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Novel genes in Sitka spruce associated with wood density identified from global transcriptomic analysis

ABSTRACT: The current study uses a transcriptomic approach to identify genes associated with differences in wood density, that are likely to be of value as candidate genes in Sitka breeding programmes for improved wood density. Following extensive wood density analysis from a Sitka spruce (Picea sitchensis (Bong) Carr.) field grown clonal trial, three detailed microarray studies were conducted to compare the transcriptome of cambial tissue from contrasting clonal lines with high and low wood density. Twenty five genes exhibited differential expression, reaching as high as 50 fold, in at least two of the three microarray experiments and this was verified using real-time PCR. Identified genes functioned in cell wall synthesis, transcriptional regulation and plant pathogen defence, amongst others. These results confirm the importance of previously-identified density-related genes, and highlight a number of novel genes with a putative role in wood quality. A wide range of processes influence wood density, but this study has allowed the identification of potential regulators in these pathways. Future studies may now use this information to understand the control of natural variation in wood density, and manipulate the expression of these genes to improve timber quality.

ORGANISM(S): Picea sitchensis Picea

PROVIDER: GSE18579 | GEO | 2010/03/01

SECONDARY ACCESSION(S): PRJNA120287

REPOSITORIES: GEO

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Project description:The current study uses a transcriptomic approach to identify genes associated with differences in wood density, that are likely to be of value as candidate genes in Sitka breeding programmes for improved wood density. Following extensive wood density analysis from a Sitka spruce (Picea sitchensis (Bong) Carr.) field grown clonal trial, three detailed microarray studies were conducted to compare the transcriptome of cambial tissue from contrasting clonal lines with high and low wood density. Twenty five genes exhibited differential expression, reaching as high as 50 fold, in at least two of the three microarray experiments and this was verified using real-time PCR. Identified genes functioned in cell wall synthesis, transcriptional regulation and plant pathogen defence, amongst others. These results confirm the importance of previously-identified density-related genes, and highlight a number of novel genes with a putative role in wood quality. A wide range of processes influence wood density, but this study has allowed the identification of potential regulators in these pathways. Future studies may now use this information to understand the control of natural variation in wood density, and manipulate the expression of these genes to improve timber quality. The Sitka spruce (Picea sitchensis (Bong) Carr.) âExperiment 35â clonal trial was grown at Newcastleton, Scotland (OS grid reference: NY506881, latitude: 55.1847, longitude: -2.77892) and set up by Forest Research, an agency of the Forestry Commission, which has been described previously (Mboyi and Lee 1999). A total of 750 trees were established from cuttings taken in 1989 of genotypes belonging to 6 unrelated full-sib families with 8 genotypes per family and 15 replicate ramets per genotype. Cambial cell scrapes were taken in summer 2004 when trees were 15 years old. A 5x2cm section of bark was cut away at a height of 1.3m from the ground for each tree selected for microarray analysis. The exposed xylem was immediately excised using a clean sharp razor blade and snap frozen in liquid Nitrogen. Samples were transported to the laboratory and ground in liquid nitrogen using a chilled mortar and pestle and stored at -80oC prior to RNA extraction. RNA was extracted and microarray hybridisation performed as described within.

Project description:In the autumn, stems of woody perennials such as forest trees undergo a transition from active growth to dormancy. We used microarray transcriptomic profiling in combination with a proteomics analysis to elucidate processes that occur during this growth-to-dormancy transition in a conifer, white spruce (Picea glauca [Moench] Voss). Several differentially expressed genes were likely associated with the developmental transition that occurs during growth cessation in the cambial zone and the concomitant completion of cell maturation in vascular tissues. Genes encoding for cell wall and membrane biosynthetic enzymes showed transcript abundance patterns consistent with completion of cell maturation, and also of cell wall and membrane modifications potentially enabling cells to withstand the harsh conditions of winter. Several differentially expressed genes were identified that encoded putative regulators of cambial activity, cell development, and of the photoperiodic pathway. Reconfiguration of carbon allocation figured centrally in the tree’s overwintering preparations. For example, genes associated with carbon-based defenses such as terpenoids were downregulated, while many genes associated with proteinbased defenses and other stress mitigation mechanisms were upregulated. Several of these correspond to proteins that were accumulated during the growth-to-dormancy transition, emphasizing the importance of stress protection in the tree’s adaptive response to overwintering. Two year old white spruce (Picea glauca [Moench] Voss) seedlings were used for all experiments, which were conducted as described by El Kayal et al. (2011). Using a complete randomized block design, seedlings were grown in growth chambers under long days (LD; 16h day / 8h night, 20°C, 50 to 60% RH) for 8-10 weeks. Shortly before seedlings were to begin bud formation, the photoperiod was changed to short days (SD; 8h day / 16h night, 20°C, 50 to 60% RH) to induce rapid and synchronous bud formation. This was designated Day 0. Lignified whole stems representing the current year’s growth (microarrays, microscopy) or previous year’s growth (protein analyses) were sampled at 0, 3, 7, 14, 28 and 70 d (10 wk) SD, and immediately frozen in liquid nitrogen. Remaining plants were maintained in SD for an additional 8-15 wk, and then transferred to low temperatures (LT, 2 - 4°C) for 3 to 4 weeks with continuing SD prior to harvest. These are referred to as LT samples.

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Novel genes in Sitka spruce associated with wood density identified from global transcriptomic analysis

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