Eucalyptus nitens
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ABSTRACT:
PROVIDER: PRJNA244011 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. Methods: We analyzed samples from the extremes of the distribution of KPY in two Eucalyptus nitens trials which also differed in growth to identify genes having differential expression between high and low KPY samples. We used reference-guided transcriptome mapping to study gene expression. Results: Several genes showed differential expression between low and high KPY samples. Gene ontology (GO) enrichment tests revealed up-regulation of stress-related gene categories and down-regulation of gene categories related to wood formation and growth in low KPY samples. More than 110,000 single nucleotide polymorphisms (SNPs) were detected in both the trials and 2103 of these showed differential allelic expression. Allelic expression of 30% of these variants was correlated with total gene expression. To identify the genes showing patterns of positive selection among the genes expressed in the cambial tissue we compared Ka/Ks ratios. The Ka/Ks ratios compare the rate of nonsynonymous substitutions (Ka) to synonymous substitutions (Ks) which can help identifying genes under selection. By comparing the two trials we observed in total 196 genes which had Ka/Ks ratios of more than 1.5 in both the trials strongly suggesting that these genes are under positive selection. A total of six GO categories were enriched in both trials for genes showing signatures of positive selection . All six categories include genes involved in apoptosis, cell death and defense responses. Conclusions: By conducting RNA-Seq analysis in two trials we identified a number of candidate genes and alleles whose expression is correlated with KPY and growth traits in E. nitens. Most of the down-regulated genes in low KPY samples are cell wall-related genes, suggesting that the identified candidate genes are biologically relevant. A number of potential functional polymorphisms were also identified that showed DAE. We detected positive selection signatures in numerous genes that are consistent with the results from RNA-Seq study in E. camaldulensis. The genes and alleles identified in this study form a valuable resource for association and genomic selection studies. Xylem mRNA profiles of Eucalyptus nitens from low and high KPY samples were generated by deep sequencing, in two trials, using Illumina HiSeq.
2014-06-03 | E-GEOD-56592 | biostudies-arrayexpress
Project description:Purpose: Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. Methods: We analyzed samples from the extremes of the distribution of KPY in two Eucalyptus nitens trials which also differed in growth to identify genes having differential expression between high and low KPY samples. We used reference-guided transcriptome mapping to study gene expression. Results: Several genes showed differential expression between low and high KPY samples. Gene ontology (GO) enrichment tests revealed up-regulation of stress-related gene categories and down-regulation of gene categories related to wood formation and growth in low KPY samples. More than 110,000 single nucleotide polymorphisms (SNPs) were detected in both the trials and 2103 of these showed differential allelic expression. Allelic expression of 30% of these variants was correlated with total gene expression. To identify the genes showing patterns of positive selection among the genes expressed in the cambial tissue we compared Ka/Ks ratios. The Ka/Ks ratios compare the rate of nonsynonymous substitutions (Ka) to synonymous substitutions (Ks) which can help identifying genes under selection. By comparing the two trials we observed in total 196 genes which had Ka/Ks ratios of more than 1.5 in both the trials strongly suggesting that these genes are under positive selection. A total of six GO categories were enriched in both trials for genes showing signatures of positive selection . All six categories include genes involved in apoptosis, cell death and defense responses. Conclusions: By conducting RNA-Seq analysis in two trials we identified a number of candidate genes and alleles whose expression is correlated with KPY and growth traits in E. nitens. Most of the down-regulated genes in low KPY samples are cell wall-related genes, suggesting that the identified candidate genes are biologically relevant. A number of potential functional polymorphisms were also identified that showed DAE. We detected positive selection signatures in numerous genes that are consistent with the results from RNA-Seq study in E. camaldulensis. The genes and alleles identified in this study form a valuable resource for association and genomic selection studies.
2014-06-03 | GSE56592 | GEO
Project description:Eucalyptus nitens transcriptome under cold stress
| PRJNA303180 | ENA
Project description:The daily cycle of night and day affects the behaviour and physiology of almost all living things. At the molecular level, many genes show daily changes in expression levels. To determine whether changes in transcript abundance occur in wood forming tissues of Eucalyptus trees we used a cDNA microarray to examine gene expression levels at roughly four hour intervals throughout the day. Experiments were performed using RNA extracted from two biological replicates - GU (Eucalyptus grandis x E. urophylla) and GC (Eucalyptus grandis x camaldulensis) trees. A loop design was used, linking six time points. A dye swap was incorporated to eliminate dye bias.
2010-06-25 | E-GEOD-11731 | 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:Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. It is essential to maximize the effectiveness of these plantations by increasing their productivity, the quality and value of their products. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven individual E. grandis trees. A 1532-probe cDNA microarray was constructed by arraying 768 cDNA-AFLP fragments and 810 cDNA library clones from seven individual E. grandis trees onto silanised slides. The results revealed that 32% of the spotted fragments showed distinct expression patterns (with a fold change of at least 1.4 or -1.4 and a p value of 0.01) and could be grouped into clusters representing co-expressed genes. Evaluation of the binary distribution of cDNA-AFLP fragments on the array showed that the individual genotypes could be discriminated. A simple, yet general method was developed for genotyping and expression profiling of wood-forming tissue of E. grandis trees differing in their splitting characteristics and in their lignin contents. Evaluation of gene expression profiles and the binary distribution of cDNA-AFLP fragments on the chip suggest that the prototype chip developed could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programmes.
2009-10-01 | GSE14707 | GEO
Project description:The daily cycle of night and day affects the behaviour and physiology of almost all living things. At the molecular level, many genes show daily changes in expression levels. To determine whether changes in transcript abundance occur in wood forming tissues of Eucalyptus trees we used a cDNA microarray to examine gene expression levels at roughly four hour intervals throughout the day.
2009-05-13 | GSE11731 | GEO
Project description:Fast growing Eucalyptus species widely distributed in eastern Australia.
| PRJNA38573 | ENA
Project description:Fast-growing Eucalyptus grandis trees are one of the most efficient producers of wood in South Africa. It is essential to maximize the effectiveness of these plantations by increasing their productivity, the quality and value of their products. We used microarray-based DNA-amplified fragment length polymorphism (AFLP) analysis in combination with expression profiling to develop fingerprints and profile gene expression of wood-forming tissue of seven individual E. grandis trees. A 1532-probe cDNA microarray was constructed by arraying 768 cDNA-AFLP fragments and 810 cDNA library clones from seven individual E. grandis trees onto silanised slides. The results revealed that 32% of the spotted fragments showed distinct expression patterns (with a fold change of at least 1.4 or -1.4 and a p value of 0.01) and could be grouped into clusters representing co-expressed genes. Evaluation of the binary distribution of cDNA-AFLP fragments on the array showed that the individual genotypes could be discriminated. A simple, yet general method was developed for genotyping and expression profiling of wood-forming tissue of E. grandis trees differing in their splitting characteristics and in their lignin contents. Evaluation of gene expression profiles and the binary distribution of cDNA-AFLP fragments on the chip suggest that the prototype chip developed could be useful for transcript profiling and for the identification of Eucalyptus trees with preferred wood quality traits in commercial breeding programmes. Transcriptional profiling and genotyping of seven E. grandis trees , namely (741-H (high lignin), 108-L (low lignin), 243-L (low lignin), 1/23/4-HS (high splitting), 1/71/6-HS (high splitting), 1/91/7-LS (low splitting) and 1/92/7-LS (low splitting), were performed with an in-house spotted cDNA microarray. All trees were characterized for their splitting qualities and lignin content and only the trees best corresponding to the selected traits were used for further analysis (Verryn and Turner 2000). RNA was isolated and cDNA synthesis was performed. A reference design microarray experiment was conducted and tree 1/23/4-HS served as a reference. Samples were fluorescently labelled with Cy5 or Cy3 dye and co-hybridized overnight. Two biological and one technical replicate (using independent labelling reactions) was performed, each replication consisting of a reverse labelling experiment.
2009-10-01 | E-GEOD-14707 | biostudies-arrayexpress