Ontology highlight
ABSTRACT:
PROVIDER: PRJNA880996 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21627242_1.fastq.gz | Fastqsanger.gz | |||
| SRR21627242_2.fastq.gz | Fastqsanger.gz | |||
| SRR21627243_1.fastq.gz | Fastqsanger.gz | |||
| SRR21627243_2.fastq.gz | Fastqsanger.gz | |||
| SRR21627244_1.fastq.gz | Fastqsanger.gz |
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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:atx1/atx3/atx4 triple mutants display significantly early flowering and early leaf senescence phenotypes. RNA-seq was used to identify gene expression changes occuring at the time of bolting, independent of leaf age.
2019-07-12 | GSE134177 | GEO
Project description:Leaf size and flatness directly affect photosynthesis and are closely related to agricultural yield. The final leaf size and shape are coordinately determined by cell proliferation, differentiation, and expansion during leaf development. Lettuce (Lactuca sativa L.) is one of the most important leafy vegetables worldwide, and lettuce leaves vary in shape and size. However, the molecular mechanisms of leaf development in lettuce are largely unknown. In this study, we showed that the lettuce APETALA2 (LsAP2) gene regulates leaf morphology. LsAP2 encodes a transcriptional repressor that contains the conserved EAR motif, which mediates interactions with the TOPLESS/TOPLESS-RELATED (TPL/TPR) corepressors. Overexpression of LsAP2 led to small and crinkly leaves, and many bulges were seen on the surface of the leaf blade. LsAP2 physically interacted with the CINCINNATA (CIN)-like TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factors and inhibited their transcriptional activation activity. RNA sequencing analysis showed that LsAP2 affected the expression of auxin- and polarity-related genes. In addition, LsAP2 directly repressed the abaxial identity gene KANADI2 (LsKAN2). Together, these results indicate that LsAP2 regulates leaf morphology by inhibiting CIN-like TCP transcription factors and repressing LsKAN2, and our work provides insights into the regulatory mechanisms of leaf development in lettuce.
2021-03-29 | GSE168886 | GEO
Project description:The first GSSM of V. vinifera was reconstructed (MODEL2408120001). Tissue-specific models for stem, leaf, and berry of the Cabernet Sauvignon cultivar were generated from the original model, through the integration of RNA-Seq data. These models have been merged into diel multi-tissue models to study the interactions between tissues at light and dark phases.
2024-09-02 | MODEL2408160001 | BioModels
Project description:Lettuce (Lactuca sativa L.) as one of the most economically important leaf vegetables, is easy bolting in high temperature condition. Early bolting loses its commodity value and edible value and bring huge losses and waste of resources. However, the initiation and molecular mechanism underlying early bolting induced by high temperature remains largely elusive. To better understand it, a comparative proteomics analysis was conducted on lettuce, in the initiation period of bolting induced by a high temperature (33 oC) and a control temperature (20 oC) using iTRAQ-based proteomics, phenotypic measures, and biological verifications using qRT-PCR. The morphologic and microscopic observation showed that the initiation of bolting was on 8 day after high temperature treatment. Fructose rapidly accumulated after high temperature. In the period of the bolting initiation, of the 3305 identified proteins, a total of 93 proteins were identified with differential abundance, among 38 of these proteins were up-regulated and 55 proteins were down-regulated. About 38% of proteins were involved in metabolic pathway and mainly clustered in energy metabolism and protein synthesis. Furthermore, some proteins involved in sugar synthesis were differentially expressed, which were also related with energy production. This is the first report on the metabolic changes involved in bolting initiation in lettuce. Our study suggested that energy metabolism and ribosomal proteins are pivotal components during bolting initiation. It may bring potential regulatory mechanism for the initiation of early bolting by high temperature and manipulations for breeding in lettuce.
2019-07-02 | PXD014464 |
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:Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the small RNA sequencing. Tissue from the msh1 mutant and dcl2,3,4,msh1 quadruple mutants used as rootstocks was similarly collected at the bolting stage and used for the small RNA sequencing.
2020-09-20 | GSE152567 | GEO
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