Quantitative proteomic analysis with iTRAQ labeling of leaf tissue samples of mutant and wild type in Chinese cabbage
Ontology highlight
ABSTRACT:
ORGANISM(S): Brassica Rapa Subsp. Pekinensis
SUBMITTER: 
Jingrui Li
PROVIDER: PXD056706 | iProX | Thu Oct 10 00:00:00 BST 2024
REPOSITORIES: iProX
Similar Datasets
Project description:The objective of this RNAseq-experiment has been to compare apical leaf halves of different mutants with that of wild type plants.
2019-10-30 | GSE136944 | GEO
Project description:Leaves are flat determinate organs derived from indeterminate shoot apical meristems. The presence of a specific leaf meristem is debated, as anatomical features typical of meristems are not present in leaves. Here we demonstrate that multiple NGATHA (NGA) and CINCINNATA-class-TCP (CIN-TCP) transcription factors act redundantly to suppress activity of a leaf margin meristem in Arabidopsis thaliana, and that their absence confers persistent marginal growth of leaves, cotyledons and floral organs. The marginal meristem is activated by the juxtaposition of adaxial and abaxial domains and maintained by WOX homeobox transcription factors, but other margin elaboration genes are dispensable for its maintenance. This genetic framework parallels the morphogenetic program of shoot apical meristems and may represent a relic from an ancestral shoot system from which seed plant leaves evolved.
2016-10-03 | GSE78693 | GEO
Project description:We study differences in gene expression between Populus P35S::BL (BL-oe) lines and control, affecting plant growth and differentiation, and dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by overexpression of BL gene. We identified an activation tagging mutant with increased leaf size and correspondingly name it BIG LEAF (BL). We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes a WD40 putative transcription regulator similar to the Arabidopsis thaliana STERILE APETALA (SAP). We recapitulated the phenotype by overexpression of the gene into the same genotype under strong constitutive promoter (P35S::BL, BL-oe). Transgenic up-regulation of the BL gene caused enhanced leaf size, early bud-break, and suppression of secondary growth. BL transcript abundance in wild type plants is in apical tissues, mostly in shoot meristem, leaf primordia and axillary meristem. Our data indicates that BL plays an important role in the process of tree growth.
2017-05-11 | GSE68859 | GEO
Project description:Certain phytophagous insects can induce leaf curling in their host plants that may provide protected and nutrient-rich habitats. However, the mechanisms of this induction remain poorly understood. The cassava mealybug, Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae), is a serious pest of the cassava and causes leaf curling. To reveal the mechanisms of leaf-curl induction, we first inoculated varying numbers of mealybugs in different locations, namely, the apical meristem and the stem, on cassava seedlings. Second, we performed transcriptome analysis using the total RNA extracted from leaves. The results showed that a single insect was able to induce leaf curling, but the intensity and frequency of the leaf curling were positively correlated with the number of insects. Furthermore, the leaf curling occurred when the mealybugs fed on or close to the apical meristem but not when they fed on the stem. Transcriptome analysis identified a total of 3,931 differentially expressed genes (DEGs) from intact plants and the plants inoculated with mealybugs at different time points. GO analysis of the biological processes revealed that the DEGs contained a series of factors for leaf development of the adaxial–abaxial axis, and auxin biosynthesis and polarity. This suggests that alterations in these functions may cause leaf curling.
2023-06-15 | GSE234712 | GEO
Project description:Rice leaves consist of three distinct regions along a proximal-distal axis, namely, the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, however,but the genetic programs underlying the development of each region are poorly understood. To capture the entire picture of rice leaf development and to discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages.
2020-10-06 | GSE159047 | GEO
Project description:Molecular characterization of leaf development has not been well studied in soybean. Studies have shown that genomic regions controlling multifoliate leaf morphology in Glycine max also regulates important agronomic characters including yield, seed weight, seed number, shattering, plant growth, and flowering. Two soybean isolines that differed in leaf phenotype were profiled by high throughput RNA and small RNA (sRNA) sequencing. A Clark isoline, homozygous for a dominant mutant allele, Lf1, that specifies a five-foliate compound leaf was compared to wild type Clark that is homozygous for the standard allele that produces trifoliate leaves. Although Lf1 is dominant, it presents variable expressivity as the young plantlets with the Lf1Lf1 genotype initially have trifoliate leaves in the first few weeks, after which they transition to five-foliate leaves. At later developmental stages, they begin to produce four-foliate or trifoliate leaves. In RNA-Seq experiments, a total of 91 and 95 million reads were generated in each lane of Illumina sequencing for the shoot tip of wild type Clark standard (CS) and mutant Clark five-foliate (CF) libraries, respectively. Of these, ~70% million reads aligned to the 78,743 target Glyma models from the reference soybean genome (cv. Williams 82) with maximum of 3 mismatches and up to 25 alignments. Where as in vegetative bud, 56 (CS) to 59 (CF) million reads were produced and of these ~80% aligned to the soybean reference genome. The comparative studies of the transcript profiles of the wild-type versus mutant line revealed a number of differentially expressed genes. A total of 1,296 and 2,083 genes were up-regulated in the shoot tip of CS and CF, respectively that showed ≥2-fold expression difference. On the contrary in the vegetative bud, much smaller number of genes 14 (CS) and 94 (CF) showed increased transcript abundance. In sRNA analysis, a collection of 200,447 and 268,508 unique sRNA sequences isolated from shoot tip tissue of CS and CF were aligned to the soybean reference genome and their target glyma models were predicted using bioinformatics. This sRNA analysis at genome level reveals differences in size distribution of classes in the CS and CF. This study provides insight into the initial understanding of leaf development in soybean by revealing a number of genes and sRNAs differentially expressed between the CS and CF.
2024-12-16 | GSE41200 | GEO
Project description:Two sets of wheat lines near-isogenic to Lr34 were used to compare gene expression profiles of wheat: 1. with and without Lr34 gene; 2. rust and mock inoculation; 3. distal and basal portion of the flag leaves. The two sets of wheat near-isogenic lines were used to subtract genetic background variations and to enrich Lr34-regulated gene expression profiles. The study is aimed to better understand the mechanisms of the well-known durable leaf rust resistance gene, Lr34, mediated resistance at the transcriptome level. Keywords: Distal and basal leaf halves of near-isogenic lines
2007-02-01 | GSE6227 | GEO
Project description:Basal branching in grasses, or tillering, is an important trait determining both form and function of crops. While similarities exist between eudicot and grass branching programs, one notable difference is that the tiller buds of grasses are covered by the subtending leaf, whereas eudicot buds are typically unconstrained. The current study shows that contact with the leaf sheath represses sorghum bud growth by providing a mechanical signal that cues the bud to refrain from rapid growth. Leaf removal resulted in massive reprogramming of the bud transcriptome that included signatures of epigenetic modifications, and also implicated several hormones in the response. Bud abscisic acid (ABA) transiently increased, then decreased following leaf removal relative to controls, and ABA was necessary to repress bud growth in the presence of the leaf. Jasmonic acid (JA) levels and signaling increased in buds following leaf removal. Remarkably, application of JA to buds in situ promoted growth. The repression of bud growth by leaf contact shares characteristics of thigmomorphogenic responses in other systems, including the involvement of JA, though the JA effect is opposite. The repression of bud growth by leaf contact may represent a mechanism to time tillering to an appropriate developmental stage of the plant.
2019-03-05 | GSE127822 | GEO
Project description:The aim of this study was to investigate the role of strigolactones (SLs) in controlling tillering and their involvement as a signal for nitrogen status. RNA-seq analysis was performed on 18-day-old hydroponically grown Tad17 triple knock-out TILLING mutant plants (SL-deficient mutant) and WT-segregant plants, 8 days after introducing them to nitrogen limiting conditions. The experiment consisted of two different treatments: High Nitrogen (10 mM N) and Low Nitrogen (0.1 mM N). Each treatment included six biological replicates. Total RNA was extracted from pooled samples of four basal node sections per biological replicate. In this study, the basal node was defined as the 0.5 cm section from the base of the main shoot, comprising the apical meristem, lateral buds, leaf meristems, etc.
2024-08-13 | E-MTAB-14014 | biostudies-arrayexpress
Project description:In this study, the cell wall proteomes of 3 different regions of alfalfa stems were compared. These three regions correspond to three phases in the stem development. The sequential extraction of cell wall proteins with CaCl2, EGTA and LiCl-complemented buffers was combined with a gel-based proteome approach and multivariate analysis. Although the highest similarities were observed between the apical and intermediate stem regions, the three proteome patterns are characteristic for each region. In the basal stem region, proteins that bind carbohydrates and have proteolytic activity, as well as enzymes involved in glycan remobilization, accumulate. Beta-amylase and ferritin likewise accumulate more in the basal stem segment. Therefore remobilization of nutrients appears to be an important process in the oldest stem segment. The intermediate and the apical region are sites of cell wall polymer remodelling, as suggested by the high abundance of proteins involved in the remodelling of the cell wall such as xyloglucan endoglucosylase, polygalacturonase non-catalytic subunit or beta-galactosidase. The most striking change between the different stem parts is however the strong accumulation of a DUF642-conserved domain containing protein in the apical region of the stem which suggests a particular role of this protein during the early development of stem tissues.
2019-11-12 | PXD010666 | Pride