Tissue-Specific Hormonal Variations in Grapes of Irrigated and Non-irrigated Grapevines (Vitis vinifera cv. “Merlot”) Growing Under Mediterranean Field Conditions

Agricultural practices in grapevines management include water restrictions due to its positive effect on wine quality, especially when applied at fruit ripening. Although the effects of water stress in some groups of phytohormones have already been described in leaves and whole grapes, information regarding tissue-specific variations in hormones during ripening in grapes is scarce. Field-grown grapevines from the cv. “Merlot” were subjected to two differential water supplies, including only rainfed, non-irrigated vines (T0) and vines additionally irrigated with 25Lweek−1 vine−1 (T1). Tissue-specific variations in the hormonal profiling of grapes [including changes in the contents of abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), the ethylene precursor 1-amino-cyclopropane-1-carboxylic acid (ACC), the auxin indole-3-acetic acid, gibberellins 1, 3, 4, and 7 (GA1, GA3, GA4, and GA7), the cytokinins trans-zeatin, and 2-isopentenyl adenine, including as well their respective ribosylated forms] were periodically evaluated from veraison to harvest. The hormonal profiling in leaves was also measured at the beginning and end of the season for comparison. Results showed that grape growth dynamics were transiently affected by the differences in water regimes, the increased water supply leading to an accelerated growth, slightly reduced accumulation of sugars, and transiently lowered pH, although grape quality did not differ between treatments at harvest. Hormonal profiling of whole berries did not reveal any difference in the endogenous contents of phytohormones between treatments, except for a transient decrease in GA4 contents in T1 compared to T0 vines, which was not confirmed at the tissular level. Hormonal profiling at the tissue level highlighted a differential accumulation of phytohormones during ripening in berry tissues, with pulps being particularly poor in ABA, JA, and SA contents, seeds particularly accumulating ACC, gibberellins, and zeatin-type cytokinins, and the skin being particularly rich in auxin and active cytokinins. Changes in water supply led to very small and transient changes in the endogenous contents of phytohormones in the seeds, pulp, and skin of berries, the most remarkable variations being observed in cytokinin contents, which increased earlier [between 5 and 12days after veraison (DAV)] but later kept more constant in the skin from T1 compared to T0 vines and were also 3-fold higher at 40 DAV in seeds of T1 compared to T0 vines. It is concluded that small changes in water supply can trigger hormonal-driven physiological adjustments at the tissular level affecting the evolution of fruit growth and quality throughout grape berry ripening.

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Increased Organic Fertilizer and Reduced Chemical Fertilizer Increased Fungal Diversity and the Abundance of Beneficial Fungi on the Grape Berry Surface in Arid Areas

Frontiers in Microbiology ◽

10.3389/fmicb.2021.628503 ◽

2021 ◽

Vol 12 ◽

Author(s):

Linnan Wu ◽

Zhiqiang Li ◽

Fengyun Zhao ◽

Benzhou Zhao ◽

Fesobi Olumide Phillip ◽

...

Keyword(s):

Fungal Diversity ◽

Organic Fertilizer ◽

Grape Juice ◽

Grape Berry ◽

Chemical Fertilizer ◽

Soluble Solids ◽

Alpha And Beta Diversity ◽

Grape Berries ◽

Grape Quality ◽

Beneficial Fungi

Fertilizer practices can significantly impact the fruit quality and microbial diversity of the orchards. The fungi on the surface of fruits are essential for fruit storability and safety. However, it is not clear whether fertilization affects the fungal diversity and community structure on the surface of grape berries. Here, grape quality and the fungal diversity on the surface of grapes harvested from three fertilizer treatments were analyzed shortly after grape picking (T0) and following 8 days of storage (T1). The study involved three treatments: (1) common chemical fertilizer for 2 years (CH); (2) increased organic fertilizer and reduced chemical fertilizer for 1 year (A.O); and (3) increased organic fertilizer and reduced chemical fertilizer for 2 years (B.O). The application of increased organic fertilizer and reduced chemical fertilizer increased the soluble solids content (SSC) of the grape berries and decreased the pH of the grape juice. A total of 827,947 high-quality fungal sequences were recovered and assigned to 527 operational taxonomic units. Members of the Ascomycota phylum were dominant in all samples and accounted for 94.41% of the total number of detected sequences, followed by the Basidiomycota (5.05%), and unidentified fungi (0.54%). Alpha and beta diversity analyses revealed significantly different fungal populations in the three fertilizer treatments over the two time periods. The fungal diversity and richness on the grape berry surface in the B.O and A.O treatments were higher than those in the CH treatment. Among the detected fungi, the B.O treatments were mainly Pichia, Aureobasidium, and Candida genera, while the CH treatments were Botrytis, Aspergillus, and Penicillium. Moreover, significant differences were revealed between the two assessment times (T0 and T1). The samples from the T0 timepoint had higher fungal richness and diversity than the samples from T1 timepoint. Increasing organic fertilizer usage in grape management could improve grape quality and went on to increase the fungal diversity, as well as the relative abundance (RA) of beneficial fungi on grape berry surfaces. The correlation analysis suggested that the pH of the grape juice was significantly negatively correlated with fungal diversity parameters.

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Performance of resistant varieties (PIWI) at two different altitudes in Southern Brazil

BIO Web of Conferences ◽

10.1051/bioconf/20191201021 ◽

2019 ◽

Vol 12 ◽

pp. 01021

Author(s):

A.L.K. de Souza ◽

A.F. Brighenti ◽

E. Brighenti ◽

V. Caliari ◽

M. Stefanini ◽

...

Keyword(s):

Climatic Conditions ◽

Soluble Solids ◽

Soluble Solids Content ◽

Southern Brazil ◽

Wine Quality ◽

Phenological Stages ◽

Lower Altitude ◽

Grape Quality ◽

Resistant Varieties ◽

Solids Content

In southern Brazil there is a predominance of labrusca and hybrid varieties for wine and juice production due to climatic conditions of high rainfall, temperature and relative humidity. Growing varieties that combine disease resistance and wine quality (PIWI) can be an alternative to improve wine quality. The objective of this work was to evaluate the performance of three PIWI varieties (Felicia, Calardis Blanc and Aromera) in two regions (Videira, 27∘01′S and 51∘08′W, altitude 830 m; and São Joaquim, 28∘13′S and 50∘04′W, altitude 1100 m) in the vintage 2018. The date of occurrence of main phenological stages, productiveindexes, clusters characteristics and grape qualitative indexes was evaluated. There was no difference for budbreak date, but flowering, veraison an maturity time varied between regions. The development of plants is slower when they are cultivated at a higher altitude. The number of clusters per plant and yield were higher at 830 m for all varieties. For productive indexes Felicia and Calardis Blanc varieties stood out in relation to Aromera in all parameters. Among the evaluated varieties, Felicia and Calardis Blanc were better adapted to the lower altitude region and had higher productivity and the same grape quality. On the other hand, Aromera presented higher productivity at 830 m but higher soluble solids content at 1100 m.

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Illuminating a plant’s tissue-specific metabolic diversity using computational metabolomics and information theory

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1610218113 ◽

2016 ◽

Vol 113 (47) ◽

pp. E7610-E7618 ◽

Cited By ~ 35

Author(s):

Dapeng Li ◽

Sven Heiling ◽

Ian T. Baldwin ◽

Emmanuel Gaquerel

Keyword(s):

Information Theory ◽

Secondary Metabolism ◽

Gene Function ◽

Tissue Level ◽

Two Dimensions ◽

Molecular Networks ◽

Specific Gene ◽

Theory Analysis ◽

Tissue Specific ◽

Metabolite Diversity

Secondary metabolite diversity is considered an important fitness determinant for plants’ biotic and abiotic interactions in nature. This diversity can be examined in two dimensions. The first one considers metabolite diversity across plant species. A second way of looking at this diversity is by considering the tissue-specific localization of pathways underlying secondary metabolism within a plant. Although these cross-tissue metabolite variations are increasingly regarded as important readouts of tissue-level gene function and regulatory processes, they have rarely been comprehensively explored by nontargeted metabolomics. As such, important questions have remained superficially addressed. For instance, which tissues exhibit prevalent signatures of metabolic specialization? Reciprocally, which metabolites contribute most to this tissue specialization in contrast to those metabolites exhibiting housekeeping characteristics? Here, we explore tissue-level metabolic specialization in Nicotiana attenuata, an ecological model with rich secondary metabolism, by combining tissue-wide nontargeted mass spectral data acquisition, information theory analysis, and tandem MS (MS/MS) molecular networks. This analysis was conducted for two different methanolic extracts of 14 tissues and deconvoluted 895 nonredundant MS/MS spectra. Using information theory analysis, anthers were found to harbor the most specialized metabolome, and most unique metabolites of anthers and other tissues were annotated through MS/MS molecular networks. Tissue–metabolite association maps were used to predict tissue-specific gene functions. Predictions for the function of two UDP-glycosyltransferases in flavonoid metabolism were confirmed by virus-induced gene silencing. The present workflow allows biologists to amortize the vast amount of data produced by modern MS instrumentation in their quest to understand gene function.

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Unraveling the association between mRNA expressions and mutant phenotypes in a genome-wide assessment of mice

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1415046112 ◽

2015 ◽

Vol 112 (15) ◽

pp. 4707-4712 ◽

Cited By ~ 10

Author(s):

Ben-Yang Liao ◽

Meng-Pin Weng

Keyword(s):

Mrna Expression ◽

Expression Profiles ◽

Tissue Level ◽

Tissue Specific ◽

Expression Phenotype ◽

Mouse Mutants ◽

Eukaryotic Genes ◽

A Genome ◽

Evolutionarily Conserved ◽

Mutant Phenotypes

High-throughput gene expression profiling has revealed substantial leaky and extraneous transcription of eukaryotic genes, challenging the perceptions that transcription is strictly regulated and that changes in transcription have phenotypic consequences. To assess the functional implications of mRNA transcription directly, we analyzed mRNA expression data derived from microarrays, RNA-sequencing, and in situ hybridization, together with phenotype data of mouse mutants as a proxy of gene function at the tissue level. The results indicated that despite the presence of widespread ectopic transcription, mRNA expression and mutant phenotypes of mammalian genes or tissues remain associated. The expression-phenotype association at the gene level was particularly strong for tissue-specific genes, and the association could be underestimated due to data insufficiency and incomprehensive phenotyping of mouse mutants; the strength of expression-phenotype association at the tissue level depended on tissue functions. Mutations on genes expressed at higher levels or expressed at earlier embryonic stages more often result in abnormal phenotypes in the tissues where they are expressed. The mRNA expression profiles that have stronger associations with their phenotype profiles tend to be more evolutionarily conserved, indicating that the evolution of transcriptome and the evolution of phenome are coupled. Therefore, mutations resulting in phenotypic aberrations in expressed tissues are more likely to occur in highly transcribed genes, tissue-specific genes, genes expressed during early embryonic stages, or genes with evolutionarily conserved mRNA expression profiles.

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Effect of composted mulch application on soil and wine grape potassium status

Soil Research ◽

10.1071/sr11084 ◽

2011 ◽

Vol 49 (5) ◽

pp. 455 ◽

Cited By ~ 8

Author(s):

K. Y. Chan ◽

D. J. Fahey

Keyword(s):

Field Trial ◽

New South ◽

New South Wales ◽

Grape Berry ◽

Wine Grape ◽

Wine Quality ◽

Exchangeable K ◽

South Wales ◽

The Mean ◽

Extractable Soil

Oversupply of potassium (K) to grape vines can result in high grape berry K and pH, leading to difficulty in wine making and low wine quality. There is concern that application of mulch to grape vines may increase K supply and the associated risks. The effect of composted mulch from green wastes was investigated in a field trial involving six vineyards in New South Wales on soils commonly used for viticulture production in Australia, over three seasons (2006–08). Significant increases in extractable soil K were detected as a result of mulch application. Higher berry K and pH were also observed due to the mulch treatments, with the changes dependent on season and mulch rate. Increases in berry K were significantly related to the higher soil exchangeable K. The mean increase in berry K due to a mulch rate of 153 m3/ha was 123 mg/kg. The mean increase in berry pH was 0.02 units observed in two seasons. Application of mulch can increase berry K and pH, but the changes are small compared with variations observed among vineyard sites and between seasons.

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A tissue-level phenome-wide network map of colocalized genes and phenotypes in the UK Biobank

10.1101/2021.04.30.441974 ◽

2021 ◽

Author(s):

Ghislain Rocheleau ◽

Iain S Forrest ◽

Áine Duffy ◽

Shantanu Bafna ◽

Amanda Dobbyn ◽

...

Keyword(s):

Clustering Algorithm ◽

Target Genes ◽

Genome Wide Association Study ◽

Wide Spectrum ◽

Association Studies ◽

Tissue Level ◽

Bipartite Network ◽

Uk Biobank ◽

Tissue Specific ◽

The Uk

Background: Phenome-wide association studies conducted in electronic health record (EHR)-linked biobanks have uncovered a large number of genomic loci associated with traits and diseases. However, interpretation of the complex relationships of associated genes and phenotypes is challenging. Results: We constructed a tissue-level phenome-wide network map of colocalized genes and phenotypes. First, we generated colocalized expression quantitative trait loci from 48 tissues of the Genotype-Tissue Expression project and from publicly available genome-wide association study summary statistics from the UK Biobank. We identified 9,151 colocalized genes for 1,411 phenotypes across 48 tissues. Then, we constructed a bipartite network using the colocalized signals to establish links between genes and phenotypes in each tissue. The majority of links are observed in a single tissue whereas only a few are present in all tissues. Finally, we applied the biLouvain clustering algorithm in each tissue-specific bipartite network to identify co-clusters of non-overlapping genes and phenotypes. The majority of co-clusters contains a small number of genes and phenotypes, and 88.6% of co-clusters are found in only one tissue. To demonstrate functionality of the phenome-wide map, we tested if these co-clusters were enriched with known biological and functional gene classes and observed several significant enrichments. Furthermore, we observed that tissue-specific co-clusters are enriched with reported drug side effects for the corresponding drug target genes in clinical trial data. Conclusions: The phenome-wide map provides links between genes, phenotypes and tissues across a wide spectrum of biological classes and can yield biological and clinical discoveries. The phenome-wide map is publicly available at https://rstudio-connect.hpc.mssm.edu/biPheMap/.

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Grape Small Auxin Upregulated RNA (SAUR) 041 Is a Candidate Regulator of Berry Size in Grape

International Journal of Molecular Sciences ◽

10.3390/ijms222111818 ◽

2021 ◽

Vol 22 (21) ◽

pp. 11818

Author(s):

Ming Li ◽

Rui Chen ◽

Hong Gu ◽

Dawei Cheng ◽

Xizhi Guo ◽

...

Keyword(s):

Gene Family ◽

Interaction Network ◽

Early Response ◽

Structural Features ◽

Grape Berry ◽

Amino Acid Residues ◽

Systematic Analysis ◽

Berry Size ◽

Grape Quality ◽

Genome Wide

Grape (Vitis vinifera) is an important horticultural crop that can be used to make juice and wine. However, the small size of the berry limits its yield. Cultivating larger berry varieties can be an effective way to solve this problem. As the largest family of auxin early response genes, SAUR (small auxin upregulated RNA) plays an important role in the growth and development of plants. Berry size is one of the important factors that determine grape quality. However, the SAUR gene family’s function in berry size of grape has not been studied systematically. We identified 60 SAUR members in the grape genome and divided them into 12 subfamilies based on phylogenetic analysis. Subsequently, we conducted a comprehensive and systematic analysis on the SAUR gene family by analyzing distribution of key amino acid residues in the domain, structural features, conserved motifs, and protein interaction network, and combined with the heterologous expression in Arabidopsis and tomato. Finally, the member related to grape berry size in SAUR gene family were screened. This genome-wide study provides a systematic analysis of grape SAUR gene family, further understanding the potential functions of candidate genes, and provides a new idea for grape breeding.

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Diversity and spoilage potential of microbial communities associated with grape sour rot in eastern coastal areas of China

PeerJ ◽

10.7717/peerj.9376 ◽

2020 ◽

Vol 8 ◽

pp. e9376

Author(s):

Huanhuan Gao ◽

Xiangtian Yin ◽

Xilong Jiang ◽

Hongmei Shi ◽

Yang Yang ◽

...

Keyword(s):

Microbial Communities ◽

High Throughput Sequencing ◽

Eastern China ◽

Grape Berry ◽

Wine Quality ◽

Bacterial Phyla ◽

Sour Rot ◽

Bacteria And Fungi ◽

Polymicrobial Disease

As a polymicrobial disease, sour rot decreases grape berry yield and wine quality. The diversity of microbial communities in sour rot-affected grapes depends on the cultivation site, but the microbes responsible for this disease in eastern coastal China, has not been reported. To identify the microbes that cause sour grape rot in this important grape-producing region, the diversity and abundance of bacteria and fungi were assessed by metagenomic analysis and cultivation-dependent techniques. A total of 15 bacteria and 10 fungi were isolated from sour rot-affected grapes. High-throughput sequencing of PCR-amplicons generated from diseased grapes revealed 1343 OTUs of bacteria and 1038 OTUs of fungi. Proteobacteria and Firmicutes were dominant phyla among the 19 bacterial phyla identified. Ascomycota was the dominant fungal phylum and the fungi Issatchenkia terricola, Colletotrichum viniferum, Hanseniaspora vineae, Saprochaete gigas, and Candida diversa represented the vast majority ofmicrobial species associated with sour rot-affected grapes. An in vitro spoilage assay confirmed that four of the isolated bacteria strains (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis) and five of the isolated fungi strains (three Aspergillus species, Alternaria tenuissima, and Fusarium proliferatum) spoiled grapes. These microorganisms, which appear responsible for spoiling grapes in eastern China, appear closely related to microbes that cause this plant disease around the world.

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Lemon maturation causes anatomical and biochemical changes at the flavedo tissue level

Botany ◽

10.1139/cjb-2021-0121 ◽

2021 ◽

Author(s):

Patricia L. Albornoz ◽

Roque Interdonato ◽

Ariadna Hammann ◽

Mariana Rosa ◽

Fernando E. Prado ◽

...

Keyword(s):

Cell Wall ◽

Agricultural Practices ◽

Tissue Level ◽

Sucrose Content ◽

Harvest Management ◽

Callose Deposition ◽

Transport Pathways ◽

Transcellular Transport ◽

Symplastic Pathway ◽

High Enzymatic Activity

Plants mobilize the photosynthates by three transport pathways: apoplastic, symplastic through plasmodesmata (PD), and transcellular. In flavedo of postharvest mature lemons, a high activity of cell wall-bound invertase (WI), an enzyme associated with transcellular transport of monosaccharides, has been detected. In order to elucidate whether this high enzymatic activity is related to restricted transport in the symplastic pathway with fruit maturation, the aim of the present work was to compare anatomical and biochemical parameters in peel tissues of immature and mature lemons. Anatomical structure focusing on cell walls, callose deposition, WI activity, and sucrose content were analyzed in peel tissues of immature and mature lemons. The parenchyma of flavedo tissue of immature lemons presented an elevated number of primary pit fields (PPF). These PPF, associated to PD or cell wall interruptions, had the appearance of a string of beads. However, in mature lemons, the number of PPF was scarce due to callose deposition. WI activity and apoplastic sucrose content increased significantly in flavedo of mature lemons in comparison to immature lemons. Present findings lay structural and functional bases relevant to understand differences between immature and mature lemons, which would help to design agricultural practices in pre- and post-harvest management.

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Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour

BMC Plant Biology ◽

10.1186/s12870-021-02889-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Elise Bizouerne ◽

Julia Buitink ◽

Benoît Ly Vu ◽

Joseph Ly Vu ◽

Eddi Esteban ◽

...

Keyword(s):

Desiccation Tolerance ◽

Genome Stability ◽

Gene Network ◽

Regulatory Networks ◽

Progressive Increase ◽

Tissue Level ◽

Seed Maturation ◽

Tomato Seed ◽

Seed Vigour ◽

Tissue Specific

Abstract Background During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures associated with desiccation tolerance, longevity, germination under water stress and dormancy. Results During maturation, 15,173 differentially expressed genes were detected, forming a gene network representing 21 expression modules, with 3 being specific to seed coat and embryo and 5 to the endosperm. A gene-trait significance measure identified a common gene module between endosperm and embryo associated with desiccation tolerance and conserved with non-endospermic seeds. In addition to genes involved in protection such LEA and HSP and ABA response, the module included antioxidant and repair genes. Dormancy was released concomitantly with the increase in longevity throughout fruit ripening until 14 days after the red fruit stage. This was paralleled by an increase in SlDOG1–2 and PROCERA transcripts. The progressive increase in seed vigour was captured by three gene modules, one in common between embryo and endosperm and two tissue-specific. The common module was enriched with genes associated with mRNA processing in chloroplast and mitochondria (including penta- and tetratricopeptide repeat-containing proteins) and post-transcriptional regulation, as well several flowering genes. The embryo-specific module contained homologues of ABI4 and CHOTTO1 as hub genes associated with seed vigour, whereas the endosperm-specific module revealed a diverse set of processes that were related to genome stability, defence against pathogens and ABA/GA response genes. Conclusion The spatio-temporal co-expression atlas of tomato seed maturation will serve as a valuable resource for the in-depth understanding of the dynamics of gene expression associated with the acquisition of seed vigour at the tissue level.

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