Sorghum axillary bud transcriptome response to leaf removal
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ABSTRACT:
ORGANISM(S): Sorghum bicolor
PROVIDER: GSE127822 | GEO | 2019/03/05
REPOSITORIES: GEO
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Project description:Phytochrome B (phyB) enables plants to modify shoot branching or tillering in response to varying light intensities and ratios of red and far-red light caused by shading and neighbor proximity. Tillering is inhibited in sorghum genotypes that lack phytochrome B (58M, phyB-1) until after floral initiation. The growth of tiller buds in the first leaf axil of wild-type (100M, PHYB) and phyB-1 sorghum genotypes is similar until 6 d after planting when buds of phyB-1 arrest growth, while wild-type buds continue growing and develop into tillers. Transcriptome analysis at this early stage of bud development identified numerous genes that were up to 50-fold differentially expressed in wild-type/phyB-1 buds. Up-regulation of terminal flower1, GA2oxidase, and TPPI could protect axillary meristems in phyB-1 from precocious floral induction and decrease bud sensitivity to sugar signals. After bud growth arrest in phyB-1, expression of dormancy-associated genes such as DRM1, GT1, AF1, and CKX1 increased and ENOD93, ACCoxidase, ARR3/6/9, CGA1, and SHY2 decreased. Continued bud outgrowth in wild-type was correlated with increased expression of genes encoding a SWEET transporter and cell wall invertases. The SWEET transporter may facilitate Suc unloading from the phloem to the apoplast where cell wall invertases generate monosaccharides for uptake and utilization to sustain bud outgrowth. Elevated expression of these genes was correlated with higher levels of cytokinin/ sugar signaling in growing buds of wild-type plants.
2017-03-30 | GSE79389 | GEO
Project description:The paraveinal mesophyll (PVM) of soybean leaves is a layer of laterally expanded cells sandwiched between the palisade and spongy mesophyll chlorenchyma. The vacuoles of PVM cells contain an abundance of a putative vegetative storage protein, VSP (α, β). VSP is is constitutively produced, but is up-regulated during sink limitation experiments involving flower, fruit, or vegetative bud removal. Soybean vegetative lipoxygenases (Vlx), consisting of 5 isozymes (Vlx, A-D), have been identified as potential storage proteins because they accumulate to high levels with experimental sink limitation and have been co-localized with VSP to the vacuoles of PVM cells. We re-investigated the sub-cellular locations of these enzymes with TEM immuno-cytochemistry. We employed laser micro-dissection to compared RNA expression of PVM cells with mesophyll chlorenchyma cells, and we performed a micro-array analysis of soybean leaf samples representing a time-course, sink-limitation, experiment. We found that none of the Vlx isozymes co-localize with putative storage proteins in PVM vacuoles, and that our sink limitation experiment (typical of those used in the past) induced a strong up-regulation of stress response genes, simultaneous with the up-regulation of the Vlx isozymes. Our findings do not support a storage function for soybean Vlx. The results reported here are from a study designed to evaluate systemic effects of a vegetative bud removal protocol that had been used previously to study accumulation and subsequent mobilization of vegetative storage proteins in soybean. During these experiments plants were grown for 30 days and then all vegetative buds were removed. Bud removal was repeated each day for 15 days (designated the "detip" phase) and then new buds were allowed to regrow (designated the "retip" phase). Samples were collected at 5 day intervals. Total RNA was extracted from selected samples for our microarray experiments. Three replicate time course experiments provided RNA samples for our microarray analysis. Samples were harvested from both bud removal ("detip/retip") plants and untreated controls of the same age that were maintained side-by-side under the same growth conditions. Bud removal plants were designated as "detip" plants during the bud removal phase and "retip" plants during the regrowth phase. Bud removal began at time-course day 30 and lasted for 15 days (designated D0 through D15). Shoot regrowth lasted an additional 15 days (designated R16 through R30). Controls were designate similarly with C0 corresponding to 30 day old plants at the the first day of bud removal and C30 corresponding to day 15 of the regrowth phase. Samples were collected at 5 day intervals. Messenger RNA was extracted from selected samples for our microarray experiments. These were from 30 day old plants ( C0, the last day of growth before detipping), 45 day old plants (C15, D15, at day 15 of bud removal), 50 day old plants (C20, R20, day 5 of shoot regeneration), and 60 old plants (C30, R30, day 15 of regrowth). RNA was extracted from leaf samples using a method developed for tissues containing abundant polysaccharides and polyphenols (Gehrig et al., 2000). In addition, the extracted RNA was further purified using the RNeasy kit (Qiagen, Valencia, CA). Each RNA sample examined (C0, C15, C20, C30, D15, R20, R30; each with a minimum of 3 replicates for a total of 22 samples) was converted to cRNA and hybridized to Affymetrix soybean GeneChips (GEO accession # GPL4592) according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA).
2012-07-25 | E-GEOD-23129 | biostudies-arrayexpress
Project description:Shoot branching of flowering plants exhibits phenotypic plasticity and variability. This plasticity is determined by the activity of axillary meristems, which in turn is influenced by endogenous and exogenous cues such as nutrients and light. In many species, not all buds on the main shoot develop into branches despite favorable growing conditions. In petunia, basal buds (buds 1-3) typically do not grow out to form branches, while more apical buds (buds 6 and 7) are competent to grow. The genetic regulation of buds was explored using transcriptome analyses of petunia axillary buds at different positions on the main stem. To suppress or promote bud outgrowth, we grew the plants in media with differing phosphate (P) levels. Using RNA-seq, we found many (>5000) differentially expressed genes between bud 6 or 7, and bud 2. In addition, more genes were differentially expressed when we transferred the plants from low P to high P medium, compared with shifting from high P to low P medium. Buds 6 and 7 had increased transcript abundance of cytokinin and auxin-related genes, whereas the basal non-growing buds (bud 2 and to a lesser extent bud 3) had higher expression of strigolactone, abscisic acid, and dormancy-related genes, suggesting the outgrowth of these basal buds was actively suppressed. Consistent with this, the expression of ABA associated genes decreased significantly in apical buds after stimulating growth by switching the medium from low P to high P. Furthermore, comparisons between our data and transcriptome data from other species suggest that the suppression of outgrowth of bud 2 was correlated with a limited supply of carbon to these axillary buds. Candidate genes that might repress bud outgrowth were identified by co-expression analysis.
2023-07-26 | GSE237985 | GEO
Project description:Analyses of expression differences in flower bud and leaf of scion and rootstock, in homografts of Arabidopsis Gene expression data of unopened developing flower buds and leaves, newly emerged after homografting, from the scion and the rootstock
2015-04-14 | E-GEOD-61631 | biostudies-arrayexpress
Project description:Aims: To determine the changes in the Arabidopsis axillary bud transcriptome in response to changes in the red light (R) to far red light (FR) ratio (R:FR). Background: The branching habit of plants is a key determinant of overall plant form and function with great relevance to modern agriculture. Shade signals transduced by phytochromes are major regulators of axillary bud outgrowth, and in turn control branching in both natural and agricultural environments. To continue our investigations into the regulation of branching by R:FR, we have developed a system using supplemental FR LEDs to tightly control the outgrowth of Arabidopsis axillary buds. Depending on the position of the bud in the rosette, outgrowth is either repressed (uppermost bud) or rapidly promoted (bud in the axil of the third leaf down) by the transition from low to high R:FR. Treatment: Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-60000 was used as the experimental material. Plants were grown individually in 25 by 50 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 Moles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24 C/18 C day/night temperatures. One day after sowing, the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis, the plants were matched and split into two treatment groups. In experiment 1, the FR source for one of the groups was switched off at 12:00 pm on the day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation. 12 samples (3 bud n and low R:FR, 3 bud n and high R:FR, 3 bud n-2 and low R:FR, 3 bud n-2 and high R:FR) were used in this experiment.
2012-11-21 | E-GEOD-42415 | biostudies-arrayexpress
Project description:The loss-of-function mutant of AtLEJ1 had well-developed anther cells and showed an increased accumulation of JA and ET in its flower bud clusters. Conversely, overexpression of AtLEJ1 caused a delay in the development of the floral organs, arrested anther cell development and secondary cell-wall biosynthesis in the endothecium cells, and reduced JA and ET contents in the flower bud clusters, resulting in male-sterility through anther indehiscence. We used microarrays to gain a comprehensive understanding of the transcriptional changes induced by AtLEJ1 gene expression, Experiment Overall Design: We performed a full genome microarray analysis (ATH1 Affymetrix chips) with the wild type, 35S:AtLEJ1/5-8 line and atlej1 mutant. Total RNAs were obtained separately from unopened flower buds at stages 1~12, when the anthers are not yet opened, and from open flowers at stages 13~14, when anthesis occurs.
2009-01-13 | E-GEOD-5449 | biostudies-arrayexpress
Project description:The paraveinal mesophyll (PVM) of soybean leaves is a layer of laterally expanded cells sandwiched between the palisade and spongy mesophyll chlorenchyma. The vacuoles of PVM cells contain an abundance of a putative vegetative storage protein, VSP (α, β). VSP is is constitutively produced, but is up-regulated during sink limitation experiments involving flower, fruit, or vegetative bud removal. Soybean vegetative lipoxygenases (Vlx), consisting of 5 isozymes (Vlx, A-D), have been identified as potential storage proteins because they accumulate to high levels with experimental sink limitation and have been co-localized with VSP to the vacuoles of PVM cells. We re-investigated the sub-cellular locations of these enzymes with TEM immuno-cytochemistry. We employed laser micro-dissection to compared RNA expression of PVM cells with mesophyll chlorenchyma cells, and we performed a micro-array analysis of soybean leaf samples representing a time-course, sink-limitation, experiment. We found that none of the Vlx isozymes co-localize with putative storage proteins in PVM vacuoles, and that our sink limitation experiment (typical of those used in the past) induced a strong up-regulation of stress response genes, simultaneous with the up-regulation of the Vlx isozymes. Our findings do not support a storage function for soybean Vlx. The results reported here are from a study designed to evaluate systemic effects of a vegetative bud removal protocol that had been used previously to study accumulation and subsequent mobilization of vegetative storage proteins in soybean. During these experiments plants were grown for 30 days and then all vegetative buds were removed. Bud removal was repeated each day for 15 days (designated the "detip" phase) and then new buds were allowed to regrow (designated the "retip" phase). Samples were collected at 5 day intervals. Total RNA was extracted from selected samples for our microarray experiments.
2012-07-26 | GSE23129 | GEO
Project description:The most effective method of micro-propagation for clonal replicates for switchgrass seed production is from the axillary buds of the lower nodes. We hypothesized that buds and nodes from low and high tillering lines from an inbred population will aid in identifying genes important for the different tillering habits of these plants. Since tiller number is directly correlated with biomass yields, identifying genes associated with high tillering trait will provide valuable biomarkers for marker-assisted selection and for QTL mapping of tillering trait in switchgrass. First-generation switchgrass inbred lines derived from selfing a parental genotype M-^QNL94 LYE 16x13M-^R, which was selected from the Oklahoma State University northern lowland breeding population in 2007 was used in this study. The NL94/298 inbred line produced fewer tillers than NL94/145. Stems of the high tillering line had 2-3 phytomers, while the low tillering line had 1-2 phytomers. Eight other inbred lines from this population that showed similar phenotypes as NL94/145 or NL94/298 and similar genotypes based on 380 genomic SSR marker profiles were selected for this study. Individual stems from these nine lines each for high and low tillering habit were harvested from field growing plants in the Agronomy field plots, Stillwater. Vegetative buds from first phytomer and node regions from second phytomer were cut out using a sharp scalpel under a dissection scope and immediately frozen in liquid nitrogen for transcriptomics analysis.
2014-01-14 | E-MTAB-1899 | biostudies-arrayexpress
Project description:Aims: To determine the changes in the Arabidopsis axillary bud transcriptome in response to changes in the red light (R) to far red light (FR) ratio (R:FR). Background: The branching habit of plants is a key determinant of overall plant form and function with great relevance to modern agriculture. Shade signals transduced by phytochromes are major regulators of axillary bud outgrowth, and in turn control branching in both natural and agricultural environments. To continue our investigations into the regulation of branching by R:FR, we have developed a system using supplemental FR LEDs to tightly control the outgrowth of Arabidopsis axillary buds. Depending on the position of the bud in the rosette, outgrowth is either repressed (uppermost bud) or rapidly promoted (bud in the axil of the third leaf down) by the transition from low to high R:FR. Treatment: Two separate experiments were conducted to evaluate the effects of R:FR on transcriptome changes in the uppermost rosette bud (bud n) and the axillary bud in the axil of the third leaf from the top (bud n-2). WT Col-60000 was used as the experimental material. Plants were grown individually in 25 by 50 mm tubes and watered and fertilized optimally. Plants were grown in a split growth chamber (providing uniform temperature and PPFD but allowing for differential R:FR) with 18 h photoperiods (185 Moles m-2 s-1 PPFD provided by T12 VHO CW fluorescent lamps) and 24oC/18oC day/night temperatures. One day after sowing, the R:FR was reduced on both sides of the chamber from 3.5 to 0.08 using FR LEDs fixed in clear overhead arrays. Prior to anthesis, the plants were matched and split into two treatment groups. In experiment 1, the FR source for one of the groups was switched off at 12:00 pm on the day of anthesis, causing the R:FR to increase to 3.5. Unelongated axillary buds in the axil of the uppermost leaves (approx. 2.5 mm long) were harvested for RNA preparation from both groups (low and transiently increased R:FR) 3 h after changing the R:FR. Each treatment was composed of three biological replicates, each containing buds from about 15-18 plants. Experiment 2 was conducted exactly the same as experiment 1, except the R:FR was altered 3 days after anthesis and the unelongated axillary buds in the axils of the third leaves down (approx. 1 mm long) were harvested for RNA preparation.
2012-11-21 | GSE42415 | GEO
Project description:Perennial plants, like fruit trees grown in temperate regions, are characterized by bud dormancy, a rest state that protects the bud from cold during winter. At the same time, these plants have developed a requirement for winter chill for correct flowering. However, winters are becoming increasingly warm in temperate regions, resulting in dramatic effects on the flowering output and therefore crop yield. A compound that successfully compensates for missing winter chill is hydrogen cyanamide, which has been used to synchronize and advance flowering time in a range of commercially important fruit crops. Hydrogen cyanamide also represents a unique tool for researchers to study controlled endodormancy release. Here, we treated dormant sweet cherry flower buds with hydrogen cyanamide, sampling flower buds at different time points after treatment. RNAseq revealed more than 6,000 hydrogen cyanamide-responsive genes. In accordance with these results, hydrogen cyanamide treatment increased the levels of jasmonoyl-isoleucine (JA-Ile) and the cytokinins trans-zeatin riboside (tZR), dihydrozeatin (DZ) and dihydrozeatin riboside (DZR). Furthermore, hydrogen cyanamide affected the expression of antioxidant- and cell wall loosening-associated transcripts. These results suggest a complex mechanism of action for hydrogen cyanamide-induced endodormancy release, including key roles for JA-Ile, zeatin-type cytokinins and hydrogen cyanide.
2017-06-01 | GSE94290 | GEO