Inflorescence development and the role of LsFT in regulating bolting in lettuce (Lactuca sativa L.)
Ontology highlight
ABSTRACT:
ORGANISM(S): Lactuca sativa
PROVIDER: GSE108260 | GEO | 2018/02/14
REPOSITORIES: GEO
Similar Datasets
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:N6-methyladenosine (m6A) is a crucial epigenetic modification in mRNA and the most abundant methylation in eukaryotes. However, research on m6A modification in radish (Raphanus sativus) is not as extensive as in model plants. In this study, we analyzed m6A modification during the vegetative and reproductive growth stages of radish using m6A-seq and RNA-seq to explore its potential role in bolting and flowering. The results showed that m6A peaks significantly increased during the reproductive growth stage compared to the vegetative stage, with more m6A modification sites in the stop codon, 3' UTR, and promoter regions. Overexpression of the RsALKBH10B gene led to a global reduction in m6A modification and resulted in an early bolting and flowering phenotype, with transcription levels of key flowering factors RsSOC1 and RsFT increasing by 10-40 fold. Correlation analysis between differential m6A modification and differentially expressed genes indicated that genes such as RsSUF4, RsAGL13, and RsCDF5 might regulate bolting and flowering. Overexpression of RsSUF4 delayed bolting and flowering and decreased overall m6A modification levels; in positive transgenic plants, higher m6A levels of RsSUF4 were associated with lower transcription levels. These findings suggest that m6A methylation may regulate gene expression related to bolting and flowering in radish by affecting mRNA stability, ultimately leading to bolting and flowering.
2024-06-22 | GSE270351 | GEO
Project description:Several pathways conferring environmental flowering responses in Arabidopsis converge on developmental processes that mediate floral transition in the shoot apical meristem. Many characterized mutations disrupt these environmental responses, but downstream developmental processes have been more refractory to mutagenesis. We constructed a quintuple mutant impaired in several environmental pathways and showed that it possesses severely reduced flowering responses to changes in photoperiod and ambient temperature. RNA-seq analysis of the quintuple mutant showed that the expression of genes encoding gibberellin biosynthesis enzymes and transcription factors involved in the age pathway correlates with flowering. Mutagenesis of the quintuple mutant generated two late-flowering mutants, quintuple ems 1 (qem1) and qem2. The mutated genes were identified by isogenic mapping and transgenic complementation. The qem1 mutant was an allele of ga20ox2, confirming the importance of gibberellin for flowering in the absence of environmental responses. By contrast, the qem2 mutation is in CHROMATIN REMODELING 4 (CHR4), which has not been genetically implicated in floral induction. Using co-immunoprecipitation, RNA-seq and ChIP-seq, we show that CHR4 interacts with transcription factors involved in floral meristem identity and affects expression of key floral regulators. We conclude that CHR4 mediates the response to endogenous flowering pathways in the inflorescence meristem to promote floral identity.
2020-03-02 | PXD016457 | Pride
Project description:How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing, producing two splice variants, FLM-β and FLM-δ, which compete for interaction with the floral repressor SVP. The SVP/FLM-β complex is predominately formed at low temperatures and prevents precocious flowering. In contrast, the competing SVP FLM-δ complex is impaired in DNA binding and acts as a dominant negative activator of flowering at higher temperatures. Our results demonstrate the importance of temperature-dependent alternative splicing in modulating the timing of the floral transition in response to environmental change.
2013-09-19 | GSE48082 | GEO
Project description:The aim of this study was to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction.
2014-12-31 | GSE55951 | GEO
Project description:Null mutations of tomato FRUITFULL-like genes FUL1, FUL2, MBP10, MBP20 caused delayed flowering and branched inflorescence, so we sequenced mRNA from vegetative meristems (VM), transition meristems (TM), floral meristems (FM), and FM of the first sympodial shoot of tomato mutant ful1/ful2/mbp10/mbp20 (slful) as well as the wild type Moneyberg (WT) to see genome-wide expression changes affected by the mutations.
2021-12-22 | GSE154419 | GEO
Project description:Temperature plays an important role in the growth and development of lettuce (Lactuca sativa L.). A high temperature can induce bolting, which decreases both the quality and production of lettuce. However, knowledge of underlying lettuce bolting is still lacking, especially in the molecular basis that high temperature promotes the premature bolting of lettuce at the phosphorylated level. In this study, we analyzed the lettuce stems during the bolting period induced by a high temperature (33oC/25oC, day/ night) and a controlled temperature (20oC/13oC, day/night) using iTRAQ-based phosphoproteome and 987 phosphoproteins were significantly changed after high-temperature treatment and a total of 3814 phosphorylation sites located in 1766 phosphopeptides were identified. Also, we found 216 phosphoproteins significantly regulated, of which 116 up-regulated and 101 down-regulated, and the abundance changed peptides after high-temperature treatment was significantly involved in the biological process (BP) of water homeostasis. Most of these phosphoproteins were associated with metabolic process, correspondingly the main molecular functions are catalytic activity and transporter activity. The top 10 signaling pathways included spliceosome, starch and sucrose metabolism, RNA transport, protein processing in endoplasmic reticulum, phosphatidylinositol signaling system, phospholipase D signaling pathway, apoptosis, protein export, tight junction, and glycerolipid metabolism. For further, we found the high-temperature influence phosphoprotein activity associated with metabolism, especially, starch and sucrose metabolism, glycerolipid metabolism, methane metabolism. The kinases, including proline-directed, acidic, basic, others and tyrosine, were predicted to be involved in signal transduction and metabolism regulation. The proline-directed motif such as ..SP..[s]P, [s]P, [t]P was the dominant class, proline-directed motifs associated with MAK kinase, and several acidic motifs are casein kinase II motif are necessary for lettuce blotting. Our study showed phosphoproteome profiling in response to high temperature and provides a better understanding of the molecular mechanisms regulated in lettuce blotting
2019-06-10 | PXD014208 |
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:The aim of this study was to explore epigenetic variations between sugar beet genotypes with distinct bolting tolerance levels and to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction.
2014-12-31 | GSE56413 | GEO
Project description:How plants control the transition to flowering in response to ambient temperature is only beginning to be understood. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process. FLM is subject to temperature-dependent alternative splicing, producing two splice variants, FLM-M-NM-2 and FLM-M-NM-4, which compete for interaction with the floral repressor SVP. The SVP/FLM-M-NM-2 complex is predominately formed at low temperatures and prevents precocious flowering. In contrast, the competing SVP FLM-M-NM-4 complex is impaired in DNA binding and acts as a dominant negative activator of flowering at higher temperatures. Our results demonstrate the importance of temperature-dependent alternative splicing in modulating the timing of the floral transition in response to environmental change. ChIP-seq A. thaliana FLM (3 replicates for gFLM and 2 replicates for FLM splice variants)
2013-09-19 | E-GEOD-48082 | biostudies-arrayexpress