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Genotyping-by-sequencing of Douglas-fir (Pseudotsuga menziesii) provenances with ApeKI and HindIII

ABSTRACT: Genotyping-by-sequencing of several coastal and interior Douglas-fir (Pseudotsuga menziesii) provenances with ApeKI and HindIII as restriction enzymes

PROVIDER: PRJEB7737 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR674690_1.fastq.gz	Fastqsanger.gz
	ERR674690_2.fastq.gz	Fastqsanger.gz
	ERR674691_1.fastq.gz	Fastqsanger.gz
	ERR674691_2.fastq.gz	Fastqsanger.gz
	ERR674692_1.fastq.gz	Fastqsanger.gz

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Genotyping-by-sequencing of Douglas-fir (Pseudotsuga menziesii) provenances with ApeKI

Project description:Genotyping-by-sequencing of several coastal and interior Douglas-fir (Pseudotsuga menziesii) provenances with ApeKI as restriction enzyme

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Transcriptome responses to natural environments in Pseudotsuga menziesii (Douglas-fir)

Project description:Local adaptation and phenotypic plasticity are important components of plant responses to variations in environmental conditions. While local adaptation has been widely studied in trees, little is known about plasticity of gene expression in adult trees in response to ever-changing environmental conditions in natural habitats. Here we investigate plasticity of gene expression in needle tissue between two douglas-fir provenances represented by 25 adult trees using deep RNA sequencing (RNA-Seq). Using linear mixed models, we investigated the effect of temperature, soil water availability and photoperiod on the abundance of 59189 detected transcripts. Expression of more than 80% of all identified transcripts revealed a response to variations in environmental conditions in the field. GO term overrepresentation analysis revealed gene expression responses to temperature, soil water availability and photoperiod that are highly conserved among many plant taxa. However, expression differences between the two Douglas-fir provenances were rather small compared to the expression differences observed between individual trees. Although the effect of environment on global transcript expression was high, the observed genotype by environment (GxE) interaction of gene expression was surprisingly low, since only 21 of all detected transcripts showed a GxE interaction.

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Project description:We report sequencing the transcriptome of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) during spring bud burst. Samples from needle tissue of two half-sibs from two families each, nested within three seed sources, were sequenced (total of six families and 12 individuals). Samples were taken at seven time points with the failure of one library, resulting in 83 total sequenced samples. Three time points were used for transcriptome assembly and 4 time point were analyzed for differential expression across time and within seed sources.

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Laccaria-Douglas fir: A Timecourse of Mycorrhizal Root Tip Development

Project description:This study characterizes the transcriptomic alterations of Laccaria bicolor S238N during interaction with Pseudotsuga menziesii. Three time-points were analyzed, two weeks, four weeks and six weeks after inoculation and compared to the transcriptome of free-living mycelium from Laccaria bicolor S238N. We performed 9 hybridizations (NimbleGen) with samples derived from Pseudotsuga menziesii /L.bicolor mycorrhizal root tips. Samples were taken after 2,4 and 6 weeks of interaction (three biological replicates). These samples were compared to free-living mycelium from Laccaria bicolor S238N (three biological replicates). All samples were labeled with Cy3.

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