Schnega, Germany; cirka@ 123456inoq.de (H.C.); philipproedel@ 123456gmx.de (P.R.); hutter@ 123456inoq.de (I.H.)
                [4 ]Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany; moya@ 123456ipk-gatersleben.de (Y.T.M.); mock@ 123456ipk-gatersleben.de (H.-P.M.); kunzeg@ 123456ipk-gatersleben.de (G.K.)
                Author notes
                [* ]Correspondence: Bettina.Hause@ 123456ipb-halle.de ; Tel.: +49-345-55821540
                Author information
                https://orcid.org/0000-0001-9697-4990
                Article
                ijms-21-07029
                10.3390/ijms21197029
                7582891
                32987747
                d3308344-d019-4cc0-9079-51d0d49d1f2a
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 28 July 2020
                : 22 September 2020
                Categories
                Article

                Molecular biology
                arbuscular mycorrhiza,brix value,carotenoids,free amino acids,fruit quality,hydroponic cultivation,phosphate,tomato,transcript profiling (rnaseq),yield

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