scholarly journals Towards the definition of a detailed transcriptomic map of berry development

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.

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

1996 ◽  
Vol 121 (5) ◽  
pp. 869-874 ◽  
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.

scholarly journals Iso-Seq allows genome-independent transcriptome profiling of grape berry development

2018 ◽  
Author(s):  
Andrea Minio ◽  
Mélanie Massonnet ◽  
Rosa Figueroa-Balderas ◽  
Amanda M. Vondras ◽  
Barbara Blanco-Ulate ◽  
...  
Keyword(s):  
Single Molecule ◽  
Transcriptional Profiling ◽  
Transcriptome Profiling ◽  
Grape Berry ◽  
Cabernet Sauvignon ◽  
Berry Development ◽  
Grape Berries ◽  
Gene Space ◽  
A Genome ◽  
Computationally Intensive

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.

scholarly journals A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.

2020 ◽  
Author(s):  
Grant R. Cramer ◽  
Noé Cochetel ◽  
Ryan Ghan ◽  
Agnès Destrac-Irvine ◽  
Serge Delrot
Keyword(s):  
Circadian Clock ◽  
Seed Dormancy ◽  
Transcript Abundance ◽  
Cabernet Sauvignon ◽  
Berry Development ◽  
Rna Seq ◽  
Cold Response ◽  
Berry Ripening ◽  
Berry Skins ◽  
Late Stages

Abstract Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.

Characterization of VvSPL18 and Its Expression in Response to Exogenous Hormones during Grape Berry Development and Ripening

2019 ◽  
Vol 159 (2) ◽  
pp. 97-108 ◽  
Author(s):  
Zhenqiang Xie ◽  
Ziwen Su ◽  
Wenran Wang ◽  
Le Guan ◽  
Yunhe Bai ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Grape Berry ◽  
Naphthalene Acetic Acid ◽  
Berry Development ◽  
Rna Seq ◽  
Chromosome 14 ◽  
Cis Element ◽  
Diverse Plant Species ◽  
Diverse Plant

The sequence and structure of grape SBP-box-like18 (VvSPL18) were identified and characterized to explore its regulatory roles during grape berry development and ripening. Homologous conservation across diverse plant species was observed, and its potential function and modulated roles in grapes were investigated. The results showed that VvSPL18 has an ORF sequence of 1,137 bp, encodes 378 amino acids, and is located on chromosome 14 of grapevine. VvSPL18 has the closest relationship with its homolog in soybeans. The promoter of VvSPL18 contains cis-elements responsive to gibberellins (GA) and salicylic acid (SA), indicating that this gene might respond to these hormones involved in the modulation of grape berry. VvSPL18 is mainly distributed in the nucleus. Expression profiles showed that VvSPL18 is highly expressed only at the veraison stage of the grape berry and is slightly expressed in other phases. RNA-seq data also revealed that VvSPL18 might participate in the modulation of grape berry development and ripening. Treatment with diverse hormones demonstrated that abscisic acid (ABA) had almost no effect on its expression, whereas naphthalene acetic acid (NAA) significantly upregulated its expression at the veraison stage. We also found that VvSPL18 has a GA-responsive cis-element but no NAA-responsive cis-element. GA could promote the expression of VvSPL18 with a peak at an earlier stage than NAA, suggesting that VvSPL18 responds faster to GA than to NAA. This result indicates that VvSPL18 might modulate berry development at this phase through an ABA-independent pathway, and it might directly respond to GA, but indirectly to NAA. Our findings provide insights into the functions of VvSPL18 in mediating grape berry development and ripening.

scholarly journals A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.

2019 ◽  
Author(s):  
Grant R. Cramer ◽  
Noé Cochetel ◽  
Ryan Ghan ◽  
Agnès Destrac-Irvine ◽  
Serge Delrot
Keyword(s):  
Circadian Clock ◽  
Seed Dormancy ◽  
Transcript Abundance ◽  
Cabernet Sauvignon ◽  
Berry Development ◽  
Rna Seq ◽  
Cold Response ◽  
Berry Ripening ◽  
Berry Skins ◽  
Late Stages

Abstract Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.

Firmness and grape berry maturation. Definition of different rheological parameters during the ripening

OENO One ◽  
1997 ◽  
Vol 31 (3) ◽  
pp. 127 ◽  
Author(s):  
Jean-Pierre Robin ◽  
Philippe Abbal ◽  
Jean-Michel Salmon
Keyword(s):  
Mechanical Properties ◽  
Mechanical Behaviour ◽  
Grape Berry ◽  
Rheological Parameters ◽  
Berry Development ◽  
Elasticity Coefficient ◽  
Grape Berries ◽  
Definition Of ◽  
Flat Tool ◽  
Berry Maturation

<p style="text-align: justify;">Mechanical properties of Shiraz and Gamay grape berries were studied in relation with their maturity state using the Penelaup<sup>TM</sup> rheometer. The analysis of the constrains registered during berry crushing with the flat tool of the device, up to the pellicular tearing, allowed the definition of different rheological parameters and the characterisation of mechanical behaviour of grape and its evolution with the degree of ripening. The analysis of the deformability curves shows, independently of the cultivar, that berry behaviour is not elastical except for some berries at the beginning and at the end of the ripening. This behaviour can be characterised by two indexes expressing the curvature sense of deformability curves, the curvature degree in a way reflecting the turgescence state of the grape. Berry firmness was also considered in two different ways: the initial firmness which represents the elasticity coefficient of the fruit at the beginning of the deformation, and the bursting firmness which can be considered as the pellicular elasticity coefficient. Others parameters, as the pellicular strength which can be expressed from the value of the displacement at berry bursting and the energy used for the deformation were also defined. The evolution of these different parameters during ripening confirms that berry softening at the véraison time depends on the cultivar and on environmental conditions as the vintage. The analysis of the evolutions also indicates that pellicular strength is maximum at this crucial period of berry development.</p>

scholarly journals Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development

BMC Genomics ◽  
2007 ◽  
Vol 8 (1) ◽  
pp. 429 ◽  
Author(s):  
Laurent G Deluc ◽  
Jérôme Grimplet ◽  
Matthew D Wheatley ◽  
Richard L Tillett ◽  
David R Quilici ◽  
...  
Keyword(s):  
Grape Berry ◽  
Cabernet Sauvignon ◽  
Berry Development

scholarly journals A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.

2019 ◽  
Author(s):  
Grant R. Cramer ◽  
Noé Cochetel ◽  
Ryan Ghan ◽  
Agnès Destrac-Irvine ◽  
Serge Delrot
Keyword(s):  
Circadian Clock ◽  
Seed Dormancy ◽  
Transcript Abundance ◽  
Cabernet Sauvignon ◽  
Berry Development ◽  
Rna Seq ◽  
Cold Response ◽  
Berry Ripening ◽  
Berry Skins ◽  
Late Stages

Abstract Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.

scholarly journals A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.

2019 ◽  
Author(s):  
Grant R. Cramer ◽  
Noé Cochetel ◽  
Ryan Ghan ◽  
Agnès Destrac-Irvine ◽  
Serge Delrot
Keyword(s):  
Circadian Clock ◽  
Seed Dormancy ◽  
Transcript Abundance ◽  
Cabernet Sauvignon ◽  
Berry Development ◽  
Rna Seq ◽  
Cold Response ◽  
Berry Ripening ◽  
Berry Skins ◽  
Late Stages

Abstract Background: Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results: To better understand the effect of “place” on berry ripening, transcript abundances in Cabernet Sauvignon berries grown in Bordeaux were compared to those in Reno during the late stages of berry development at similar berry sugar levels (19 to 26 °Brix, total soluble solids (TSS)). Day lengths were similar in both locations but day temperatures were warmer and night temperatures were cooler in Reno. TSS was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-seq analysis identified 4,455 differentially expressed genes (DEGs) between Bordeaux and Reno grape skins at 22°Brix. Top DEG gene ontology categories involved response to stimulus (1464 genes), biosynthesis (1260 genes) and response to stress (834 genes). Some DEGS included genes encoding terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. The plant temperature sensor phytochrome B was linked with Reveille 1 expression, which is part of the circadian clock output pathway that affects seed dormancy. Bordeaux berries had higher transcript abundance with DEGs associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with DEGs involved in water deprivation, cold response, ABA signaling and Fe homeostasis. Conclusions: Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-seq analysis identified a common core set of ripening genes that do not depend on rootstock, vineyard management, plant age, soil and climatic conditions. Most DEGs could be associated with different environmental conditions that affected the berries in the two locations and may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result. Temperature, light, water status and fungal infection were identified to be some of the most influential factors that affected differential gene expression and the quality trait pathways associated with them.

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

1978 ◽  
Vol 5 (4) ◽  
pp. 415 ◽  
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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