Genome-Wide Analysis of TCP Transcription FactorFamily in Sunflower and Identification of HaTCP1 Involved in the Regulation of Shoot Branching
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ABSTRACT:
PROVIDER: PRJNA912670 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22750823_1.fastq.gz | Fastqsanger.gz | |||
| SRR22750823_2.fastq.gz | Fastqsanger.gz | |||
| SRR22750824_1.fastq.gz | Fastqsanger.gz | |||
| SRR22750824_2.fastq.gz | Fastqsanger.gz | |||
| SRR22750825_1.fastq.gz | Fastqsanger.gz |
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Project description:Previous study we have reported the cucumber TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) family gene BRANCHED1 (CsBRC1) as a main transcription factor functions to regulate shoot branching. Here, we found CsBRC1 (CsTCP18b in this study) had a paralogous gene CsTCP18a. To investigate whether the function of CsTCP18a was same as CsTCP18b, we carried out biochemical experiments and genetic transformation. The Real-Time PCR and in situ hybridization showed that CsTCP18a displayed different expression patterns in cucumber compared with CsTCP18b. Ectopic expression of CsTCP18a in Arabidopsis tcp18 (brc1) mutants resulted in a decreased number of rosette branches and rosette leaves, whereas silencing CsTCP18a in cucumber only led to a deformed true leaf of seedling without influencing the shoot branching. RNA-seq analysis of wild-type plants and CsTCP18a-RNAi lines implicated that CsTCP18a regulated early leaf development of cucumber through affecting the transcripts of auxin and cytokinin related genes. Further studies indicated that CsTCP18a could directly interact with CsTCP10 and CsTCP18b in vitro and in vivo. Therefore, our data suggested that CsTCP18a had functional redundancy with CsTCP18b in inhibiting axillary buds outgrowth, and it could also regulate leaf development during cucumber seedling.
2022-11-20 | GSE140737 | GEO
Project description:These findings could lay a critical foundation for further exploring the functions of HaTCPs.
2022-12-26 | GSE221055 | GEO
Project description:Plant-specific DOF-type transcription factors regulate various biological processes. Here, we characterized a silique-abundant gene AtDOF4.2 for its functions in Arabidopsis. AtDOF4.2 is localized in the nuclear region and has transcriptional activation activity in both yeast and plant protoplast assays. The Thr-Met-Asp motif in AtDOF4.2 is essential for its activation. AtDOF4.2-overexpressing plants exhibit an increased branching phenotype, and the mutation of Thr-Met-Asp motif in AtDOF4.2 significantly reduces the branching in transgenic plants. AtDOF4.2 may achieve this function through the upregulation of three branching-related genes, AtSTM, AtTFL1 and AtCYP83B1. The seeds of an AtDOF4.2-overexpressing plant show collapse-like morphology in epidermal cells of the seed coat. Mucilage contents and the concentration and composition of mucilage monosaccharides are significantly changed in the seed coat of transgenic plants. AtDOF4.2 may exert its effects on the seed epidermis through the direct binding and activation of the cell wall loosening-related gene AtEXPA9. The dof4.2 mutant did not exhibit changes in branching or its seed coat; however, the silique length and seed yield were increased. AtDOF4.4, which is a close homolog of AtDOF4.2, also promotes shoot branching and affects silique size and seed yield. Manipulation of these genes should have a practical use in the improvement of agronomic traits in important crops. Two-week-old seedlings (aerial part) of Col-0 and AtDOF4.4-overexpressing transgenic lines 4.4-1 and 4.4-5, grown on MS, were used for extraction of total RNA and subjected to chip analysis using Agilent Arabidopsis Oligo Microarray (4X44K) in SHANGHAIBIO CORPORATION (www.ebioservice.com; Shanghai, China).
2012-10-19 | E-GEOD-41682 | biostudies-arrayexpress
Project description:Plant architecture greatly depends on its branching patterns. Branches are formed from meristems initiated in the axils of leaves. Axillary meristems may develop immediately giving new shoots or they may become arrested after a short period of growth as dormant axillary buds. This decision is affected by endogenous and environmental factors. We are studying two Arabidopsis genes coding for TCP transcription factors, BRANCHED1 (BRC1) and BRANCHED2 (BRC2) that control this key decision. Several endogenous and environmental stimuli affect this process one of them is the quality of ambient light. Plants have developed sophisticated mechanisms that allow them to detect the presence of nearby plants and trigger responses of development to avoid the shade. This set of responses is known as shade avoidance. One response to this syndrome, with high agronomic relevance, is the suppression of branching. The genetic basis of this response is still largely unknown. Our goal is to carry out, in Arabidopsis, a systematic study of the genetic control of the removal of branching during the escape response of the shadow. We found that Arabidopsis plants produce fewer branches when grown at high density. We also found that the removal of high-density branch is accompanied by up-regulation of BRC1. On the other hand, short light treatment enriched in far-red (which simulate the shade plant) also cause an accumulation of BRC1 mRNA levels in plants grown at low density. Besides initial data off transcriptomic analysis (wt vs. brc1-2) indicate that BRC1 could be involved in signaling / response to light in the axillary buds. In this study we have identified several potential target genes of BRC1 involved in the response to light. One is PIL2 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 2), a gene that encodes a bHLH transcription factor that interacts with APRR1/TOC1. We are currently characterizing in more detail at the genetic and molecular level the BRC1 relationship with this and other potential target genes and their role in the control of branching patterns. The microarray analysis was performed using RNA samples obtained from three independent plant pools grown under identical conditions. The cDNA synthesized from RNA of wild type or brc1-2 plants grown either in white light (WT-WL, brc1-2-WL) or red+far red light (WT-FR, brc1-2-FR) was hybridized.
2014-05-11 | E-GEOD-23407 | biostudies-arrayexpress
Project description:Plant-specific DOF-type transcription factors regulate various biological processes. Here, we characterized a silique-abundant gene AtDOF4.2 for its functions in Arabidopsis. AtDOF4.2 is localized in the nuclear region and has transcriptional activation activity in both yeast and plant protoplast assays. The Thr-Met-Asp motif in AtDOF4.2 is essential for its activation. AtDOF4.2-overexpressing plants exhibit an increased branching phenotype, and the mutation of Thr-Met-Asp motif in AtDOF4.2 significantly reduces the branching in transgenic plants. AtDOF4.2 may achieve this function through the upregulation of three branching-related genes, AtSTM, AtTFL1 and AtCYP83B1. The seeds of an AtDOF4.2-overexpressing plant show collapse-like morphology in epidermal cells of the seed coat. Mucilage contents and the concentration and composition of mucilage monosaccharides are significantly changed in the seed coat of transgenic plants. AtDOF4.2 may exert its effects on the seed epidermis through the direct binding and activation of the cell wall loosening-related gene AtEXPA9. The dof4.2 mutant did not exhibit changes in branching or its seed coat; however, the silique length and seed yield were increased. AtDOF4.4, which is a close homolog of AtDOF4.2, also promotes shoot branching and affects silique size and seed yield. Manipulation of these genes should have a practical use in the improvement of agronomic traits in important crops.
2012-10-19 | GSE41682 | GEO
Project description:Plant architecture greatly depends on its branching patterns. Branches are formed from meristems initiated in the axils of leaves. Axillary meristems may develop immediately giving new shoots or they may become arrested after a short period of growth as dormant axillary buds. This decision is affected by endogenous and environmental factors. We are studying two Arabidopsis genes coding for TCP transcription factors, BRANCHED1 (BRC1) and BRANCHED2 (BRC2) that control this key decision. Several endogenous and environmental stimuli affect this process one of them is the quality of ambient light. Plants have developed sophisticated mechanisms that allow them to detect the presence of nearby plants and trigger responses of development to avoid the shade. This set of responses is known as shade avoidance. One response to this syndrome, with high agronomic relevance, is the suppression of branching. The genetic basis of this response is still largely unknown. Our goal is to carry out, in Arabidopsis, a systematic study of the genetic control of the removal of branching during the escape response of the shadow. We found that Arabidopsis plants produce fewer branches when grown at high density. We also found that the removal of high-density branch is accompanied by up-regulation of BRC1. On the other hand, short light treatment enriched in far-red (which simulate the shade plant) also cause an accumulation of BRC1 mRNA levels in plants grown at low density. Besides initial data off transcriptomic analysis (wt vs. brc1-2) indicate that BRC1 could be involved in signaling / response to light in the axillary buds. In this study we have identified several potential target genes of BRC1 involved in the response to light. One is PIL2 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 2), a gene that encodes a bHLH transcription factor that interacts with APRR1/TOC1. We are currently characterizing in more detail at the genetic and molecular level the BRC1 relationship with this and other potential target genes and their role in the control of branching patterns.
2014-05-11 | GSE23407 | GEO
Project description:The objective of this study was to evaluate the role of cytochrome P450 monooxygenases (P450s) and other detoxification-related proteins in Imisun sunflower resistance. Two sunflower inbred lines were used: HA 425 and HA 89, imidazolinone (IMI)-resistant and susceptible, respectively. Growth response to imazethapyr herbicide in combination with P450s inhibitors 1-aminobenzotriazole (ABT) and piperonyl butoxide (PBO) was evaluated in 15-day-old sunflower plantlets. Roots were collected and label-free quantitation (LFQ) proteomic analysis were carried out in order to characterize plant response to IMI. Roots of 15-day-old plants treated with 0 and 3.3 µM imazethapyr were frozen in liquid nitrogen. Protein extraction was performed as described in Wu et al. (2014) from 1 g root tissue per genotype/treatment combination.
2020-03-25 | PXD014689 | Pride
Project description:BRANCHED1-like gene CsTCP18a contributes to shoot branching and leaf development in cucumber
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Project description:Chickpea and lentil are two important pulse crops used for human consumption as sources of vegetable protein, rich in amino acids and bioactive compounds. The search for elite cultivars with better architecture has been a demand by farmers of these two crops, which aims to systematize their mechanized planting and harvesting on a large scale. Therefore, the identification of genes associated with the regulation of the branching and architecture of these plants has currently gained great importance. This work aimed to gain insight into transcriptomic changes of two contrasting chickpea and lentil cultivars in terms of branching pattern (little versus highly branched cultivars). In addition, we aimed to identify candidate genes involved in the regulation of shoot branching that could be used as future targets for molecular breeding. The axillary and apical buds of chickpea cultivars Blanco lechoso and FLIP07-318C, and lentil cultivars Castellana and Campisi, considered as little and highly branched, respectively, were harvested.
2024-05-31 | E-MTAB-13679 | biostudies-arrayexpress
Project description:Background: Respiratory allergy triggered by pollen allergens is increasing at an alarming rate worldwide. Sunflower pollen is thought to be an important source of inhalant allergens. Present study aims to identify the prevalence of sunflower pollinosis among the Indian allergic population and characterizes the pollen allergens using immuno-proteomic tools. Methodology: Clinico-immunological tests were performed to understand the prevalence of sensitivity towards sunflower pollen among the atopic population. Sera from selected sunflower positive patients were used as probe to detect the IgE-reactive proteins from the one and two dimensionally separated proteome of sunflower pollen. The antigenic nature of the sugar moiety of the glycoprotein allergens was studied by meta-periodate modification of IgE-immunoblot. Finally, these allergens were identified by mass-spectrometry (MALDI TOF/TOF and LC ESI qTOF). MASCOT searching was performed against NCBInr database. However, Helianthus annuus genome is not fully sequenced and partially annotated. So in case of low confidence (p> 0.05) protein identification, searching was performed against EST library of Helianthus annuus. Results: Prevalence of sunflower pollen allergy was observed among 21% of the atopic population and associated with elevated level of specific IgE and histamine in the sera of these patients. Immunoscreening of sunflower pollen proteome with patient serum detected seven IgE-reactive proteins with varying molecular weight and pI. Hierarchical clustering of 2D-immunoblot data highlighted three allergens characterized by a more frequent immuno-reactivity and increased levels of IgE antibodies in the sera of susceptible patients. These allergens were considered as the major allergens of sunflower pollen and were found to have their glycan moiety critical for inducing IgE response. Homology driven search of MS/MS data of these IgE-reactive proteins identified seven previously unreported allergens from sunflower pollen. Three major allergenic proteins were identified as two non-isoformic pectate lyases and a cystein protease. Conclusion: Novelty of the present report is the identification of a panel of seven sunflower pollen allergens for the first time at immuno-biochemical and proteomic level, which substantiated the clinical evidence of sunflower allergy. Further purification and recombinant expression of these allergens will improve component-resolved diagnosis and therapy of pollen allergy.
2015-10-05 | PXD002397 | Pride