Phylogenetic Analysis of 5′-Noncoding Regions From the ABA-Responsive rab16/17 Gene Family of Sorghum, Maize and Rice Provides Insight Into the Composition, Organization and Function of cis-Regulatory ModulesSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession no. AY177889.

Buchanan, Christina D.; Klein, Patricia E.; Mullet, John E.

doi:10.1534/genetics.104.030346

Cited by 17 publications

(12 citation statements)

References 70 publications

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“…However, sorghum genes encoding dehydrins related to dhn2 were in general expressed at 10-to 20-fold higher levels in the roots of nonstressed plants. These observations are consistent with the idea that different members of the dehydrin gene family are regulated by an overlapping but diverse set of signaling pathways, ciselements and transcription factors (Buchanan et al, 2004). Genes encoding oleosins and dermal proteins were also induced by ABA, NaCl and PEG treatment.…”

Section: Genes Involved In the Protection Of Sorghum From Abiotic Andsupporting

confidence: 89%

“…The expression data obtained in this study can also be utilized to identify cis-elements through analysis of co-regulated sets of genes (Spellman et al, 1998) and through phylogenetic analysis (Buchanan et al, 2004) to further elucidate the connections between transcription factors and genes that comprise regulons.…”

Section: Genes Involved In Regulation and Gene Expressionmentioning

confidence: 99%

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Sorghum bicolor’s Transcriptome Response to Dehydration, High Salinity and ABA

et al. 2005

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Genome wide changes in gene expression were monitored in the drought tolerant C4 cereal Sorghum bicolor, following exposure of seedlings to high salinity (150 mM NaCl), osmotic stress (20% polyethylene glycol) or abscisic acid (125 microM ABA). A sorghum cDNA microarray providing data on 12,982 unique gene clusters was used to examine gene expression in roots and shoots at 3- and 27-h post-treatment. Expression of approximately 2200 genes, including 174 genes with currently unknown functions, of which a subset appear unique to monocots and/or sorghum, was altered in response to dehydration, high salinity or ABA. The modulated sorghum genes had homology to proteins involved in regulation, growth, transport, membrane/protein turnover/repair, metabolism, dehydration protection, reactive oxygen scavenging, and plant defense. Real-time PCR was used to quantify changes in relative mRNA abundance for 333 genes that responded to ABA, NaCl or osmotic stress. Osmotic stress inducible sorghum genes identified for the first time included a beta-expansin expressed in shoots, actin depolymerization factor, inositol-3-phosphate synthase, a non-C4 NADP-malic enzyme, oleosin, and three genes homologous to 9-cis-epoxycarotenoid dioxygenase that may be involved in ABA biosynthesis. Analysis of response profiles demonstrated the existence of a complex gene regulatory network that differentially modulates gene expression in a tissue- and kinetic-specific manner in response to ABA, high salinity and water deficit. Modulation of genes involved in signal transduction, chromatin structure, transcription, translation and RNA metabolism contributes to sorghum's overlapping but nonetheless distinct responses to ABA, high salinity, and osmotic stress. Overall, this study provides a foundation of information on sorghum's osmotic stress responsive gene complement that will accelerate follow up biochemical, QTL and comparative studies.

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Section: Genes Involved In the Protection Of Sorghum From Abiotic Andsupporting

confidence: 89%

Section: Genes Involved In Regulation and Gene Expressionmentioning

confidence: 99%

Sorghum bicolor’s Transcriptome Response to Dehydration, High Salinity and ABA

et al. 2005

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“…Phylogenetic footprinting and shadowing have emerged as powerful techniques for the identification of candidates for functionally conserved domains in cis-transcriptional regulators of plant genes (Koch et al, 2001b;Colinas et al, 2002;Ayre et al, 2003;Guo and Moose, 2003;Hong et al, 2003;Bao et al, 2004;Buchanan et al, 2004;Lee et al, 2005). Sequence identity is not attributable solely to conservation of function; it is also retained as a stochastic consequence of common history.…”

Section: Global Analysis Of 5# Regulatory Regionsmentioning

confidence: 99%

Partial Shotgun Sequencing of the Boechera stricta Genome Reveals Extensive Microsynteny and Promoter Conservation with Arabidopsis

et al. 2006

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Comparative genomics provides insight into the evolutionary dynamics that shape discrete sequences as well as whole genomes. To advance comparative genomics within the Brassicaceae, we have end sequenced 23,136 medium-sized insert clones from Boechera stricta, a wild relative of Arabidopsis (Arabidopsis thaliana). A significant proportion of these sequences, 18,797, are nonredundant and display highly significant similarity (BLASTn e-value # 10 230) to low copy number Arabidopsis genomic regions, including more than 9,000 annotated coding sequences. We have used this dataset to identify orthologous gene pairs in the two species and to perform a global comparison of DNA regions 5# to annotated coding regions. On average, the 500 nucleotides upstream to coding sequences display 71.4% identity between the two species. In a similar analysis, 61.4% identity was observed between 5# noncoding sequences of Brassica oleracea and Arabidopsis, indicating that regulatory regions are not as diverged among these lineages as previously anticipated. By mapping the B. stricta end sequences onto the Arabidopsis genome, we have identified nearly 2,000 conserved blocks of microsynteny (bracketing 26% of the Arabidopsis genome). A comparison of fully sequenced B. stricta inserts to their homologous Arabidopsis genomic regions indicates that indel polymorphisms .5 kb contribute substantially to the genome size difference observed between the two species. Further, we demonstrate that microsynteny inferred from end-sequence data can be applied to the rapid identification and cloning of genomic regions of interest from nonmodel species. These results suggest that among diploid relatives of Arabidopsis, smallto medium-scale shotgun sequencing approaches can provide rapid and cost-effective benefits to evolutionary and/or functional comparative genomic frameworks.

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“…, 1994). Phylogenetic analysis of 5′‐noncoding regions from the Rab16/17 gene family of sorghum, maize and rice revealed the absence of some important cis ‐elements in the promoters, which could explain some differences in the expression of Rab17 ‐like genes in these plants (Buchanan et al. , 2004).…”

Section: Introductionmentioning

confidence: 99%

Improvement of stress tolerance of wheat and barley by modulation of expression of DREB/CBF factors

Morran¹,

Eini²,

Pyvovarenko³

et al. 2011

Plant Biotechnology Journal

402

251

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SummaryTranscription factors have been shown to control the activity of multiple stress response genes in a coordinated manner and therefore represent attractive targets for application in molecular plant breeding. We investigated the possibility of modulating the transcriptional regulation of drought and cold responses in the agriculturally important species, wheat and barley, with a view to increase drought and frost tolerance. Transgenic wheat and barley plants were generated showing constitutive (double 35S) and drought-inducible (maize Rab17) expression of the TaDREB2 and TaDREB3 transcription factors isolated from wheat grain. Transgenic populations with constitutive over-expression showed slower growth, delayed flowering and lower grain yields relative to the nontransgenic controls. However, both the TaDREB2 and TaDREB3 transgenic plants showed improved survival under severe drought conditions relative to nontransgenic controls. There were two components to the drought tolerance: real (activation of drought-stress-inducible genes) and 'seeming' (consumption of less water as a result of smaller size and ⁄ or slower growth of transgenics compared to controls). The undesired changes in plant development associated with the 'seeming' component of tolerance could be alleviated by using a drought-inducible promoter. In addition to drought tolerance, both TaDREB2 and TaDREB3 transgenic plants with constitutive over-expression of the transgene showed a significant improvement in frost tolerance. The increased expression of TaDREB2 and TaDREB3 lead to elevated expression in the transgenics of 10 other CBF ⁄ DREB genes and a large number of stress responsive LEA ⁄ COR ⁄ DHN genes known to be responsible for the protection of cell from damage and desiccation under stress.

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Cited by 17 publications

References 70 publications

Sorghum bicolor’s Transcriptome Response to Dehydration, High Salinity and ABA

Sorghum bicolor’s Transcriptome Response to Dehydration, High Salinity and ABA

Partial Shotgun Sequencing of the Boechera stricta Genome Reveals Extensive Microsynteny and Promoter Conservation with Arabidopsis

Improvement of stress tolerance of wheat and barley by modulation of expression of DREB/CBF factors

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