Project description:A microarray analysis of whole-genome gene expression in leaves was carried out in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Resultant data contributed to the analysis of the genetic architecture of gene expression in leaves of Populus.
Project description:A microarray analysis of whole-genome gene expression in roots was carried out in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Resultant data contributed to the analysis of the genetic architecture of gene expression in roots of Populus.
Project description:A microarray analysis of whole-genome gene expression and single feature polymorphism in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Concurrently, sequence-level polymorphism was analyzed based on dedicated probes identified in a pilot study comprised of the two parent genotypes (GPL7169). Resultant data contributed to a high density genetic map and to analysis of the genetic architecture of gene expression in Populus. Keywords: Genetic analysis of gene expression and polymorphism, eQTL
Project description:We investigated differential gene expression patterns in Populus vegetative buds between paradormant, endodormant, and ecodormant dormancy states. Our primary objectives were to (1) identify which individual genes, biological processes, molecular functions, and regulatory pathways were differentially expressed among dormancy states, (2) classify the differentially expressed genes into contrasting gene expression patterns, and (3) identify cis-acting elements associated with each gene expression group. For more details consult Howe et al. (Frontiers in Plant Science, 2015, pending). Nimblegen whole genome microarrays (n=10 arrays) were hybridized with total RNA isolated from axillary buds collected on five dates between August and March. On each date, RNA was isolated from two P. trichocarpa trees (clone Nisqually-1) growing in the field. After cDNA synthesis and labeling, the samples were sent to NimbleGen for fragmentation, hybridization, and detection. The Nimblegen microarray was designed for the Populus v1.0 genome assembly, but for data analysis, the 60-mer probes were reassigned to the Populus v3.0 gene models.
Project description:Populus deltoides and Populus trichocarpa were exposed to either ambient air or an acute ozone exposure of 200 ppb for 9 hrs and ozone response was profiled for each genotype by hybridising control against ozone-exposed samples per genotype. Keywords: stress response, genotype comparrison, ozone exposure
Project description:Comparison of wild type Populus to transgenics expressing either a miRNA-resistant Populus ortholog of ATHB15/CORONA or miRNA-resistant Populus ortholog of REVOLUTA
Project description:Illumina HiSeq2000 technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after 3 months of contact in order to identify mycorrhiza-regulated transcripts. 100bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) reference genome.
