Analysis of global transcriptomic response of lettuce seedlings (Lactuca sativa L.) to microalgae extract used as biostimulant agents
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ABSTRACT:
PROVIDER: PRJNA945382 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23883520_1.fastq.gz | Fastqsanger.gz | |||
| SRR23883520_2.fastq.gz | Fastqsanger.gz | |||
| SRR23883521_1.fastq.gz | Fastqsanger.gz | |||
| SRR23883521_2.fastq.gz | Fastqsanger.gz | |||
| SRR23883522_1.fastq.gz | Fastqsanger.gz |
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Project description:The use of new natural eco-sustainable products is becoming an interesting option in order to reduce the use of chemical fertilizers and increase crop yields. Seaweed extracts are gained major attention as plant biostimulants due to their positive effect on plant-growth as well as on improving plants’ tolerance against abiotic stresses. Among the horticulture crops, lettuce (Lactuca sativa L.) is a major fresh vegetable crop in the Mediterranean area, which often requires the use of natural biostimulants to improve both the quantity and quality of production. The aim of this work was to assess the effect of either Chlorella vulgaris or Scenedesmus quadricauda extracts on lettuce seedlings (Lactuca sativa L.) by motoring the induced transcriptomic modifications using a RNASeq approach. The results showed that both C. vulgaris and S. quadricauda extracts positively influence the growth of lettuce seedlings. However, a higher reprogramming of the gene expression occurred in the case of C. vulgaris treatment than in S. quadricauda extract. Considering the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional enrichments, the main KEGG terms are in the “Biosynthesis of secondary metabolites”, “Metabolic pathways”, “Carbon metabolism” and “Biosynthesis of amino acids” categories. This study lays the basis for understanding the mechanisms and processes triggered by the use of microalgal extracts, which can represent an easier-to-handle and cheaper method for an eco-sustainable cultivation of lettuce plants than the application of chemicals.
2023-07-13 | GSE227491 | GEO
Project description:To reduce the use of chemical fertilizers and maximize agricultural yields, the use of microalgae extracts as biostimulants has recently attracted significant attention due to their favourable impact on both plant growth and their ability to induce tolerance towards environmental stressors. Lettuce (Lactuca sativa) is one of the most important fresh vegetables that often requires applications of chemical fertilizers to increase quality and productivity. Accordingly, the purpose of this study was to analyse the transcriptome reprogramming of lettuce (L. sativa) seedlings in response to either Chlorella vulgaris or Scenedesmus quadricauda extracts by applying an RNAseq approach. Differential gene expression analysis revealed that the core gene set that responded to microalgal treatments in a species-independent manner includes 1330 clusters, 1184 of which were down-regulated and 146 up-regulated, clearly suggesting that the repression of gene expression is the main effect of algal treatments. The deregulation of 7197 transcripts in the C. vulgaris treated seedlings compared to control samples (LsCv vs. LsCK) and 7118 transcripts in the S. quadricauda treated seedlings compared to control samples (LsSq vs. LsCK) were counted. Although the number of deregulated genes turned out to be similar between the algal treatments, the level of deregulation was higher in LsCv versus LsCK than in LsSq versus LsCK. In addition, 2439 deregulated transcripts were observed in the C. vulgaris treated seedlings compared to S. quadricauda treated samples (LsCv vs. LsSq comparison) suggesting that a specific transcriptomic profile was induced by the single algal extracts. 'Plant hormone signal transduction' category includes a very elevated number of DEGs, many of them specifically indicating that C. vulgaris actives both genes involved in the auxin biosynthesis and transduction pathways, whereas S. quadricauda up-regulates genes implicated in the cytokinin biosynthesis pathway. Finally, algal treatments induced the deregulation of genes encoding small hormone-like molecules that are known to act alone or by interacting with major plant hormones. In conclusion, this study offers the groundwork to draw up a list of putative gene targets with the aim of lettuce genetic improvement that will allow a limited or even null use of synthetic fertilizers and pesticides in the management of this crop.
| S-EPMC10332502 | biostudies-literature
Project description:Bolting is a key process in the growth and development of lettuce (Lactuca sativa L.). High temperature can induce earlier bolting which decreases in both quality and production of lettuce. However, knowledge underlying lettuce bolting is still lacking. To better understand the molecular basis of bolting, a comparative proteomics analysis was conducted on lettuce stems in the bolting period induced by high temperature (33 °C) compared with a control (20 °C) using iTRAQ-based proteomics, phenotypic measures, and biological verifications. High temperature induced lettuce bolting, while control temperature did not. Of the 6656 proteins identified, 758 proteins significantly altered their expression level induced by high-temperature relative to the control, of which 409 were up-regulated and 349 down-regulated. Proteins with abundance level change were mainly involved in photosynthesis, carbohydrate metabolism, stress response, hormone synthesis, and signal transduction. These differential proteins were mainly enriched in pathways associated with photosynthesis and tryptophan metabolism involving in auxin (IAA) biosynthesis. Among the differentially expressed proteins associated with photosynthesis and tryptophan metabolism were up-regulated. Moreover, in gibberellin (GA) biosynthesis pathway, 10 of main enzymes of P450 were up-regulated. Proteins related to SAUR and GRP, implicated in IAA and GA signal transduction were up-regulated, and the phosphorylation and ubiquitination related proteins regulating IAA and GA signal transduction were also induced. These findings indicate that a high temperature enhances the function of photosynthesis, IAA and GA synthesis and signal transduction to promote the process of bolting, which is in line with the physiology and transcription levels of IAA and GA metabolism. Our data provide a first comprehensive dataset for gaining novel understanding of the molecular basis underlying lettuce bolting induced by high temperature. It is potentially important for further functional analysis and genetic manipulation for molecular breeding to breed new cultivar of lettuce to restrain early bolting, which is vital for improving vegetable quality.
2019-11-12 | PXD008610 | Pride
Project description:Lettuce (Lactuca sativa L.) is one of the most important leafy vegetable that is consumed during its vegetative growth. The transition from vegetative to reproductive growth is induced by high temperature, which has significant economic effect on lettuce production. However, the progression of floral transition and the molecular regulation of bolting are largely unknown. Here we morphologically characterized the inflorescence development and functionally analyzed the FLOWERING LOCUS T (LsFT) gene during bolting regulation in lettuce. We described the 8 developmental stages during floral transition process. The expression of LsFT was negatively correlated with bolting in different lettuce varieties, and was promoted by heat treatment. Overexpression of LsFT could recover the late-flowering phenotype of ft-2 mutant. Knockdown of LsFT by RNA interference dramatically delayed bolting in lettuce, and failed to respond to high temperature. Therefore, this study dissects the process of inflorescence development and characterizes the role of LsFT in bolting regulation in lettuce.
2018-02-14 | GSE108260 | GEO
Project description:Lettuce (Lactuca sativa L.) is a highly perishable horticultural crop with a relatively short shelf life due to leaf senescence that limits its commercial value and contributes to food waste. Postharvest senescence varies with influences of both environmental and genetic factors. Preharvest genetic factors can be indicative of postharvest quality. Discovery of additional preharvest markers to assess lettuce shelf life is an important step towards increasing the efficiency of lettuce breeding efforts for improved shelf life. We selected and evaluated three romaine lettuces with variable shelf lives with the aim of identifying preharvest markers of lettuce postharvest shelf life. We evaluated leaf morphological characteristics for each of the three cultivars. To assess molecular indicators of shelf life, we used an RNA sequencing approach to construct transcriptomic profiles of two of the cultivars, a short shelf life (SSL) breeding line 60184 and a long shelf life (LSL) cultivar ‘Okeechobee’ at maturity. We identified 552 upregulated and 315 downregulated differentially expressed (DE) genes between the genotypes. We found that 27 % of the DE lettuce genes had an Arabidopsis thaliana ortholog characterized as senescence-associated, indicating that variable expression of senescence-associated genes (SAGs) could serve as a tool for preharvest markers of postharvest shelf life. Notably, we identified several SAGs and functional groupings with highly differential expression between the cultivars. This includes several jasmonate ZIM-domain (JAZ), jasmonic acid (JA) signaling genes, chlorophyll a-b binding (CAB) chloroplast-associated genes, and cell wall modification genes including pectate lyases (PL) and expansins (EXP). This study presented an innovative approach for identifying molecular markers for preharvest factors linked to postharvest traits for prolonged shelf. These genes could potentially be developed further as preharvest predictors of shelf life for lettuce breeding
2024-02-27 | GSE226302 | GEO
Project description:Circular RNA (circRNA) is a covalently-closed single-stranded RNA molecule that plays an important role in transcriptional regulation of gene expression in a variety of species. Light intensity is a pivotal environmental factor affecting plant growth and development. However, little is known regarding photoresponsive plant circRNAs. Here, we aimed to investigate the expression and function of circRNAs in lettuce leaves in response to different light intensity treatments. We performed RNA sequencing (RNA-Seq) on leaves of lettuce (Lactuca sativa) to determine circRNA expression profiles and reverse-transcription polymerase chain reaction (PCR) to validate the candidate circRNA molecules. We then combined bioinformatics approach to explore the function of the parental genes of circRNA, including network, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. We identified 1650 circRNAs in lettuce, of which 1508 (86.40%) were derived from exons. Using real-time PCR, we characterized 10 validated differentially expressed circRNAs and their parental genes, all of which showed expression patterns consistent with RNA-Seq data. Interestingly, the expression of circRNA was, in some cases, inversely correlated with the expression of the parental gene. Furthermore, analysis of the circRNA–microRNA–mRNA network suggests that circRNAs may be involved in plant hormone signaling and chlorophyll metabolism during photoreactivity. These findings provide an essential reference basis for studying circRNAs’ biological mechanisms in light-treated plants.
2020-04-14 | GSE148578 | GEO
Project description:Lettuce is a widely consumed leafy vegetable, valued for its nutritional benefits and culinary versatility. Various breeding initiatives have yielded lettuce varieties such as romaine or cos lettuce (Lactuca sativa var. longifolia), characterized by pigmented germplasm and enhanced tolerance to elevated temperatures. Despite its significance, a notable need exists for targeted study investigations into its chemical composition. Thus, this study aims to define the volatile and non-volatile components of the red romaine Thurinus RZ lettuce cultivar using LC-MS and GC-MS analysis. For LC-MS analysis, a C18 column will be accompanied by gradient elution using (A) water and (B) acetonitrile, each containing 0.1% formic acid as the mobile phase. For GC-MS analysis, the HP-5 column will be accompanied by Helium as the carrier gas. The molecules determined will then be ionized, and fragments will be interpreted and annotated using the mass-to-charge (m/z) ratio, which will further be tabulated.
2025-04-10 | MSV000097600 | MassIVE
Project description:The small RNAs and their targets were characterized in lettuce (Lactuca sativa) genome by deep sequencing the small RNA populations of leaf tissues (cv. Salinas, Cobham and Diana), inoculated with Bremia and mock. The small RNA targets were also validated using PARE/degradome data derived from the same tissues.
2017-04-13 | GSE84280 | GEO
Project description:Salinization poses a significant challenge in agriculture, exacerbated by anthropogenic global warming. Biostimulants, derived from living microorganisms or natural extracts, have emerged as valuable tools for conventional and organic agriculture. However, our understanding of the molecular mechanisms underlying the effects of biostimulants is very limited, especially in crops under real cultivation conditions. In this study, we adopted an integrative approach to investigate the effectiveness of the combined application of plant growth-promoting bacterium (Bacillus megaterium strain BM08) and a non-microbial biostimulant under control conditions (normal watering) and salt stress. After confirming the yield increase under both conditions, we investigated the molecular mechanisms underlying the observed effect by measuring a number of physiological parameters (i.e., lipid peroxidation, antioxidants, chlorophylls, total phenolics and phytohormone content), as well as RNA sequencing and primary metabolite analyses. Our findings reveal that the combined effect of the microbial and non-microbial biostimulants led to a decrease in the antioxidant response and an up-regulation of genes involved in cytokinin biosynthesis under salt stress conditions. This, in turn, resulted in a higher concentration of the bioactive cytokinin, isopentenyladenosine, in roots and leaves and an increase in γ-aminobutyric acid, a non-proteic amino acid related to abiotic stress responses. In addition, we observed a decrease in malic acid, along with an abscisic acid (ABA)-independent up-regulation of SR-kinases, a family of protein kinases associated with abiotic stress responses. Furthermore, we observed that the single application of the non-microbial biostimulant triggers an ABA-dependent response under salt stress; however, when combined with the microbial biostimulant, it potentiated the mechanisms triggered by the BM08 bacterial strain. This comprehensive investigation shows that the combination of two biostimulants is able to elicit a cytokinin-dependent response that may explain the observed yield increase under salt stress conditions.
2024-10-15 | GSE279211 | GEO
Project description:UV-B radiation is one of the major environmental stresses that triggers a variety of plant responses. However, limited information is available regarding plant biological reactions which help to circumvent the potentially harmful effects of UV-B radiation in lettuce (Lactuca sativa L.). In this study, RNA-seq was performed to identify differentially expressed genes in response to UV-B radiation.
2018-02-18 | GSE105821 | GEO