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Ibrahim Hmmam

Bio: Ibrahim Hmmam is an academic researcher from University of Padua. The author has contributed to research in topics: Horticulture & WRKY protein domain. The author has an hindex of 5, co-authored 8 publications receiving 175 citations.

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Journal ArticleDOI
TL;DR: 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, and enrichment of cis-regulatory motifs for diverse TFs reinforced the notion of transcriptional coordination and interaction between MYBs and other regulators.
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.

110 citations

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TL;DR: Genome-wide gene co-expression analysis using two separate transcriptome compendia based on microarray and RNA sequencing data revealed that WRKY TFs were the top TF family correlated with STS genes, and four WRKY genes were further shortlisted and functionally validated.
Abstract: Stilbene synthase (STS) is the key enzyme leading to the biosynthesis of resveratrol. Recently we reported two R2R3-MYB transcription factor (TF) genes that regulate the stilbene biosynthetic pathway in grapevine: VviMYB14 and VviMYB15. These genes are strongly co-expressed with STS genes under a range of stress and developmental conditions, in agreement with the specific activation of STS promoters by these TFs. Genome-wide gene co-expression analysis using two separate transcriptome compendia based on microarray and RNA sequencing data revealed that WRKY TFs were the top TF family correlated with STS genes. On the basis of correlation frequency, four WRKY genes, namely VviWRKY03, VviWRKY24, VviWRKY43 and VviWRKY53, were further shortlisted and functionally validated. Expression analyses under both unstressed and stressed conditions, together with promoter-luciferase reporter assays, suggested different hierarchies for these TFs in the regulation of the stilbene biosynthetic pathway. In particular, VviWRKY24 seems to act as a singular effector in the activation of the VviSTS29 promoter, while VviWRKY03 acts through a combinatorial effect with VviMYB14, suggesting that these two regulators may interact at the protein level as previously reported in other species.

83 citations

Journal ArticleDOI
TL;DR: In this article, carboxymethyl cellulose (CMC) and guar gum-based silver nanoparticles (AgNPs) were used as fruit coatings, and their effects on postharvest storage behavior and quality attributes were investigated.
Abstract: Mango fruit (cv. Seddik) is known as a delicate fruit for storage after harvest. Herein, carboxymethyl cellulose (CMC) and guar gum-based silver nanoparticles (AgNPs) were used as fruit coatings, and their effects on postharvest storage behavior and quality attributes were investigated. AgNPs were synthesized using a chemical reduction approach and then combined with CMC and guar gum as coating bases. Mango fruits were coated with the developed and pre-characterized CMC-AgNPs and guar gum-AgNPs, and then packed and stored at 13 °C for 4 weeks. The results showed an increase in weight loss, respiration rate, total soluble solids (TSS), total sugars, and total carotenoids over the storage period. However, this increase was comparatively less significant in coated fruits compared to uncoated fruits. Firmness and titratable acidity (TA) significantly decreased during storage, but this decrease was less in coated fruits. Silver traces in fruit pulp samples were not detected. These findings showed the efficacy of CMC-AgNP and guar gum-AgNP coatings in delaying mango fruit ripening and maintaining fruit quality during cold storage. Therefore, these coatings could be promising alternative materials for extending the postharvest life and marketing period of mango fruit.

17 citations

01 Jan 2011
TL;DR: The results showed that the transplant length, leaves number/transplant, leaf area, leaves content of N, P, K, Ca, Na, Cl and chlorophyll were decreased with increasing water stress conditions, while there were no significantly differences between treatments in proline content.
Abstract: The present study was carried out during the period from 2009 to 2010 in the greenhouse of Pomology Department, Faculty of Agriculture, Cairo University to study the effect of water stress (Irrigation at 100, 75, 50 and 25% from field capacity) on vegetative characteristics and leaves chemical constituents on five olive (Olea europaea L.) cultivars (Picual, Koroneiki, Manzanillo, Coratina and Eggizi Shami). The results showed that the transplant length, leaves number/transplant, leaf area, leaves content of N, P, K, Ca, Na, Cl and chlorophyll were decreased with increasing water stress conditions, while there were no significantly differences between treatments in proline content.

12 citations

Journal ArticleDOI
TL;DR: Analysis of olive cultivars and cultivar groups within the olive cultivation area in Veneto by using discriminant SSR markers to obtain a systematic genetic survey of the Veneto regional olive germplasm patrimony finds that regionally the most common variety was “Casaliva”, corresponding to the widely diffused cultivar “Frantoio”.
Abstract: Olive (Olea europaea L.) is one of the most important tree crops of the Mediterranean regions. In spite of the increasing appreciation of typical extra virgin olive oils at world level, based on the use of local traditional varieties, very few studies have focused on the genetic characterisation of olive cultivars of regional interest, such as those grown in Veneto, a North-Eastern Italy region. A deep knowledge of the varieties cultivated in this territory is a key step to address the product quality, to increase market demand and to certify the origin of local olive oils. Here we have analyzed olive cultivars and cultivar groups within the olive cultivation area in Veneto, from the Garda Lake to the Euganean and Trevisan hills, by using discriminant SSR markers, in order to obtain a systematic genetic survey of the Veneto regional olive germplasm patrimony. A total of 203 previously uncharacterized olive samples were collected from ancient trees still grown by local farmers. The analyzed samples included also 36 olive reference cultivars from Veneto and neighbour Regions. We found 57 unique molecular profiles out of this set of olive accessions that were split into 15 cultivar groups corresponding to genetically distinct STRUCTURE clusters. Based on a common SSR database, our 239 Venetian accessions were compared with 280 olive reference genotypes representative of the Mediterranean cultivation area. From the genetic structure analysis, it has been observed that 80% of Venetian cultivars clustered in the central Mediterranean group, about 9% and 2% with the eastern and western varieties, respectively, and all the others resulted intermixed among two or three populations. We found that regionally the most common variety was “Casaliva”, corresponding to the widely diffused cultivar “Frantoio”, while others showed identity with known varieties grown in close regions, such as “Leccino”, “Miniol”, “Capolga” and “Bianchera”. Besides these genotypes, others were not matching any known reference and therefore they could be classified as true local varieties of indigenous origin, possibly deriving from the hybridization and selection made by farmers and from their adaptation to the local soil and climate conditions.

8 citations


Cited by
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Journal ArticleDOI
TL;DR: Phenylpropanoids are a large class of plant secondary metabolites derived from aromatic amino acids phenylalanine in most plants or tyrosine in partial monocots as discussed by the authors.
Abstract: Phenylpropanoids are a large class of plant secondary metabolites derived from aromatic amino acids phenylalanine in most plants or tyrosine in partial monocots. It mainly includes flavonoids, mono...

269 citations

Journal ArticleDOI
TL;DR: The relation between miRNAs and TFs is studied by consolidating the research findings from different plant species which will help plant scientists in understanding the mechanism of action and interaction between these regulators in the plant growth and development under normal and stress environmental conditions.
Abstract: Recent achievements in plant microRNA (miRNA), a large class of small and non-coding RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular cloning, bioinformatic analysis, and the latest technology, deep sequencing have greatly advanced miRNA discovery. A tiny miRNA sequence has the ability to target single/multiple mRNA targets. Most of the miRNA targets are transcription factors (TFs) which have paramount importance in regulating the plant growth and development. Various families of TFs, which have regulated a range of regulatory networks, may assist plants to grow under normal and stress environmental conditions. This present review focuses on the regulatory relationships between miRNAs and different families of TFs like; NF-Y, MYB, AP2, TCP, WRKY, NAC, GRF and SPL. For instance NF-Y play important role during drought tolerance and flower development, MYB are involved in signal transduction and biosynthesis of secondary metabolites, AP2 regulate the floral development and nodule formation, TCP direct leaf development and growth hormones signalling. WRKY have known roles in multiple stress tolerances, NAC regulate lateral root formation, GRF are involved in root growth, flower, and seed development, and SPL regulate plant transition from juvenile to adult. We also studied the relation between miRNAs and TFs by consolidating the research findings from different plant species which will help plant scientists in understanding the mechanism of action and interaction between these regulators in the plant growth and development under normal and stress environmental conditions.

230 citations

Journal ArticleDOI
TL;DR: A new version of the grapevine reference genome assembly and of its annotation and its VCost.v3 gene annotation in Genbank format is presented.
Abstract: :The dataset comprises 12X.v2 grapevine reference genome assembly and its VCost.v3 gene annotation in Genbank format. The 12X.v2 chromosome assembly is based on the scaffolds of the grapevine reference genome build (FN594950-FN597014, EMBL release 102; Vitis vinifera cv. PN40024). The data set is provided in support of the data paper: “A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)” by Canaguier A, Grimplet J, Di Gaspero G, Scalabrin S, Duchene E, Mohellibi N, Guichard C, Choisne N, Rombault S, Le Clainche I, Berard A, Chauveau A, Bounon R, Ruztenholtz C, Morgante M, Le Paslier M-C, Brunel D, Adam-Blondon A-F (Genomic Data, 2017, https://doi.org/10.1016/j.gdata.2017.09.002)

183 citations

Journal ArticleDOI
13 May 2021-Agronomy
TL;DR: The shikimate pathway and the aromatic amino acids produced in this pathway are the precursors of a range of secondary metabolites including terpenoids, alkaloids, and sulfur- and nitrogen-containing compounds and how the biosynthesis of important metabolites is altered by several genes related to secondary metabolite biosynthesis pathways are detailed.
Abstract: Plant secondary metabolites (SMs) play important roles in plant survival and in creating ecological connections between other species. In addition to providing a variety of valuable natural products, secondary metabolites help protect plants against pathogenic attacks and environmental stresses. Given their sessile nature, plants must protect themselves from such situations through accumulation of these bioactive compounds. Indeed, secondary metabolites act as herbivore deterrents, barriers against pathogen invasion, and mitigators of oxidative stress. The accumulation of SMs are highly dependent on environmental factors such as light, temperature, soil water, soil fertility, and salinity. For most plants, a change in an individual environmental factor can alter the content of secondary metabolites even if other factors remain constant. In this review, we focus on how individual environmental factors affect the accumulation of secondary metabolites in plants during both biotic and abiotic stress conditions. Furthermore, we discuss the application of abiotic and biotic elicitors in culture systems as well as their stimulating effects on the accumulation of secondary metabolites. Specifically, we discuss the shikimate pathway and the aromatic amino acids produced in this pathway, which are the precursors of a range of secondary metabolites including terpenoids, alkaloids, and sulfur- and nitrogen-containing compounds. We also detail how the biosynthesis of important metabolites is altered by several genes related to secondary metabolite biosynthesis pathways. Genes responsible for secondary metabolite biosynthesis in various plant species during stress conditions are regulated by transcriptional factors such as WRKY, MYB, AP2/ERF, bZIP, bHLH, and NAC, which are also discussed here.

178 citations

Journal ArticleDOI
TL;DR: A R2R3-MYB repressor in peach, designated PpMYB18, is reported on, which acts as a negative regulator of anthocyanin and PA accumulation and serves as a model for balancing secondary metabolite accumulation at the transcriptional level.
Abstract: Anthocyanin and proanthocyanidin (PA) accumulation is regulated by both myeloblastosis (MYB) activators and repressors, but little information is available on hierarchical interactions between the positive and negative regulators. Here, we report on a R2R3-MYB repressor in peach, designated PpMYB18, which acts as a negative regulator of anthocyanin and PA accumulation. PpMYB18 can be activated by both anthocyanin- and PA-related MYB activators, and is expressed both at fruit ripening and juvenile stages when anthocyanins or PAs, respectively, are being synthesized. The PpMYB18 protein competes with MYB activators for binding to basic Helix Loop Helixes (bHLHs), which develops a fine-tuning regulatory loop to balance PA and anthocyanin accumulation. In addition, the bHLH binding motif in the R3 domain and the C1 and C2 repression motifs in the C-terminus of PpMYB18 both confer repressive activity of PpMYB18. Our study also demonstrates a modifying negative feedback loop, which prevents cells from excess accumulation of anthocyanin and PAs, and serves as a model for balancing secondary metabolite accumulation at the transcriptional level.

142 citations