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Item Phytochrome B Controls Shoot Architecture by Regulating Phytochrome Interacting Factors and Phytohormones(2014-04-30) Holalu, Srinidhi VPlant architectural responses to changes in the ratio of red light to far-red light (R: FR) are mediated by phytochromes (phy), especially phyB. phyB function is transduced through interactions with the PHYTOCHROME INTERACTING FACTORS (PIFs) family of transcription factors. This study assessed the roles of Arabidopsis thaliana PIF4, PIF5 and PIF7 in mediating shoot architectural responses to high and low R:FR. The genetic interactions between various PIFs and phyB were also examined. The results indicated that PIF4/PIF5 and PIF7 are required for suppression of branch outgrowth under low R:FR, or with the loss of functional phyB. Compared to wild-type, lower levels of axillary bud abscisic acid (ABA) were detected in the pif7 and pif4pif5 mutants under low R:FR. The loss of functional phyB elevated axillary bud sensitivity to exogenous ABA. It was also demonstrated that the abscisic acid biosynthetic enzyme NCED3 was essential for aspects of phyB mediated regulation of branching. The analysis of transcript abundances of a panel of auxin-responsive genes in pif and phyB mutants in the study suggested that PIF4/PIF5 may mediate branching responses by regulating the transcription of auxin-signaling genes. PIF7 mediated effects on bud outgrowth may involve regulation of both ABA abundances and sensitivity in buds. In summary, PIF4/PIF5 and PIF7 affect branching by regulating auxin-signaling in shoots, ABA biosynthesis and sensitivity in buds in response to the R:FR in coordination with phyB. Assessment of the kinetics of axillary bud outgrowth and ABA levels in buds revealed a significant change in bud ABA levels as early as 1 h after alteration of the R:FR. This indicates that buds are able to rapidly respond to variations in the R:FR. Ethylene is known to mediate plant responses to variation in the R:FR. The assessment of plant architectural changes in the ethylene insensitive mutants ein2-1 and etr1-2 revealed a minor contribution of ethylene in mediating branch outgrowth responses to the R:FR. EIN2 and ETR1 were shown to regulate normal gravitropic responses in rosette branches.Item Regulation of Branching by Phytochrome and Phytohormones(2012-07-16) Krishnareddy, Srirama R.Light is the fundamental source of energy and information throughout the plant life cycle. Light signals regulate plant architecture and branching, key processes that determine biomass production and grain yield. Low red (R) to far-red (FR) light ratios (R:FR) perceived by phytochromes serve as a warning signal about impending competition for light resources and lead to shade avoidance responses (SARs), including reduced branching. The R:FR regulates branching in both a bud autonomous and non-bud autonomous manner, however a detailed mechanistic understanding of the process remains unclear. We hypothesized that high R:FR promotes bud outgrowth by differentially regulating branching-related genes (transcriptome) within the axillary bud and that increased apical dominance under low R:FR or with phyB deficiency is mediated by auxin or other novel signal/s. We analyzed the branching phenotype of Arabidopsis Columbia-60000 ecotype in response to different R:FR treatments and conducted a microarray study to identify early (within 3 hours) changes in the transcriptome of buds from different rosette positions in response to altered R:FR. Physiological experiments were also conducted to determine if auxin concentration, transport rate, sensitivity, and establishment of an auxin transport stream were important in determining the branching phenotype of shade avoiding plants. The results revealed that the duration of low R:FR determines plant architecture and the branching phenotype and that bud outgrowth is regulated by the R:FR in a spatial and temporal manner. Low R:FR promoted the elongation of branches at top rosette nodes while it suppressed the outgrowth of axillary buds at lower nodes. High R:FR could reverse the effects of previous low R:FR by promoting the outgrowth of buds from lower axils within 24 hours of treatment. Transcriptomic analysis revealed that the R:FR differentially regulated the expression of genes related to hormone biosynthesis/transport/signaling, cell-cycle regulation and cell wall modification. Cis-elements responsive to light and hormone signaling pathways were overrepresented in several gene clusters. Apical dominance related studies discovered that loss of phyB function results in a slower auxin transport rate, fewer xylem parenchyma cells, and reduced sensitivity to auxin. These results, in addition to estimates of correlative inhibition, suggested that auxin is at least partially responsible for increased apical dominance under low R:FR or with phyB deficiency, but may be acting in conjunction with other undefined regulators.Item Regulation of branching by phytochrome B and PPFD in Arabidopsis thaliana(Texas A&M University, 2008-10-10) Chou, Nan-yenThe branching or tillering of crops is an important agronomic trait with a major impact on yield. Maintaining an appropriate number of branches allows the plant to use limited light resources and to produce biomass or yield more effectively. The branching process includes the initiation of the axillary meristem leading to bud formation and the further outgrowth of the axillary buds. Phytohormones, including cytokinins and auxin, are known to play major roles in regulating axillary bud outgrowth. Light signals, including light quantity and light quality, are among the most important factors regulating plant growth and are perceived by the action of specialized photoreceptors, including phytochromes. Phytochromes sense red (R) and far-red (FR) light and allow some plants to perceive and respond to competing neighbors by evoking the shade avoidance syndrome (SAS). One component of the SAS is inhibition of branching. Phytochrome B (phyB) is especially important in sensing shade signals and loss of phyB function results in a constitutive shade avoidance phenotype, including reduced branching. While it has been anecdotally reported that phyB-deficient Arabidopsis branches less than wild type, a detailed study of the defects in the process is lacking. In this research, the interactions between light signals, phytochromes and phytohormones in the regulation of branching were assessed using an integrated physiological, molecular and genetic approach.