Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development

AbstractTranscriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in grape are performed using the available genome sequence, PN40024, as reference. However, differences in gene content among grape accessions, which contribute to phenotypic differences among cultivars, suggest that a single reference genome does not represent the species’ entire gene space. Though whole genome assembly and annotation can reveal the relatively unique or “private” gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (Iso-Seq) to sequence full-length cDNA and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, Illumina short reads from ripening berries were used to error-correct low-expression isoforms and to profile isoform expression. By comparing the annotated gene space of Cabernet Sauvignon to other grape cultivars, we demonstrate that the transcriptome reference built with Iso-Seq data represents most of the expressed genes in the grape berries and includes 1,501 cultivar-specific genes. Iso-Seq produced transcriptome profiles similar to those obtained after mapping on a complete genome reference. Together, these results justify the application of Iso-Seq to identify cultivar-specific genes and build a comprehensive reference for transcriptional profiling that circumvents the necessity of a genome reference with its associated costs and computational weight.

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Influence of Light on Grape Berry Growth and Composition Varies during Fruit Development

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.121.5.869 ◽

1996 ◽

Vol 121 (5) ◽

pp. 869-874 ◽

Cited By ~ 128

Author(s):

N.K. Dokoozlian ◽

W.M. Kliewer

Keyword(s):

Fruit Development ◽

Light Exposure ◽

Grape Berry ◽

Pinot Noir ◽

Stage Iii ◽

Cabernet Sauvignon ◽

Fruit Softening ◽

Berry Development ◽

Development Stages ◽

Final Sample

Potted `Cabernet Sauvignon' and `Pinot noir' grapevines (Vitis vinifera L.) grown in a sunlit phytotron were used to study the influence of cluster light exposure during various stages of fruit development on berry growth and composition. Clusters grown without light during berry development stages I and II, stage III, or stages I, II, and III, were compared to clusters exposed to light throughout fruit development (control). The temperature of light-exposed and nonexposed fruit was similar. The weights and diameters of berries grown without light during stages I and II, or stages I, II, and III, were similar and significantly lower than those of the control. Fruit softening in both cultivars, as well as the initiation of berry coloration, was delayed when berries were grown without light during stages I and II. Following fruit softening, berries grown without light during stages I, II, and III were lower in sugar than the control. On the final sample date, `Cabernet Sauvignon' berries grown without light during stages I, II, and III were higher in malate compared to the control. `Pinot noir' berries grown without light during stages I and II, or stages I, II, and III, were lower in malate before fruit softening, and higher in malate following fruit softening, than the control. Control berries had greater skin anthocyanins and phenolics compared to the remaining treatments. Berries grown without light during stages I and II, or stage III, were greater in anthocyanins and phenolics than fruit grown without light during stages I, II, and III. Light had no effect on fruit tartrate concentration or juice pH. Light had its greatest impact on fruit development during the initial stages of berry growth. Berry growth was reduced and ripening delayed when fruit were grown without light during stages I and II. Normal fruit development was not fully restored when these fruit were exposed to light during stage III.

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Towards the definition of a detailed transcriptomic map of berry development

BIO Web of Conferences ◽

10.1051/bioconf/20191301001 ◽

2019 ◽

Vol 13 ◽

pp. 01001

Author(s):

Marianna Fasoli ◽

Chandra L. Richter ◽

Sara Zenoni ◽

Marco Sandri ◽

Paola Zuccolotto ◽

...

Keyword(s):

Gene Expression Analysis ◽

Grape Berry ◽

Pinot Noir ◽

Cabernet Sauvignon ◽

Berry Development ◽

Rna Seq ◽

Molecular Events ◽

Molecular Information ◽

Definition Of ◽

Transcriptomic Level

The progress of the grapevine genomics and the development of high-throughput technologies for gene expression analysis stimulated the investigation of the physical, biochemical and physiological changes of grape berry growth and maturation at transcriptomic level. The molecular information generated in the last decade is however still fragmented since it relies upon detailed analysis of few stages and thus lacks continuity over grape development. To identify the molecular events associated with berry development at a higher temporal resolution and define a transcriptomic map, we performed RNA-seq analysis of berry samples collected every week from fruit-set to maturity in Pinot noir and Cabernet Sauvignon for three consecutive years, resulting in 219 samples. Using the most variable portion of the transcriptome, we built a preliminary transcriptomic model of berry development based on the Cabernet Sauvignon samples. The Pinot noir samples were then aligned onto this preliminary ripening map to investigate its performance in describing the development of another grape variety. A further step for testing the model was the projection of RNA-seq samples of fruit development of five red-skin Italian cultivars. For all these surveys, the transcriptomic route allowed a precise definition of the progression of berry development during both formation and ripening phases.

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Compositional Changes During Grape Berry Development in Relation to Abscisic Acid and Salinity

Functional Plant Biology ◽

10.1071/pp9780415 ◽

1978 ◽

Vol 5 (4) ◽

pp. 415 ◽

Cited By ~ 13

Author(s):

WJS Downton ◽

BR Loveys

Keyword(s):

Abscisic Acid ◽

Chemical Composition ◽

Grape Berry ◽

Reducing Sugar ◽

Cabernet Sauvignon ◽

Berry Development ◽

Grape Berries ◽

Low Salt ◽

Compositional Changes

Changes in the chemical composition of developing Cabernet Sauvignon berries from salt-treated and low-salt vines were followed. Although salinity advanced the timing of veraison, the sequence of changes in the salt-affected berries remained the same as in berries from control plants, viz. concentrations of abscisic acid and reducing sugar increased before proline, arginine, potassium and chloride increased, and before acidity declined. The contribution of these substances to osmotic changes within developing grape berries is discussed.

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Transcriptomic Analyses of Root Restriction Effects on Phytohormone Content and Signal Transduction during Grape Berry Development and Ripening

International Journal of Molecular Sciences ◽

10.3390/ijms19082300 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2300 ◽

Cited By ~ 1

Author(s):

Feng Leng ◽

Jinping Cao ◽

Shiping Wang ◽

Ling Jiang ◽

Xian Li ◽

...

Keyword(s):

Signal Transduction ◽

High Resolution Mass Spectrometry ◽

Transcript Abundance ◽

Ultra Performance Liquid Chromatography ◽

Grape Berry ◽

Enzyme Linked Immunosorbent Assay ◽

Signal Transduction Pathways ◽

Berry Development ◽

Seedless Grape ◽

Root Restriction

Phytohormones strongly influence growth, development and nutritional quality of agricultural products by modulating molecular and biochemical changes. The purpose of the present study was to investigate the influence of root restriction (RR) treatment on the dynamic changes of main phytohormones during the berry development and ripening of “Summer Black” early ripening seedless grape (Vitis vinifera × V. labrusca), and to analyze the changes in the biosynthesis and signal transduction pathways of phytohormones by transcriptomics. Enzyme-linked immunosorbent assay (ELISA) and Ultra Performance Liquid Chromatography-High Resolution Mass Spectrometry (UPLC-HRMS) were used to quantify the phytohormone levels, and RNA-Seq was used to analyze the transcript abundance. The results showed that 23 transcripts involved in the phytohormone biosynthesis and 34 transcripts involved in the signal transduction pathways were significantly changed by RR treatment. RR also increased abscisic acid, brassinosteroid, ethylene, jasmonic acid and salicylic acid levels, while decreasing auxin, cytokinin, and gibberellin contents. The results of the present study suggest that RR treatment can accelerate the grape ripening process, and specific candidate genes were identified for further functional analysis.

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Interactions between auxin and quercetin during grape berry development

Scientia Horticulturae ◽

10.1016/j.scienta.2016.04.018 ◽

2016 ◽

Vol 205 ◽

pp. 45-51

Author(s):

Mei Luo ◽

Sibao Wan ◽

Xiangyu Sun ◽

Tingting Ma ◽

Weidong Huang ◽

...

Keyword(s):

Grape Berry ◽

Berry Development

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The Effect of Elevated CO2 on Berry Development and Bunch Structure of Vitis vinifera L. cvs. Riesling and Cabernet Sauvignon

Applied Sciences ◽

10.3390/app10072486 ◽

2020 ◽

Vol 10 (7) ◽

pp. 2486 ◽

Cited By ~ 2

Author(s):

Yvette Wohlfahrt ◽

Susanne Tittmann ◽

Dominik Schmidt ◽

Doris Rauhut ◽

Bernd Honermeier ◽

...

Keyword(s):

Carbon Dioxide ◽

Vitis Vinifera ◽

Elevated Co2 ◽

Fruit Quality ◽

Growth And Yield ◽

Nutrition Status ◽

Vitis Vinifera L ◽

Cabernet Sauvignon ◽

Berry Development ◽

Non Invasive

Carbon dioxide (CO2) as one of the main factors driving climate change is known to increase grapevine growth and yield and could, therefore, have an impact on the fruit quality of vines. This study reports the effects of elevated CO2 (eCO2) on berry development and bunch structure of two grapevine cultivars (Vitis vinifera L. cvs. Riesling and Cabernet Sauvignon) within the VineyardFACE (Free-Air Carbon Dioxide enrichment) experiment, using must analysis and non-invasive fluorescence sensor technology. Berry development was examined on five dates over three consecutive years by analyzing total soluble solids (TSS), pH, total acidity, organic acids, nutrition status, and non-invasive Multiplex measurements. Before harvest, secondary bunches were collected to examine bunch and berry parameters. Results showed that eCO2 had little impact on berry composition of Riesling and Cabernet Sauvignon during berry development, which could be related to bunch structure or single berry weight within single seasons. Elevated CO2 (eCO2) did not result in modified TSS accumulation during ripening but was directly related to the chlorophyll index SFR_R. Higher single berry weights (SBW), higher malic acid (MA), and lower tartaric acid (TAA) were examined at some stages during development of berries under eCO2 levels. Our study provides evidence that eCO2 did alter some bunch and berry parameters without a negative impact on fruit quality.

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