Identification of genes involved in secondary cell wall development in the hypocotyls of short day grown Arabidopsis
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE6153 | GEO | 2007/01/22
SECONDARY ACCESSION(S): PRJNA97697
REPOSITORIES: GEO
Similar Datasets
Project description:Arabidopsis, when grown under short day conditions (16 hours dark, 8 hours light, 22oC) develop extensive secondary thickened hypocotyls with both a vascular and cork cambium (Chaffey et al, 2002, Phys. Plant., 114:594-600). It has been found that once secondary xylem development is completed within the Arabidopsis hypocotyls, it closely resembles the structure of the wood of angiosperm trees (Chaffey et al, 2002, Phys. Plant., 114:594-600). We can utilise this model Arabidopsis tree to identify genes that are important for secondary cell wall formation in xylem cells and therefore important for wood development. Columbia plants were grown for 3 months under short day conditions and secondary thickened hypocotyls were snap-frozen in liquid nitrogen. RNA was isolated from these hypocotyls and submitted to NASC for probing against the ATH1-121501 full GeneChip.
2022-11-21 | E-NASC-58 | biostudies-arrayexpress
Project description:Arabidopsis, when grown under short day conditions (16 hours dark, 8 hours light, 22oC) develop extensive secondary thickened hypocotyls with both a vascular and cork cambium (Chaffey et al, 2002, Phys. Plant., 114:594-600). It has been found that once secondary xylem development is completed within the Arabidopsis hypocotyls, it closely resembles the structure of the wood of angiosperm trees (Chaffey et al, 2002, Phys. Plant., 114:594-600). We can utilise this model Arabidopsis tree to identify genes that are important for secondary cell wall formation in xylem cells and therefore important for wood development. Columbia plants were grown for 3 months under short day conditions and secondary thickened hypocotyls were snap-frozen in liquid nitrogen. RNA was isolated from these hypocotyls and submitted to NASC for probing against the ATH1-121501 full GeneChip. Experiment Overall Design: 2 samples
2008-06-14 | E-GEOD-6153 | biostudies-arrayexpress
Project description:The douple mutant Arabidopsis thaliana soc1 ful, in contrast with WT, produces an interfascicular cambium and a large wood cylinder is the flowering stem. We present the RNAseq data for polyA mRNA of different developmental stages of cambium and wood formation in Arabidopsis thaliana. We sequenced 7 stages; 4 in the woody mutant soc1-6 ful-7 (herbaceous, cambium initiation, wood initiation and leaf) and 3 stages in the WT Col-0 (herbaceous, cambium and leaf). The corresponding stem anatomy is also presented in the manuscript indicating the stage of cambium development and the production of secondary xylem.
2016-05-21 | GSE69167 | GEO
Project description:The Arabidopsis hypocotyl is an excellent model for understanding radial growth in plants. Division of the cambial cells and their subsequent differentiation into xylem and phloem drives radial expansion of the hypocotyl. Following the transition to reproductive growth, a phase change occurs in the Arabidopsis hypocotyl. During this second phase, the relative rate of xylem production is dramatically increased compared to that of phloem and xylem fibres containing thick secondary cell walls also form, which results in the production of xylem tissue comparable to the wood of trees. Abscisic acid (ABA) is a phytohormone known to have a major role in various plant processes, including in the response to changes in environmental conditions and in the promotion of seed dormancy. Using two different genetic backgrounds and different environmental conditions, we identified a set of core of transcriptional changes associated with the switch to the second phase of growth in the hypocotyl. ABA signalling pathways were identified as being as significantly over-represented in this set of core genes. Reverse genetic analysis demonstrated that mutants defective in ABA-biosynthesis enzymes exhibited significantly delayed fibre production without affecting the xylem:phloem ratio. The altered morphology is also reflected at the transcript level, with a reduced expression of marker genes associated with fibre formation in aba1 mutants. The application of exogenous ABA to the mutant rescued the phenotype, restoring fibre differentiation to wild-type levels. Taken together the data reveals an essential role for ABA in the regulation of fibre formation. We used microarrays to probe transcripome changes I Arabidopsis hypocotyls following transition from phase I to phase II
2018-05-19 | GSE114638 | GEO
Project description:Wood is one of the most important and enormous biomass that is widely used in our life. It is formed by successive addition of secondary xylem that develops continuously from cambium. The transcriptome of nst1 nst3 “double-knockout” lines was examined to know the effect of mutations on wood formation. Keywords: mutant vs wt comparison
2006-10-28 | GSE5187 | GEO
Project description:* In response to gravitational stresses, angiosperm trees form tension wood in the upper sides of branches and leaning stems in which cellulose content is higher, microfibrils are typically aligned closely with the fibre axis and the fibres often have a thick inner gelatinous cell wall layer (G-layer). * Gene expression was studied in Eucalyptus nitens branches oriented at 45° using microarrays containing 4 900 xylem cDNAs, and wood fibre characteristics revealed by X-ray diffraction, chemical and histochemical methods. * Xylem fibres in tension wood (upper branch) had a low microfibril angle, contained few fibres with G-layers and had higher cellulose and decreased Klason lignin compared to lower branch wood. Expression of two closely related fasciclin-like arabinogalactan proteins and a B-tubulin was inversely correlated with microfibril angle in upper and lower xylem from branches. * Structural and chemical modifications throughout the secondary cell walls of fibres sufficient to resist tension forces in branches can occur in the absence of G-layer enriched fibres and some important genes involved in responses to gravitational stress in eucalypt xylem are identified. Keywords: tissue comparison
2011-05-19 | GSE8816 | GEO
Project description:Currently little is known about the genetic mechanisms regulating the vascular cambium or the secondary growth of stems. We show here that the Populus Class I KNOX homeobox gene ARBORKNOX2 (ARK2) regulates both cell division in the cambium region and the differentiation of daughter cells in secondary xylem and phloem. ARK2 is expressed in the shoot apical meristem, and the vascular cambium region, reflecting some overlap in the regulation of these meristems. ARK2 is expressed broadly in the cambium region and in differentiating lignified cells types before becoming progressively restricted to the cambium. Populus overexpressing ARK2 present stem phenotypes with precocious cambium formation, delayed differentiation of cambium daughter cells, a wider cambium region, and ultimately less phloem fibers and secondary xylem. In contrast, Populus expressing RNAi or amicroRNA that target ARK2 transcripts present precocious differentiation of secondary phloem fibers and xylem, and ultimately more secondary xylem tissue and thicker secondary cell walls in phloem fibers and secondary xylem cells. These phenotypes in turn correlate with changes in the expression of genes affecting cell division, auxin, and cell wall synthesis and lignification that indicate that ARK2 primarily affects woody tissue development by regulation of cell differentiation. Notably, wood properties associated with secondary cell wall synthesis are negatively associated with ARK2 expression, including lignin and cellulose content. Together, our results suggest that ARK2 functions primarily by negatively regulating cell differentiation during secondary growth. We propose that ARK2 may identify a co-evolved regulatory module that influences complex wood properties relevant to ecological, industrial, and biofuels applications.
2009-10-01 | GSE15595 | GEO
Project description:* In response to gravitational stresses, angiosperm trees form tension wood in the upper sides of branches and leaning stems in which cellulose content is higher, microfibrils are typically aligned closely with the fibre axis and the fibres often have a thick inner gelatinous cell wall layer (G-layer). * Gene expression was studied in Eucalyptus nitens branches oriented at 45° using microarrays containing 4 900 xylem cDNAs, and wood fibre characteristics revealed by X-ray diffraction, chemical and histochemical methods. * Xylem fibres in tension wood (upper branch) had a low microfibril angle, contained few fibres with G-layers and had higher cellulose and decreased Klason lignin compared to lower branch wood. Expression of two closely related fasciclin-like arabinogalactan proteins and a B-tubulin was inversely correlated with microfibril angle in upper and lower xylem from branches. * Structural and chemical modifications throughout the secondary cell walls of fibres sufficient to resist tension forces in branches can occur in the absence of G-layer enriched fibres and some important genes involved in responses to gravitational stress in eucalypt xylem are identified. Keywords: tissue comparison Two nine-year-old Eucalyptus nitens trees were used as a source of biological material. RNA was isolated from xylem from the vertical main stem and from the upper and lower quarter of branches oriented at approximately 45° from vertical. For each tree, slides were hybridized with probes synthesized from vertical xylem and one or other of upper or lower branch xylem.
2011-05-19 | E-GEOD-8816 | biostudies-arrayexpress
Project description:Wood in conifers is mainly composed of tracheids. Some taxa, such as Pinus, present tracheids also in the rays, but are axial tracheids which constitute the vast majority of secondary xylem. Nevertheless, radial and axial parenchyma surrounding constitutive and traumatic resin ducts is known to serve as crucial reserve storage. These reserves are mobilized in response to traumatism, insect and pathogen attacks and defoliation, allowing the synthesis of resin, healing and, in few taxa, even resprouting. However, due to the low proportion of parenchymatic cells in secondary xylem relevant genes involved in their differentiation may have been missed in studies of transcriptomics of conifer wood formation. In this study we have used Pinus canariensis as a model species, given its comparatively high proportion of axial parenchyma. We have prepared two normalized libraries from its cambial zone, covering early- and late-wood differentiation. We have de novo assembled a transcriptome, and have analyzed the transcriptional profiles during the growing season, getting a more complete picture of wood formation in conifers. SUBMITTER_CITATION: Chano, V., López de Heredia, U., Collada, C., et al. (2017). Transcriptomic analysis of juvenile wood formation during the growing season in Pinus canariensis. Holzforschung, 0(0), pp. -. Retrieved 8 Aug. 2017, from doi:10.1515/hf-2017-0014
2016-09-01 | GSE82217 | GEO
Project description:PtrHSFB3-1 and PtrMYB092 are xylem specific genes in xylem of P. trichocarpa, and their expression levels are down regulated most significantly in tension wood. These two transcription factors were transiently overexpressed in stem differentiating xylem (SDX) of P. trichocarpa , and transcriptomic sequencing was performed to identify the regulatory effects of the two transcription factors on wood formation related genes.
2020-07-11 | GSE154167 | GEO