scholarly journals Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Pascale Maillot ◽  
Amandine Velt ◽  
Camille Rustenholz ◽  
Gisèle Butterlin ◽  
Didier Merdinoglu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Gene Expression Regulation ◽  
Grape Berry ◽  
Vitis Vinifera L ◽  
Splicing Regulation ◽  
Berry Development ◽  
Phenotypic Characteristics ◽  
Berry Ripening ◽  
Green Stage ◽  
Selection Of

Abstract Background Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties. Results A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome. Conclusions The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change.

scholarly journals Transcriptomic analysis of grape berry softening during ripening

OENO One ◽  
2008 ◽  
Vol 42 (1) ◽  
pp. 1 ◽  
Author(s):  
David Glissant ◽  
Fabienne Dédaldéchamp ◽  
Serge Delrot
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Molecular Markers ◽  
Expression Pattern ◽  
Molecular Basis ◽  
Grape Berry ◽  
Berry Development ◽  
Cell Wall Metabolism ◽  
Study Gene Expression ◽  
Berry Ripening

<p style="text-align: justify;"><strong>Aims</strong>: The aim of this paper was to use recent transcriptomic tools available for grape in order to understand berry softening.</p><p style="text-align: justify;"><strong>Methods and results</strong>: A microarray bearing specific 50 mer oligonucleotide for 3,200 genes was used to study gene expression along 8 stages of berry development in Chardonnay and Shiraz berries. Transcripts corresponding to aquaporin genes and to genes involved in cell wall metabolism were studied in detail and ranked according to their pattern of expression.</p><p style="text-align: justify;"><strong>Conclusion</strong>: Several structural and regulatory genes whose expression pattern correlated with the late phases of ripening were identified. Significance and impact of study: This study provides a preliminary molecular basis to identify molecular markers of berry ripening.</p>

scholarly journals Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Pietro Delfino ◽  
Sara Zenoni ◽  
Zahra Imanifard ◽  
Giovanni Battista Tornielli ◽  
Diana Bellin
Keyword(s):  
Candidate Genes ◽  
Genetic Control ◽  
Developmental Stages ◽  
Regulation Of Gene Expression ◽  
Climatic Conditions ◽  
Grape Berry ◽  
Genetic Maps ◽  
Berry Development ◽  
Comprehensive Overview ◽  
Berry Ripening

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.

Delaying Riesling grape berry ripening with a synthetic auxin affects malic acid metabolism and sugar accumulation, and alters wine sensory characters

2012 ◽  
Vol 39 (9) ◽  
pp. 745 ◽  
Author(s):  
Christine Böttcher ◽  
Paul K. Boss ◽  
Christopher Davies
Keyword(s):  
Malic Acid ◽  
Grape Berry ◽  
Hormonal Control ◽  
Sugar Accumulation ◽  
Vitis Vinifera L ◽  
Naphthaleneacetic Acid ◽  
Synthetic Auxin ◽  
Significant Difference ◽  
Berry Ripening ◽  
Rate Of Decline

An improved understanding of the hormonal control of grape (Vitis vinifera L.) berry ripening and the ability to manipulate it are of interest scientifically and commercially. Grapes are nonclimacteric fruit with ethylene unlikely to have a principal role in berry ripening but there are several other hormones thought to be involved. In this work, a significant delay in Riesling berry ripening was achieved through preripening treatments with the synthetic auxin 1-naphthaleneacetic acid (NAA). The initiation of sugar accumulation was delayed and the rate of sugar accumulation was lower in NAA-treated fruit, resulting in a 15-day delay in harvest. NAA treatments also reduced the rate of decline in malic acid levels that occurs during ripening, and increased the synchronicity of malic acid and berry sugar accumulation. Sensory panel assessment revealed a significant difference between wine made from control and NAA-treated fruit. Analysis of the volatile composition of the wines’ headspace showed that the concentration of several compounds was altered significantly by the NAA treatment. These data provide further support for the involvement of auxins in inhibiting ripening and suggest that auxin treatments may be useful in controlling both winery intake, and fruit and wine composition.

scholarly journals A Grape Berry (Vitis vinifera L.) Cation/Proton Antiporter is Associated with Berry Ripening

2007 ◽  
Vol 48 (6) ◽  
pp. 804-811 ◽  
Author(s):  
M. Hanana ◽  
O. Cagnac ◽  
T. Yamaguchi ◽  
S. Hamdi ◽  
A. Ghorbel ◽  
...  
Keyword(s):  
Vitis Vinifera ◽  
Grape Berry ◽  
Vitis Vinifera L ◽  
Berry Ripening

Evolution of the grapevine (Vitis vinifera L.) imprinted by natural and human factorsThis review is one of a selection of papers presented at the symposium on Vitis at the XVII International Botanical Congress held in Vienna, Austria, in 2005.

2007 ◽  
Vol 85 (8) ◽  
pp. 679-690 ◽  
Author(s):  
Roger Bessis
Keyword(s):  
Vegetative Reproduction ◽  
Molecular Characteristics ◽  
Vitis Vinifera L ◽  
Biological Interactions ◽  
Direct Effects ◽  
Parasitic Fungi ◽  
International Botanical ◽  
International Botanical Congress ◽  
Environmental Agents ◽  
Selection Of

This paper is concerned with vegetative reproduction, which is the only mode of propagation in cultivated grapevines. After a brief summary of the systematics of the Vitaceae the question of the nomenclature of cultivated grapevines is discussed. Intra-varietal variability is discussed using morphological and molecular characteristics. The origins of variation are presented: mutations, foreign nucleic acids, and memory of previous environmental conditions. Grapevines provide characteristic products, leading viticulturalists to make selections among the diversity observed in the vineyard, thus decreasing diversity. Grapevines interact with various environmental agents. One example, the natural defence provided by resveratrol, is analysed, showing its direct effects against parasitic fungi and its indirect effects, both metabolic and genetic, on other organisms. Thus, the grapevine, viticulturalists, and their environment form a web of biological interactions.

scholarly journals Nova Regulates GABAA Receptor γ2 Alternative Splicing via a Distal Downstream UCAU-Rich Intronic Splicing Enhancer

2003 ◽  
Vol 23 (13) ◽  
pp. 4687-4700 ◽  
Author(s):  
B. Kate Dredge ◽  
Robert B. Darnell
Keyword(s):  
Alternative Splicing ◽  
Rna Binding ◽  
Splice Acceptor Site ◽  
Acceptor Site ◽  
Splicing Regulation ◽  
Globin Genes ◽  
Enhancer Element ◽  
Intronic Splicing Enhancer ◽  
Splicing Enhancer

ABSTRACT Nova is a neuron-specific RNA binding protein targeted in patients with the autoimmune disorder paraneoplastic opsoclonus-myoclonus ataxia, which is characterized by failure of inhibition of brainstem and spinal motor systems. Here, we have biochemically confirmed the observation that splicing regulation of the inhibitory GABAA receptor γ2 (GABAARγ2) subunit pre-mRNA exon E9 is disrupted in mice lacking Nova-1. To elucidate the mechanism by which Nova-1 regulates GABAARγ2 alternative splicing, we systematically screened minigenes derived from the GABAARγ2 and human β-globin genes for their ability to support Nova-dependent splicing in transient transfection assays. These studies demonstrate that Nova-1 acts directly on GABAARγ2 pre-mRNA to regulate E9 splicing and identify an intronic region that is necessary and sufficient for Nova-dependent enhancement of exon inclusion, which we term the NISE (Nova-dependent intronic splicing enhancer) element. The NISE element (located 80 nucleotides upstream of the splice acceptor site of the downstream exon E10) is composed of repeats of the sequence YCAY, consistent with previous studies of the mechanism by which Nova binds RNA. Mutation of these repeats abolishes binding of Nova-1 to the RNA in vitro and Nova-dependent splicing regulation in vivo. These data provide a molecular basis for understanding Nova regulation of GABAARγ2 alternative splicing and suggest that general dysregulation of Nova's splicing enhancer function may underlie the neurologic defects seen in Nova's absence.

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