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Malacarne G, Lagreze J, Rojas San Martin B, Malnoy M, Moretto M, Moser C, Dalla Costa L. Insights into the cell-wall dynamics in grapevine berries during ripening and in response to biotic and abiotic stresses. PLANT MOLECULAR BIOLOGY 2024; 114:38. [PMID: 38605193 PMCID: PMC11009762 DOI: 10.1007/s11103-024-01437-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/26/2024] [Indexed: 04/13/2024]
Abstract
The cell wall (CW) is the dynamic structure of a plant cell, acting as a barrier against biotic and abiotic stresses. In grape berries, the modifications of pulp and skin CW during softening ensure flexibility during cell expansion and determine the final berry texture. In addition, the CW of grape berry skin is of fundamental importance for winemaking, controlling secondary metabolite extractability. Grapevine varieties with contrasting CW characteristics generally respond differently to biotic and abiotic stresses. In the context of climate change, it is important to investigate the CW dynamics occurring upon different stresses, to define new adaptation strategies. This review summarizes the molecular mechanisms underlying CW modifications during grapevine berry fruit ripening, plant-pathogen interaction, or in response to environmental stresses, also considering the most recently published transcriptomic data. Furthermore, perspectives of new biotechnological approaches aiming at modifying the CW properties based on other crops' examples are also presented.
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Affiliation(s)
- Giulia Malacarne
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, 38098, Trento, Italy.
| | - Jorge Lagreze
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, 38098, Trento, Italy
- Centre Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, 38098, Trento, Italy
| | - Barbara Rojas San Martin
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, 38098, Trento, Italy
- Centre Agriculture Food Environment (C3A), University of Trento, San Michele all'Adige, 38098, Trento, Italy
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, 38098, Trento, Italy
| | - Marco Moretto
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, 38098, Trento, Italy
| | - Claudio Moser
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, 38098, Trento, Italy
| | - Lorenza Dalla Costa
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, 38098, Trento, Italy
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2
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Ameen M, Zafar A, Mahmood A, Zia MA, Kamran K, Javaid MM, Yasin M, Khan BA. Melatonin as a master regulatory hormone for genetic responses to biotic and abiotic stresses in model plant Arabidopsis thaliana: a comprehensive review. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23248. [PMID: 38310885 DOI: 10.1071/fp23248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/09/2024] [Indexed: 02/06/2024]
Abstract
Melatonin is a naturally occurring biologically active amine produced by plants, animals and microbes. This review explores the biosynthesis of melatonin in plants, with a particular focus on its diverse roles in Arabidopsis thaliana , a model species. Melatonin affects abiotic and biotic stress resistance in A. thaliana . Exogenous and endogenous melatonin is addressed in association with various conditions, including cold stress, high light stress, intense heat and infection with Botrytis cinerea or Pseudomonas , as well as in seed germination and lateral root formation. Furthermore, melatonin confers stress resistance in Arabidopsis by initiating the antioxidant system, remedying photosynthesis suppression, regulating transcription factors involved with stress resistance (CBF, DREB, ZAT, CAMTA, WRKY33, MYC2, TGA) and other stress-related hormones (abscisic acid, auxin, ethylene, jasmonic acid and salicylic acid). This article additionally addresses other precursors, metabolic components, expression of genes (COR , CBF , SNAT , ASMT , PIN , PR1 , PDF1.2 and HSFA ) and proteins (JAZ, NPR1) associated with melatonin and reducing both biological and environmental stressors. Furthermore, the future perspective of melatonin rich agri-crops is explored to enhance plant tolerance to abiotic and biotic stresses, maximise crop productivity and enhance nutritional worth, which may help improve food security.
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Affiliation(s)
- Muaz Ameen
- Department of Botany, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Asma Zafar
- Department of Botany, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Athar Mahmood
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Anjum Zia
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Kashif Kamran
- Department of Physics, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Mansoor Javaid
- Department of Agronomy, College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan
| | - Muhammad Yasin
- Department of Agronomy, College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan
| | - Bilal Ahmad Khan
- Department of Agronomy, College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan
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Ferrandino A, Pagliarani C, Pérez-Álvarez EP. Secondary metabolites in grapevine: crosstalk of transcriptional, metabolic and hormonal signals controlling stress defence responses in berries and vegetative organs. FRONTIERS IN PLANT SCIENCE 2023; 14:1124298. [PMID: 37404528 PMCID: PMC10315584 DOI: 10.3389/fpls.2023.1124298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/26/2023] [Indexed: 07/06/2023]
Abstract
Abiotic stresses, such as temperature, heat waves, water limitation, solar radiation and the increase in atmospheric CO2 concentration, significantly influence the accumulation of secondary metabolites in grapevine berries at different developmental stages, and in vegetative organs. Transcriptional reprogramming, miRNAs, epigenetic marks and hormonal crosstalk regulate the secondary metabolism of berries, mainly the accumulation of phenylpropanoids and of volatile organic compounds (VOCs). Currently, the biological mechanisms that control the plastic response of grapevine cultivars to environmental stress or that occur during berry ripening have been extensively studied in many worlds viticultural areas, in different cultivars and in vines grown under various agronomic managements. A novel frontier in the study of these mechanisms is the involvement of miRNAs whose target transcripts encode enzymes of the flavonoid biosynthetic pathway. Some miRNA-mediated regulatory cascades, post-transcriptionally control key MYB transcription factors, showing, for example, a role in influencing the anthocyanin accumulation in response to UV-B light during berry ripening. DNA methylation profiles partially affect the berry transcriptome plasticity of different grapevine cultivars, contributing to the modulation of berry qualitative traits. Numerous hormones (such as abscisic and jasmomic acids, strigolactones, gibberellins, auxins, cytokynins and ethylene) are involved in triggering the vine response to abiotic and biotic stress factors. Through specific signaling cascades, hormones mediate the accumulation of antioxidants that contribute to the quality of the berry and that intervene in the grapevine defense processes, highlighting that the grapevine response to stressors can be similar in different grapevine organs. The expression of genes responsible for hormone biosynthesis is largely modulated by stress conditions, thus resulting in the numeourous interactions between grapevine and the surrounding environment.
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Affiliation(s)
- Alessandra Ferrandino
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Grugliasco, Italy
| | - Chiara Pagliarani
- National Research Council, Institute for Sustainable Plant Protection (CNR-IPSP), Torino, Italy
| | - Eva Pilar Pérez-Álvarez
- Grupo VIENAP. Finca La Grajera, Instituto de Ciencias de la Vid y del Vino (ICVV), Logroño, La Rioja, Spain
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Fu Y, Song Y, van Tuyl JM, Visser RGF, Arens P. The use of a candidate gene approach to study Botrytis cinerea resistance in Gerbera hybrida. FRONTIERS IN PLANT SCIENCE 2023; 14:1100416. [PMID: 37035068 PMCID: PMC10073661 DOI: 10.3389/fpls.2023.1100416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Candidate genes (CG) for Botrytis cinerea resistance described in literature were mapped on gerbera linkage maps for which several QTL for Botrytis resistance had been found previously using a rapid, low-cost platform for SNP genotyping. In total, 29 CGs were mapped in either of two mapping populations. Four CGs were mapped within the previous identified QTL intervals and three co-localized with QTL. Two of these CGs for resistance against B. cinerea, PG1 (polygalacturonase gene) and sit (sitiens, ABA-aldehyde oxidase gene) that mapped in QTL regions for the ray floret disease resistance test were studied in detail. Virus-induced gene silencing (VIGS) was used for gene function analysis to determine the CGs' role in gerbera resistance to Botrytis. Ray florets, of which the CGs were silenced, showed a significantly delayed growth of lesions upon Botrytis infection compared to controls. Combining QTL analysis, candidate gene mapping and VIGS showed to be an useful combination to identify possible causal genes and for understanding the molecular mechanisms of Botrytis resistance in gerbera. The two genes seem to act as partial S-genes and are likely among the determining genes leading to the variation observed for B. cinerea resistance in gerbera.
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Affiliation(s)
- Yiqian Fu
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Yin Song
- Phytopathology, Wageningen University and Research, Wageningen, Netherlands
| | - Jaap M. van Tuyl
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | | | - Paul Arens
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
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Silva CJ, Adaskaveg JA, Mesquida-Pesci SD, Ortega-Salazar IB, Pattathil S, Zhang L, Hahn MG, van Kan JAL, Cantu D, Powell ALT, Blanco-Ulate B. Botrytis cinerea infection accelerates ripening and cell wall disassembly to promote disease in tomato fruit. PLANT PHYSIOLOGY 2023; 191:575-590. [PMID: 36053186 PMCID: PMC9806607 DOI: 10.1093/plphys/kiac408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Postharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes to facilitate infections and promote disease in tomato (Solanum lycopersicum). Assessments of ripening progression revealed that B. cinerea accelerated external coloration, ethylene production, and softening in unripe fruit, while mRNA sequencing of inoculated unripe fruit confirmed the corresponding upregulation of host genes involved in ripening processes, such as ethylene biosynthesis and cell wall degradation. Furthermore, an enzyme-linked immunosorbent assay (ELISA)-based glycomics technique used to assess fruit cell wall polysaccharides revealed remarkable similarities in the cell wall polysaccharide changes caused by both infections of unripe fruit and ripening of healthy fruit, particularly in the increased accessibility of pectic polysaccharides. Virulence and additional ripening assessment experiments with B. cinerea knockout mutants showed that induction of ripening depends on the ability to infect the host and break down pectin. The B. cinerea double knockout Δbc polygalacturonase1 Δbc polygalacturonase2 lacking two critical pectin degrading enzymes was incapable of emerging from quiescence even long after the fruit had ripened at its own pace, suggesting that the failure to accelerate ripening severely inhibits fungal survival on unripe fruit. These findings demonstrate that active induction of ripening in unripe tomato fruit is an important infection strategy for B. cinerea.
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Affiliation(s)
- Christian J Silva
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Jaclyn A Adaskaveg
- Department of Plant Sciences, University of California, Davis, California, USA
| | | | | | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
- Mascoma LLC (Lallemand, Inc.), Lebanon, New Hampshire 03766, USA
| | - Lisha Zhang
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, California, USA
| | - Ann L T Powell
- Department of Plant Sciences, University of California, Davis, California, USA
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Pan X, Li T, Liao C, Zhu Y, Yang M. The influences of fungal endophytes inoculation on the biochemical status of grape cells of different varieties in vitro. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:335-343. [PMID: 37283619 PMCID: PMC10240921 DOI: 10.5511/plantbiotechnology.22.0730a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/30/2022] [Indexed: 06/08/2023]
Abstract
The metabolic patterns of grape cells can be specifically shaped by different strains of dual-cultured fungal endophytes. In this work, a solid co-culture system was furtherly proposed to illustrate the different impacts of endophytic fungi on the biochemical status of grape cells of different varieties. By measuring the metabolic impacts of contact fungal endophytes on grape cells of the varieties 'Rose honey' (RH) and 'Cabernet sauvignon' (CS), we observed that most of the fungal strains used had promoting effects on grape cellular biochemistry parameters. Compared with the control, inoculation with most of the fungal strains increased the superoxide dismutase (SOD) and phenylalanine ammonia-lyase (PAL) activities as well as the total flavonoid (TF) and total phenolics (TPh) contents in both types of grape cells. Among the tested strains, RH34, RH49 and MDR36 had relatively stronger biochemical impacts on grape cells. More interestingly, in addition to the varietal specificity, a certain degree of fungal genus specificity was also observed during the metabolic interactions between fungal endophytes and grape cells, as fungal endophytes from the same genus tended to be clustered into the same group based on the affected biochemical traits. This work revealed the differential biochemical status effects of fungal endophytes on different varietal grape cells and raised the possibility of reshaping grape qualities by applying endophytes.
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Affiliation(s)
- Xiaoxia Pan
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education, School of Ethnic Medicine, Yunnan Minzu University, Kunming 650504, China
| | - Tong Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Changmei Liao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
| | - Youyong Zhu
- Key Laboratory for Agro-biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Mingzhi Yang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, China
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Savoi S, Santiago A, Orduña L, Matus JT. Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits. FRONTIERS IN PLANT SCIENCE 2022; 13:937927. [PMID: 36340350 PMCID: PMC9630917 DOI: 10.3389/fpls.2022.937927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.
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Affiliation(s)
- Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
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Abo-Kadoum MA, Abouelela ME, Al Mousa AA, Abo-Dahab NF, Mosa MA, Helmy YA, Hassane AMA. Resveratrol biosynthesis, optimization, induction, bio-transformation and bio-degradation in mycoendophytes. Front Microbiol 2022; 13:1010332. [PMID: 36304949 PMCID: PMC9593044 DOI: 10.3389/fmicb.2022.1010332] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/23/2022] [Indexed: 11/13/2022] Open
Abstract
Resveratrol (3,4,5-trihydroxystilbene) is a naturally occurring polyphenolic stilbene compound produced by certain plant species in response to biotic and abiotic factors. Resveratrol has sparked a lot of interest due to its unique structure and approved therapeutic properties for the prevention and treatment of many diseases such as neurological disease, cardiovascular disease, diabetes, inflammation, cancer, and Alzheimer's disease. Over the last few decades, many studies have focused on the production of resveratrol from various natural sources and the optimization of large-scale production. Endophytic fungi isolated from various types of grapevines and Polygonum cuspidatum, the primary plant sources of resveratrol, demonstrated intriguing resveratrol-producing ability. Due to the increasing demand for resveratrol, one active area of research is the use of endophytic fungi and metabolic engineering techniques for resveratrol's large-scale production. The current review addresses an overview of endophytic fungi as a source for production, as well as biosynthesis pathways and relevant genes incorporated in resveratrol biosynthesis. Various approaches for optimizing resveratrol production from endophytic fungi, as well as their bio-transformation and bio-degradation, are explained in detail.
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Affiliation(s)
- M. A. Abo-Kadoum
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - Mohamed E. Abouelela
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, United States
| | - Amal A. Al Mousa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nageh F. Abo-Dahab
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - Mohamed A. Mosa
- Nanotechnology and Advanced Nano-Materials Laboratory (NANML), Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Yosra A. Helmy
- Department of Veterinary Science, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, United States
- Department of Animal Hygiene, Zoonoses and Animal Ethology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Abdallah M. A. Hassane
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut, Egypt
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Song G, Du S, Sun H, Liang Q, Wang H, Yan M, Zhang J. Antifungal mechanism of (E)-2-hexenal against Botrytis cinerea growth revealed by transcriptome analysis. Front Microbiol 2022; 13:951751. [PMID: 36071976 PMCID: PMC9444101 DOI: 10.3389/fmicb.2022.951751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022] Open
Abstract
Gray mold caused by Botrytis cinerea, a necrotrophic plant pathogen, is one of the most damaging diseases of tomato, resulting in both pre- and post-harvest losses. (E)-2-Hexenal dose-dependently inhibited the mycelial growth of B. cinerea, and caused distortion of mycelia and loss of the cytoplasm content, thus altering the morphology of B. cinerea hyphae. To understand molecular processes in response to (E)-2-hexenal, transcriptome sequencing was carried out using RNA-Seq technology. RNA-Seq results revealed that a total of 3,893 genes were differentially expressed in B. cinerea samples treated with (E)-2-hexenal fumigation. Among these genes, 1,949 were upregulated and 1,944 were downregulated. Moreover, further analysis results showed 2,113 unigenes were mapped onto 259 pathways in Kyoto Encyclopedia of Genes and Genomes (KEGG). Moreover, (E)-2-hexenal stress affected the expression of genes involved in the pathways of cell wall, cell membrane, and energy metabolism. KEGG pathway analysis showed that the terpenoid backbone biosynthesis and steroid biosynthesis were the most enriched in ergosterol biosynthetic process transcriptome data. Particularly, (E)-2-hexenal fumigation had influenced ergosterol biosynthetic gene expression levels (e.g., ERG1, ERG3, ERG4, ERG7, ERG12, ERG13, ERG24, ERG25, ERG26, and ERG27), which were in good agreement with the experimental measurement results, and the ergosterol content decreased. Collectively, the results of this study increase our current understanding of (E)-2-hexenal inhibition mechanisms in B. cinerea and provide relevant information on postharvest shelf life extension and preservation of fruits and vegetables.
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Affiliation(s)
- Ge Song
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Hunan University of Science and Technology, Xiangtan, China
| | - Shenglong Du
- Department of Chemical Engineering, Xiangtan University, Xiangtan, China
| | - Helong Sun
- Department of Chemical Engineering, Xiangtan University, Xiangtan, China
| | - Quanwu Liang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Hunan University of Science and Technology, Xiangtan, China
| | - Haihua Wang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Hunan University of Science and Technology, Xiangtan, China
| | - Mingli Yan
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Hunan University of Science and Technology, Xiangtan, China
| | - Jihong Zhang
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, Hunan University of Science and Technology, Xiangtan, China
- *Correspondence: Jihong Zhang,
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Hegyi ÁI, Otto M, Geml J, Hegyi-Kaló J, Kun J, Gyenesei A, Pierneef R, Váczy KZ. Metatranscriptomic Analyses Reveal the Functional Role of Botrytis cinerea in Biochemical and Textural Changes during Noble Rot of Grapevines. J Fungi (Basel) 2022; 8:jof8040378. [PMID: 35448609 PMCID: PMC9030449 DOI: 10.3390/jof8040378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 02/04/2023] Open
Abstract
Botrytis cinerea, can lead to the formation of noble rot (NR) of grape berries under certain environmental conditions, resulting in favored metabolic and physical changes necessary for producing highly regarded botrytized wines. The functional genes involved in the textural and biochemical processes are still poorly characterized. We generated and analyzed metatranscriptomic data from healthy (H) berries and from berries representing the four stages of NR from the Tokaj wine region in Hungary over three months. A weighted gene co-expression network analysis (WGCNA) was conducted to link B. cinerea functional genes to grape berry physical parameters berry hardness (BH), berry skin break force (F_sk), berry skin elasticity (E_sk), and the skin break energy (W_sk). Clustered modules showed that genes involved in carbohydrate and protein metabolism were significantly enriched in NR, highlighting their importance in the grape berry structural integrity. Carbohydrate active enzymes were particularly up-regulated at the onset of NR (during the transition from phase I to II) suggesting that the major structural changes occur early in the NR process. In addition, we identified genes expressed throughout the NR process belonging to enriched pathways that allow B. cinerea to dominate and proliferate during this state, including sulphate metabolizing genes and genes involved in the synthesis of antimicrobials.
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Affiliation(s)
- Ádám István Hegyi
- Food and Wine Research Institute, Eszterházy Károly Catholic University, H-3300 Eger, Hungary; (Á.I.H.); (J.G.); (J.H.-K.)
| | - Margot Otto
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, H-3300 Eger, Hungary;
| | - József Geml
- Food and Wine Research Institute, Eszterházy Károly Catholic University, H-3300 Eger, Hungary; (Á.I.H.); (J.G.); (J.H.-K.)
- ELKH-EKKE Lendület Environmental Microbiome Research Group, Eszterházy Károly Catholic University, H-3300 Eger, Hungary;
| | - Júlia Hegyi-Kaló
- Food and Wine Research Institute, Eszterházy Károly Catholic University, H-3300 Eger, Hungary; (Á.I.H.); (J.G.); (J.H.-K.)
| | - József Kun
- Genomics and Bioinformatics Core Facility, University of Pécs, H-7601 Pécs, Hungary; (J.K.); (A.G.)
- Department of Pharmacology and Parmacotherapy, University of Pécs Medical School, H-7624 Pécs, Hungary
| | - Attila Gyenesei
- Genomics and Bioinformatics Core Facility, University of Pécs, H-7601 Pécs, Hungary; (J.K.); (A.G.)
| | - Rian Pierneef
- Biotechnology Platform, Agricultural Research Council-Onderstepoort Veterinary Research, Pretoria 0110, South Africa;
| | - Kálmán Zoltán Váczy
- Food and Wine Research Institute, Eszterházy Károly Catholic University, H-3300 Eger, Hungary; (Á.I.H.); (J.G.); (J.H.-K.)
- Correspondence:
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Pogány M, Dankó T, Hegyi-Kaló J, Kámán-Tóth E, Szám DR, Hamow KÁ, Kalapos B, Kiss L, Fodor J, Gullner G, Váczy KZ, Barna B. Redox and Hormonal Changes in the Transcriptome of Grape (Vitis vinifera) Berries during Natural Noble Rot Development. PLANTS 2022; 11:plants11070864. [PMID: 35406844 PMCID: PMC9003472 DOI: 10.3390/plants11070864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 01/18/2023]
Abstract
Noble rot is a favorable form of the interaction between grape (Vitis spp.) berries and the phytopathogenic fungus Botrytis cinerea. The transcriptome pattern of grapevine cells subject to natural noble rot development in the historic Hungarian Tokaj wine region has not been previously published. Furmint, a traditional white Tokaj variety suited to develop great quality noble rot was used in the experiments. Exploring a subset of the Furmint transcriptome redox and hormonal changes distinguishing between noble rot and bunch rot was revealed. Noble rot is defined by an early spike in abscisic acid (ABA) accumulation and a pronounced remodeling of ABA-related gene expression. Transcription of glutathione S-transferase isoforms is uniquely upregulated, whereas gene expression of some sectors of the antioxidative apparatus (e.g., catalases, carotenoid biosynthesis) is downregulated. These mRNA responses are lacking in berries exposed to bunch rot. Our results help to explain molecular details behind the fine and dynamic balance between noble rot and bunch rot development.
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Affiliation(s)
- Miklós Pogány
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
- Correspondence:
| | - Tamás Dankó
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Júlia Hegyi-Kaló
- Food and Wine Research Institute, Eszterházy Károly Catholic University, 3300 Eger, Hungary; (J.H.-K.); (K.Z.V.)
| | - Evelin Kámán-Tóth
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Dorottya Réka Szám
- Georgikon Campus, Hungarian University of Agriculture and Life Sciences, 8360 Keszthely, Hungary;
| | - Kamirán Áron Hamow
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Balázs Kalapos
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Levente Kiss
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - József Fodor
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Gábor Gullner
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
| | - Kálmán Zoltán Váczy
- Food and Wine Research Institute, Eszterházy Károly Catholic University, 3300 Eger, Hungary; (J.H.-K.); (K.Z.V.)
| | - Balázs Barna
- Centre for Agricultural Research, 2462 Martonvásár, Hungary; (T.D.); (E.K.-T.); (K.Á.H.); (B.K.); or (L.K.); (J.F.); (G.G.); (B.B.)
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12
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Rienth M, Vigneron N, Walker RP, Castellarin SD, Sweetman C, Burbidge CA, Bonghi C, Famiani F, Darriet P. Modifications of Grapevine Berry Composition Induced by Main Viral and Fungal Pathogens in a Climate Change Scenario. FRONTIERS IN PLANT SCIENCE 2021; 12:717223. [PMID: 34956249 PMCID: PMC8693719 DOI: 10.3389/fpls.2021.717223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 11/01/2021] [Indexed: 06/14/2023]
Abstract
The grapevine is subject to high number of fungal and viral diseases, which are responsible for important economic losses in the global wine sector every year. These pathogens deteriorate grapevine berry quality either directly via the modulation of fruit metabolic pathways and the production of endogenous compounds associated with bad taste and/or flavor, or indirectly via their impact on vine physiology. The most common and devastating fungal diseases in viticulture are gray mold, downy mildew (DM), and powdery mildew (PM), caused, respectively by Botrytis cinerea, Plasmopara viticola, and Erysiphe necator. Whereas B. cinerea mainly infects and deteriorates the ripening fruit directly, deteriorations by DM and PM are mostly indirect via a reduction of photosynthetic leaf area. Nevertheless, mildews can also infect berries at certain developmental stages and directly alter fruit quality via the biosynthesis of unpleasant flavor compounds that impair ultimate wine quality. The grapevine is furthermore host of a wide range of viruses that reduce vine longevity, productivity and berry quality in different ways. The most widespread virus-related diseases, that are known nowadays, are Grapevine Leafroll Disease (GLRD), Grapevine Fanleaf Disease (GFLD), and the more recently characterized grapevine red blotch disease (GRBD). Future climatic conditions are creating a more favorable environment for the proliferation of most virus-insect vectors, so the spread of virus-related diseases is expected to increase in most wine-growing regions. However, the impact of climate change on the evolution of fungal disease pressure will be variable and depending on region and pathogen, with mildews remaining certainly the major phytosanitary threat in most regions because their development rate is to a large extent temperature-driven. This paper aims to provide a review of published literature on most important grapevine fungal and viral pathogens and their impact on grape berry physiology and quality. Our overview of the published literature highlights gaps in our understanding of plant-pathogen interactions, which are valuable for conceiving future research programs dealing with the different pathogens and their impacts on grapevine berry quality and metabolism.
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Affiliation(s)
- Markus Rienth
- Changins College for Viticulture and Oenology, University of Sciences and Art Western Switzerland, Nyon, Switzerland
| | - Nicolas Vigneron
- Changins College for Viticulture and Oenology, University of Sciences and Art Western Switzerland, Nyon, Switzerland
| | - Robert P. Walker
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Simone Diego Castellarin
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Crystal Sweetman
- College of Science & Engineering, Flinders University, Bedford Park, SA, Australia
| | - Crista A. Burbidge
- School of Agriculture and Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Glen Osmond, SA, Australia
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova Agripolis, Legnaro, Italy
| | - Franco Famiani
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Philippe Darriet
- Univ. Bordeaux, Unité de recherche Œnologie EA 4577, USC 1366 INRAE, Institut des Sciences de la Vigne et du Vin, Villenave d’Ornon, France
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13
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Chen P, Li Z, Zhang D, Shen W, Xie Y, Zhang J, Jiang L, Li X, Shen X, Geng D, Wang L, Niu C, Bao C, Yan M, Li H, Li C, Yan Y, Zou Y, Micheletti D, Koot E, Ma F, Guan Q. Insights into the effect of human civilization on Malus evolution and domestication. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2206-2220. [PMID: 34161653 PMCID: PMC8541786 DOI: 10.1111/pbi.13648] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/02/2021] [Accepted: 06/05/2021] [Indexed: 05/09/2023]
Abstract
The evolutionary history of the Malus genus has not been well studied. In the current study, we presented genetic evidence on the origin of the Malus genus based on genome sequencing of 297 Malus accessions, revealing the genetic relationship between wild species and cultivated apples. Our results demonstrated that North American and East Asian wild species are closer to the outgroup (pear) than Central Asian species, and hybrid species including natural (separated before the Pleistocene, about 2.5 Mya) and artificial hybrids (including ornamental trees and rootstocks) are between East and Central Asian wild species. Introgressions from M. sylvestris in cultivated apples appeared to be more extensive than those from M. sieversii, whose genetic background flowed westward across Eurasia and eastward to wild species including M. prunifolia, M. × asiatica, M. × micromalus, and M. × robust. Our results suggested that the loss of ancestral gene flow from M. sieversii in cultivated apples accompanied the movement of European traders around the world since the Age of Discovery. Natural SNP variations showed that cultivated apples had higher nucleotide diversity than wild species and more unique SNPs than other apple groups. An apple ERECTA-like gene that underwent selection during domestication on 15th chromosome was identified as a likely major determinant of fruit length and diameter, and an NB-ARC domain-containing gene was found to strongly affect anthocyanin accumulation using a genome-wide association approach. Our results provide new insights into the origin and domestication of apples and will be useful in new breeding programmes and efforts to increase fruit crop productivity.
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Affiliation(s)
- Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Dehui Zhang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Wenyun Shen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Jing Zhang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Lijuan Jiang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Liping Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Chana Bao
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Mingjia Yan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Haiyan Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Cuiying Li
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yan Yan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yangjun Zou
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | | | - Emily Koot
- The New Zealand Institute for Plant and Food Research LimitedPalmerston NorthNew Zealand
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of HorticultureNorthwest A&F UniversityYanglingChina
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14
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Weiller F, Schückel J, Willats WGT, Driouich A, Vivier MA, Moore JP. Tracking cell wall changes in wine and table grapes undergoing Botrytis cinerea infection using glycan microarrays. ANNALS OF BOTANY 2021; 128:527-543. [PMID: 34192306 PMCID: PMC8422895 DOI: 10.1093/aob/mcab086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS The necrotrophic fungus Botrytis cinerea infects a broad range of fruit crops including domesticated grapevine Vitis vinifera cultivars. Damage caused by this pathogen is severely detrimental to the table and wine grape industries and results in substantial crop losses worldwide. The apoplast and cell wall interface is an important setting where many plant-pathogen interactions take place and where some defence-related messenger molecules are generated. Limited studies have investigated changes in grape cell wall composition upon infection with B. cinerea, with much being inferred from studies on other fruit crops. METHODS In this study, comprehensive microarray polymer profiling in combination with monosaccharide compositional analysis was applied for the first time to investigate cell wall compositional changes in the berries of wine (Sauvignon Blanc and Cabernet Sauvignon) and table (Dauphine and Barlinka) grape cultivars during Botrytis infection and tissue maceration. This was used in conjunction with scanning electron microscopy (SEM) and X-ray computed tomography (CT) to characterize infection progression. KEY RESULTS Grapes infected at veraison did not develop visible infection symptoms, whereas grapes inoculated at the post-veraison and ripe stages showed evidence of significant tissue degradation. The latter was characterized by a reduction in signals for pectin epitopes in the berry cell walls, implying the degradation of pectin polymers. The table grape cultivars showed more severe infection symptoms, and corresponding pectin depolymerization, compared with wine grape cultivars. In both grape types, hemicellulose layers were largely unaffected, as was the arabinogalactan protein content, whereas in moderate to severely infected table grape cultivars, evidence of extensin epitope deposition was present. CONCLUSIONS Specific changes in the grape cell wall compositional profiles appear to correlate with fungal disease susceptibility. Cell wall factors important in influencing resistance may include pectin methylesterification profiles, as well as extensin reorganization.
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Affiliation(s)
- Florent Weiller
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, South Africa
| | - Julia Schückel
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- DKMS Life Science Lab, Dresden, Germany
| | - William G T Willats
- School of Agriculture, Food and Rural Development, Newcastle University, Newcastle-upon-Tyne, UK
| | - Azeddine Driouich
- Université de ROUEN Normandie, Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale, UPRES-EA 4358, Fédération de Recherche ‘Normandie-Végétal’-FED 4277, F-76821 Mont-Saint-Aignan, France
| | - Melané A Vivier
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, South Africa
| | - John P Moore
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, South Africa
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15
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Chen T, Zhang Z, Li B, Qin G, Tian S. Molecular basis for optimizing sugar metabolism and transport during fruit development. ABIOTECH 2021; 2:330-340. [PMID: 36303881 PMCID: PMC9590571 DOI: 10.1007/s42994-021-00061-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022]
Abstract
Sugars are fundamental metabolites synthesized in leaves and further delivered to fruit in fruit crops. They not only provide "sweetness" as fruit quality traits, but also function as signaling molecules to modulate the responses of fruit to environmental stimuli. Therefore, the understanding to the molecular basis for sugar metabolism and transport is crucial for improving fruit quality and dissecting responses to abiotic/biotic factors. Here, we provide a review for molecular components involved in sugar metabolism and transport, crosstalk with hormone signaling, and the roles of sugars in responses to abiotic and biotic stresses. Moreover, we also envisage the strategies for optimizing sugar metabolism during fruit quality maintenance.
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Affiliation(s)
- Tong Chen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Zhanquan Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
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16
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Ma Y, Xu Y, Tang K. Aroma of Icewine: A Review on How Environmental, Viticultural, and Oenological Factors Affect the Aroma of Icewine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6943-6957. [PMID: 34143625 DOI: 10.1021/acs.jafc.1c01958] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The aroma of a wine is mostly driven by not only the factors in the vineyard, such as the grape variety and harvest time, but also the fermentation process. Icewine is a unique, intensely sweet wine made from late harvested grapes that have frozen naturally on the vine. Different from normal table wines, the grapes used in icewine naturally undergo a dehydration process and freeze-thaw cycles, and the must for icewine making has to be pressed from frozen grapes. This pressing process leaves water behind as ice crystals and allows the grape juice to be concentrated with more sugars, acids, and other dissolved solids, resulting in a slower than normal fermentation. These special procedures can lead to a unique aroma characteristic of icewine. This review delves into recent advances in chemical compounds related to icewine aroma characteristics and addresses how changes in these aroma characteristics and composition are influenced by environmental, viticultural, and oenological factors in the vineyard and winery. Deficiencies in previous studies and future trends related to the flavor science of icewine were also briefly addressed.
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Affiliation(s)
- Yue Ma
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, People's Republic of China
- Centre des Sciences du Goût et de l'Alimentation, INRAE, CNRS, AgroSup Dijon, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, People's Republic of China
| | - Ke Tang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, People's Republic of China
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17
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Wan R, Guo C, Hou X, Zhu Y, Gao M, Hu X, Zhang S, Jiao C, Guo R, Li Z, Wang X. Comparative transcriptomic analysis highlights contrasting levels of resistance of Vitis vinifera and Vitis amurensis to Botrytis cinerea. HORTICULTURE RESEARCH 2021; 8:103. [PMID: 33931625 PMCID: PMC8087793 DOI: 10.1038/s41438-021-00537-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 02/23/2021] [Accepted: 03/08/2021] [Indexed: 05/08/2023]
Abstract
Botrytis cinerea is a major grapevine (Vitis spp.) pathogen, but some genotypes differ in their degree of resistance. For example, the Vitis vinifera cultivar Red Globe (RG) is highly susceptible, but V. amurensis Rupr Shuangyou (SY) is highly resistant. Here, we used RNA sequencing analysis to characterize the transcriptome responses of these two genotypes to B. cinerea inoculation at an early infection stage. Approximately a quarter of the genes in RG presented significant changes in transcript levels during infection, the number of which was greater than that in the SY leaves. The genes differentially expressed between infected leaves of SY and RG included those associated with cell surface structure, oxidation, cell death and C/N metabolism. We found evidence that an imbalance in the levels of reactive oxygen species (ROS) and redox homeostasis probably contributed to the susceptibility of RG to B. cinerea. SY leaves had strong antioxidant capacities and improved ROS homeostasis following infection. Regulatory network prediction suggested that WRKY and MYB transcription factors are associated with the abscisic acid pathway. Weighted gene correlation network analysis highlighted preinfection features of SY that might contribute to its increased resistance. Moreover, overexpression of VaWRKY10 in Arabidopsis thaliana and V. vinifera Thompson Seedless enhanced resistance to B. cinerea. Collectively, our study provides a high-resolution view of the transcriptional changes of grapevine in response to B. cinerea infection and novel insights into the underlying resistance mechanisms.
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Affiliation(s)
- Ran Wan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
- College of Horticulture, Henan Agricultural University, 450002, Zhengzhou, Henan, China
| | - Chunlei Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, 066004, Qinhuangdao, Hebei, China
| | - Xiaoqing Hou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
| | - Yanxun Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
| | - Min Gao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
| | - Xiaoyan Hu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, 066004, Qinhuangdao, Hebei, China
| | - Songlin Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
| | - Chen Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Rongrong Guo
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, 53000, Nanning, Guangxi, China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, 712100, Yangling, Xianyang, Shaanxi, China.
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18
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Reiter T, Montpetit R, Byer S, Frias I, Leon E, Viano R, Mcloughlin M, Halligan T, Hernandez D, Figueroa-Balderas R, Cantu D, Steenwerth K, Runnebaum R, Montpetit B. Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes. mSystems 2021; 6:e00033-21. [PMID: 33850038 PMCID: PMC8546962 DOI: 10.1128/msystems.00033-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/16/2021] [Indexed: 01/04/2023] Open
Abstract
Ribosomal DNA amplicon sequencing of grape musts has demonstrated that microorganisms occur nonrandomly and are associated with the vineyard of origin, suggesting a role for the vineyard, grape, and wine microbiome in shaping wine fermentation outcomes. Here, ribosomal DNA amplicon sequencing from grape musts and RNA sequencing of eukaryotic transcripts from primary fermentations inoculated with the wine yeast Saccharomyces cerevisiae RC212 were used to profile fermentations from 15 vineyards in California and Oregon across two vintages. These data demonstrate that the relative abundance of fungal organisms detected by ribosomal DNA amplicon sequencing correlated with neither transcript abundance from those same organisms within the RNA sequencing data nor gene expression of the inoculated RC212 yeast strain. These data suggest that the majority of the fungi detected in must by ribosomal DNA amplicon sequencing were not active during the primary stage of these inoculated fermentations and were not a major factor in determining RC212 gene expression. However, unique genetic signatures were detected within the ribosomal DNA amplicon and eukaryotic transcriptomic sequencing that were predictive of vineyard site and region. These signatures included S. cerevisiae gene expression patterns linked to nitrogen, sulfur, and thiamine metabolism. These genetic signatures of site offer insight into specific environmental factors to consider with respect to fermentation outcomes and vineyard site and regional wine characteristics.IMPORTANCE The wine industry generates billions of dollars of revenue annually, and economic productivity is in part associated with regional distinctiveness of wine sensory attributes. Microorganisms associated with grapes and wineries are influenced by region of origin, and given that some microorganisms play a role in fermentation, it is thought that microbes may contribute to the regional distinctiveness of wine. In this work, as in previous studies, it is demonstrated that specific bacteria and fungi are associated with individual wine regions and vineyard sites. However, this work further shows that their presence is not associated with detectable fungal gene expression during the primary fermentation or the expression of specific genes by the inoculate Saccharomyces cerevisiae strain RC212. The detected RC212 gene expression signatures associated with region and vineyard site also allowed the identification of flavor-associated metabolic processes and environmental factors that could impact primary fermentation outcomes. These data offer novel insights into the complexities and subtleties of vineyard-specific inoculated wine fermentation and starting points for future investigations into factors that contribute to regional wine distinctiveness.
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Affiliation(s)
- Taylor Reiter
- Food Science Graduate Group, University of California Davis, Davis, California, USA
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
- Department of Population Health and Reproduction, University of California, Davis, California, USA
| | - Rachel Montpetit
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Shelby Byer
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Isadora Frias
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Esmeralda Leon
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Robert Viano
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Michael Mcloughlin
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Thomas Halligan
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Desmon Hernandez
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Kerri Steenwerth
- Crops Pathology and Genetics Research Unit, USDA Agricultural Research Service, Davis, California, USA
| | - Ron Runnebaum
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
- Department of Chemical Engineering, University of California, Davis, California, USA
| | - Ben Montpetit
- Food Science Graduate Group, University of California Davis, Davis, California, USA
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
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19
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Griggs RG, Steenwerth KL, Mills DA, Cantu D, Bokulich NA. Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing. Front Microbiol 2021; 12:673810. [PMID: 33927711 PMCID: PMC8076609 DOI: 10.3389/fmicb.2021.673810] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 03/22/2021] [Indexed: 01/05/2023] Open
Abstract
Microbiomes are integral to viticulture and winemaking – collectively termed winegrowing – where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.
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Affiliation(s)
- Reid G Griggs
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States
| | - Kerri L Steenwerth
- USDA-ARS, Crops Pathology and Genetics Research Unit, Department of Land, Air and Water Resources, University of California, Davis, Davis, CA, United States
| | - David A Mills
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States.,Department of Food Science and Technology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States.,Foods for Health Institute, University of California, Davis, Davis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, Robert Mondavi Institute for Wine and Food Science, University of California, Davis, Davis, CA, United States
| | - Nicholas A Bokulich
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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20
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Burbidge CA, Ford CM, Melino VJ, Wong DCJ, Jia Y, Jenkins CLD, Soole KL, Castellarin SD, Darriet P, Rienth M, Bonghi C, Walker RP, Famiani F, Sweetman C. Biosynthesis and Cellular Functions of Tartaric Acid in Grapevines. FRONTIERS IN PLANT SCIENCE 2021; 12:643024. [PMID: 33747023 PMCID: PMC7970118 DOI: 10.3389/fpls.2021.643024] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/09/2021] [Indexed: 05/29/2023]
Abstract
Tartaric acid (TA) is an obscure end point to the catabolism of ascorbic acid (Asc). Here, it is proposed as a "specialized primary metabolite", originating from carbohydrate metabolism but with restricted distribution within the plant kingdom and lack of known function in primary metabolic pathways. Grapes fall into the list of high TA-accumulators, with biosynthesis occurring in both leaf and berry. Very little is known of the TA biosynthetic pathway enzymes in any plant species, although recently some progress has been made in this space. New technologies in grapevine research such as the development of global co-expression network analysis tools and genome-wide association studies, should enable more rapid progress. There is also a lack of information regarding roles for this organic acid in plant metabolism. Therefore this review aims to briefly summarize current knowledge about the key intermediates and enzymes of TA biosynthesis in grapes and the regulation of its precursor, ascorbate, followed by speculative discussion around the potential roles of TA based on current knowledge of Asc metabolism, TA biosynthetic enzymes and other aspects of fruit metabolism.
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Affiliation(s)
| | | | | | - Darren Chern Jan Wong
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Yong Jia
- Western Barley Genetic Alliance, Murdoch University, Perth, WA, Australia
| | | | - Kathleen Lydia Soole
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Simone Diego Castellarin
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Philippe Darriet
- Université Bordeaux, Unité de recherche OEnologie, EA 4577, USC 1366 INRAE, Institut des Sciences de la Vigne et du Vin, Villenave d’Ornon, France
| | - Markus Rienth
- University of Sciences and Art Western Switzerland, Changins College for Viticulture and Oenology, Nyon, Switzerland
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Robert Peter Walker
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Franco Famiani
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Crystal Sweetman
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
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21
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Leng F, Ye Y, Zhu X, Zhang Y, Zhang Z, Shi J, Shen N, Jia H, Wang L. Comparative transcriptomic analysis between 'Summer Black' and its bud sport 'Nantaihutezao' during developmental stages. PLANTA 2021; 253:23. [PMID: 33403440 DOI: 10.1007/s00425-020-03543-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
4-coumarate-CoA ligase (VIT_02s0109g00250) and copper amine oxidase (VIT_17s0000g09100) played essential roles in contributing to the total soluble solid and total anthocyanin variations induced by bud sport in grape berries. Taste and color, which are important organoleptic qualities of grape berry, undergo rapid and substantial changes during development and ripening. In this study, we used two cultivars 'Summer Black' and its bud sport 'Nantaihutezao' to explore and identify differentially expressed genes associated with total soluble solid and anthocyanin during developmental stages using RNA-Seq. Overall, substantial differences in expression were observed across berry development between the two cultivars. 5388 genes were detected by weighted gene co-expression network analysis (WGCNA) associated with the total soluble solid (TSS) and anthocyanin contents variations. Several of these genes were significantly enriched in the phenylalanine metabolism pathway; two hub genes 4-coumarate-CoA ligase (VIT_02s0109g00250) and copper amine oxidase (VIT_17s0000g09100) played the most essential roles in relating to the total soluble solid and total anthocyanin variations induced by bud sport through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and co-expression network analysis. These findings provide insights into the molecular mechanism responsible for the bud sport phenotype.
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Affiliation(s)
- Feng Leng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yunling Ye
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Xiaoheng Zhu
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement of the Ministry of Agriculture/Department of Horticulture, Zhejiang University, Hangzhou, 310058, China
| | - Yue Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Ziyue Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Jiayu Shi
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Nan Shen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Huijuan Jia
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement of the Ministry of Agriculture/Department of Horticulture, Zhejiang University, Hangzhou, 310058, China.
| | - Li Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China.
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22
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Hegyi-Kaló J, Hegyi ÁI, Geml J, Zsófi Z, Pálfi X, Váczy KZ. Physico-Chemical Characteristics and Culturable Microbial Communities of Grape Berries Change Strongly during Noble Rot Development. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1809. [PMID: 33371257 PMCID: PMC7766896 DOI: 10.3390/plants9121809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 11/23/2022]
Abstract
Botrytis cinerea is a well-known pathogen of grapevine. However, under certain microclimatic conditions, Botrytis infection results in noble rot, an essential process in the production of the world-known Tokaji aszú wines in Hungary. We investigated the physico-chemical characteristics and culturable microorganisms associated with grape berries through several noble rot phases in the two main cultivars grown in Tokaj: Vitisvinifera cv. "Furmint" and "Hárslevelű". We measured physical and analytical parameters routinely tested in viticulture and analyzed the ITS rDNA sequence data of fungi isolated from the sampled berries. We observed significant differences in the physico-chemical parameters among the noble rot phases as well as sampling dates. The greatest variation in berry texture and microbial structure was observed in the initial phases, with variables converging as the noble rot progressed. By finding a bijection between the examined chemical properties and the factorial parameters (e.g., noble rot phase, collection time, cultivar), an appropriate sweet winemaking material can be designed. Fungal community differed significantly among cultivars, with higher number of species observed in Hárslevelű. Our results reveal that there is more to noble rot than only Botrytiscinerea and other microorganisms may play important roles in the aszú process.
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Affiliation(s)
- Júlia Hegyi-Kaló
- Food and Wine Research Institute, Eszterházy Károly University, 6 Leányka Street, H-3300 Eger, Hungary; (J.H.-K.); (Á.I.H.); (Z.Z.); (X.P.)
- Department of Microbiology and Biotechnology, SZIU, 14-16 Somlói Street, H-1118 Budapest, Hungary
| | - Ádám István Hegyi
- Food and Wine Research Institute, Eszterházy Károly University, 6 Leányka Street, H-3300 Eger, Hungary; (J.H.-K.); (Á.I.H.); (Z.Z.); (X.P.)
| | - József Geml
- MTA-EKE Lendület Environmental Microbiome Research Group, Eszterházy Károly University, 6 Leányka Street, H-3300 Eger, Hungary;
| | - Zsolt Zsófi
- Food and Wine Research Institute, Eszterházy Károly University, 6 Leányka Street, H-3300 Eger, Hungary; (J.H.-K.); (Á.I.H.); (Z.Z.); (X.P.)
| | - Xénia Pálfi
- Food and Wine Research Institute, Eszterházy Károly University, 6 Leányka Street, H-3300 Eger, Hungary; (J.H.-K.); (Á.I.H.); (Z.Z.); (X.P.)
| | - Kálmán Zoltán Váczy
- Food and Wine Research Institute, Eszterházy Károly University, 6 Leányka Street, H-3300 Eger, Hungary; (J.H.-K.); (Á.I.H.); (Z.Z.); (X.P.)
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23
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Xie S, Lei Y, Chen H, Li J, Chen H, Zhang Z. R2R3-MYB Transcription Factors Regulate Anthocyanin Biosynthesis in Grapevine Vegetative Tissues. FRONTIERS IN PLANT SCIENCE 2020; 11:527. [PMID: 32457776 PMCID: PMC7221203 DOI: 10.3389/fpls.2020.00527] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/07/2020] [Indexed: 06/02/2023]
Abstract
Anthocyanins with important physiological functions mainly accumulate in grape berry, but teinturier grape cultivars can accumulate anthocyanins in both reproductive and vegetative tissues. The molecular regulatory mechanisms of anthocyanin biosynthesis in grapevine reproductive and vegetative tissues are different. Therefore, teinturier grapevine cultivar provides opportunities to investigate transcriptional regulation of vegetative anthocyanins, and to compare with mechanisms that regulate grape berry anthocyanins. Yan73 is a teinturier Vitis vinifera variety with vegetative tissues able to accumulate anthocyanins, but the anthocyanin pattern and the molecular mechanism regulating anthocyanin biosynthesis in these tissues remain uncharacterized. We analyzed the anthocyanin metabolic and transcriptome profiles of the vegetative tissues of Yan73 and its male parent with HPLC-ESI-MS/MS and RNA-sequencing technologies. Yan73 vegetative tissues had relatively high 3'-OH, acylated, and methoxylated anthocyanins. Furthermore, peonidin-3-O-(trans-6-coumaryl)-glucoside is the most abundant anthocyanin in Yan73 grapevine vegetative tissues. A total of 30,17 and 10 anthocyanin biosynthesis genes showed up-regulated expression in Yan73 leaf, stem and tendril, respectively, indicating anthocyanin biosynthesis in Yan73 vegetative tissues is regulated by transcription factors. The up-regulated expression of VvMYBA1 on chromosome 2 and VvMYBA5, VvMYBA6, and VvMYBA7 on chromosome 14 are responsible for the anthocyanin patterns of Yan73 vegetative tissues. The expression of a set of R2R3-MYB C2 repressor genes is activated and may negatively regulate anthocyanin biosynthesis in Yan73 vegetative tissues. These findings enhance our understanding of anthocyanin biosynthesis in grapevine.
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Affiliation(s)
- Sha Xie
- College of Enology, Northwest A&F University, Xianyang, China
| | - Yujuan Lei
- College of Food Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China
| | - Huawei Chen
- College of Enology, Northwest A&F University, Xianyang, China
| | - Junnan Li
- College of Enology, Northwest A&F University, Xianyang, China
| | - Huangzhao Chen
- College of Enology, Northwest A&F University, Xianyang, China
- College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Zhenwen Zhang
- College of Enology, Northwest A&F University, Xianyang, China
- Shaanxi Engineering Research Center for Viti-Viniculture, Xianyang, China
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24
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Breia R, Conde A, Pimentel D, Conde C, Fortes AM, Granell A, Gerós H. VvSWEET7 Is a Mono- and Disaccharide Transporter Up-Regulated in Response to Botrytis cinerea Infection in Grape Berries. FRONTIERS IN PLANT SCIENCE 2020; 10:1753. [PMID: 32047506 PMCID: PMC6996298 DOI: 10.3389/fpls.2019.01753] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 12/13/2019] [Indexed: 05/24/2023]
Abstract
The newly-identified SWEETs are high-capacity, low-affinity sugar transporters with important roles in numerous physiological mechanisms where sugar efflux is critical. SWEETs are desirable targets for manipulation by pathogens and their expression may be transcriptionally reprogrammed during infection. So far, few plant SWEET transporters have been functionally characterized, especially in grapevine. In this study, in the Botrytis-susceptible variety "Trincadeira," we thoroughly analyzed modifications in the gene expression profile of key SWEET genes in Botrytis cinerea-infected grape berries. VvSWEET7 and VvSWEET15 are likely to play an important role during fruit development and Botrytis infection as they are strongly expressed at the green and mature stage, respectively, and were clearly up-regulated in response to infection. Also, B. cinerea infection down-regulated VvSWEET17a expression at the green stage, VvSWEET10 and VvSWEET17d expression at the veraison stage, and VvSWEET11 expression at the mature stage. VvSWEET7 was functionally characterized by heterologous expression in Saccharomyces cerevisiae as a low-affinity, high-capacity glucose and sucrose transporter with a K m of 15.42 mM for glucose and a K m of 40.08 mM for sucrose. VvSWEET7-GFP and VvSWEET15-GFP fusion proteins were transiently expressed in Nicotiana benthamiana epidermal cells and confocal microscopy allowed to observe that both proteins clearly localize to the plasma membrane. In sum, VvSWEETs transporters are important players in sugar mobilization during grape berry development and their expression is transcriptionally reprogrammed in response to Botrytis infection.
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Affiliation(s)
- Richard Breia
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Artur Conde
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Diana Pimentel
- University of Lisbon, Lisbon Science Faculty, BioISI, Campo Grande, Lisbon, Portugal
| | - Carlos Conde
- i3S-Institute of Research and Innovation in Health, University of Porto, Porto, Portugal
- IBMC-Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
| | - Ana Margarida Fortes
- University of Lisbon, Lisbon Science Faculty, BioISI, Campo Grande, Lisbon, Portugal
| | - Antonio Granell
- Institute of Molecular and Cellular Biology of Plants, Spanish National Research Council (CSIC), Polytechnic University of Valencia, Valencia, Spain
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
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25
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Lopez-Delacalle M, Camejo DM, García-Martí M, Nortes PA, Nieves-Cordones M, Martínez V, Rubio F, Mittler R, Rivero RM. Using Tomato Recombinant Lines to Improve Plant Tolerance to Stress Combination Through a More Efficient Nitrogen Metabolism. FRONTIERS IN PLANT SCIENCE 2020; 10:1702. [PMID: 32038679 PMCID: PMC6983915 DOI: 10.3389/fpls.2019.01702] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/03/2019] [Indexed: 05/18/2023]
Abstract
The development of plant varieties with a better nitrogen use efficiency (NUE) is a means for modern agriculture to decrease environmental pollution due to an excess of nitrate and to maintain a sufficient net income. However, the optimum environmental conditions for agriculture will tend to be more adverse in the coming years, with increases in temperatures, water scarcity, and salinity being the most important productivity constrains for plants. NUE is inherently a complex trait, as each step, including N uptake, translocation, assimilation, and remobilization, is governed by multiple interacting genetic and environmental factors. In this study, two recombinant inbred lines (RIL-66 and RIL-76) from a cross between Solanum lycopersicum and Solanum pimpinellifoilum with different degree of tolerance to the combination of salinity and heat were subjected to a physiological, ionomic, amino acid profile, and gene expression study to better understand how nitrogen metabolism is affected in tolerant plants as compared to sensitive ones. The ionomics results showed a different profile between the two RILs, with K+ and Mg2+ being significantly lower in RIL-66 (low tolerant) as compared to RIL-76 (high tolerant) under salinity and heat combination. No differences were shown between the two RILs in N total content; however, N-NO3 - was significantly higher in RIL-66, whereas N-Norg was lower as compared to the other genotype, which could be correlated with its tolerance to the combination of salinity and heat. Total proteins and total amino acid concentration were significantly higher in RIL-76 as compared to the sensitive recombinant line under these conditions. Glutamate, but more importantly glutamine, was also highly synthesized and accumulated in RIL-76 under the combination of salinity and heat, which was in agreement with the upregulation of the nitrogen metabolism related transcripts studied (SlNR, SlNiR, SlGDH, SlGLT1, SlNRT1.2, SlAMT1, and SlAMT2). This study emphasized the importance of studying abiotic stress in combination and how recombinant material with different degrees of tolerance can be highly important for the improvement of nitrogen use efficiency in horticultural plants through the targeting of N-related markers.
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Affiliation(s)
| | | | | | | | | | | | | | - Ron Mittler
- The Division of Plant Sciences, College of Agriculture, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
- University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Rosa M. Rivero
- Department of Plant Nutrition, CEBAS-CSIC, Murcia, Spain
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26
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Lin J, Massonnet M, Cantu D. The genetic basis of grape and wine aroma. HORTICULTURE RESEARCH 2019; 6:81. [PMID: 31645942 PMCID: PMC6804543 DOI: 10.1038/s41438-019-0163-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/12/2019] [Accepted: 05/14/2019] [Indexed: 05/23/2023]
Abstract
The grape is one of the oldest and most important horticultural crops. Grape and wine aroma has long been of cultural and scientific interest. The diverse compound classes comprising aroma result from multiple biosynthetic pathways. Only fairly recently have researchers begun to elucidate the genetic mechanisms behind the biosynthesis and metabolism of grape volatile compounds. This review summarizes current findings regarding the genetic bases of grape and wine aroma with an aim towards highlighting areas in need of further study. From the literature, we compiled a list of functionally characterized genes involved in berry aroma biosynthesis and present them with their corresponding annotation in the grape reference genome.
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Affiliation(s)
- Jerry Lin
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, One Shields Ave, Davis, CA 95616 USA
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27
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Minio A, Massonnet M, Figueroa-Balderas R, Vondras AM, Blanco-Ulate B, Cantu D. Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development. G3 (BETHESDA, MD.) 2019; 9:755-767. [PMID: 30642874 PMCID: PMC6404599 DOI: 10.1534/g3.118.201008] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/09/2019] [Indexed: 01/13/2023]
Abstract
Transcriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in grape are performed using the available genome sequence, PN40024, as reference. However, differences in gene content among grape accessions, which contribute to phenotypic differences among cultivars, suggest that a single reference genome does not represent the species' entire gene space. Though whole genome assembly and annotation can reveal the relatively unique or "private" gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (SMRT) to sequence full-length cDNA (Iso-Seq) and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, short reads from ripening berries were used to error-correct low-expression isoforms and to profile isoform expression. By comparing the annotated gene space of Cabernet Sauvignon to other grape cultivars, we demonstrate that the transcriptome reference built with Iso-Seq data represents most of the expressed genes in the grape berries and includes 1,501 cultivar-specific genes. Iso-Seq produced transcriptome profiles similar to those obtained after mapping on a complete genome reference. Together, these results justify the application of Iso-Seq to identify cultivar-specific genes and build a comprehensive reference for transcriptional profiling that circumvents the necessity of a genome reference with its associated costs and computational weight.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | | | - Amanda M Vondras
- Department of Viticulture and Enology, University of California Davis, Davis, CA
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA
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28
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Hily JM, Candresse T, Garcia S, Vigne E, Tannière M, Komar V, Barnabé G, Alliaume A, Gilg S, Hommay G, Beuve M, Marais A, Lemaire O. High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member. Front Microbiol 2018; 9:1782. [PMID: 30210456 PMCID: PMC6123372 DOI: 10.3389/fmicb.2018.01782] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/16/2018] [Indexed: 12/20/2022] Open
Abstract
In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more "reductionist" view focusing on one or a few known agents, HTS-based approaches are able to give a "holistic snapshot" of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.
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Affiliation(s)
- Jean-Michel Hily
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, Bordeaux, France
| | - Shahinez Garcia
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Emmanuelle Vigne
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Mélanie Tannière
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Véronique Komar
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Guillaume Barnabé
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Antoine Alliaume
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Sophie Gilg
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Gérard Hommay
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Monique Beuve
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, Villenave d'Ornon, Bordeaux, France
| | - Olivier Lemaire
- UMR 1131 Santé de la Vigne et Qualité du Vin, INRA-Université de Strasbourg, Colmar, France
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Karasinski J, Elguera JCT, Ibarra AAG, Wrobel K, Bulska E, Wrobel K. Comparative Evaluation of Red Wine from Various European Regions Using Mass Spectrometry Tools. ANAL LETT 2018. [DOI: 10.1080/00032719.2018.1442472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Jakub Karasinski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | | | | | - Kazimierz Wrobel
- Department of Chemistry, University of Guanajuato, Guanajuato, Mexico
| | - Ewa Bulska
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Katarzyna Wrobel
- Department of Chemistry, University of Guanajuato, Guanajuato, Mexico
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Wong DCJ, Ariani P, Castellarin S, Polverari A, Vandelle E. Co-expression network analysis and cis-regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases. Sci Rep 2018; 8:3151. [PMID: 29453355 PMCID: PMC5816651 DOI: 10.1038/s41598-018-21377-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 02/02/2018] [Indexed: 02/06/2023] Open
Abstract
Arabidopsis thaliana Toxicos en Levadura (ATL) proteins are a subclass of the RING-H2 zinc finger binding E3 ubiquitin ligases. The grapevine (Vitis vinifera) ATL family was recently characterized, revealing 96 members that are likely to be involved in several physiological processes through protein ubiquitination. However, the final targets and biological functions of most ATL E3 ligases are still unknown. We analyzed the co-expression networks among grapevine ATL genes across a set of transcriptomic data related to defense and abiotic stress, combined with a condition-independent dataset. This revealed strong correlations between ATL proteins and diverse signal transduction components and transcriptional regulators, in particular those involved in immunity. An enrichment analysis of cis-regulatory elements in ATL gene promoters and related co-expressed genes highlighted the importance of hormones in the regulation of ATL gene expression. Our work identified several ATL proteins as candidates for further studies aiming to decipher specific grapevine resistance mechanisms activated in response to pathogens.
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Affiliation(s)
- Darren C J Wong
- Wine Research Centre, University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Pietro Ariani
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, 37134, Italy
| | - Simone Castellarin
- Wine Research Centre, University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Annalisa Polverari
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, 37134, Italy.
| | - Elodie Vandelle
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, 37134, Italy.
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Morales‐Cruz A, Allenbeck G, Figueroa‐Balderas R, Ashworth VE, Lawrence DP, Travadon R, Smith RJ, Baumgartner K, Rolshausen PE, Cantu D. Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk disease complex. MOLECULAR PLANT PATHOLOGY 2018; 19:490-503. [PMID: 28218463 PMCID: PMC6638111 DOI: 10.1111/mpp.12544] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/13/2017] [Indexed: 05/20/2023]
Abstract
Grapevines, like other perennial crops, are affected by so-called 'trunk diseases', which damage the trunk and other woody tissues. Mature grapevines typically contract more than one trunk disease and often multiple grapevine trunk pathogens (GTPs) are recovered from infected tissues. The co-existence of different GTP species in complex and dynamic microbial communities complicates the study of the molecular mechanisms underlying disease development, especially under vineyard conditions. The objective of this study was to develop and optimize a community-level transcriptomics (i.e. metatranscriptomics) approach that could monitor simultaneously the virulence activities of multiple GTPs in planta. The availability of annotated genomes for the most relevant co-infecting GTPs in diseased grapevine wood provided the unprecedented opportunity to generate a multi-species reference for the mapping and quantification of DNA and RNA sequencing reads. We first evaluated popular sequence read mappers using permutations of multiple simulated datasets. Alignment parameters of the selected mapper were optimized to increase the specificity and sensitivity for its application to metagenomics and metatranscriptomics analyses. Initial testing on grapevine wood experimentally inoculated with individual GTPs confirmed the validity of the method. Using naturally infected field samples expressing a variety of trunk disease symptoms, we show that our approach provides quantitative assessments of species composition, as well as genome-wide transcriptional profiling of potential virulence factors, namely cell wall degradation, secondary metabolism and nutrient uptake for all co-infecting GTPs.
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Affiliation(s)
- Abraham Morales‐Cruz
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | - Gabrielle Allenbeck
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | | | - Vanessa E. Ashworth
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCA92521USA
| | - Daniel P. Lawrence
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Renaud Travadon
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Rhonda J. Smith
- University of California Cooperative Extension, Sonoma CountySanta RosaCA95403USA
| | - Kendra Baumgartner
- United States Department of Agriculture ‐ Agricultural Research ServiceCrops Pathology and Genetics Research UnitDavisCA95616USA
| | - Philippe E. Rolshausen
- Department of Botany and Plant SciencesUniversity of California RiversideRiversideCA92521USA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
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Massonnet M, Morales‐Cruz A, Figueroa‐Balderas R, Lawrence DP, Baumgartner K, Cantu D. Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum. MOLECULAR PLANT PATHOLOGY 2018; 19:21-34. [PMID: 27608421 PMCID: PMC6637977 DOI: 10.1111/mpp.12491] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 05/24/2023]
Abstract
The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability to colonize woody tissue, combined with the secretion of phytotoxic compounds, is thought to underlie its pathogenicity and virulence. Here, we describe the repertoire of virulence factors and their transcriptional dynamics as the fungus feeds on different substrates and colonizes the woody stem. We assembled and annotated a highly contiguous genome using single-molecule real-time DNA sequencing. Transcriptome profiling by RNA sequencing determined the genome-wide patterns of expression of virulence factors both in vitro (potato dextrose agar or medium amended with grape wood as substrate) and in planta. Pairwise statistical testing of differential expression, followed by co-expression network analysis, revealed that physically clustered genes coding for putative virulence functions were induced depending on the substrate or stage of plant infection. Co-expressed gene clusters were significantly enriched not only in genes associated with secondary metabolism, but also in those associated with cell wall degradation, suggesting that dynamic co-regulation of transcriptional networks contributes to multiple aspects of N. parvum virulence. In most of the co-expressed clusters, all genes shared at least a common motif in their promoter region, indicative of co-regulation by the same transcription factor. Co-expression analysis also identified chromatin regulators with correlated expression with inducible clusters of virulence factors, suggesting a complex, multi-layered regulation of the virulence repertoire of N. parvum.
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Affiliation(s)
- Mélanie Massonnet
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | - Abraham Morales‐Cruz
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
| | | | - Daniel P. Lawrence
- Department of Plant PathologyUniversity of California DavisDavisCA95616USA
| | - Kendra Baumgartner
- US Department of Agriculture ‐ Agricultural Research ServiceCrops Pathology and Genetics Research UnitDavisCA95616USA
| | - Dario Cantu
- Department of Viticulture and EnologyUniversity of California DavisDavisCA95616USA
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Harris ZN, Kovacs LG, Londo JP. RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar 'Riesling'. BMC Genomics 2017; 18:937. [PMID: 29197332 PMCID: PMC5712117 DOI: 10.1186/s12864-017-4346-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work is an attempt to utilize a de novo-assembled transcriptome of the V. vinifera cultivar 'Riesling' to improve annotation of the grapevine reference genome sequence. RESULTS Here we show that the transcriptome assembly of a single V. vinifera cultivar is insufficient for a complete genome annotation of the grapevine reference genome constructed from V. vinifera PN40024. Further, we provide evidence that the gene models we identified cannot be completely anchored to the previously published V. vinifera PN40024 gene models. In addition to these findings, we present a computational pipeline for the de novo identification of lncRNAs. Our results demonstrate that, in grapevine, lncRNAs are significantly different from protein coding transcripts in such metrics as length, GC-content, minimum free energy, and length-corrected minimum free energy. CONCLUSIONS In grapevine, high-level heterozygosity necessitates that transcriptome characterization be based on cultivar-specific reference genome sequences. Our results strengthen the hypothesis that lncRNAs have thermodynamically different properties than protein-coding RNAs. The analyses of both coding and non-coding RNAs will be instrumental in uncovering inter-cultivar variation in wild and cultivated grapevine species.
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Affiliation(s)
- Zachary N. Harris
- Missouri State University, Biology Department, 901 S. National Ave, Springfield, MO USA
- Present address: Saint Louis University, Department of Biology, 1 N. Grand Blvd, Saint Louis, MO USA
| | - Laszlo G. Kovacs
- Missouri State University, Biology Department, 901 S. National Ave, Springfield, MO USA
| | - Jason P. Londo
- United States Department of Agriculture, Agricultural Research Service, Grape Genetics Research Unit, 630 W. North Street, Geneva, NY USA
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Abstract
Ozone, a powerful oxidative stressor, has been recently used in wine industry as sanitizing agent to reduce spoilage microflora on grapes. In this study, we evaluated ozone-induced metabolic and molecular responses during postharvest grape dehydration. Ozone increased the contents of total volatile organic compounds (VOCs), which have a great impact on the organoleptic properties of grapes and wines. Among terpenes, responsible for floral and fruity aroma, linalool, geraniol and nerol were the major aromatic markers of Moscato bianco grapes. They were significantly affected by the long-term ozone treatment, increasing their concentration in the last phases of dehydration (>20% weight loss). At molecular level, our results demonstrated that both postharvest dehydration and ozone exposure induce the biosynthesis of monoterpenes via methylerythritol phosphate (MEP) pathway and of aldehydes from lipoxygenase-hydroperoxide lyase (LOX-HPL) pathway. Therefore, transcriptional changes occurred and promoted the over-production of many important volatile compounds for the quality of white grapes.
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Zhou Y, Massonnet M, Sanjak JS, Cantu D, Gaut BS. Evolutionary genomics of grape ( Vitis vinifera ssp. vinifera) domestication. Proc Natl Acad Sci U S A 2017; 114:11715-11720. [PMID: 29042518 PMCID: PMC5676911 DOI: 10.1073/pnas.1709257114] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We gathered genomic data from grapes (Vitis vinifera ssp. vinifera), a clonally propagated perennial crop, to address three ongoing mysteries about plant domestication. The first is the duration of domestication; archaeological evidence suggests that domestication occurs over millennia, but genetic evidence indicates that it can occur rapidly. We estimated that our wild and cultivated grape samples diverged ∼22,000 years ago and that the cultivated lineage experienced a steady decline in population size (Ne ) thereafter. The long decline may reflect low-intensity management by humans before domestication. The second mystery is the identification of genes that contribute to domestication phenotypes. In cultivated grapes, we identified candidate-selected genes that function in sugar metabolism, flower development, and stress responses. In contrast, candidate-selected genes in the wild sample were limited to abiotic and biotic stress responses. A genomic region of high divergence corresponded to the sex determination region and included a candidate male sterility factor and additional genes with sex-specific expression. The third mystery concerns the cost of domestication. Annual crops accumulate putatively deleterious variants, in part due to strong domestication bottlenecks. The domestication of perennial crops differs from that of annuals in several ways, including the intensity of bottlenecks, and it is not yet clear if they accumulate deleterious variants. We found that grape accessions contained 5.2% more deleterious variants than wild individuals, and these were more often in a heterozygous state. Using forward simulations, we confirm that clonal propagation leads to the accumulation of recessive deleterious mutations but without decreasing fitness.
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Affiliation(s)
- Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California, Davis, CA 95616
| | - Jaleal S Sanjak
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, CA 95616
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697;
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Hu D, Fan Y, Tan Y, Tian Y, Liu N, Wang L, Zhao D, Wang C, Wu A. Metabolic Profiling on Alternaria Toxins and Components of Xinjiang Jujubes Incubated with Pathogenic Alternaria alternata and Alternaria tenuissima via Orbitrap High-Resolution Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:8466-8474. [PMID: 28882039 DOI: 10.1021/acs.jafc.7b03243] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Xinjiang jujubes (Zizyphus rhamnaceae) are important agro-economical foods with the highest planting area and yields in China; however, black spot disease and contaminated Alternaria toxins have unfortunately caused a decline or loss of jujube nutritional quality in recent years. In this study, we used ultrahigh-performance liquid chromatography coupled to Orbitrap high-resolution mass spectrometry to profile both Alternaria toxins and components in three representative Xinjiang jujubes, Hami Huang, Hetian Jun, and Ruoqiang Hui. Before liquid chromatography-mass spectrometry analysis, jujubes were inoculated with two main pathogens of Alternaria alternata (Aa) and Alternaria tenuissima (At). Different combinations of jujube varieties with pathogenic isolates display different metabolic profiles, as expected. Moreover, four major Alternaria toxins, alternariol, alternariol monomethyl ether, altenuene, and tenuazonic acid, were detected in all samples. The inoculation of both pathogens significantly decreased the levels of nutrients and metabolites in jujube, including four saponins, three organic acids, and three alkaloids, whereas it increased the level of several glycerol phosphates. The flavonoid profiles are diverse. Lastly, inoculation of Aa changes more metabolites in jujubes than At. Our data provide insights to better understand the detrimental contamination of Alternaria pathogens in Xinjiang jujubes and improve food safety of jujubes.
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Affiliation(s)
- Dongqiang Hu
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, Key Laboratory of Food Safety Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai 200031, People's Republic of China
| | - Yingying Fan
- Institute of Quality Standards and Testing Technology for Agro-Products, Key Laboratory of Agro-Products Quality and Safety of Xinjiang, Laboratory of Quality and Safety Risk Assessment for Agro-Products (Urumqi), Ministry of Agriculture, Xinjiang Academy of Agricultural Sciences , Urumqi, Xinjiang 830091, People's Republic of China
| | - Yanglan Tan
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, Key Laboratory of Food Safety Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai 200031, People's Republic of China
| | - Ye Tian
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, Key Laboratory of Food Safety Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai 200031, People's Republic of China
| | - Na Liu
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, Key Laboratory of Food Safety Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai 200031, People's Republic of China
| | - Lan Wang
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, Key Laboratory of Food Safety Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai 200031, People's Republic of China
| | - Duoyong Zhao
- Institute of Quality Standards and Testing Technology for Agro-Products, Key Laboratory of Agro-Products Quality and Safety of Xinjiang, Laboratory of Quality and Safety Risk Assessment for Agro-Products (Urumqi), Ministry of Agriculture, Xinjiang Academy of Agricultural Sciences , Urumqi, Xinjiang 830091, People's Republic of China
| | - Cheng Wang
- Institute of Quality Standards and Testing Technology for Agro-Products, Key Laboratory of Agro-Products Quality and Safety of Xinjiang, Laboratory of Quality and Safety Risk Assessment for Agro-Products (Urumqi), Ministry of Agriculture, Xinjiang Academy of Agricultural Sciences , Urumqi, Xinjiang 830091, People's Republic of China
| | - Aibo Wu
- SIBS-UGENT-SJTU Joint Laboratory of Mycotoxin Research, Key Laboratory of Food Safety Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai 200031, People's Republic of China
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Massonnet M, Figueroa-Balderas R, Galarneau ERA, Miki S, Lawrence DP, Sun Q, Wallis CM, Baumgartner K, Cantu D. Neofusicoccum parvum Colonization of the Grapevine Woody Stem Triggers Asynchronous Host Responses at the Site of Infection and in the Leaves. FRONTIERS IN PLANT SCIENCE 2017; 8:1117. [PMID: 28702038 PMCID: PMC5487829 DOI: 10.3389/fpls.2017.01117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/09/2017] [Indexed: 05/09/2023]
Abstract
Grapevine trunk diseases cause important economic losses in vineyards worldwide. Neofusicoccum parvum, one of the most aggressive causal agents of the trunk disease Botryosphaeria dieback, colonizes cells and tissues of the grapevine wood, leading to the formation of an internal canker. Symptoms then extend to distal shoots, with wilting of leaves and bud mortality. Our aim was to characterize the transcriptional dynamics of grapevine genes in the woody stem and in the leaves during Neofusicoccum parvum colonization. Genome-wide transcriptional profiling at seven distinct time points (0, 3, and 24 hours; 2, 6, 8, and 12 weeks) showed that both stems and leaves undergo extensive transcriptomic reprogramming in response to infection of the stem. While most intense transcriptional responses were detected in the stems at 24 hours, strong responses were not detected in the leaves until the next sampling point at 2 weeks post-inoculation. Network co-expression analysis identified modules of co-expressed genes common to both organs and showed most of these genes were asynchronously modulated. The temporal shift between stem vs. leaf responses affected transcriptional modulation of genes involved in both signal perception and transduction, as well as downstream biological processes, including oxidative stress, cell wall rearrangement and cell death. Promoter analysis of the genes asynchronously modulated in stem and leaves during N. parvum colonization suggests that the temporal shift of transcriptional reprogramming between the two organs might be due to asynchronous co-regulation by common transcriptional regulators. Topology analysis of stem and leaf co-expression networks pointed to specific transcription factor-encoding genes, including WRKY and MYB, which may be associated with the observed transcriptional responses in the two organs.
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Affiliation(s)
- Mélanie Massonnet
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
| | - Erin R. A. Galarneau
- Department of Plant Pathology, University of California, DavisDavis, CA, United States
| | - Shiho Miki
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
- Department of Agriculture and Forest Science, Faculty of Life and Environmental Science, Shimane UniversityMatsue, Japan
| | - Daniel P. Lawrence
- Department of Plant Pathology, University of California, DavisDavis, CA, United States
| | - Qiang Sun
- Department of Biology, University of WisconsinStevens Point, WI, United States
| | - Christopher M. Wallis
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences CenterParlier, CA, United States
| | - Kendra Baumgartner
- United States Department of Agriculture-Agricultural Research Service, Crops Pathology and Genetics Research UnitDavis, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
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Negri S, Lovato A, Boscaini F, Salvetti E, Torriani S, Commisso M, Danzi R, Ugliano M, Polverari A, Tornielli GB, Guzzo F. The Induction of Noble Rot ( Botrytis cinerea) Infection during Postharvest Withering Changes the Metabolome of Grapevine Berries ( Vitis vinifera L., cv. Garganega). FRONTIERS IN PLANT SCIENCE 2017; 8:1002. [PMID: 28680428 PMCID: PMC5478704 DOI: 10.3389/fpls.2017.01002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/26/2017] [Indexed: 05/27/2023]
Abstract
The natural or induced development of noble rot caused by the fungus Botrytis cinerea during the late stages of grapevine (Vitis vinifera L.) berry ripening is used in some traditional viticulture areas to produce high-quality wines such as Sauternes and Tokaji. In this research, we wanted to verify if by changing the environmental conditions during post-harvest withering we could induce the noble rot development on harvested berries in order to positively change the wine produced from withered Garganega berries. Therefore, we exposed the berries to postharvest withering under normal or artificially humid conditions, the latter to induce noble rot. The presence of noble rot symptoms was associated with the development of B. cinerea in the berries maintained under humid conditions. The composition of infected and non-infected berries was investigated by untargeted metabolomics using liquid chromatography/mass spectrometry. We also explored the effects of the two withering methods on the abundance of volatile organic compounds in wine by yeast-inoculated micro-fermentation followed by targeted gas chromatography/mass spectrometry. These experiments revealed significant metabolic differences between berries withered under normal and humid conditions, indicating that noble rot affects berry metabolism and composition. As well as well-known botrytization markers, we detected two novel lipids that have not been observed before in berries infected with noble rot. Unraveling the specific metabolic profile of berries infected with noble rot may help to determine the compounds responsible for the organoleptic quality traits of botrytized Garganega wines.
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Affiliation(s)
- Stefano Negri
- Biotechnology Department, University of VeronaVerona, Italy
| | - Arianna Lovato
- Biotechnology Department, University of VeronaVerona, Italy
| | | | - Elisa Salvetti
- Biotechnology Department, University of VeronaVerona, Italy
| | | | - Mauro Commisso
- Biotechnology Department, University of VeronaVerona, Italy
| | | | | | | | | | - Flavia Guzzo
- Biotechnology Department, University of VeronaVerona, Italy
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Costantini L, Kappel CD, Trenti M, Battilana J, Emanuelli F, Sordo M, Moretto M, Camps C, Larcher R, Delrot S, Grando MS. Drawing Links from Transcriptome to Metabolites: The Evolution of Aroma in the Ripening Berry of Moscato Bianco ( Vitis vinifera L.). FRONTIERS IN PLANT SCIENCE 2017; 8:780. [PMID: 28559906 PMCID: PMC5432621 DOI: 10.3389/fpls.2017.00780] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/25/2017] [Indexed: 05/29/2023]
Abstract
Monoterpenes confer typical floral notes to "Muscat" grapevine varieties and, to a lesser extent, to other aromatic non-Muscat varieties. Previous studies have led to the identification and functional characterization of some enzymes and genes in this pathway. However, the underlying genetic map is still far from being complete. For example, the specific steps of monoterpene metabolism and its regulation are largely unknown. With the aim of identifying new candidates for the missing links, we applied an integrative functional genomics approach based on the targeted metabolic and genome-wide transcript profiling of Moscato Bianco ripening berries. In particular, gas chromatography-mass spectrometry analysis of free and bound terpenoid compounds was combined with microarray analysis in the skins of berries collected at five developmental stages from pre-veraison to over-ripening. Differentially expressed metabolites and probes were identified in the pairwise comparison between time points by using the early stage as a reference. Metabolic and transcriptomic data were integrated through pairwise correlation and clustering approaches to discover genes linked with particular metabolites or groups of metabolites. These candidate transcripts were further checked for co-localization with quantitative trait loci (QTLs) affecting aromatic compounds. Our findings provide insights into the biological networks of grapevine secondary metabolism, both at the catalytic and regulatory levels. Examples include a nudix hydrolase as component of a terpene synthase-independent pathway for monoterpene biosynthesis, genes potentially involved in monoterpene metabolism (cytochrome P450 hydroxylases, epoxide hydrolases, glucosyltransferases), transport (vesicle-associated proteins, ABCG transporters, glutathione S-transferases, amino acid permeases), and transcriptional control (transcription factors of the ERF, MYB and NAC families, intermediates in light- and circadian cycle-mediated regulation with supporting evidence from the literature and additional regulatory genes with a previously unreported association to monoterpene accumulation).
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Affiliation(s)
- Laura Costantini
- Grapevine Genetics and Breeding Unit, Genomics and Biology of Fruit Crop Department, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Christian D. Kappel
- UMR Ecophysiology and Grape Functional Genomics, Institut des Sciences de la Vigne et du Vin, University of BordeauxVillenave d'Ornon, France
| | - Massimiliano Trenti
- Grapevine Genetics and Breeding Unit, Genomics and Biology of Fruit Crop Department, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Juri Battilana
- Grapevine Genetics and Breeding Unit, Genomics and Biology of Fruit Crop Department, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Francesco Emanuelli
- Grapevine Genetics and Breeding Unit, Genomics and Biology of Fruit Crop Department, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Maddalena Sordo
- Grapevine Genetics and Breeding Unit, Genomics and Biology of Fruit Crop Department, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Marco Moretto
- Computational Biology Platform, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Céline Camps
- UMR Ecophysiology and Grape Functional Genomics, Institut des Sciences de la Vigne et du Vin, University of BordeauxVillenave d'Ornon, France
| | - Roberto Larcher
- Experiment and Technological Services Department, Technology Transfer Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Serge Delrot
- UMR Ecophysiology and Grape Functional Genomics, Institut des Sciences de la Vigne et du Vin, University of BordeauxVillenave d'Ornon, France
| | - Maria S. Grando
- Grapevine Genetics and Breeding Unit, Genomics and Biology of Fruit Crop Department, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
- Center Agriculture Food Environment, University of TrentoSan Michele all'Adige, Italy
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Blanco-Ulate B, Hopfer H, Figueroa-Balderas R, Ye Z, Rivero RM, Albacete A, Pérez-Alfocea F, Koyama R, Anderson MM, Smith RJ, Ebeler SE, Cantu D. Red blotch disease alters grape berry development and metabolism by interfering with the transcriptional and hormonal regulation of ripening. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1225-1238. [PMID: 28338755 PMCID: PMC5444480 DOI: 10.1093/jxb/erw506] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Grapevine red blotch-associated virus (GRBaV) is a major threat to the wine industry in the USA. GRBaV infections (aka red blotch disease) compromise crop yield and berry chemical composition, affecting the flavor and aroma properties of must and wine. In this study, we combined genome-wide transcriptional profiling with targeted metabolite analyses and biochemical assays to characterize the impact of the disease on red-skinned berry ripening and metabolism. Using naturally infected berries collected from two vineyards, we were able to identify consistent berry responses to GRBaV across different environmental and cultural conditions. Specific alterations of both primary and secondary metabolism occurred in GRBaV-infected berries during ripening. Notably, GRBaV infections of post-véraison berries resulted in the induction of primary metabolic pathways normally associated with early berry development (e.g. thylakoid electron transfer and the Calvin cycle), while inhibiting ripening-associated pathways, such as a reduced metabolic flux in the central and peripheral phenylpropanoid pathways. We show that this metabolic reprogramming correlates with perturbations at multiple regulatory levels of berry development. Red blotch caused the abnormal expression of transcription factors (e.g. NACs, MYBs, and AP2-ERFs) and elements of the post-transcriptional machinery that function during red-skinned berry ripening. Abscisic acid, ethylene, and auxin pathways, which control both the initiation of ripening and stress responses, were also compromised. We conclude that GRBaV infections disrupt normal berry development and stress responses by altering transcription factors and hormone networks, which result in the inhibition of ripening pathways involved in the generation of color, flavor, and aroma compounds.
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Affiliation(s)
- Barbara Blanco-Ulate
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | - Helene Hopfer
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Zirou Ye
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Rosa M Rivero
- CEBAS-CSIC, Campus de Espinardo, 30100, Murcia, Spain
| | | | | | - Renata Koyama
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
- Department of Agronomy, Londrina State University, Celso Garcia Cid Road, Londrina, PR, 86057-970, Brazil
| | - Michael M Anderson
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Rhonda J Smith
- University of California Cooperative Extension, Sonoma County, Santa Rosa, CA 95403, USA
| | - Susan E Ebeler
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
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Serrano A, Espinoza C, Armijo G, Inostroza-Blancheteau C, Poblete E, Meyer-Regueiro C, Arce A, Parada F, Santibáñez C, Arce-Johnson P. Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Responses. FRONTIERS IN PLANT SCIENCE 2017; 8:1486. [PMID: 28936215 PMCID: PMC5594091 DOI: 10.3389/fpls.2017.01486] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/10/2017] [Indexed: 05/21/2023]
Abstract
Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I), lag (II), and ripening (III), in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process. In this review, we focus on the integration of global approaches, including proteomics, metabolomics, and especially transcriptomics, to understand grape berry development. Several aspects will be considered, including seed development and the production of seedless fruits; veraison, at which anthocyanin accumulation begins in the berry skin of colored varieties; and hormonal regulation of berry development and signaling throughout ripening, focusing on the transcriptional regulation of hormone receptors, protein kinases, and genes related to secondary messenger sensing. Finally, berry responses to different environmental factors, including abiotic (temperature, water-related stress and UV-B radiation) and biotic (fungi and viruses) stresses, and how they can significantly modify both, development and composition of vine fruit, will be discussed. Until now, advances have been made due to the application of Omics tools at different molecular levels. However, the potential of these technologies should not be limited to the study of single-level questions; instead, data obtained by these platforms should be integrated to unravel the molecular aspects of grapevine development. Therefore, the current challenge is the generation of new tools that integrate large-scale data to assess new questions in this field, and to support agronomical practices.
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Affiliation(s)
- Alejandra Serrano
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Carmen Espinoza
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Grace Armijo
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Claudio Inostroza-Blancheteau
- Núcleo de Investigación en Producción Alimentaría, Facultad de Recursos Naturales, Escuela de Agronomía, Universidad Católica de TemucoTemuco, Chile
| | - Evelyn Poblete
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Carlos Meyer-Regueiro
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Anibal Arce
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Francisca Parada
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Claudia Santibáñez
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
- Ecophysiology and Functional Genomic of Grapevine, Institut des Sciences de la Vigne et du Vin, Institut National de la Recherche Agronomique, Université de BordeauxBordeaux, France
| | - Patricio Arce-Johnson
- Laboratorio de Biología Molecular y Biotecnología Vegetal, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de ChileSantiago, Chile
- *Correspondence: Patricio Arce-Johnson,
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Ariani P, Regaiolo A, Lovato A, Giorgetti A, Porceddu A, Camiolo S, Wong D, Castellarin S, Vandelle E, Polverari A. Genome-wide characterisation and expression profile of the grapevine ATL ubiquitin ligase family reveal biotic and abiotic stress-responsive and development-related members. Sci Rep 2016; 6:38260. [PMID: 27910910 PMCID: PMC5133618 DOI: 10.1038/srep38260] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/08/2016] [Indexed: 01/09/2023] Open
Abstract
The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes. Most of the grapevine ATL genes lacked introns and were scattered among the 19 chromosomes, with a high level of duplication retention. Expression profiling revealed that some ATL genes are expressed specifically during early or late development and may participate in the juvenile to mature plant transition, whereas others may play a role in pathogen and/or abiotic stress responses, making them key candidates for further functional analysis. Our data offer the first genome-wide overview and annotation of the grapevine ATL family, and provide a basis for investigating the roles of specific family members in grapevine physiology and stress responses, as well as potential biotechnological applications.
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Affiliation(s)
- Pietro Ariani
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Alice Regaiolo
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Arianna Lovato
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Alejandro Giorgetti
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Andrea Porceddu
- Università degli Studi di Sassari, Dipartimento di Agraria, SACEG, Via Enrico De Nicola 1, Sassari, 07100, Italy
| | - Salvatore Camiolo
- Università degli Studi di Sassari, Dipartimento di Agraria, SACEG, Via Enrico De Nicola 1, Sassari, 07100, Italy
| | - Darren Wong
- Wine Research Centre, University of British Columbia, 326-2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Simone Castellarin
- Wine Research Centre, University of British Columbia, 326-2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Elodie Vandelle
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Annalisa Polverari
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
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Yang MZ, Ma MD, Yuan MQ, Huang ZY, Yang WX, Zhang HB, Huang LH, Ren AY, Shan H. Fungal Endophytes as a Metabolic Fine-Tuning Regulator for Wine Grape. PLoS One 2016; 11:e0163186. [PMID: 27656886 PMCID: PMC5033586 DOI: 10.1371/journal.pone.0163186] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/02/2016] [Indexed: 11/17/2022] Open
Abstract
Endophytes proved to exert multiple effects on host plants, including growth promotion, stress resistance. However, whether endophytes have a role in metabolites shaping of grape has not been fully understood. Eight endophytic fungal strains which originally isolated from grapevines were re-inoculated to field-grown grapevines in this study, and their effects on both leaves and berries of grapevines at maturity stage were assessed, with special focused on secondary metabolites and antioxidant activities. High-density inoculation of all these endophytic fungal strains modified the physio-chemical status of grapevine to different degrees. Fungal inoculations promoted the content of reducing sugar (RS), total flavonoids (TF), total phenols (TPh), trans-resveratrol (Res) and activities of phenylalanine ammonia-lyase (PAL), in both leaves and berries of grapevine. Inoculation of endophytic fungal strains, CXB-11 (Nigrospora sp.) and CXC-13 (Fusarium sp.) conferred greater promotion effects in grape metabolic re-shaping, compared to other used fungal strains. Additionally, inoculation of different strains of fungal endophytes led to establish different metabolites patterns of wine grape. The work implies the possibility of using endophytic fungi as fine-tuning regulator to shape the quality and character of wine grape.
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Affiliation(s)
- Ming-Zhi Yang
- School of Life Science, Yunnan University, Kunming, China
| | - Mian-Di Ma
- School of Life Science, Yunnan University, Kunming, China
| | - Ming-Quan Yuan
- School of Chemistry Science and Technology, Yunnan University, Kunming, China
| | - Zhi-Yu Huang
- School of Life Science, Yunnan University, Kunming, China
| | - Wei-Xi Yang
- College of Food and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Han-Bo Zhang
- School of Life Science, Yunnan University, Kunming, China
| | - Li-Hua Huang
- School of Life Science, Yunnan University, Kunming, China
| | - An-Yun Ren
- School of Life Science, Yunnan University, Kunming, China
| | - Hui Shan
- School of Life Science, Yunnan University, Kunming, China
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Salvetti E, Campanaro S, Campedelli I, Fracchetti F, Gobbi A, Tornielli GB, Torriani S, Felis GE. Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions. Front Microbiol 2016; 7:937. [PMID: 27445999 PMCID: PMC4917526 DOI: 10.3389/fmicb.2016.00937] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/31/2016] [Indexed: 12/20/2022] Open
Abstract
Vitis vinifera L. cv. Corvina grape forms the basis for the production of unique wines, such as Amarone, whose distinctive sensory features are strongly linked to the post-harvest grape withering process. Indeed, this process increases sugar concentration and changes must characteristics. While microorganisms involved in must fermentation have been widely investigated, few data are available on the microbiota of withered grapes. Thus, in this paper, a whole metagenome sequencing (WMS) approach was used to analyse the microbial consortium associated with Corvina berries at the end of the withering process performed in two different conditions ("traditional withering," TW or "accelerated withering," AW), and to unveil whether changes of drying parameters could have an impact on microbial diversity. Samples of healthy undamaged berries were collected and washed, to recover microorganisms from the surface and avoid contamination with grapevine genetic material. Isolated DNA was sequenced and the data obtained were analyzed with several bioinformatics methods. The eukaryotic community was mainly composed by members of the phylum Ascomycota, including Eurotiomycetes, Sordariomycetes, and Dothideomycetes. Moreover, the distribution of the genera Aspergillus and Penicillium (class Eurotiomycetes) varied between the withered berry samples. Instead, Botryotinia, Saccharomyces, and other wine technologically useful microorganisms were relatively scarce in both samples. For prokaryotes, 25 phyla were identified, nine of which were common to both conditions. Environmental bacteria belonging to the class Gammaproteobacteria were dominant and, in particular, the TW sample was characterized by members of the family Pseudomonadaceae, while members of the family Enterobacteriaceae dominated the AW sample, in addition to Sphyngobacteria and Clostridia. Finally, the binning procedure discovered 15 putative genomes which dominated the microbial community of the two samples, and included representatives of genera Erwinia, Pantoea, Pseudomonas, Clostridium, Paenibacillus, and of orders Lactobacillales and Actinomycetales. These results provide insights into the microbial consortium of Corvina withered berries and reveal relevant variations attributable to post-harvest withering conditions, underling how WMS could open novel perspectives in the knowledge and management of the withering process of Corvina, with an impact on the winemaking of important Italian wines.
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Affiliation(s)
- Elisa Salvetti
- Department of Biotechnology, University of VeronaVerona, Italy
| | | | | | | | - Alex Gobbi
- Department of Biotechnology, University of VeronaVerona, Italy
| | | | - Sandra Torriani
- Department of Biotechnology, University of VeronaVerona, Italy
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Savoi S, Wong DCJ, Arapitsas P, Miculan M, Bucchetti B, Peterlunger E, Fait A, Mattivi F, Castellarin SD. Transcriptome and metabolite profiling reveals that prolonged drought modulates the phenylpropanoid and terpenoid pathway in white grapes (Vitis vinifera L.). BMC PLANT BIOLOGY 2016; 16:67. [PMID: 27001212 PMCID: PMC4802899 DOI: 10.1186/s12870-016-0760-1] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/15/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Secondary metabolism contributes to the adaptation of a plant to its environment. In wine grapes, fruit secondary metabolism largely determines wine quality. Climate change is predicted to exacerbate drought events in several viticultural areas, potentially affecting the wine quality. In red grapes, water deficit modulates flavonoid accumulation, leading to major quantitative and compositional changes in the profile of the anthocyanin pigments; in white grapes, the effect of water deficit on secondary metabolism is still largely unknown. RESULTS In this study we investigated the impact of water deficit on the secondary metabolism of white grapes using a large scale metabolite and transcript profiling approach in a season characterized by prolonged drought. Irrigated grapevines were compared to non-irrigated grapevines that suffered from water deficit from early stages of berry development to harvest. A large effect of water deficit on fruit secondary metabolism was observed. Increased concentrations of phenylpropanoids, monoterpenes, and tocopherols were detected, while carotenoid and flavonoid accumulations were differentially modulated by water deficit according to the berry developmental stage. The RNA-sequencing analysis carried out on berries collected at three developmental stages-before, at the onset, and at late ripening-indicated that water deficit affected the expression of 4,889 genes. The Gene Ontology category secondary metabolic process was overrepresented within up-regulated genes at all the stages of fruit development considered, and within down-regulated genes before ripening. Eighteen phenylpropanoid, 16 flavonoid, 9 carotenoid, and 16 terpenoid structural genes were modulated by water deficit, indicating the transcriptional regulation of these metabolic pathways in fruit exposed to water deficit. An integrated network and promoter analyses identified a transcriptional regulatory module that encompasses terpenoid genes, transcription factors, and enriched drought-responsive elements in the promoter regions of those genes as part of the grapes response to drought. CONCLUSION Our study reveals that grapevine berries respond to drought by modulating several secondary metabolic pathways, and particularly, by stimulating the production of phenylpropanoids, the carotenoid zeaxanthin, and of volatile organic compounds such as monoterpenes, with potential effects on grape and wine antioxidant potential, composition, and sensory features.
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Affiliation(s)
- Stefania Savoi
- />Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Italy
- />Dipartimento di Scienze Agro-alimentari, Ambientali e Animali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy
| | - Darren C. J. Wong
- />Wine Research Centre, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4 Canada
| | - Panagiotis Arapitsas
- />Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Italy
| | - Mara Miculan
- />Dipartimento di Scienze Agro-alimentari, Ambientali e Animali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy
- />Istituto di Genomica Applicata, Parco Scientifco e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Barbara Bucchetti
- />Dipartimento di Scienze Agro-alimentari, Ambientali e Animali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy
| | - Enrico Peterlunger
- />Dipartimento di Scienze Agro-alimentari, Ambientali e Animali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy
| | - Aaron Fait
- />The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Fulvio Mattivi
- />Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Italy
| | - Simone D. Castellarin
- />Dipartimento di Scienze Agro-alimentari, Ambientali e Animali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy
- />Wine Research Centre, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4 Canada
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