Transcriptomics

Dataset Information

22

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. Overall design: The Sitka spruce (Picea sitchensis (Bong) Carr.) ‘Experiment 35’ 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.

INSTRUMENT(S): Treenomix spruce 21.8K cDNA microarray

ORGANISM(S): Picea sitchensis  

SUBMITTER: Patrick Stephenson 

PROVIDER: GSE18579 | GEO | 2010-03-01

SECONDARY ACCESSION(S): PRJNA120287

REPOSITORIES: GEO

Similar Datasets

2010-05-07 | E-GEOD-18579 | ArrayExpress
2012-02-18 | E-GEOD-35922 | ArrayExpress
2011-11-28 | E-GEOD-27476 | ArrayExpress
2011-11-28 | GSE27476 | GEO
2011-10-17 | GSE31090 | GEO
2015-01-21 | E-GEOD-60277 | ArrayExpress
| GSE71094 | GEO
2011-10-16 | E-GEOD-31090 | ArrayExpress
2012-08-02 | E-GEOD-32086 | ArrayExpress
2014-05-06 | E-GEOD-57301 | ArrayExpress