Sorghum axillary bud transcriptome response to leaf removal
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ABSTRACT:
PROVIDER: PRJNA525462 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8667880_1.fastq.gz | Fastqsanger.gz | |||
| SRR8667880_2.fastq.gz | Fastqsanger.gz | |||
| SRR8667890.fastq.gz | Fastqsanger.gz | |||
| SRR8667900_1.fastq.gz | Fastqsanger.gz | |||
| SRR8667900_2.fastq.gz | Fastqsanger.gz |
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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 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: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.
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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.
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