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Transcriptome profiling of the basal region of poplar stems during the early gravitropic response

ABSTRACT: Young poplar stems show a preponderantly primary growth in the top internodes and differential cambium activity in the basal internodes after inclination with some tension wood formed after 45 min. This study was conducted in order to characterize the early changes in gene expression during early stages of the gravitropic response in the poplar.

ORGANISM(S): Populus tremula x Populus alba Populus trichocarpa x Populus deltoides

PROVIDER: GSE44981 | GEO | 2013/04/12

SECONDARY ACCESSION(S): PRJNA196854

REPOSITORIES: GEO

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Transcriptome profiling of the basal region of poplar stems during the early gravitropic response

Project description:Young poplar stems show a preponderantly primary growth in the top internodes and differential cambium activity in the basal internodes after inclination with some tension wood formed after 45 min. This study was conducted in order to characterize the early changes in gene expression during early stages of the gravitropic response in the poplar. Hybridizations were performed to compare gravistimulated poplar stems (basal region) after 45 min of inclination and untreated control stems. Two biological replicates were done. Two hybridizations with a dye swap for each tree pair were done, making a total of four hybridizations.

2013-04-12 | E-GEOD-44981 | biostudies-arrayexpress

circad_pop1-circadian rhythm in the expression of genes involved in the formation of poplar wood

Project description:affy_orleans_circad - circad_pop1 - Global transcriptome analysis of tension wood in poplar over a 24h period. Young differentiating xylem was harvested on the tension wood side of 6 month-old poplar trees grown in greenhouse conditions. The samples were harvested at 6 hour intervals throughout the day. The bioinformatic analysis will permit the identification of genes expressed in tension wood and that cycle with a nycthemeral oscillation pattern. Keywords: time course

2010-06-05 | GSE16459 | GEO

circad_pop1-circadian rhythm in the expression of genes involved in the formation of poplar wood

2010-06-16 | E-GEOD-16459 | biostudies-arrayexpress

Integrative analysis from the transcriptome to proteome uncovers brassinosteroid-mediated regulation of cambium initiation and patterning in woody stems

Project description:Wood formation involves sequential developmental events, requiring the coordination of multiple hormones. Brassinosteroids (BRs) play a key role in wood development, but little is known about the cellular and molecular processes that underlie wood formation in tree species. Here, we generated transgenic poplar lines editing one or several members of PdBRI1s, the orthologs of Arabidopsis vascular-enriched BR receptors, and showed how inhibition of BR signaling influences wood development at the mRNA level. Six Populus PdBRI1 genes form three gene pairs and each exhibits high expression in the basal stems. Simultaneous mutation of PdBRI1-1, 2, 3 and 6, the orthologs of Arabidopsis vascular-enriched BR receptors BRI1, BRL1 and BRL3, resulted in a severe defect in growth. Particularly, the stems of these mutant lines displayed a discontinuous ring of cambium and patterning defects in derived secondary vascular tissues. Abnormal formation of cambia within cortical parenchyma was also observed in the stem of pdbri1-1;2;3;6. Transgenic poplars editing PdBRI1-1 or PdBRI1-1;2;6 had phenotypic alterations in stem development at 4.5 months of growth, indicating functional redundancy among these PdBRI1 genes. An integrated analysis of the transcriptome from pdbri1-1;2;3;6 stems revealed differential expression of a number of genes associated with wood development and hormones.

2022-02-02 | GSE179471 | GEO

Expression data from poplar stems

Project description:Expression data from poplar stems

| PRJNA480161 | ENA

Analysis of Expression Profile of Over-expressed Brassinolide Synthase DET2 in Poplar

Project description:We overexpressed the brassinolide synthase DET2 in 84K poplar and obtained an overexpression material.It was found that the brassinolide content of the overexpression material increased significantly.And it was found that the plant height, diameter, and number of internodes of the overexpression material increased significantly.However,the mechanism of this phenotype is unknown.We collected two-month-old DET2 overexpression material and 84K wild-type material in three parts, apex,cambium,and xylem,and conducted high-throughput sequencing.The sequencing results were mined, and the difference genes that were significantly changed in the DET2 overexpression material and the 84K wild-type material were found.Find out how the increase in brassinolide content promotes the development of wood.

2022-09-20 | GSE176470 | GEO

Expression data from poplar stems

Project description:We study differences in gene expression between Populus P35S::PLGT , RNAi_PLGT and control/WT plants, affecting tropic responses and stem development. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by th etransgenic manipulations of PLGT gene. By screening activation tagging population we identified the PLAGIOTROPICA (PLGT) mutant. The mutant is severely impaired in gravitropic responses and displays consistent south orientation of the shoot tip in the overexpressing plants. We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes an ortholog of the OCTOPUS gene from Arabidopsis. We fully recapitulated the phenotype by overexpression of the gene into the same genotype under strong constitutive promoter (P35S::PLGT). We further downregulated the gene using RNAi approach. The gene was most highly expressed in young stems and phloem tissues.

2020-07-01 | GSE116762 | GEO

Transcriptome profiles and comparison of Arabidopsis thaliana woody (soc1-ful) and WT (Col-0) stems.

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

Genes expression during stem growth of Populus alba x Populus tremula var. glandulosa

Project description:To obtain genes expression in different parts of 84k poplar stems, transcriptome sequencing was performed using Illumina Novaseq 6000 second-generation sequencing platform from Shanghai BIOZERON Co. Ltd (www.biozeron.com). Selecte three stem segments of plants REPEAT 1, 2 and 3 with good and similar growth to use: 2nd-3rd internodes (poplar stem top: PST1, PST2, PST3); 9th-10th internodes (poplar stem middle: PSM1, PSM2, PSM3); 14th-15th internodes (poplar stem bottom: PSB1, PSB2, PSB3). [Or the three repeating organisms are also called poplar A, B, C. From top to bottom, the three parts of the stem are also called stem 1, 2, 3.]

2021-10-28 | GSE186743 | GEO

Expression data from NPA treated stems of Arabidopsis thaliana.

Project description:In-vivo induced establishment and activity of the interfascicular cambium in Arabidopsis thaliana stems under NPA treatments. We used microarrays to detail the global programme of gene expression underlying the establishment and activity of the interfascicular cambium.

2011-09-01 | GSE24763 | GEO

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