1
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Zhang C, Dai Z, Ferrier T, Orduña L, Santiago A, Peris A, Wong DCJ, Kappel C, Savoi S, Loyola R, Amato A, Kozak B, Li M, Liang A, Carrasco D, Meyer-Regueiro C, Espinoza C, Hilbert G, Figueroa-Balderas R, Cantu D, Arroyo-Garcia R, Arce-Johnson P, Claudel P, Errandonea D, Rodríguez-Concepción M, Duchêne E, Huang SSC, Castellarin SD, Tornielli GB, Barrieu F, Matus JT. MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries. Plant Cell 2023; 35:4238-4265. [PMID: 37648264 PMCID: PMC10689149 DOI: 10.1093/plcell/koad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/13/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Variegation is a rare type of mosaicism not fully studied in plants, especially fruits. We examined red and white sections of grape (Vitis vinifera cv. 'Béquignol') variegated berries and found that accumulation of products from branches of the phenylpropanoid and isoprenoid pathways showed an opposite tendency. Light-responsive flavonol and monoterpene levels increased in anthocyanin-depleted areas in correlation with increasing MYB24 expression. Cistrome analysis suggested that MYB24 binds to the promoters of 22 terpene synthase (TPS) genes, as well as 32 photosynthesis/light-related genes, including carotenoid pathway members, the flavonol regulator HY5 HOMOLOGUE (HYH), and other radiation response genes. Indeed, TPS35, TPS09, the carotenoid isomerase gene CRTISO2, and HYH were activated in the presence of MYB24 and MYC2. We suggest that MYB24 modulates ultraviolet and high-intensity visible light stress responses that include terpene and flavonol synthesis and potentially affects carotenoids. The MYB24 regulatory network is developmentally triggered after the onset of berry ripening, while the absence of anthocyanin sunscreens accelerates its activation, likely in a dose-dependent manner due to increased radiation exposure. Anthocyanins and flavonols in variegated berry skins act as effective sunscreens but for different wavelength ranges. The expression patterns of stress marker genes in red and white sections of 'Béquignol' berries strongly suggest that MYB24 promotes light stress amelioration but only partly succeeds during late ripening.
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Affiliation(s)
- Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Thilia Ferrier
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Arnau Peris
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm 14476, Germany
| | - Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin 10124, Italy
| | - Rodrigo Loyola
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Bartosz Kozak
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia V1V 1V7, Canada
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Akun Liang
- Departamento de Física Aplicada-ICMUV-MALTA Consolider Team, Universitat de València, Burjassot 46100, Valencia, Spain
| | - David Carrasco
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid-INIA, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Carlos Meyer-Regueiro
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Carmen Espinoza
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8380453, Chile
| | - Ghislaine Hilbert
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Rosa Figueroa-Balderas
- 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
| | - Rosa Arroyo-Garcia
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid-INIA, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Patricio Arce-Johnson
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería Universidad Autónoma deChile
| | | | - Daniel Errandonea
- Departamento de Física Aplicada-ICMUV-MALTA Consolider Team, Universitat de València, Burjassot 46100, Valencia, Spain
| | - Manuel Rodríguez-Concepción
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, Valencia 46022, Spain
| | - Eric Duchêne
- SVQV, University of Strasbourg, INRAE, Colmar 68000, France
| | - Shao-shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Simone Diego Castellarin
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia V1V 1V7, Canada
| | | | - Francois Barrieu
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
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2
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Wang Y, Shang B, Génard M, Hilbert-Masson G, Delrot S, Gomès E, Poni S, Keller M, Renaud C, Kong J, Chen J, Liang Z, Dai Z. Model-assisted analysis for tuning anthocyanin composition in grape berries. Ann Bot 2023; 132:1033-1050. [PMID: 37850481 PMCID: PMC10808033 DOI: 10.1093/aob/mcad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Anthocyanin composition is responsible for the red colour of grape berries and wines, and contributes to their organoleptic quality. However, anthocyanin biosynthesis is under genetic, developmental and environmental regulation, making its targeted fine-tuning challenging. We constructed a mechanistic model to simulate the dynamics of anthocyanin composition throughout grape ripening in Vitis vinifera, employing a consensus anthocyanin biosynthesis pathway. The model was calibrated and validated using six datasets from eight cultivars and 37 growth conditions. Tuning the transformation and degradation parameters allowed us to accurately simulate the accumulation process of each individual anthocyanin under different environmental conditions. The model parameters were robust across environments for each genotype. The coefficients of determination (R2) for the simulated versus observed values for the six datasets ranged from 0.92 to 0.99, while the relative root mean square errors (RRMSEs) were between 16.8 and 42.1 %. The leave-one-out cross-validation for three datasets showed R2 values of 0.99, 0.96 and 0.91, and RRMSE values of 28.8, 32.9 and 26.4 %, respectively, suggesting a high prediction quality of the model. Model analysis showed that the anthocyanin profiles of diverse genotypes are relatively stable in response to parameter perturbations. Virtual experiments further suggested that targeted anthocyanin profiles may be reached by manipulating a minimum of three parameters, in a genotype-dependent manner. This model presents a promising methodology for characterizing the temporal progression of anthocyanin composition, while also offering a logical foundation for bioengineering endeavours focused on precisely adjusting the anthocyanin composition of grapes.
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Affiliation(s)
- Yongjian Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Boxing Shang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Michel Génard
- INRAE, UR1115, Unité Plantes et Systèmes de Culture Horticoles, Avignon, France
| | | | - Serge Delrot
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Eric Gomès
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Stefano Poni
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Markus Keller
- Department of Viticulture and Enology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Christel Renaud
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Junhua Kong
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Jinliang Chen
- Center for Agricultural Water Research in China, China Agricultural University, Beijing, 100083, China
| | - Zhenchang Liang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanwu Dai
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Guo Y, Li D, Liu T, Li Y, Liu J, He M, Cui X, Liu Z, Chen M. Genome-Wide Identification of PAP1 Direct Targets in Regulating Seed Anthocyanin Biosynthesis in Arabidopsis. Int J Mol Sci 2023; 24:16049. [PMID: 38003239 PMCID: PMC10671800 DOI: 10.3390/ijms242216049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Anthocyanins are widespread water-soluble pigments in the plant kingdom. Anthocyanin accumulation is activated by the MYB-bHLH-WD40 (MBW) protein complex. In Arabidopsis, the R2R3-MYB transcription factor PAP1 activates anthocyanin biosynthesis. While prior research primarily focused on seedlings, seeds received limited attention. This study explores PAP1's genome-wide target genes in anthocyanin biosynthesis in seeds. Our findings confirm that PAP1 is a positive regulator of anthocyanin biosynthesis in Arabidopsis seeds. PAP1 significantly increased anthocyanin content in developing and mature seeds in Arabidopsis. Transcriptome analysis at 12 days after pollination reveals the upregulation of numerous genes involved in anthocyanin accumulation in 35S:PAP1 developing seeds. Chromatin immunoprecipitation and dual luciferase reporter assays demonstrate PAP1's direct promotion of ten key genes and indirect upregulation of TT8, TTG1, and eight key genes during seed maturation, thus enhancing seed anthocyanin accumulation. These findings enhance our understanding of PAP1's novel role in regulating anthocyanin accumulation in Arabidopsis seeds.
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Affiliation(s)
- Yuan Guo
- Shaanxi Key Laboratory of Crop Heterosis, National Yangling Agricultural Biotechnology and Breeding Center, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.G.); (T.L.); (Y.L.); (J.L.); (M.H.); (X.C.); (Z.L.)
| | - Dong Li
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai 264025, China;
| | - Tiantian Liu
- Shaanxi Key Laboratory of Crop Heterosis, National Yangling Agricultural Biotechnology and Breeding Center, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.G.); (T.L.); (Y.L.); (J.L.); (M.H.); (X.C.); (Z.L.)
| | - Yuxin Li
- Shaanxi Key Laboratory of Crop Heterosis, National Yangling Agricultural Biotechnology and Breeding Center, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.G.); (T.L.); (Y.L.); (J.L.); (M.H.); (X.C.); (Z.L.)
| | - Jiajia Liu
- Shaanxi Key Laboratory of Crop Heterosis, National Yangling Agricultural Biotechnology and Breeding Center, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.G.); (T.L.); (Y.L.); (J.L.); (M.H.); (X.C.); (Z.L.)
| | - Mingyuan He
- Shaanxi Key Laboratory of Crop Heterosis, National Yangling Agricultural Biotechnology and Breeding Center, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.G.); (T.L.); (Y.L.); (J.L.); (M.H.); (X.C.); (Z.L.)
| | - Xiaohui Cui
- Shaanxi Key Laboratory of Crop Heterosis, National Yangling Agricultural Biotechnology and Breeding Center, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.G.); (T.L.); (Y.L.); (J.L.); (M.H.); (X.C.); (Z.L.)
| | - Zijin Liu
- Shaanxi Key Laboratory of Crop Heterosis, National Yangling Agricultural Biotechnology and Breeding Center, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.G.); (T.L.); (Y.L.); (J.L.); (M.H.); (X.C.); (Z.L.)
| | - Mingxun Chen
- Shaanxi Key Laboratory of Crop Heterosis, National Yangling Agricultural Biotechnology and Breeding Center, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.G.); (T.L.); (Y.L.); (J.L.); (M.H.); (X.C.); (Z.L.)
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4
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Azuma A, Kobayashi S. Demethylation of the 3' LTR region of retrotransposon in VvMYBA1 BEN allele enhances anthocyanin biosynthesis in berry skin and flesh in 'Brazil' grape. Plant Sci 2022; 322:111341. [PMID: 35667250 DOI: 10.1016/j.plantsci.2022.111341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 05/10/2023]
Abstract
Black-skinned and red-fleshed grape 'Brazil' is a bud sport of rosy-skinned 'Benitaka'. 'Brazil' has a much higher anthocyanin content in the skin than that of 'Benitaka' and is characterized by the accumulation of anthocyanins in the flesh. Our genomic analysis of the VvMYBA loci, which regulate anthocyanin biosynthesis, suggested that the difference in skin and flesh color between 'Brazil' and 'Benitaka' cannot be explained by genomic alteration at the loci. Expression levels of VvMYBA1 and anthocyanin biosynthesis-related genes in skin and flesh were significantly higher in 'Brazil' than in 'Benitaka' throughout berry development. DNA methylation levels in the 3' long terminal repeat (LTR) of a retrotransposon in the upstream region of VvMYBA1BEN allele were clearly higher in the skin and flesh of 'Benitaka' than in those of 'Brazil' throughout berry development. These findings suggest that a dramatic decrease in DNA methylation level in the 3' LTR of the retrotransposon in the VvMYBA1BEN allele in 'Brazil' increases the expression levels of VvMYBA1 and anthocyanin accumulation in skin and flesh. Our findings also suggest that skin and flesh colors are inherited together and vary depending on the presence or absence of the VvMYBA1BEN allele.
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Affiliation(s)
- Akifumi Azuma
- Division of Grape and Persimmon Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Higashihiroshima, Hiroshima 739-2494, Japan.
| | - Shozo Kobayashi
- Division of Grape and Persimmon Research, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Higashihiroshima, Hiroshima 739-2494, Japan
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6
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Flutre T, Le Cunff L, Fodor A, Launay A, Romieu C, Berger G, Bertrand Y, Terrier N, Beccavin I, Bouckenooghe V, Roques M, Pinasseau L, Verbaere A, Sommerer N, Cheynier V, Bacilieri R, Boursiquot JM, Lacombe T, Laucou V, This P, Péros JP, Doligez A. A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs. G3 (Bethesda) 2022; 12:6575896. [PMID: 35485948 PMCID: PMC9258538 DOI: 10.1093/g3journal/jkac103] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/21/2022] [Indexed: 12/11/2022]
Abstract
To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.
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Affiliation(s)
- Timothée Flutre
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France.,Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Loïc Le Cunff
- UMT Géno-Vigne, 34398 Montpellier, France.,IFV, 30240 Le Grau-du-Roi, France
| | - Agota Fodor
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Amandine Launay
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Charles Romieu
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Gilles Berger
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Yves Bertrand
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Nancy Terrier
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | | | | | - Maryline Roques
- UMT Géno-Vigne, 34398 Montpellier, France.,IFV, 30240 Le Grau-du-Roi, France
| | - Lucie Pinasseau
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | - Arnaud Verbaere
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | - Nicolas Sommerer
- SPO, Univ Montpellier, INRAE, Institut Agro, 34060 Montpellier, France
| | | | - Roberto Bacilieri
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Jean-Michel Boursiquot
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Thierry Lacombe
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Valérie Laucou
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Patrice This
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Jean-Pierre Péros
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
| | - Agnès Doligez
- AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France.,UMT Géno-Vigne, 34398 Montpellier, France
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7
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Tirumalai V, Narjala A, Swetha C, Sundar GVH, Sujith TN, Shivaprasad PV. Cultivar-specific miRNA-mediated RNA silencing in grapes. Planta 2022; 256:17. [PMID: 35737180 DOI: 10.1007/s00425-022-03934-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
In-depth comparative degradome analysis of two domesticated grape cultivars with diverse secondary metabolite accumulation reveals differential miRNA-mediated targeting. Small (s)RNAs such as micro(mi)RNAs and secondary small interfering (si) often work as negative switches of gene expression. In plants, it is well known that miRNAs target and cleave mRNAs that have high sequence complementarity. However, it is not known if there are variations in miRNA-mediated targeting between subspecies and cultivars that have been subjected to vast genetic modifications through breeding and other selections. Here, we have used PAREsnip2 tool for analysis of degradome datasets derived from two contrasting domesticated grape cultivars having varied fruit color, habit and leaf shape. We identified several interesting variations in sRNA targeting using degradome and 5'RACE analysis between two contrasting grape cultivars that was further correlated using RNA-seq analysis. Several of the differences we identified are associated with secondary metabolic pathways. We propose possible means by which sRNAs might contribute to diversity in secondary metabolites and other development pathways between two domesticated cultivars of grapes.
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Affiliation(s)
- Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - G Vivek Hari Sundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - T N Sujith
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, 560065, India.
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8
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Alahakoon D, Fennell A, Helget Z, Bates T, Karn A, Manns D, Mansfield AK, Reisch BI, Sacks G, Sun Q, Zou C, Cadle-davidson L, Londo JP. Berry Anthocyanin, Acid, and Volatile Trait Analyses in a Grapevine-Interspecific F2 Population Using an Integrated GBS and rhAmpSeq Genetic Map. Plants 2022; 11:696. [PMID: 35270166 PMCID: PMC8912348 DOI: 10.3390/plants11050696] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 11/29/2022]
Abstract
Increased map density and transferability of markers are essential for the genetic analysis of fruit quality and stress tolerance in interspecific grapevine populations. We used 1449 GBS and 2000 rhAmpSeq markers to develop a dense map for an interspecific F2 population (VRS-F2) that was derived by selfing a single F1 from a Vitis riparia x ‘Seyval blanc’ cross. The resultant map contained 2519 markers spanning 1131.3 cM and was highly collinear with the Vitis vinifera ‘PN40024’ genome. Quantitative trait loci (QTL) for berry skin color and flower type were used to validate the map. Four rhAmpSeq transferable markers were identified that can be used in pairs (one pistillate and one hermaphroditic) to predict pistillate and hermaphrodite flower type with ≥99.7% accuracy. Total and individual anthocyanin diglucoside QTL mapped to chromosome 9 near a 5-O-GLUCOSYLTRANSFERASE candidate gene. Malic acid QTL were observed on chromosome 1 and 6 with two MALATE DEHYRDROGENASE CYTOPLASMIC 1 and ALUMINUM-ACTIVATED MALATE TRANSPORTER 2-LIKE (ALMT) candidate genes, respectively. Modeling malic acid identified a potential QTL on chromosome 8 with peak position in proximity of another ALMT. A first-ever reported QTL for the grassy smelling volatile (E)-2-hexenal was found on chromosome 2 with a PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE candidate gene near peak markers.
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9
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Navarro-Payá D, Santiago A, Orduña L, Zhang C, Amato A, D’Inca E, Fattorini C, Pezzotti M, Tornielli GB, Zenoni S, Rustenholz C, Matus JT. The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement. Front Plant Sci 2022; 12:803977. [PMID: 35111182 PMCID: PMC8801485 DOI: 10.3389/fpls.2021.803977] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/20/2021] [Indexed: 05/06/2023]
Abstract
Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species' pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes. Well-established research communities studying model organisms have created and maintained, through public and private funds, a diverse range of online tools and databases serving as repositories of genomes and gene function data. The lack of such resources for the non-model, but economically important, Vitis vinifera species has driven the need for a standardised collection of genes within the grapevine community. In an effort led by the Integrape COST Action CA17111, we have recently developed the first grape gene reference catalogue, where genes are ascribed to functional data, including their accession identifiers from different genome-annotation versions (https://integrape.eu/resources/genes-genomes/). We present and discuss this gene repository together with a validation-level scheme based on varied supporting evidence found in current literature. The catalogue structure and online submission form provided permits community curation. Finally, we present the Gene Cards tool, developed within the Vitis Visualization (VitViz) platform, to visualize the data collected in the catalogue and link gene function with tissue-specific expression derived from public transcriptomic data. This perspective article aims to present these resources to the community as well as highlight their potential use, in particular for plant-breeding applications.
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Affiliation(s)
- David Navarro-Payá
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Erica D’Inca
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Chiara Fattorini
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Mario Pezzotti
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Sara Zenoni
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Valencia, Spain
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10
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Cai J, Mo X, Wen C, Gao Z, Chen X, Xue C. FvMYB79 Positively Regulates Strawberry Fruit Softening via Transcriptional Activation of FvPME38. Int J Mol Sci 2021; 23:101. [PMID: 35008526 DOI: 10.3390/ijms23010101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/18/2022] Open
Abstract
Strawberry is a soft fruit with short postharvest life, due to a rapid loss of firmness. Pectin methylesterase (PME)-mediated cell wall remodeling is important to determine fruit firmness and softening. Previously, we have verified the essential role of FvPME38 in regulation of PME-mediated strawberry fruit softening. However, the regulatory network involved in PME-mediated fruit softening is still largely unknown. Here, we identified an R2R3-type MYB transcription factor FvMYB79, which activates the expression level of FvPME38, thereby accelerating fruit softening. During fruit development, FvMYB79 co-expressed with FvPME38, and this co-expression pattern was opposite to the change of fruit firmness in the fruit of 'Ruegen' which significantly decreased during fruit developmental stages and suddenly became very low after the color turning stage. Via transient transformation, FvMYB79 could significantly increase the transcriptional level of FvPME38, leading to a decrease of firmness and acceleration of fruit ripening. In addition, silencing of FvMYB79 showed an insensitivity to ABA-induced fruit ripening, suggesting a possible involvement of FvMYB79 in the ABA-dependent fruit softening process. Our findings suggest FvMYB79 acts as a novel regulator during strawberry ripening via transcriptional activation of FvPME38, which provides a novel mechanism for improvement of strawberry fruit firmness.
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11
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Karn A, Diaz-Garcia L, Reshef N, Zou C, Manns DC, Cadle-Davidson L, Mansfield AK, Reisch BI, Sacks GL. The Genetic Basis of Anthocyanin Acylation in North American Grapes ( Vitis spp.). Genes (Basel) 2021; 12:1962. [PMID: 34946911 PMCID: PMC8701791 DOI: 10.3390/genes12121962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022] Open
Abstract
Hydroxycinnamylated anthocyanins (or simply 'acylated anthocyanins') increase color stability in grape products, such as wine. Several genes that are relevant for anthocyanin acylation in grapes have been previously described; however, control of the degree of acylation in grapes is complicated by the lack of genetic markers quantitatively associated with this trait. To characterize the genetic basis of anthocyanin acylation in grapevine, we analyzed the acylation ratio in two closely related biparental families, Vitis rupestris B38 × 'Horizon' and 'Horizon' × Illinois 547-1, for 2 and 3 years, respectively. The acylation ratio followed a bimodal and skewed distribution in both families, with repeatability estimates larger than 0.84. Quantitative trait locus (QTL) mapping with amplicon-based markers (rhAmpSeq) identified a strong QTL from 'Horizon' on chromosome 3, near 15.85 Mb in both families and across years, explaining up to 85.2% of the phenotypic variance. Multiple candidate genes were identified in the 14.85-17.95 Mb interval, in particular, three copies of a gene encoding an acetyl-CoA-benzylalcohol acetyltransferase-like protein within the two most strongly associated markers. Additional population-specific QTLs were found in chromosomes 9, 10, 15, and 16; however, no candidate genes were described. The rhAmpSeq markers reported here, which were previously shown to be highly transferable among the Vitis genus, could be immediately implemented in current grapevine breeding efforts to control the degree of anthocyanin acylation and improve the quality of grapes and their products.
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Affiliation(s)
- Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (L.C.-D.); (B.I.R.)
| | - Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Campo Experimental Pabellón, Aguascalientes 20676, Mexico
| | - Noam Reshef
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA;
| | - David C. Manns
- Department of Food Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (D.C.M.); (A.K.M.)
| | - Lance Cadle-Davidson
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (L.C.-D.); (B.I.R.)
- USDA-Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Anna Katharine Mansfield
- Department of Food Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (D.C.M.); (A.K.M.)
| | - Bruce I. Reisch
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY 14456, USA; (A.K.); (L.C.-D.); (B.I.R.)
| | - Gavin L. Sacks
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
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12
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García-Pastor ME, Giménez MJ, Serna-Escolano V, Guillén F, Valero D, Serrano M, García-Martínez S, Terry LA, Alamar MC, Zapata PJ. Oxalic Acid Preharvest Treatment Improves Colour and Quality of Seedless Table Grape 'Magenta' Upregulating on-Vine Abscisic Acid Metabolism, Relative VvNCED1 Gene Expression, and the Antioxidant System in Berries. Front Plant Sci 2021; 12:740240. [PMID: 34790211 PMCID: PMC8591251 DOI: 10.3389/fpls.2021.740240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
The effect of oxalic acid (OA) in determining poorly coloured table grape quality remains relatively unknown. Some red cultivars, such as seedless table grape 'Magenta' are characterised by a poor berry colour, an attribute highly demanded by the consumer. The aim of this research was to elucidate the effect of a preharvest OA treatment (5 mM) on berry colour and quality of table grape by investigating its role in berry development, on-vine ripening, and postharvest senescence. We found that OA significantly increased abscisic acid (ABA) and ABA glucose ester (ABA-GE) content in treated berries. This increase was mediated by changes in the ABA biosynthetic pathway, specifically by the upregulation of the 9-cis-epoxycarotenoid dioxygenase (VvNCED1) gene. The accumulation of ABA in treated berries resulted in colour improvement and a higher individual and total anthocyanins content at harvest compared with control; whereas at harvest, OA-treated table grapes showed a significantly lower glucose and fructose content and a higher content of tartaric, ascorbic, and succinic acids. Furthermore, antioxidant enzyme activity was increased during berry development in OA-treated berries. On the other hand, those berries treated with OA showed a delay in loss of firmness and colour during cold storage, as well as less susceptibility to postharvest decay incidence. This effect of OA delaying the senescence process was also related to enzymatic antioxidant system stimulation. For the first time, the role of OA on increasing quality, mainly colour, in table grapes was elucidated, highlighting that this treatment upregulated ABA metabolism, relative VvNCED1 gene expression and antioxidant system, delaying postharvest berry senescence.
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Affiliation(s)
| | - María J. Giménez
- Department of Food Technology, EPSO, University Miguel Hernández, Alicante, Spain
| | | | - Fabián Guillén
- Department of Food Technology, EPSO, University Miguel Hernández, Alicante, Spain
| | - Daniel Valero
- Department of Food Technology, EPSO, University Miguel Hernández, Alicante, Spain
| | - María Serrano
- Department of Applied Biology, EPSO, University Miguel Hernández, Alicante, Spain
| | | | - Leon A. Terry
- Plant Science Laboratory, Cranfield University, Bedfordshire, United Kingdom
| | - M. Carmen Alamar
- Plant Science Laboratory, Cranfield University, Bedfordshire, United Kingdom
| | - Pedro J. Zapata
- Department of Food Technology, EPSO, University Miguel Hernández, Alicante, Spain
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13
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Kim DH, Lee J, Rhee J, Lee JY, Lim SH. Loss of the R2R3 MYB Transcription Factor RsMYB1 Shapes Anthocyanin Biosynthesis and Accumulation in Raphanus sativus. Int J Mol Sci 2021; 22:10927. [PMID: 34681588 PMCID: PMC8535906 DOI: 10.3390/ijms222010927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 11/26/2022] Open
Abstract
The red or purple color of radish (Raphanus sativus L.) taproots is due to anthocyanins, which have nutritional and aesthetic value, as well as antioxidant properties. Moreover, the varied patterns and levels of anthocyanin accumulation in radish roots make them an interesting system for studying the transcriptional regulation of anthocyanin biosynthesis. The R2R3 MYB transcription factor RsMYB1 is a key positive regulator of anthocyanin biosynthesis in radish. Here, we isolated an allele of RsMYB1, named RsMYB1Short, in radish cultivars with white taproots. The RsMYB1Short allele carried a 4 bp insertion in the first exon causing a frame-shift mutation of RsMYB1, generating a truncated protein with only a partial R2 domain at the N-terminus. Unlike RsMYB1Full, RsMYB1Short was localized to the nucleus and the cytoplasm and failed to interact with their cognate partner RsTT8. Transient expression of genomic or cDNA sequences for RsMYB1Short in radish cotyledons failed to induce anthocyanin accumulation, but that for RsMYB1Full activated it. Additionally, RsMYB1Short showed the lost ability to induce pigment accumulation and to enhance the transcript level of anthocyanin biosynthetic genes, while RsMYB1Full promoted both processes when co-expressed with RsTT8 in tobacco leaves. As the result of the transient assay, co-expressing RsTT8 and RsMYB1Full, but not RsMYB1Short, also enhanced the promoter activity of RsCHS and RsDFR. We designed a molecular marker for RsMYB1 genotyping, and revealed that the RsMYB1Short allele is common in white radish cultivars, underscoring the importance of variation at the RsMYB1 locus in anthocyanin biosynthesis in the radish taproot. Together, these results indicate that the nonsense mutation of RsMYB1 generated the truncated protein, RsMYB1Short, that had the loss of ability to regulate anthocyanin biosynthesis. Our findings highlight that the frame shift mutation of RsMYB1 plays a key role in anthocyanin biosynthesis in the radish taproot.
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Affiliation(s)
- Da-Hye Kim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Korea;
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea;
| | - Jundae Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea;
| | - JuHee Rhee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea;
| | - Jong-Yeol Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea;
| | - Sun-Hyung Lim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong 17579, Korea;
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14
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Gomès É, Maillot P, Duchêne É. Molecular Tools for Adapting Viticulture to Climate Change. Front Plant Sci 2021; 12:633846. [PMID: 33643361 PMCID: PMC7902699 DOI: 10.3389/fpls.2021.633846] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.
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Affiliation(s)
- Éric Gomès
- EGFV, University of Bordeaux – Bordeaux Sciences-Agro – INRAE, Villenave d’Ornon, France
| | - Pascale Maillot
- SVQV, INRAE – University of Strasbourg, Colmar, France
- University of Haute Alsace, Mulhouse, France
| | - Éric Duchêne
- SVQV, INRAE – University of Strasbourg, Colmar, France
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15
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Bigard A, Romieu C, Sire Y, Torregrosa L. Vitis vinifera L. Diversity for Cations and Acidity Is Suitable for Breeding Fruits Coping With Climate Warming. Front Plant Sci 2020; 11:01175. [PMID: 33072139 PMCID: PMC7536366 DOI: 10.3389/fpls.2020.01175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/20/2020] [Indexed: 05/31/2023]
Abstract
The selection of grapevine varieties is considered to be the smartest strategy for adapting the viticulture to climate warming. Present knowledge of the diversity of grape solutes known to be influenced by temperature is too limited to perform genetic improvement strategies. This study aimed to characterize the diversity for major cations (K+, Mg2+, Ca2+, NH4 +) of the Vitis vinifera fruit and their effect on acidity. Two developmental stages were targeted: the end of green growth, when organic acids reach a maximum, and the physiological ripe stage defined by the stopping of solutes and water import at the maximum volume of the berry. Twelve varieties and 21 microvines from the same segregating population were selected from preliminary phenotyping. The concentration of cations depended on the stage of fruit development, the genotype and the environment with GxE effects. In the ripe grape, K+ concentration varied from 28 to 57 mmol.L-1 with other cations being less concentrated. Combined with the variation in organic acids, cation concentration diversity resulted in titratable acidity of the ripe fruit ranging from 38 to 215 meq.L-1. These results open new perspectives for the selection of varieties to mitigate the adverse effects of climate warming on grape quality.
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Affiliation(s)
- Antoine Bigard
- AGAP, University of Montpellier, CIRAD, INRAe, Institut Agro, Montpellier, France
- UE INRAe de Pech Rouge, University of Montpellier, INRAe, Gruissan, France
| | - Charles Romieu
- AGAP, University of Montpellier, CIRAD, INRAe, Institut Agro, Montpellier, France
- GENOVIGNE, University of Montpellier, IFV, INRAe, Institut Agro, Montpellier, France
| | - Yannick Sire
- UE INRAe de Pech Rouge, University of Montpellier, INRAe, Gruissan, France
| | - Laurent Torregrosa
- AGAP, University of Montpellier, CIRAD, INRAe, Institut Agro, Montpellier, France
- UE INRAe de Pech Rouge, University of Montpellier, INRAe, Gruissan, France
- GENOVIGNE, University of Montpellier, IFV, INRAe, Institut Agro, Montpellier, France
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16
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Tan LQ, Yang CJ, Zhou B, Wang LB, Zou Y, Chen W, Xia T, Tang Q. Inheritance and quantitative trait loci analyses of the anthocyanins and catechins of Camellia sinensis cultivar 'Ziyan' with dark-purple leaves. Physiol Plant 2020; 170:109-119. [PMID: 32333383 DOI: 10.1111/ppl.13114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/12/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
Owing to the potential health benefits, anthocyanin-rich teas (Camellia sinensis) have attracted interest over the past decade. Previously, we developed the cultivar 'Ziyan,' which has dark-purple leaves because of the accumulation of a high amount of anthocyanins. In this study, we performed a genetic analysis of this anthocyanin-rich tea cultivar and 176 of its naturally pollinated offspring. For two consecutive years, we quantified the anthocyanins and catechins of 'Ziyan' and the offspring population. While >60% of the offspring accumulated less than half of the amount of anthocyanins of 'Ziyan,' 17 (2018) and 15 (2019) individuals exceeded 'Ziyan' in anthocyanin content. A negative correlation between anthocyanin and total catechin content (r = -0.59, P < 0.001) was observed. The population was genotyped with 131 SSR markers spanning all linkage groups of the C. sinensis genome. Kruskal-Wallis tests identified 10 markers significantly associated with anthocyanins, catechins and their ratios in both years. Quantitative trait locus (QTL) analyses using the interval mapping method detected 13 QTLs, suggesting the dark-purple trait of 'Ziyan' is because of the pyramiding of anthocyanin-promoting alleles on at least five linkage groups. Two genetic loci reversely related to anthocyanin and total catechin contents were identified. This study provides valuable information for genetic improvement of purple tea cultivars and for fine-mapping related genes.
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Affiliation(s)
- Li-Qiang Tan
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chun-Jing Yang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Bin Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liu-Bin Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yao Zou
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qian Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
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17
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Sun L, Li S, Jiang J, Tang X, Fan X, Zhang Y, Liu J, Liu C. New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map. BMC Plant Biol 2020; 20:302. [PMID: 32605636 PMCID: PMC7325011 DOI: 10.1186/s12870-020-02517-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/23/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Berry color is an important trait in grapes and is mainly determined by the anthocyanin content and composition. To further explore the coloring mechanism of grape berries, the F1 population of Vitis vinifera 'Red Globe' × 'Muscat Hamburg' was used to map the color locus, and transcriptome analysis was performed to assist in screening candidate genes. RESULTS A total of 438,407 high-quality single-nucleotide polymorphisms (SNPs) were obtained from whole-genome resequencing (WGS) of the population, and 27,454 SNPs were selected to construct a high-density genetic map. The selected SNPs were clustered into 19 linkage groups (LGs) spanning a genetic distance of 1442.638 cM. Berry color was evaluated by color grade, chromatic aberration, total anthocyanin content and anthocyanin composition. The Pearson correlation coefficients of these phenotypes in 2017 and 2018 were significant at the 0.01 level. The major color locus of MYBA1 and MYBA2 on LG2 was identified, explaining between 26 and 63.6% of all phenotypic variance. Furthermore, 9 additional QTLs with smaller effects were detected on Chr2, Chr4, Chr6, Chr11 and Chr17. Combined with the gene annotation and RNA-seq data, multiple new candidate genes were selected from the above QTLs. CONCLUSION These results indicated that grape berry color is a quantitative trait controlled by a major color locus and multiple minor loci. Though the major color locus was consistent with previous studies, several minor QTLs and candidate genes associated with grape berry color and anthocyanin accumulation were identified in this study. And the specific regulatory mechanism still needs to be further explored.
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Affiliation(s)
- Lei Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Shenchang Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jianfu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaoping Tang
- Pomology Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| | - Xiucai Fan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Ying Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jihong Liu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China.
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.
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18
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Alseekh S, Perez de Souza L, Benina M, Fernie AR. The style and substance of plant flavonoid decoration; towards defining both structure and function. Phytochemistry 2020; 174:112347. [PMID: 32203741 DOI: 10.1016/j.phytochem.2020.112347] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 05/19/2023]
Abstract
Over 8000 different flavonoids have been described and a considerable number of new flavonoid structures are being elucidated every year. The advent of metabolomics alongside the development of phytochemical genetics - wherein the genetic basis underlying the regulation of the levels of plant metabolites is determined - has provided a massive boost to such efforts. That said our understanding of the individual function(s) of the vast majority of the metabolites that constitute this important class of phytochemicals remains unknown. Here we review what is known concerning the major decorative modifications of flavonoids in plants, namely hydroxylation, glycosylation, methylation and acylation. Our major focus is with regard to the in planta function of these modified compounds, however, we also highlight the demonstrated bioactive roles which they possess. We additionally performed a comprehensive survey of the flavonoids listed in the KNApSAcK database in order to assess the frequency of occurrence of each type of flavonoid modification. We conclude that whilst considerable research has been carried out regarding the biological roles of flavonoids most studies to date have merely provided information on the compound class or sub-classes thereof as a whole with too little currently known on the specific role of individual metabolites. We, therefore, finally suggest a framework based on currently available tools by which the relative importance of the individual compounds can be assessed under various biological conditions in order to fill this knowledge-gap.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Maria Benina
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
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19
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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. Front Plant Sci 2020; 11:527. [PMID: 32457776 PMCID: PMC7221203 DOI: 10.3389/fpls.2020.00527] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Underhill AN, Hirsch CD, Clark MD. Evaluating and Mapping Grape Color Using Image-Based Phenotyping. Plant Phenomics 2020; 2020:8086309. [PMID: 33313563 PMCID: PMC7706331 DOI: 10.34133/2020/8086309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/05/2020] [Indexed: 05/19/2023]
Abstract
Grape berry color is an economically important trait that is controlled by two major genes influencing anthocyanin synthesis in the skin. Color is often described qualitatively using six major categories; however, this is a subjective rating that often fails to describe variation within these six classes. To investigate minor genes influencing berry color, image analysis was used to quantify berry color using different color spaces. An image analysis pipeline was developed and utilized to quantify color in a segregating hybrid wine grape population across two years. Images were collected from grape clusters immediately after harvest and segmented by color to determine the red, green, and blue (RGB); hue, saturation, and intensity (HSI); and lightness, red-green, and blue-yellow values (L∗a∗b∗) of berries. QTL analysis identified known major QTL for color on chromosome 2 along with several previously unreported smaller-effect QTL on chromosomes 1, 5, 6, 7, 10, 15, 18, and 19. This study demonstrated the ability of an image analysis phenotyping system to characterize berry color and to more effectively capture variability within a population and identify genetic regions of interest.
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Affiliation(s)
- A. N. Underhill
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA
| | - C. D. Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - M. D. Clark
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA
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21
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Fan L, Xu L, Wang Y, Tang M, Liu L. Genome- and Transcriptome-Wide Characterization of bZIP Gene Family Identifies Potential Members Involved in Abiotic Stress Response and Anthocyanin Biosynthesis in Radish ( Raphanus sativus L.). Int J Mol Sci 2019; 20:ijms20246334. [PMID: 31888167 PMCID: PMC6941039 DOI: 10.3390/ijms20246334] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 01/20/2023] Open
Abstract
Basic leucine zipper (bZIP) transcription factors play crucial roles in various abiotic stress responses as well as anthocyanin accumulation. Anthocyanins are most abundant in colorful skin radish, which exhibit strong antioxidant activity that offers benefits for human health. Here, a total of 135 bZIP-encoding genes were identified from radish genome. Synteny analysis showed that 104 radish and 63 ArabidopsisbZIP genes were orthologous. Transcriptome analysis revealed that 10 RsbZIP genes exhibited high-expression levels in radish taproot (RPKM>10). Specifically, RsbZIP010 exhibited down-regulated expression under Cd, Cr and Pb stresses, whereas RsbZIP031 and RsbZIP059 showed significant down-regulation under heat and salt stresses, respectively. RT-qPCR analysis indicated that RsbZIP011 and RsbZIP102 were significantly up-regulated in the tissues of radish with high anthocyanin contents. Furthermore, the promoter sequences of 39 anthocyanin-related genes were found to contain G-box or ACE-box elements that could be recognized by bZIP family members. Taken together, several RsbZIPs might be served as critical regulators in radish taproot under Cd, Cr, Pb, heat and salt stresses. RsbZIP011 and RsbZIP102 were the potential participants in anthocyanin biosynthesis pathway of radish. These results facilitate further investigation on functional characterization of bZIP genes in response to abiotic stress and anthocyanin biosynthesis in radish.
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22
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Xie S, Qiao X, Chen H, Nan H, Zhang Z. Coordinated Regulation of Grape Berry Flesh Color by Transcriptional Activators and Repressors. J Agric Food Chem 2019; 67:11815-11824. [PMID: 31550160 DOI: 10.1021/acs.jafc.9b05234] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Yan73 is a teinturier Vitis vinifera variety with red berry flesh, but the molecular mechanisms underlying its flesh coloration remain unclear. We analyzed the flavonoid metabolic and transcriptome profiles of Yan73 berry red and white flesh using HPLC-ESI-MS/MS and RNA-sequencing technologies. Anthocyanins are the main flavonoids responsible for Yan73 berry flesh color, and the coloration is coordinately regulated by the VvMYBA1 transcriptional activator and VvMYBC2-L1 transcriptional repressor. Furthermore, yeast one- and two-hybrid, dual luciferase, and bimolecular fluorescence complementation assays suggested that VvMYBA1 positively regulates Yan73 berry flesh color via interactions with VvWDR1 and the activation of the VvCHI3, VvOMT, and VvGST4 promoters, whereas VvMYBC2-L1 negatively regulates Yan73 berry flesh color, possibly by competing with the R2R3-MYB transcriptional activators for bHLH partners or by repressing VvOMT and VvGST4 expression. Our findings provide new insights into the molecular mechanisms regulating grape flesh color.
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Affiliation(s)
- Sha Xie
- College of Enology , Northwest A&F University , No. 22 Xinong Road , Yangling , Shaanxi 712100 , China
| | - Xinlong Qiao
- Laboratory of Interdisciplinary Research Institute of Biophysics , Chinese Academy of Sciences , Beijing 100101 , China
- University of the Chinese Academy of Sciences , Beijing 100049 , China
| | - Huawei Chen
- College of Enology , Northwest A&F University , No. 22 Xinong Road , Yangling , Shaanxi 712100 , China
| | - Hao Nan
- College of Life Sciences , Northwest A&F University , Yangling , Shaanxi 712100 , China
| | - Zhenwen Zhang
- College of Enology , Northwest A&F University , No. 22 Xinong Road , Yangling , Shaanxi 712100 , China
- Shaanxi Engineering Research Center for Viti-Viniculture , Yangling , Shaanxi 712100 , China
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23
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Delfino P, Zenoni S, Imanifard Z, Tornielli GB, Bellin D. Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data. BMC Genomics 2019; 20:739. [PMID: 31615398 PMCID: PMC6794750 DOI: 10.1186/s12864-019-6124-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/20/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High temperature during grape berry ripening impairs the quality of fruits and wines. Veraison time, which marks ripening onset, is a key factor for determining climatic conditions during berry ripening. Understanding its genetic control is crucial to successfully breed varieties more adapted to a changing climate. Quantitative trait loci (QTL) studies attempting to elucidate the genetic determinism of developmental stages in grapevine have identified wide genomic regions. Broad scale transcriptomic studies, by identifying sets of genes modulated during berry development and ripening, also highlighted a huge number of putative candidates. RESULTS With the final aim of providing an overview about available information on the genetic control of grapevine veraison time, and prioritizing candidates, we applied a meta-QTL analysis for grapevine phenology-related traits and checked for co-localization of transcriptomic candidates. A consensus genetic map including 3130 markers anchored to the grapevine genome assembly was compiled starting from 39 genetic maps. Two thousand ninety-three QTLs from 47 QTL studies were projected onto the consensus map, providing a comprehensive overview about distribution of available QTLs and revealing extensive co-localization especially across phenology related traits. From 141 phenology related QTLs we generated 4 veraison meta-QTLs located on linkage group (LG) 1 and 2, and 13 additional meta-QTLs connected to the veraison time genetic control, among which the most relevant were located on LG 14, 16 and 18. Functional candidates in these intervals were inspected. Lastly, taking advantage of available transcriptomic datasets, expression data along berry development were integrated, in order to pinpoint among positional candidates, those differentially expressed across the veraison transition. CONCLUSION Integration of meta-QTLs analysis on available phenology related QTLs and data from transcriptomic dataset allowed to strongly reduce the number of candidate genes for the genetic control of the veraison transition, prioritizing a list of 272 genes, among which 78 involved in regulation of gene expression, signal transduction or development.
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Affiliation(s)
- Pietro Delfino
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy.,Present address: Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Zahra Imanifard
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | | | - Diana Bellin
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134, Verona, Italy.
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24
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Crupi P, Alba V, Masi G, Caputo AR, Tarricone L. Effect of two exogenous plant growth regulators on the color and quality parameters of seedless table grape berries. Food Res Int 2019; 126:108667. [PMID: 31732072 DOI: 10.1016/j.foodres.2019.108667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 08/04/2019] [Accepted: 09/09/2019] [Indexed: 12/16/2022]
Abstract
Some red-pink table grape varieties, cultivated in warm climates, can fail in achieving the right level of anthocyanins responsible for the intense and uniform red color of berries. Nowadays, this is becoming an important technological issue in the Mediterranean area, which may result in decreasing market acceptance and potential economic value of table grape. Usually, plant growth regulators or phytohormones, such as S-ABA, can overcome this problem because they drive the accumulation of anthocyanins over the ripening season. Harpin proteins (HrP), which enhance the plant disease resistance, may be supposed to stimulate the anthocyanins biosynthesis in grape skin if applied close to veraison. Therefore, this research aimed at comparing the effect of HrP and S-ABA over the anthocyanin and color improvement of Crimson Seedless table grape grown in Southern Italy. For the first time, the exogenous treatment with HrP showed as effective as the less sustainable S-ABA one in favoring the anthocyanin accumulation, leading to peonidin-3-O-glucoside, cyanidin-3-O-glucoside, and malvidin-3-O-glucoside values up to 4 folds higher than control grapes and giving rise to a greater concentration of the more stable acylated anthocyanins. Overall, the color of berries was improved but keeping high the other quality characteristics.
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Affiliation(s)
- Pasquale Crupi
- CREA-VE, Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via Casamassima, 148, 70010 Turi, BA, Italy.
| | - Vittorio Alba
- CREA-VE, Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via Casamassima, 148, 70010 Turi, BA, Italy
| | - Gianvito Masi
- CREA-VE, Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via Casamassima, 148, 70010 Turi, BA, Italy
| | - Angelo Raffaele Caputo
- CREA-VE, Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via Casamassima, 148, 70010 Turi, BA, Italy
| | - Luigi Tarricone
- CREA-VE, Council for Agricultural Research and Economics - Research Centre for Viticulture and Enology, Via Casamassima, 148, 70010 Turi, BA, Italy
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25
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Wang P, Dai L, Ai J, Wang Y, Ren F. Identification and functional prediction of cold-related long non-coding RNA (lncRNA) in grapevine. Sci Rep 2019; 9:6638. [PMID: 31036931 DOI: 10.1038/s41598-019-43269-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 04/18/2019] [Indexed: 11/09/2022] Open
Abstract
Plant long non-coding RNA (lncRNA) undergoes dynamic regulation and acts in developmental and stress regulation. In this study, we surveyed the expression dynamics of lncRNAs in grapevine (Vitis vinifera L.) under cold stress using high-throughput sequencing. Two-hundred and three known lncRNAs were significantly up-regulated and 144 known lncRNAs were significantly down-regulated in cold-treated grapevine. In addition, 2 088 novel lncRNA transcripts were identified in this study, with 284 novel lncRNAs significantly up-regulated and 182 novel lncRNAs significantly down-regulated in cold-treated grapevine. Two-hundred and forty-two differentially expressed grapevine lncRNAs were predicted to target 326 protein-coding genes in a cis-regulatory relationship. Many differentially expressed grapevine lncRNAs targeted stress response-related genes, such as CBF4 transcription factor genes, late embryogenesis abundant protein genes, peroxisome biogenesis protein genes, and WRKY transcription factor genes. Sixty-two differentially expressed grapevine lncRNAs were predicted to target 100 protein-coding genes in a trans-regulatory relationship. The expression of overall target genes in both cis and trans-regulatory relationships were positively related to the expression of lncRNAs in grapevines under cold stress. We identified 31 known lncRNAs as 34 grapevine micro RNA (miRNA) precursors and some miRNAs may be derived from multiple lncRNAs. We found 212 lncRNAs acting as targets of miRNAs in grapevines, involving 150 miRNAs; additionally, 120 grapevine genes were predicted as targets of grapevine miRNAs and lncRNAs. We found one gene cluster that was up-regulated and showed the same expression trend. In this cluster, many genes may be involved in abiotic stress response such as WRKY, Hsf, and NAC transcription factor genes.
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26
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Xue C, Yao JL, Xue YS, Su GQ, Wang L, Lin LK, Allan AC, Zhang SL, Wu J. PbrMYB169 positively regulates lignification of stone cells in pear fruit. J Exp Bot 2019; 70:1801-1814. [PMID: 30715420 DOI: 10.1093/jxb/erz039] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/17/2019] [Indexed: 05/09/2023]
Abstract
Stone cells negatively affect fruit quality because of their firm and lignified cell walls, so are targets for reduction in pear breeding programmes. However, there is only limited knowledge of the molecular mechanisms underlying the formation of stone cells. Here, we show that PbrMYB169, an R2R3 MYB transcription factor, of Pyrus bretschneideri positively regulates lignification of stone cells in pear fruit. PbrMYB169 was shown to be co-expressed with lignin biosynthesis genes during pear fruit development, and this co-expression pattern was coincident with stone cell formation in the fruit of Pyrus bretschneideri 'Dangshansuli'. The PbrMYB169 expression level was also positively correlated with stone cell content in 36 pear cultivars tested. PbrMYB169 protein significantly activated the promoter of lignin genes C3H1, CCR1, CCOMT2, CAD, 4CL1, 4CL2, HCT2, and LAC18 via binding to AC elements [ACC(T/A)ACC] in these promoters. Furthermore, overexpression of PbrMYB169 in transgenic Arabidopsis plants enhanced the expression of lignin genes, and increased lignin deposition and cell wall thickness of vessel elements, but did not change the ratio of syringyl and guaiacyl lignin monomers. In conclusion, PbrMYB169 appears to be a transcriptional activator of lignin biosynthesis and regulates secondary wall formation in fruit stone cells. This study advances the understanding of the regulation of lignin biosynthesis and provides valuable molecular genetic information for reducing stone cell content in pear fruit.
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Affiliation(s)
- Cheng Xue
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jia-Long Yao
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Yong-Song Xue
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Guan-Qing Su
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Liang Wang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Li-Kun Lin
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Andrew C Allan
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag, Auckland, New Zealand
| | - Shao-Ling Zhang
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jun Wu
- Center of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
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27
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Vezzulli S, Malacarne G, Masuero D, Vecchione A, Dolzani C, Goremykin V, Mehari ZH, Banchi E, Velasco R, Stefanini M, Vrhovsek U, Zulini L, Franceschi P, Moser C. The Rpv3-3 Haplotype and Stilbenoid Induction Mediate Downy Mildew Resistance in a Grapevine Interspecific Population. Front Plant Sci 2019; 10:234. [PMID: 30894868 PMCID: PMC6414455 DOI: 10.3389/fpls.2019.00234] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/12/2019] [Indexed: 05/04/2023]
Abstract
The development of new resistant varieties to the oomycete Plasmopara viticola (Berk.& Curt) is a promising way to combat downy mildew (DM), one of the major diseases threatening the cultivated grapevine (Vitis vinifera L.). Taking advantage of a segregating population derived from "Merzling" (a mid-resistant hybrid) and "Teroldego" (a susceptible landrace), 136 F1 individuals were characterized by combining genetic, phenotypic, and gene expression data to elucidate the genetic basis of DM resistance and polyphenol biosynthesis upon P. viticola infection. An improved consensus linkage map was obtained by scoring 192 microsatellite markers. The progeny were screened for DM resistance and production of 42 polyphenols. QTL mapping showed that DM resistance is associated with the herein named Rpv3-3 specific haplotype and it identified 46 novel metabolic QTLs linked to 30 phenolics-related parameters. A list of the 95 most relevant candidate genes was generated by specifically exploring the stilbenoid-associated QTLs. Expression analysis of 11 genes in Rpv3-3 +/- genotypes displaying disparity in DM resistance level and stilbenoid accumulation revealed significant new candidates for the genetic control of stilbenoid biosynthesis and oligomerization. These overall findings emphasized that DM resistance is likely mediated by the major Rpv3-3 haplotype and stilbenoid induction.
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Affiliation(s)
- Silvia Vezzulli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giulia Malacarne
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Domenico Masuero
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Antonella Vecchione
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Chiara Dolzani
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Vadim Goremykin
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Zeraye Haile Mehari
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Ethiopian Institute of Agricultural Research, Addis Ababa, Ethiopia
| | - Elisa Banchi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Riccardo Velasco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- CREA Research Centre for Viticulture and Enology, Conegliano, Italy
| | - Marco Stefanini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Urska Vrhovsek
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Luca Zulini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Pietro Franceschi
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Claudio Moser
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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28
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Lin Y, Jiang L, Chen Q, Li Y, Zhang Y, Luo Y, Zhang Y, Sun B, Wang X, Tang H. Comparative Transcriptome Profiling Analysis of Red- and White-Fleshed Strawberry (Fragaria�ananassa) Provides New Insight into the Regulation of the Anthocyanin Pathway. Plant Cell Physiol 2018; 59:1844-1859. [PMID: 29800352 DOI: 10.1093/pcp/pcy098] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/14/2018] [Indexed: 05/07/2023]
Abstract
Anthocyanins are water-soluble pigments in plants. They confer both economic and healthy profits for humans. To gain a deeper insight into the regulation of anthocyanin biosynthesis in octoploid strawberry (Fragaria�ananassa; Fa), a widely consumed economically important fruit, we performed comparative transcriptomic analysis of red- and white-fleshed strawberry cultivars in two ripening stages. In total, 365,455 non-redundant transcripts were assembled from the RNA sequencing (RNAseq) data. Of this collection, 377 were annotated as putative anthocyanin-related transcripts. Differential expression analysis revealed that 57 anthocyanin biosynthesis transcripts were down-regulated, and 89 transcription factors (TFs) were either down- or up-regulated under anthocyanin deficiency. Additionally, amongst the 50,601 putative long non-coding RNAs (lncRNAs) identified here, 68 lncRNAs were differentially expressed and co-expressed with differentially expressed anthocyanin-related mRNAs; 2,070 co-expressing lncRNA-mRNA pairs were generated. Expression profile analysis revealed that it was the limited expression of FaF3'H (flavonoid 3'-hydroxylase) that blocked the cyanidin 3-glucoside accumulation in the two investigated strawberry cultivars. This was further supported by a transient overexpression experiment with FaMYB10. The down-regulated lncRNAs might participate in anthocyanin regulation by acting as targets for microRNAs (miRNAs). The level of competitive intensity in miRNA and lncRNA for the same mRNA targets was probably lower in the white-fleshed strawberries, which can release the repression effect of the mRNAs in red-fleshed strawberry as a result. This study for the first time presents lncRNAs related to anthocyanins in strawberries, provides new insights into the anthocyanin regulatory network and also lays the foundation for identifying new anthocyanin regulators in strawberry.
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Affiliation(s)
- Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Leiyu Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yali Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Pomology & Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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Bontpart T, Ferrero M, Khater F, Marlin T, Vialet S, Vallverdù-Queralt A, Pinasseau L, Ageorges A, Cheynier V, Terrier N. Focus on putative serine carboxypeptidase-like acyltransferases in grapevine. Plant Physiol Biochem 2018; 130:356-366. [PMID: 30055344 DOI: 10.1016/j.plaphy.2018.07.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/18/2018] [Indexed: 05/23/2023]
Abstract
Grapevine (Vitis vinifera L.) berry synthesizes and accumulates a large array of phenolic compounds (e.g. flavonoids and hydroxycinnamic acid derivatives), some of which result from acylation mechanisms. In grapevine, the genes encoding enzymes responsible for such acylation are largely unknown. Enzymes classified as serine carboxypeptidases (SCPs), able to transfer acyl moieties from a glucose ester, have previously been characterized in plants, and named serine carboxypeptidase-like acyltransferases (SCL-ATs). We performed genome-wide identification of SCP sequences in V. vinifera. Phylogenetic analysis revealed that only 12 grapevine SCPs, grouped in clade IA with previously characterized SCPL-AT could have an acylation function. Interestingly, seven putative SCP-ATs are grouped in a 400 kb cluster in chromosome 3. The expression level of putative SCPL-ATs has been evaluated at key stages of grape berry development in the main tissues and compared with the content of acylated phenolic compounds in the corresponding samples. The expression levels of VvGAT1 and VvGAT2 and that of VvSCP5 were increased in hairy-roots overexpressing transcription factors inducing the biosynthesis of proanthocyanidins and anthocyanins, respectively. These findings open the way for the functional characterization of the identified putative SCPL-AT from grapevine.
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Affiliation(s)
- Thibaut Bontpart
- SPO, INRA, Montpellier Supagro, Univ Montpellier, Montpellier, France.
| | - Manuela Ferrero
- Laboratory of Plant Physiology, DISAFA - Turin University, Grugliasco, 10095, TO, Italy
| | - Fida Khater
- SPO, INRA, Montpellier Supagro, Univ Montpellier, Montpellier, France
| | - Thérèse Marlin
- SPO, INRA, Montpellier Supagro, Univ Montpellier, Montpellier, France
| | - Sandrine Vialet
- SPO, INRA, Montpellier Supagro, Univ Montpellier, Montpellier, France
| | | | - Lucie Pinasseau
- SPO, INRA, Montpellier Supagro, Univ Montpellier, Montpellier, France
| | - Agnès Ageorges
- SPO, INRA, Montpellier Supagro, Univ Montpellier, Montpellier, France
| | | | - Nancy Terrier
- SPO, INRA, Montpellier Supagro, Univ Montpellier, Montpellier, France
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Marrano A, Micheletti D, Lorenzi S, Neale D, Grando MS. Genomic signatures of different adaptations to environmental stimuli between wild and cultivated Vitis vinifera L. Hortic Res 2018; 5:34. [PMID: 29977570 PMCID: PMC6026492 DOI: 10.1038/s41438-018-0041-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/23/2018] [Accepted: 04/06/2018] [Indexed: 05/03/2023]
Abstract
The application of population genetic methods in combination with gene mapping strategies can help to identify genes and mutations selected during the evolution from wild plants to crops and to explore the considerable genetic variation still maintained in natural populations. We genotyped a grapevine germplasm collection of 44 wild (Vitis vinifera subsp. sylvestris) and 48 cultivated (V. vinifera subsp. sativa) accessions at 54 K single-nucleotide polymorphisms (SNPs) to perform a whole-genome comparison of the main population genetic statistics. The analysis of Wright Fixation Index (FST) along the whole genome allowed us to identify several putative "signatures of selection" spanning over two thousand SNPs significantly differentiated between sativa and sylvestris. Many of these genomic regions included genes involved in the adaptation to environmental changes. An overall reduction of nucleotide diversity was observed across the whole genome within sylvestris, supporting a small effective population size of the wild grapevine. Tajima's D resulted positive in both wild and cultivated subgroups, which may indicate an ongoing balancing selection. Association mapping for six domestication-related traits was performed in combination with population genetics, providing further evidence of different perception and response to environmental stresses between sativa and sylvestris.
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Affiliation(s)
- Annarita Marrano
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
| | - Diego Micheletti
- Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
| | - Silvia Lorenzi
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
| | - David Neale
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - M. Stella Grando
- Department of Genomics and Biology of Fruit Crops, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all ‘Adige (TN), Italy
- Center Agriculture Food Environment (C3A), University of Trento, San Michele all ‘Adige (TN), Italy
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Bigard A, Berhe DT, Maoddi E, Sire Y, Boursiquot JM, Ojeda H, Péros JP, Doligez A, Romieu C, Torregrosa L. Vitis vinifera L. Fruit Diversity to Breed Varieties Anticipating Climate Changes. Front Plant Sci 2018; 9:455. [PMID: 29765379 PMCID: PMC5938353 DOI: 10.3389/fpls.2018.00455] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/22/2018] [Indexed: 05/04/2023]
Abstract
The wine industry is facing critical issues due to climate changes since production is established on very tight Genotype × Environment interaction bases. While, some cultivation practices may reduce adverse effects of abiotic stresses on the vines, e.g., the use of irrigation to mitigate drought, the deleterious impacts of warming on fruit development are difficult to manage. Elevated temperature alters grapevine fruit growth and composition, with a critical increase of the sugars/organic acids ratio. Select grapes with improved metabolite balances to offset high temperature effects is a valuable option to sustain viticulture. Unfortunately, the lack of knowledge about the genetic diversity for fruit traits impacted by temperature impairs the design of breeding programs. This study aimed to assess the variation in berry volume, main sugars and organic acids amounts in genetic resources. Fruit phenotyping focused on two critical stages of development: the end of green lag phase when organic acidity reaches its maximum, and the ripe stage when sugar unloading and water uptake stop. For that purpose, we studied a panel of 33 genotypes, including 12 grapevine varieties and 21 microvine offspring. To determine the date of sampling for each critical stage, fruit texture and growth were carefully monitored. Analyses at both stages revealed large phenotypic variation for malic and tartaric acids, as well as for sugars and berry size. At ripe stage, fruit fresh weight ranged from 1.04 to 5.25 g and sugar concentration from 751 to 1353 mmol.L-1. The content in organic acids varied both in quantity (from 80 to 361 meq.L-1) and in composition, with malic to tartaric acid ratio ranging from 0.13 to 3.62. At the inter-genotypic level, data showed no link between berry growth and osmoticum accumulation per fruit unit, suggesting that berry water uptake is not dependent only on fruit osmotic potential. Diversity among varieties for berry size, sugar accumulation and malic to tartaric acid ratio could be exploited through cross-breeding. This provides interesting prospects for improving grapevine to mitigate some adverse effects of climate warming on grapevine fruit volume and quality.
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Affiliation(s)
- Antoine Bigard
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- UE INRA de Pech-Rouge, University of Montpellier, INRA, Montpellier, France
| | - Dargie T Berhe
- UE INRA de Pech-Rouge, University of Montpellier, INRA, Montpellier, France
- SNNPRS, Dilla University, Dilla, Ethiopia
| | - Eleonora Maoddi
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Yannick Sire
- UE INRA de Pech-Rouge, University of Montpellier, INRA, Montpellier, France
| | | | - Hernan Ojeda
- UE INRA de Pech-Rouge, University of Montpellier, INRA, Montpellier, France
- UE INRA de Vassal, Grapevine Biological Resource Centre, University of Montpellier, INRA, Montpellier, France
| | - Jean-Pierre Péros
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Agnès Doligez
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Charles Romieu
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Laurent Torregrosa
- AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- UE INRA de Pech-Rouge, University of Montpellier, INRA, Montpellier, France
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Zhou Y, Yuan C, Ruan S, Zhang Z, Meng J, Xi Z. Exogenous 24-Epibrassinolide Interacts with Light to Regulate Anthocyanin and Proanthocyanidin Biosynthesis in Cabernet Sauvignon (Vitis vinifera L.). Molecules 2018; 23:molecules23010093. [PMID: 29315208 PMCID: PMC6017727 DOI: 10.3390/molecules23010093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 12/04/2022] Open
Abstract
Anthocyanins and proanthocyanidins (PAs) are crucial factors that affect the quality of grapes and the making of wine, which were stimulated by various stimuli and environment factors (sugar, hormones, light, and temperature). The aim of the study was to investigate the influence of exogenous 24-Epibrassinolide (EBR) and light on the mechanism of anthocyanins and PAs accumulation in grape berries. Grape clusters were sprayed with EBR (0.4 mg/L) under light and darkness conditions (EBR + L, EBR + D), or sprayed with deionized water under light and darkness conditions as controls (L, D), at the onset of veraison. A large amount of anthocyanins accumulated in the grape skins and was measured under EBR + L and L treatments, whereas EBR + D and D treatments severely suppressed anthocyanin accumulation. This indicated that EBR treatment could produce overlay effects under light, in comparison to that in dark. Real-time quantitative PCR analysis indicated that EBR application up-regulated the expression of genes (VvCHI1, VvCHS2, VvCHS3, VvDFR, VvLDOX, VvMYBA1) under light conditions. Under darkness conditions, only early biosynthetic genes of anthocyanin biosynthesis responded to EBR. Furthermore, we also analyzed the expression levels of the BR-regulated transcription factor VvBZR1 (Brassinazole-resistant 1) and light-regulated transcription factor VvHY5 (Elongated hypocotyl 5). Our results suggested that EBR and light had synergistic effects on the expression of genes in the anthocyanin biosynthesis pathway.
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Affiliation(s)
- Yali Zhou
- College of Enology, Northwest A&F University, Yangling 712100, China.
| | - Chunlong Yuan
- College of Enology, Northwest A&F University, Yangling 712100, China.
- Shaanxi Engineering Research Center for Viti-Viniculture, Yangling 712100, China.
| | - Shicheng Ruan
- Chateau Changyu Rena Co., Ltd., Xianyang 712000, China.
| | - Zhenwen Zhang
- College of Enology, Northwest A&F University, Yangling 712100, China.
- Shaanxi Engineering Research Center for Viti-Viniculture, Yangling 712100, China.
| | - Jiangfei Meng
- College of Enology, Northwest A&F University, Yangling 712100, China.
- Shaanxi Engineering Research Center for Viti-Viniculture, Yangling 712100, China.
| | - Zhumei Xi
- College of Enology, Northwest A&F University, Yangling 712100, China.
- Shaanxi Engineering Research Center for Viti-Viniculture, Yangling 712100, China.
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Wang P, Su L, Gao H, Jiang X, Wu X, Li Y, Zhang Q, Wang Y, Ren F. Genome-Wide Characterization of bHLH Genes in Grape and Analysis of their Potential Relevance to Abiotic Stress Tolerance and Secondary Metabolite Biosynthesis. Front Plant Sci 2018; 9:64. [PMID: 29449854 PMCID: PMC5799661 DOI: 10.3389/fpls.2018.00064] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/12/2018] [Indexed: 05/17/2023]
Abstract
Basic helix-loop-helix (bHLH) transcription factors are involved in many abiotic stress responses as well as flavonol and anthocyanin biosynthesis. In grapes (Vitis vinifera L.), flavonols including anthocyanins and condensed tannins are most abundant in the skins of the berries. Flavonols are important phytochemicals for viticulture and enology, but grape bHLH genes have rarely been examined. We identified 94 grape bHLH genes in a genome-wide analysis and performed Nr and GO function analyses for these genes. Phylogenetic analyses placed the genes into 15 clades, with some remaining orphans. 41 duplicate gene pairs were found in the grape bHLH gene family, and all of these duplicate gene pairs underwent purifying selection. Nine triplicate gene groups were found in the grape bHLH gene family and all of these triplicate gene groups underwent purifying selection. Twenty-two grape bHLH genes could be induced by PEG treatment and 17 grape bHLH genes could be induced by cold stress treatment including a homologous form of MYC2, VvbHLH007. Based on the GO or Nr function annotations, we found three other genes that are potentially related to anthocyanin or flavonol biosynthesis: VvbHLH003, VvbHLH007, and VvbHLH010. We also performed a cis-acting regulatory element analysis on some genes involved in flavonoid or anthocyanin biosynthesis and our results showed that most of these gene promoters contained G-box or E-box elements that could be recognized by bHLH family members.
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Monticolo F, Colantuono C, Chiusano ML. Shaping the evolutionary tree of green plants: evidence from the GST family. Sci Rep 2017; 7:14363. [PMID: 29084977 DOI: 10.1038/s41598-017-14316-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/05/2017] [Indexed: 12/13/2022] Open
Abstract
Glutathione-S-transferases (GSTs) are encoded by genes belonging to a wide ubiquitous family in aerobic species and catalyze the conjugation of electrophilic substrates to glutathione (GSH). GSTs are divided in different classes, both in plants and animals. In plants, GSTs function in several pathways, including those related to secondary metabolites biosynthesis, hormone homeostasis, defense from pathogens and allow the prevention and detoxification of damage from heavy metals and herbicides. 1107 GST protein sequences from 20 different plant species with sequenced genomes were analyzed. Our analysis assigns 666 unclassified GSTs proteins to specific classes, remarking the wide heterogeneity of this gene family. Moreover, we highlighted the presence of further subclasses within each class. Regarding the class GST-Tau, one possible subclass appears to be present in all the Tau members of ancestor plant species. Moreover, the results highlight the presence of members of the Tau class in Marchantiophytes and confirm previous observations on the absence of GST-Tau in Bryophytes and green algae. These results support the hypothesis regarding the paraphyletic origin of Bryophytes, but also suggest that Marchantiophytes may be on the same branch leading to superior plants, depicting an alternative model for green plants evolution.
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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.). Front Plant Sci 2017; 8:780. [PMID: 28559906 PMCID: PMC5432621 DOI: 10.3389/fpls.2017.00780] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Koyama K, Kamigakiuchi H, Iwashita K, Mochioka R, Goto-Yamamoto N. Polyphenolic diversity and characterization in the red-purple berries of East Asian wild Vitis species. Phytochemistry 2017; 134:78-86. [PMID: 27887737 DOI: 10.1016/j.phytochem.2016.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 09/10/2016] [Accepted: 10/11/2016] [Indexed: 05/20/2023]
Abstract
Grapes (Vitis spp.) produce diverse polyphenolic compounds, which are phytochemicals that contribute to human health. In this study, the polyphenolic profiles of the red-purple berries of two wild grape species native to Japan, Vitis ficifolia and V. coignetiae, and their interspecific hybrid cultivars were investigated and compared with the profiles of V. vinifera and V. × labruscana cultivars. Proanthocyanidins (PAs) were present at lower concentrations in both skins and seeds of wild grape species and their hybrid cultivars than those in V. vinifera cultivars. They also differed in their composition, consisting mainly of epicatechin in wild grape species, but containing considerable amounts of both epigallocatechin in the skins and epicatechin gallate in the seeds of V. vinifera. In contrast, V. ficifolia varieties and their hybrid cultivars accumulated high concentrations of diverse anthocyanins, and whose compositions of anthocyanins and flavonols differed between species in their degree of modification by glucosylation, acylation, methylation and B-ring hydroxylation. Principal component analysis (PCA) indicated that the polyphenolic constituents clearly separate V. vinifera and V. × labruscana cultivars from the wild grape species as well as between wild grape species, V. coignetiae and V. ficifolia. Intermediate compositions were also observed in the hybrid cultivars between these wild grape species and V. vinifera.
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Affiliation(s)
- Kazuya Koyama
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.
| | - Hiroshi Kamigakiuchi
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan
| | - Kazuhiro Iwashita
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan
| | - Ryosuke Mochioka
- University Farm, Faculty of Agriculture, Kagawa University, Showa, Sanuki, Kagawa, 769-2304, Japan
| | - Nami Goto-Yamamoto
- National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan
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Wong DCJ, Matus JT. Constructing Integrated Networks for Identifying New Secondary Metabolic Pathway Regulators in Grapevine: Recent Applications and Future Opportunities. Front Plant Sci 2017; 8:505. [PMID: 28446914 PMCID: PMC5388765 DOI: 10.3389/fpls.2017.00505] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/22/2017] [Indexed: 05/19/2023]
Abstract
Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Whereas, some studies have used gene co-expression networks to find common pathways and putative targets for transcription factors related to development and metabolism, others have defined networks of primary and secondary metabolites for characterizing the main metabolic differences between cultivars throughout fruit ripening. Lately, proteomic-related networks and those integrating genome-wide analyses of promoter regulatory elements have also been generated. The integration of all these data in multilayered networks allows building complex maps of molecular regulation and interaction. This perspective article describes the currently available network data and related resources for grapevine. With the aim of illustrating data integration approaches into network construction and analysis in grapevine, we searched for berry-specific regulators of the phenylpropanoid pathway. We generated a composite network consisting of overlaying maps of co-expression between structural and transcription factor genes, integrated with the presence of promoter cis-binding elements, microRNAs, and long non-coding RNAs (lncRNA). This approach revealed new uncharacterized transcription factors together with several microRNAs potentially regulating different steps of the phenylpropanoid pathway, and one particular lncRNA compromising the expression of nine stilbene synthase (STS) genes located in chromosome 10. Application of network-based approaches into multi-omics data will continue providing supplementary resources to address important questions regarding grapevine fruit quality and composition.
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Affiliation(s)
- Darren C. J. Wong
- Ecology and Evolution, Research School of Biology, Australian National UniversityActon, ACT, Australia
| | - José Tomás Matus
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UBBarcelona, Spain
- *Correspondence: José Tomás Matus
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Sun L, Fan X, Zhang Y, Jiang J, Sun H, Liu C. Transcriptome analysis of genes involved in anthocyanins biosynthesis and transport in berries of black and white spine grapes ( Vitis davidii). Hereditas 2016; 153:17. [PMID: 28096779 PMCID: PMC5226110 DOI: 10.1186/s41065-016-0021-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 11/30/2016] [Indexed: 12/22/2022] Open
Abstract
Background The color of berry skin is an important economic trait for grape and is essentially determined by the components and content of anthocyanins. The fruit color of Chinese wild grapes is generally black, and the profile of anthocyanins in Chinese wild grapes is significantly different from that of Vitis vinifera. However, V. davidii is the only species that possesses white berry varieties among Chinese wild grape species. Thus, we performed a transcriptomic analysis to compare the difference of transcriptional level in black and white V. davidii, in order to find some key genes that are related to anthocyanins accumulation in V. davidii. Results The results of anthocyanins detection revealed that 3,5-O-diglucoside anthocyanins is the predominant anthocyanins in V. davidii. It showed obvious differences from V. vinifera in the profile of the composition of anthocyanins. The transcriptome sequencing by Illumina mRNA-Seq technology generated an average of 57 million 100-base pair clean reads from each sample. Differential gene expression analysis revealed thousands of differential expression genes (DEGs) in the pairwise comparison of different fruit developmental stages between and within black and white V. davidii. After the analysis of functional category enrichment and differential expression patterns of DEGs, 46 genes were selected as the candidate genes. Some genes have been reported as being related to anthocyanins accumulation, and some genes were newly found in our study as probably being related to anthocyanins accumulation. We inferred that 3AT (VIT_03s0017g00870) played an important role in anthocyanin acylation, GST4 (VIT_04s0079g00690) and AM2 (VIT_16s0050g00910) played important roles in anthocyanins transport in V. davidii. The expression of some selected DEGs was further confirmed by quantitative real-time PCR (qRT-PCR). Conclusions The present study investigated the transcriptomic profiles of berry skin from black and white spine grapes at three fruit developmental stages by Illumina mRNA-Seq technology. It revealed the variety specificity of anthocyanins accumulation in V. davidi at the transcriptional level. The data reported here will provide a valuable resource for understanding anthocyanins accumulation in grapes, especially in V. davidii. Electronic supplementary material The online version of this article (doi:10.1186/s41065-016-0021-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lei Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Xiucai Fan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Ying Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Jianfu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Haisheng Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Chonghuai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
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Wong DCJ, Schlechter R, Vannozzi A, Höll J, Hmmam I, Bogs J, Tornielli GB, Castellarin SD, Matus JT. A systems-oriented analysis of the grapevine R2R3-MYB transcription factor family uncovers new insights into the regulation of stilbene accumulation. DNA Res 2016; 23:451-466. [PMID: 27407139 PMCID: PMC5066171 DOI: 10.1093/dnares/dsw028] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/17/2016] [Indexed: 01/12/2023] Open
Abstract
R2R3-MYB transcription factors (TFs) belong to a large and functionally diverse protein superfamily in plants. In this study, we explore the evolution and function of this family in grapevine (Vitis vinifera L.), a high-value fruit crop. We identified and manually curated 134 genes using RNA-Seq data, and named them systematically according to the Super-Nomenclature Committee. We identified novel genes, splicing variants and grapevine/woody-specific duplicated subgroups, suggesting possible neo- and sub-functionalization events. Regulatory network analysis ascribed biological functions to uncharacterized genes and validated those of known genes (e.g. secondary cell wall biogenesis and flavonoid biosynthesis). A comprehensive analysis of different MYB binding motifs in the promoters of co-expressed genes predicted grape R2R3-MYB binding preferences and supported evidence for putative downstream targets. Enrichment of cis-regulatory motifs for diverse TFs reinforced the notion of transcriptional coordination and interaction between MYBs and other regulators. Analysis of the network of Subgroup 2 showed that the resveratrol-related VviMYB14 and VviMYB15 share common co-expressed STILBENE SYNTHASE genes with the uncharacterized VviMYB13. These regulators have distinct expression patterns within organs and in response to biotic and abiotic stresses, suggesting a pivotal role of VviMYB13 in regulating stilbene accumulation in vegetative tissues and under biotic stress conditions.
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Affiliation(s)
| | | | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, 35020 Legnaro, Padova, Italy
| | - Janine Höll
- Centre for Organismal Studies Heidelberg, University of Heidelberg, 69120 Heidelberg, Germany
| | - Ibrahim Hmmam
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, 35020 Legnaro, Padova, Italy
| | - Jochen Bogs
- Dienstleistungszentrum Laendlicher Raum Rheinpfalz, Breitenweg 71, Viticulture and Enology Group, 67435 Neustadt/W, Germany.,Fachhochschule Bingen, Berlinstr. 109, 55411 Bingen am Rhein, Germany
| | | | | | - José Tomás Matus
- Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona 08193, Spain
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Malacarne G, Coller E, Czemmel S, Vrhovsek U, Engelen K, Goremykin V, Bogs J, Moser C. The grapevine VvibZIPC22 transcription factor is involved in the regulation of flavonoid biosynthesis. J Exp Bot 2016; 67:3509-22. [PMID: 27194742 PMCID: PMC4892739 DOI: 10.1093/jxb/erw181] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In grapevine, flavonoids constitute one of the most abundant subgroups of secondary metabolites, influencing the quality, health value, and typicity of wines. Their synthesis in many plant species is mainly regulated at the transcriptional level by modulation of flavonoid pathway genes either by single regulators or by complexes of different regulators. In particular, bZIP and MYB factors interact synergistically in the recognition of light response units present in the promoter of some genes of the pathway, thus mediating light-dependent flavonoid biosynthesis. We recently identified VvibZIPC22, a member of clade C of the grapevine bZIP family, in a quantitative trait locus (QTL) specifically associated with kaemperol content in mature berries. Here, to validate the involvement of this candidate gene in the fine regulation of flavonol biosynthesis, we characterized its function by in vitro and in vivo experiments. A role for this gene in the control of flavonol biosynthesis was indeed confirmed by its highest expression at flowering and during UV light-mediated induction, paralleled by accumulation of the flavonol synthase 1 transcript and flavonol compounds. The overexpression of VvibZIPC22 in tobacco caused a significant increase in several flavonoids in the flower, via induction of general and specific genes of the pathway. In agreement with this evidence, VvibZIPC22 was able to activate the promoters of specific genes of the flavonoid pathway, alone or together with other factors, as revealed by transient reporter assays. These findings, supported by in silico indications, allowed us to propose VvibZIPC22 as a new regulator of flavonoid biosynthesis in grapevine.
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Affiliation(s)
- Giulia Malacarne
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Emanuela Coller
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Stefan Czemmel
- Centre for Organismal Studies Heidelberg, University of Heidelberg, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Urska Vrhovsek
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Kristof Engelen
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Vadim Goremykin
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Jochen Bogs
- Centre for Organismal Studies Heidelberg, University of Heidelberg, Im Neuenheimer Feld 360, D-69120 Heidelberg, Germany Studiengang Weinbau und Oenologie, Dienstleistungszentrum Laendlicher Raum Rheinpfalz, Breitenweg 71, D-67435 Neustadt, Germany
| | - Claudio Moser
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, 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 Biol 2016; 16:67. [PMID: 27001212 PMCID: PMC4802899 DOI: 10.1186/s12870-016-0760-1] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Rustioni L, De Lorenzis G, Hârţa M, Failla O. Pink berry grape (Vitis vinifera L.) characterization: Reflectance spectroscopy, HPLC and molecular markers. Plant Physiol Biochem 2016; 98:138-45. [PMID: 26687319 DOI: 10.1016/j.plaphy.2015.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 05/27/2023]
Abstract
Color has a fundamental role for the qualitative evaluation and cultivar characterization of fruits. In grape, a normally functional pigment biosynthesis leads to the accumulation of a high quantity of anthocyanins. In this work, 28 Vitis vinifera L. cultivars accumulating low anthocyanins in berries were studied to characterize the biosynthetic dysfunctions in both a phenotypic and genotypic point of view. Reflectance spectroscopy, HPLC profiles and molecular markers related to VvMybA1 and VvMybA2 genes allowed a detailed description of the pigment-related characteristics of these cultivars. Data were consistent concerning the heterozygosity of the non-functional allele in both investigated genes, resulting in a low colored phenotype as described by reflectance. However, the variability in berry colour among our samples was not fully explained by MybA locus, probably due to specific interferences among the biosynthetic pathways, as suggested by the anthocyanin profile variations detected among our samples. The results presented in this work confirmed the importance of the genetic background: grapes accumulating high levels of cyanidin-3-O-glucosides (di-substituted anthocyanin) are generally originated by white cultivar retro-mutations and they seem to preserve the anomalies in the flavonoid hydroxylases enzymes which negatively affect the synthesis of tri-substituted anthocyanins.
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Affiliation(s)
- Laura Rustioni
- CIRIVE, Centro Interdipartimentale di Ricerca per l'Innovazione in Viticoltura ed Enologia, Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy.
| | - Gabriella De Lorenzis
- CIRIVE, Centro Interdipartimentale di Ricerca per l'Innovazione in Viticoltura ed Enologia, Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Monica Hârţa
- Life Science Institute, Faculty of Horticulture, University of Agricultural Sciences and Veterinary Medicine, 3-5 Mănăştur st., 400372, Cluj-Napoca Romania
| | - Osvaldo Failla
- CIRIVE, Centro Interdipartimentale di Ricerca per l'Innovazione in Viticoltura ed Enologia, Dipartimento di Scienze Agrarie e Ambientali - Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
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Moretto M, Sonego P, Pilati S, Malacarne G, Costantini L, Grzeskowiak L, Bagagli G, Grando MS, Moser C, Engelen K. VESPUCCI: Exploring Patterns of Gene Expression in Grapevine. Front Plant Sci 2016; 7:633. [PMID: 27242836 PMCID: PMC4862315 DOI: 10.3389/fpls.2016.00633] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/25/2016] [Indexed: 05/20/2023]
Abstract
Large-scale transcriptional studies aim to decipher the dynamic cellular responses to a stimulus, like different environmental conditions. In the era of high-throughput omics biology, the most used technologies for these purposes are microarray and RNA-Seq, whose data are usually required to be deposited in public repositories upon publication. Such repositories have the enormous potential to provide a comprehensive view of how different experimental conditions lead to expression changes, by comparing gene expression across all possible measured conditions. Unfortunately, this task is greatly impaired by differences among experimental platforms that make direct comparisons difficult. In this paper, we present the Vitis Expression Studies Platform Using COLOMBOS Compendia Instances (VESPUCCI), a gene expression compendium for grapevine which was built by adapting an approach originally developed for bacteria, and show how it can be used to investigate complex gene expression patterns. We integrated nearly all publicly available microarray and RNA-Seq expression data: 1608 gene expression samples from 10 different technological platforms. Each sample has been manually annotated using a controlled vocabulary developed ad hoc to ensure both human readability and computational tractability. Expression data in the compendium can be visually explored using several tools provided by the web interface or can be programmatically accessed using the REST interface. VESPUCCI is freely accessible at http://vespucci.colombos.fmach.it.
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Affiliation(s)
- Marco Moretto
- Department of Computational Biology, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
- Department of Biology, University of PadovaPadova, Italy
| | - Paolo Sonego
- Department of Computational Biology, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
| | - Stefania Pilati
- Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
| | - Giulia Malacarne
- Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
| | - Laura Costantini
- Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
| | - Lukasz Grzeskowiak
- Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
| | - Giorgia Bagagli
- Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
| | - Maria Stella Grando
- Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
| | - Claudio Moser
- Department of Genomics and Biology of Fruit Crop, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
| | - Kristof Engelen
- Department of Computational Biology, Research and Innovation Center, Fondazione Edmund MachTrento, Italy
- *Correspondence: Kristof Engelen,
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Blanco-Ulate B, Amrine KCH, Collins TS, Rivero RM, Vicente AR, Morales-Cruz A, Doyle CL, Ye Z, Allen G, Heymann H, Ebeler SE, Cantu D. Developmental and Metabolic Plasticity of White-Skinned Grape Berries in Response to Botrytis cinerea during Noble Rot. Plant Physiol 2015; 169:2422-43. [PMID: 26450706 PMCID: PMC4677888 DOI: 10.1104/pp.15.00852] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/06/2015] [Indexed: 05/24/2023]
Abstract
Noble rot results from exceptional infections of ripe grape (Vitis vinifera) berries by Botrytis cinerea. Unlike bunch rot, noble rot promotes favorable changes in grape berries and the accumulation of secondary metabolites that enhance wine grape composition. Noble rot-infected berries of cv Sémillon, a white-skinned variety, were collected over 3 years from a commercial vineyard at the same time that fruit were harvested for botrytized wine production. Using an integrated transcriptomics and metabolomics approach, we demonstrate that noble rot alters the metabolism of cv Sémillon berries by inducing biotic and abiotic stress responses as well as ripening processes. During noble rot, B. cinerea induced the expression of key regulators of ripening-associated pathways, some of which are distinctive to the normal ripening of red-skinned cultivars. Enhancement of phenylpropanoid metabolism, characterized by a restricted flux in white-skinned berries, was a common outcome of noble rot and red-skinned berry ripening. Transcript and metabolite analyses together with enzymatic assays determined that the biosynthesis of anthocyanins is a consistent hallmark of noble rot in cv Sémillon berries. The biosynthesis of terpenes and fatty acid aroma precursors also increased during noble rot. We finally characterized the impact of noble rot in botrytized wines. Altogether, the results of this work demonstrated that noble rot causes a major reprogramming of berry development and metabolism. This desirable interaction between a fruit and a fungus stimulates pathways otherwise inactive in white-skinned berries, leading to a greater accumulation of compounds involved in the unique flavor and aroma of botrytized wines.
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Affiliation(s)
- Barbara Blanco-Ulate
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Katherine C H Amrine
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Thomas S Collins
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Rosa M Rivero
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Ariel R Vicente
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Abraham Morales-Cruz
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Carolyn L Doyle
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Zirou Ye
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Greg Allen
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Hildegarde Heymann
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Susan E Ebeler
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, California 95616 (B.B.-U., K.C.H.A., T.S.C., A.M.-C., C.L.D., Z.Y., H.H., S.E.E., D.C.);Viticulture and Enology Program, Washington State University, Tri-Cities, Richland, Washington 99354 (T.S.C.);Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, 30100 Murcia, Spain (R.M.R.);Consejo Nacional de Investigaciones Científicas y Técnicas, 1900 La Plata, Argentina (A.R.V.);Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de La Plata, 1900 La Plata, Argentina (A.R.V.); andDolce Winery, Oakville, California 94562 (G.A.)
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Rinaldo AR, Cavallini E, Jia Y, Moss SMA, McDavid DAJ, Hooper LC, Robinson SP, Tornielli GB, Zenoni S, Ford CM, Boss PK, Walker AR. A Grapevine Anthocyanin Acyltransferase, Transcriptionally Regulated by VvMYBA, Can Produce Most Acylated Anthocyanins Present in Grape Skins. Plant Physiol 2015; 169:1897-916. [PMID: 26395841 PMCID: PMC4634099 DOI: 10.1104/pp.15.01255] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 08/13/2015] [Indexed: 05/21/2023]
Abstract
Anthocyanins are flavonoid compounds responsible for red/purple colors in the leaves, fruit, and flowers of many plant species. They are produced through a multistep pathway that is controlled by MYB transcription factors. VvMYBA1 and VvMYBA2 activate anthocyanin biosynthesis in grapevine (Vitis vinifera) and are nonfunctional in white grapevine cultivars. In this study, transgenic grapevines with altered VvMYBA gene expression were developed, and transcript analysis was carried out on berries using a microarray technique. The results showed that VvMYBA is a positive regulator of the later stages of anthocyanin synthesis, modification, and transport in cv Shiraz. One up-regulated gene, ANTHOCYANIN 3-O-GLUCOSIDE-6″-O-ACYLTRANSFERASE (Vv3AT), encodes a BAHD acyltransferase protein (named after the first letter of the first four characterized proteins: BEAT [for acetyl CoA:benzylalcohol acetyltransferase], AHCT [for anthocyanin O-hydroxycinnamoyltransferase], HCBT [for anthranilate N-hydroxycinnamoyl/benzoyltransferase], and DAT [for deacetylvindoline 4-O-acetyltransferase]), belonging to a clade separate from most anthocyanin acyltransferases. Functional studies (in planta and in vitro) show that Vv3AT has a broad anthocyanin substrate specificity and can also utilize both aliphatic and aromatic acyl donors, a novel activity for this enzyme family found in nature. In cv Pinot Noir, a red-berried grapevine mutant lacking acylated anthocyanins, Vv3AT contains a nonsense mutation encoding a truncated protein that lacks two motifs required for BAHD protein activity. Promoter activation assays confirm that Vv3AT transcription is activated by VvMYBA1, which adds to the current understanding of the regulation of the BAHD gene family. The flexibility of Vv3AT to use both classes of acyl donors will be useful in the engineering of anthocyanins in planta or in vitro.
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Affiliation(s)
- Amy R Rinaldo
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Erika Cavallini
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Yong Jia
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Sarah M A Moss
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Debra A J McDavid
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Lauren C Hooper
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Simon P Robinson
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Giovanni B Tornielli
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Sara Zenoni
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Christopher M Ford
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Paul K Boss
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
| | - Amanda R Walker
- Commonwealth Scientific and Industrial Research Organization-Agriculture, Wine Innovation West, Hartley Grove, South Australia 5064, Australia (A.R.R., S.M.A.M., D.A.J.M., L.C.H., S.P.R., P.K.B., A.R.W.);School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5005, Australia (A.R.R., Y.J., S.M.A.M., C.M.F.); andDepartment of Biotechnology, University of Verona, 37134 Verona, Italy (E.C., G.B.T., S.Z.)
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Malacarne G, Costantini L, Coller E, Battilana J, Velasco R, Vrhovsek U, Grando MS, Moser C. Regulation of flavonol content and composition in (Syrah×Pinot Noir) mature grapes: integration of transcriptional profiling and metabolic quantitative trait locus analyses. J Exp Bot 2015; 66:4441-53. [PMID: 26071529 PMCID: PMC4507773 DOI: 10.1093/jxb/erv243] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Flavonols are a ubiquitous class of flavonoids that accumulate preferentially in flowers and mature berries. Besides their photo-protective function, they play a fundamental role during winemaking, stabilizing the colour by co-pigmentation with anthocyanins and contributing to organoleptic characteristics. Although the general flavonol pathway has been genetically and biochemically elucidated, the genetic control of flavonol content and composition at harvest is still not clear. To this purpose, the grapes of 170 segregating F1 individuals from a 'Syrah'×'Pinot Noir' population were evaluated at the mature stage for the content of six flavonol aglycons in four seasons. Metabolic data in combination with genetic data enabled the identification of 16 mQTLs (metabolic quantitative trait loci). For the first time, major genetic control by the linkage group 2 (LG 2)/MYBA region on flavonol variation, in particular of tri-hydroxylated flavonols, is demonstrated. Moreover, seven regions specifically associated with the fine control of flavonol biosynthesis are identified. Gene expression profiling of two groups of individuals significantly divergent for their skin flavonol content identified a large set of differentially modulated transcripts. Among these, the transcripts coding for MYB and bZIP transcription factors, methyltranferases, and glucosyltranferases specific for flavonols, proteins, and factors belonging to the UV-B signalling pathway and co-localizing with the QTL regions are proposed as candidate genes for the fine regulation of flavonol content and composition in mature grapes.
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Affiliation(s)
- Giulia Malacarne
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Laura Costantini
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Emanuela Coller
- Computational Biology Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Juri Battilana
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Riccardo Velasco
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Urska Vrhovsek
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Maria Stella Grando
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
| | - Claudio Moser
- Genomics and Biology of Fruit Crops Department, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S. Michele all'Adige, Trento, Italy
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