Transcriptome reorganization during wood maturation in Pinus radiata
Ontology highlight
ABSTRACT:
ORGANISM(S): Pinus radiata
SUBMITTER: Xinguo Li
PROVIDER: E-GEOD-20535 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Wood stiffness is the most important wood quality trait of forest trees for structural timber production. We investigated genes differentially transcribed in radiate pine trees with distinct wood stiffness using bulked segregant analysis (BSA) and cDNA microarrays. Transcript accumulation in earlywood (EW) and latewood (LW) of high (HS) and low stiffness (LS) trees in two progeny trials was compared. Radiata pine trees used for microarray experiment were selected from two progeny trials planted at Flynn and Kromelite, Australia. Based on the IML-based MOE measurement, five families with highest and lowest MOE each were selected from each trial, which represented two segregant populations with contrasting wood stiffness. Two individuals from each selected family were further sampled. Developing xylem tissues of selected trees in Flynn trial were sampled in spring (October) and autumn (April), representing earlywood (EW) and latewood (LW) of juvenile aged trees, respectively. Collection of xylem tissues from Kromelite trial was arranged in summer (late November) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. In Flynn trial EW and LW tissues were collected from the same sampled trees on opposite sides of the trunk. Transcript accumulation was compared in trees with highest (HS) and lowest stiffness (LS) using xylem samples from Flynn collected in spring (EW) and autumn (LW), as well as Kromelite in summer (LW), respectively. Bulked segregant analysis (BSA) was used for the experiment design. Total RNA samples extracted from the five trees with HS were pooled at equal amount, and compared to the bulked five individuals with LS. This pooling strategy can partly minimize the genetic variation among different genotypes. Dye swaps were applied in each biological replicate.
2011-06-01 | E-GEOD-23020 | biostudies-arrayexpress
Project description:Seasonal wood development results in two distinct wood types: earlywood (EW) and latewood (LW), which is the major cause of wood qaulity variation. We investigate transcriptome reorganization during seasonal wood development in radiata pine using a newly developed 18k cDNA microarrays. Three sampling trees each at juvenile (5 yrs), transition (9 yrs) and mature (14 yrs) ages (based on the wood rings at breast height) were selected from a plantation forest of radiata pine at Bondo, NSW , Australia (35º 16' 44.04 S, 148º 26' 54.66 E). The sampling trees at juvenile and mature ages were grown within 50 m distance and under similar environment. Two sampling trees at rotation age (30 yrs) were chosen at Yarralumla, ACT, Australia (35° 18' 27'' S, 149° 7' 27.9'' E).
2010-10-08 | E-GEOD-15230 | biostudies-arrayexpress
Project description:Wood density is a foundamental quality trait for structural timber, bioenergy and pulp industries. We investigated genes differentially transcribed in radiate pine juvneile trees with distinct wood density using cDNA microarrays. Radiata pine trees were selected from a progeny trial planted at Flynn, Australia. Based on the gravitical measurement of wood cores, 12 families with highest and lowest density each were selected, representing two groups of trees with contrasting wood density. One individual with higher or lower density were further sampled in each selected family. Developing xylem tissues of selected trees were sampled in autumn (April) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. Wood cores of the sampled trees were further measured using SilviScan 2. Total RNA extracted from ten developing xylem tissues with confirmed distinct density in each tree group were pooled into two bulks (five trees each), and the two bulks of HD were compared with two LD bulks in the microarray experiment (named the bulk experiment). Six developing xylem tissues with the most distinct density from each tree group were further chosen. Six xylem tissues with HD were individually compared with bulked six xylem tissues with LD in the second microarray experiment (named individual experiment). These two different pooling strategies can partly minimize the genetic variation among different genotypes. Dye swaps were applied in each biological replicate.
2012-08-02 | E-GEOD-32086 | biostudies-arrayexpress
Project description:Compression (CW) and opposite wood (OW) are formed in the uniderside and upperside of conifer branches respectively in response to gravity stress. We investigated genes differentially transcribed between the underside and upside of radiate pine branches using cDNA microarrays with a view to plant gravitropism. Six trees with well-developed branches were selected from a radiata pine commercial plantation (aged 13 years) located at Bondo, NSW, Australia (35º 16' 44.04 S, 148º 26' 54.66 E). The largest branch from each tree was further selected for sampling, including three branches sampled in April 2007 (autumn in Bondo) and three sampled in October 2007 (spring). Bark was removed from the base part (about 10 cm in length) of each branch. Developing xylem tissues were scraped from the exposed upperside and underside surface respectively with a sharp chisel. Samples were immediately placed into 50 ml BD FalconTM tubes filled with liquid nitrogen. Gene expression in the underside and upperside of branches was compared using radiata pine cDNA microarrays.
2014-05-30 | E-GEOD-47167 | biostudies-arrayexpress
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:In order to pinpoint the most differentially expressed genes between Eucalyptus grandis leaf blades and vascular (xylem) tissues as well as between E. grandis and Eucalyptus globulus xylem tissues, a total number of nine 50mer-oligoprobes covering the length of each one of 21,432 unique sequences derived from the Genolyptus EST dataset were synthesized “on-chip” in duplicate, randomly distributed in two blocks of each slide. Probes were also synthesized from ten cDNA sequences encoding known human proteins as negative controls, totaling 21,442 sequences. Leaves and xylem samples were taken from two E. grandis clonal trees, i.e., both derived from the same matrix tree and harboring the same genotype. Two additional xylem samples were collected from two other E. grandis clonal trees of a different genotype, as well as from two E. globulus clonal trees. Therefore, ten cDNA samples and ten identical chips were produced at Roche NimbleGen for the microarray assays, with a total number of 385,956 features per slide. Besides the discovery of differentially expressed genes between leaf and xylem, we wanted to test the validity of the assumed “technical” and “biological duplicates” since all trees were field-grown and four years-old in age. A ten chip study using total RNA recovered from mature leaf and vascular (xylem) tissues of Eucalyptus grandis and xylem from Eucalyptus globulus trees. Two clonal trees of E. grandis (E.grandis_Clone A_Ramet 1 and E.grandis_Clone A_Ramet 2), derived from a single matrix tree and therefore genomically identical, were the source of two samples of leaf RNA and two samples of xylem RNA, individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Two other clonal trees of E. grandis (E.grandis_Clone B_Ramet 1 and E.grandis_Clone B_Ramet 2), derived from a different matrix tree, were the source of two additional samples of xylem RNA individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Likewise, two pairs of clonal trees of E. globulus (E.globulus_Clone A_Ramet 1 and E.globulus_Clone A_Ramet 2/ E.globulus_Clone B_Ramet 1 and E.globulus_Clone B_Ramet 2), derived from two distinct matrix trees, were the source of four additional samples of xylem RNA, individually hybridized to four chips after cDNA synthesis/Cy3 labeling. Each chip measures the expression level of 21,432 genes from Eucalyptus sp. and ten human genes (negative controls) with nine 50-mer probe pairs (PM/MM) per gene in two separate blocks per chip (technical duplicate), totalizing 18 hybridization signal values per gene per chip.
2011-12-31 | E-GEOD-31696 | biostudies-arrayexpress
Project description:Woody plant material represents a renewable resource that has the potential to produce biofuels and/or novel materials with greatly reduced CO2 emissions. The study of viral infection in plants has largely focussed on detrimental symptoms, such as leaf yellowing or cell death that result in reduced crop yields. Apple rubbery wood (ARW) disease is the result of a viral infection that causes woody stems to exhibit increased flexibility. Biochemical and histochemical studies suggest the phenotype is a result of reduced lignification, specifically within the fibre cells of woody xylem. Expression analysis and proteomic data suggests that the downregulation of phenylalanine ammonia lyase (PAL) is responsible for decreased lignification. PAL is required for the first committed step in the phenylpropanoid pathway that leads to lignin biosynthesis. This is consistent with a large increase in soluble phenolics, including the lignin precursor phenylalanine, in symptomatic xylem. Downregulation of PAL appears to result from a widespread siRNA induction by the infected host, triggered by the virus. Symptomatic wood exhibited increased digestibility comparable to those seen in genetically engineered plants that alter lignin biosynthesis. To our knowledge this is the first example of a virus that alters lignin metabolism and offers a unique route to address the problem of the recalcitrant nature of plant biomass and a possible route to generating wood with altered mechanical properties.
2023-01-12 | E-MTAB-11409 | biostudies-arrayexpress
Project description:Woody plant material represents a renewable resource that has the potential to produce biofuels and/or novel materials with greatly reduced CO2 emissions. The study of viral infection in plants has largely focussed on detrimental symptoms, such as leaf yellowing or cell death that result in reduced crop yields. Apple rubbery wood (ARW) disease is the result of a viral infection that causes woody stems to exhibit increased flexibility. Biochemical and histochemical studies suggest the phenotype is a result of reduced lignification, specifically within the fibre cells of woody xylem. Expression analysis and proteomic data suggests that the downregulation of phenylalanine ammonia lyase (PAL) is responsible for decreased lignification. PAL is required for the first committed step in the phenylpropanoid pathway that leads to lignin biosynthesis. This is consistent with a large increase in soluble phenolics, including the lignin precursor phenylalanine, in symptomatic xylem. Downregulation of PAL appears to result from a widespread siRNA induction by the infected host, triggered by the virus. Symptomatic wood exhibited increased digestibility comparable to those seen in genetically engineered plants that alter lignin biosynthesis. To our knowledge this is the first example of a virus that alters lignin metabolism and offers a unique route to address the problem of the recalcitrant nature of plant biomass and a possible route to generating wood with altered mechanical properties.
2023-01-12 | E-MTAB-11410 | biostudies-arrayexpress
Project description:Wood maturation produces two distinct wood tissues: juvenile wood (JW) and mature wood (LW), which are the major cause of wood qaulity variation within a tree. We investigate transcriptome reorganization during wood maturation process in radiata pine using a newly developed 18k cDNA microarrays.
2011-06-01 | GSE20535 | GEO
Project description:In a field study, trees from two sites in Lower Saxony, Germany, were compared. RNA-seq (performed on an Illumina HiSeq 2000) was conducted on RNA from developing xylem tissue from 4 different harvests throughout the growth season to analyze transcriptional changes related to variations in wood formation and development. A transcriptome contig database was created from the combined raw reads using ABySS. Mapping of reads from distinct samples to the contig database was performed using Bowtie.
2016-07-03 | E-MTAB-3615 | biostudies-arrayexpress