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Transcriptomics of Axillary Bud Outgrowth Regulation by Shade Signals in Arabidopsis

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE42415 | GEO | 2012/11/21

SECONDARY ACCESSION(S): PRJNA181353

REPOSITORIES: GEO

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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 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.

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 lightÂ (WT-WL, brc1-2-WL) or red+far red light (WT-FR, brc1-2-FR) was hybridized.

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Transcriptomics of Axillary Bud Outgrowth Regulation by Shade Signals in Arabidopsis

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