Auxin and ABA act as central regulators of developmental networks associated with paradormancy in Canada thistle (Cirsium arvense).

USDA-Agricultural Research Service, Biosciences Research Laboratory, U.S. Department of Agriculture, 1605 Albrecht Blvd., Fargo, ND 58102-2765, USA.
Functional & Integrative Genomics (Impact Factor: 2.69). 05/2012; 12(3):515-31. DOI: 10.1007/s10142-012-0280-5
Source: PubMed

ABSTRACT Dormancy in underground vegetative buds of Canada thistle, an herbaceous perennial weed, allows escape from current control methods and contributes to its invasive nature. In this study, ~65 % of root sections obtained from greenhouse propagated Canada thistle produced new vegetative shoots by 14 days post-sectioning. RNA samples obtained from sectioned roots incubated 0, 24, 48, and 72 h at 25°C under 16:8 h light-dark conditions were used to construct four MID-tagged cDNA libraries. Analysis of in silico data obtained using Roche 454 GS-FLX pyrosequencing technologies identified molecular networks associated with paradormancy release in underground vegetative buds of Canada thistle. Sequencing of two replicate plates produced ~2.5 million ESTs with an average read length of 362 bases. These ESTs assembled into 67358 unique sequences (21777 contigs and 45581 singlets) and annotation against the Arabidopsis database identified 15232 unigenes. Among the 15232 unigenes, we identified processes enriched with transcripts involved in plant hormone signaling networks. To follow-up on these results, we examined hormone profiles in roots, which identified changes in abscisic acid (ABA) and ABA metabolites, auxins, and cytokinins post-sectioning. Transcriptome and hormone profiling data suggest that interaction between auxin- and ABA-signaling regulate paradormancy maintenance and release in underground adventitious buds of Canada thistle. Our proposed model shows that sectioning-induced changes in polar auxin transport alters ABA metabolism and signaling, which further impacts gibberellic acid signaling involving interactions between ABA and FUSCA3. Here we report that reduced auxin and ABA-signaling, in conjunction with increased cytokinin biosynthesis post-sectioning supports a model where interactions among hormones drives molecular networks leading to cell division, differentiation, and vegetative outgrowth.

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    ABSTRACT: The present review suggests the significance of various phytohormones in the regulation of cell division and the endoreduplication process in plant cells. Here, molecular pathways are designed that clearly elucidate the role of phytohormones in the regulation of the cell division and endoreduplication process. This determines the stages at which the cell division cycle diverts towards the endoreduplication process. Phytohormones manage the activity of CDK/CYC complexes and RBR proteins at various stages of the cell cycle by controlling the transcription and destruction of E2F proteins. For example, cytokinin stimulates the G1 phase by activating the CDKA/CYCD complex, ABA regulates the activity of CDKA in the G1 and G2 phase using CDK inhibitor proteins, GA stimulates activation of CDK/CYC complexes using CAKs, auxin regulates the progress of the cell cycle from the G1/S transition to the G2/M transition, JA regulates the signaling of GA using DELLA proteins and ethylene regulates the activity of CDK B. Hyperphosphorylation or hypophosphorylation of RBR protein by the CDK/CYC complex will determine whether the cell cycle shifts towards cell division or endoreduplication. The activity of the E2F transcription factors is most significant during these processes, which is in turn regulated by phytohormones. Accumulation of E2F A in the G1 phase will drive the cell cycle towards the S phase. E2FB will give a signal to the mitotic inducing factor CDKB/CYCD complex, which will lead the cell cycle towards mitosis. E2FB is a key target of auxin, in determining whether the cell with undergo mitosis or endoreduplication. Auxin also regulates the activity of E2FC using a RUB–cullin signaling pathway, whose over-expression leads the cell cycle towards the endocycling process
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    ABSTRACT: Background In temperate regions, the time lag between vegetative bud burst and bud set determines the duration of the growing season of trees (i.e. the duration of wood biomass production). Dormancy, the period during which the plant is not growing, allows trees to avoid cold injury resulting from exposure to low temperatures. An understanding of the molecular machinery controlling the shift between these two phenological states is of key importance in the context of climatic change. The objective of this study was to identify genes upregulated during endo- and ecodormancy, the two main stages of bud dormancy. Sessile oak is a widely distributed European white oak species. A forcing test on young trees was first carried out to identify the period most likely to correspond to these two stages. Total RNA was then extracted from apical buds displaying endo- and ecodormancy. This RNA was used for the generation of cDNA libraries, and in-depth transcriptome characterization was performed with 454 FLX pyrosequencing technology. Results Pyrosequencing produced a total of 495,915 reads. The data were cleaned, duplicated reads removed, and sequences were mapped onto the oak UniGene data. Digital gene expression analysis was performed, with both R statistics and the R-Bioconductor packages (edgeR and DESeq), on 6,471 contigs with read numbers ≥ 5 within any contigs. The number of sequences displaying significant differences in expression level (read abundance) between endo- and ecodormancy conditions ranged from 75 to 161, depending on the algorithm used. 13 genes displaying significant differences between conditions were selected for further analysis, and 11 of these genes, including those for glutathione-S-transferase (GST) and dehydrin xero2 (XERO2) were validated by quantitative PCR. Conclusions The identification and functional annotation of differentially expressed genes involved in the “response to abscisic acid”, “response to cold stress” and “response to oxidative stress” categories constitutes a major step towards characterization of the molecular network underlying vegetative bud dormancy, an important life history trait of long-lived organisms.
    BMC Genomics 04/2013; 14(1):236. DOI:10.1186/1471-2164-14-236 · 4.04 Impact Factor
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    ABSTRACT: Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.
    BMC Genomics 02/2015; 16(1):112. DOI:10.1186/s12864-015-1331-9 · 4.04 Impact Factor


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