Dataset Information

Pinus radiata tissues (root, adult and juvenil needle, bud) proteomics

ABSTRACT: Roots and needles were harvested from 6 juvenile Pinus radiata seedlings (3 biological pool constituted by 2 seedlings each). Needles and floral buds were harvested from 6 adult Pinus radiata plants (3 biological pools constituted by 2 plants each).

INSTRUMENT(S):

ORGANISM(S): Pinus Radiata (monterey Pine)

TISSUE(S): Plant Cell, Root, Flower Bud, Leaf

SUBMITTER: Victor Roces

LAB HEAD: Luis Valledor

PROVIDER: PXD047869 | Pride | 2025-05-16

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	LuisValledor_sol23-17_Set2_AA1-.msf	Msf
	LuisValledor_sol23-17_Set2_AA1-1_14062017_170714111722.raw	Raw
	LuisValledor_sol23-17_Set2_AA1-2_14062017_170714140145.raw	Raw
	LuisValledor_sol23-17_Set2_AA1-3_14062017_170714164602.raw	Raw
	LuisValledor_sol23-17_Set2_AA2-.msf	Msf

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Publications

Pra-GE-ATLAS: Empowering Pinus radiata stress and breeding research through a multi-omics database.

Roces Víctor V Cañal María Jesús MJ Mateo Juan Luis JL Valledor Luis L

Journal of integrative plant biology 20250612 8

In recent decades, research on model organisms has significantly increased our understanding of core biological processes in plant science. However, this focus has created a substantial knowledge bottleneck due to the limited phylogenetic and ecological spectrum covered. Gymnosperms, especially conifers, represent a molecular and ecological diversity hotspot among seed plants. Despite their importance, research on these species is notably underrepresented, primarily due to a slower pace of inves ...[more]

PMID: 40504102

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Project description:Comparison of transcriptomes from bark, developing xylem and xylem of P. radiata saplings exposed to 0 or 1mg of Ethephon in lanolin for 1 or 8 weeks We developed an oligonucleotide microarray using sequences (mostly from Pinus taeda) from public sequence databases. These sequences were reconstituted into a non-redundant database by CAP3 assembly and used as templates for automated design of 60-mer oligonucleotide probes through eArray, AgilentM-bM-^@M-^Ys online facility. The microarray slides, manufactured by Agilent, were used to monitor gene expression in an Ethephon-induction experiment. Ethephon was dispersed in lanolin paste and applied in a 3 cm band near the base of the stem of 2-year old Pinus radiata saplings. RNA was extracted from bark, cambial region, also known as M-bM-^@M-^\developing xylemM-bM-^@M-^], and xylem tissues exposed for 1 or 8 weeks to Ethephon. The transcriptomes from these extracts were compared by hybridization onto the All-Pinus microarray slides. Statistically significant differentially expressed genes identified by limma (Linear Models for Microarray Data) were subsequently analysed by singular enrichment analysis through the Database for Annotation, Visualization and Integrated Discovery (DAVID) portal. Results revealed that bark, cambial region and xylem generate mostly mutually exclusive cohorts of genes and Gene Ontology (GO) classes. Ethephon induction led to the upregulation of xylem genes related to the metabolism of phenylpropanoids and flavonoids and to defence responses, specifically, fungal/insect attack and oxidative stress. Independent validation of the microarray data for five genes was obtained by quantitative RT-PCR. The results are also interpreted in reference to gross and microscopic morphological changes. These results confirm the utility of the All-Pinus microarray for transcriptomic research in P. radiata. Series of 2-color, 2 condition experiments in 12 180k arrays. Main comparison is within tissues exposed to 0 [control] or 1 mg Ethephon. 2nd level of comparison is between tissues [bark, xylem scraping, xylem]. Third level of comparison is between time [1 or 8 week exposure]. One slide is hybridized with cRNA generated from control and treated tissues with the same duration of exposure to Ethephon. Two biological replicates [each biological rep is a 2 y old cutting propagated clone] for treated plants whilst control consists of RNA pooled, in equal proportions [estimated by UV absorbance], from 2 untreated biological replicates.]. Dyes used for each sample are indicated in sample description.