Original Paper

Tree Genetics & Genomes

, Volume 9, Issue 4, pp 1031-1041

First online:

Transcriptome characterization and detection of gene expression differences in aspen (Populus tremuloides)

  • Hardeep S. RaiAffiliated withEcology Center and Department of Wildland Resources, Utah State University
  • , Karen E. MockAffiliated withEcology Center and Department of Wildland Resources, Utah State University
  • , Bryce A. RichardsonAffiliated withRocky Mountain Research Station, USDA Forest Service
  • , Richard C. CronnAffiliated withPacific Northwest Research Station, USDA Forest Service
  • , Katherine J. HaydenAffiliated withDepartment of Environmental Science, Policy, and Management, University of California
  • , Jessica W. WrightAffiliated withPacific Southwest Research Station, USDA- Forest Service
  • , Brian J. KnausAffiliated withPacific Northwest Research Station, USDA Forest Service
  • , Paul G. WolfAffiliated withEcology Center and Department of Biology, Utah State University Email author 

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Aspen (Populus tremuloides) is a temperate North American tree species with a geographical distribution more extensive than any other tree species on the continent. Because it is economically important for pulp and paper industries and ecologically important for its role as a foundation species in forest ecosystems, the decline of aspen in large portions of its range is of serious concern. The availability and annotation of the black cottonwood (Populus trichocarpa) genome enables a range of high throughput sequencing approaches that can be used to understand rangewide patterns of genetic variation, adaptation, and responses to environmental challenges in other Populus species, including aspen. Gene expression studies are particularly useful for understanding the molecular basis of ecological responses, but are limited by the availability of transcriptome data. We explored the aspen transcriptome through the use of high-throughput sequencing with two main goals: (1) characterization of the expressed portion of the P. tremuloides genome in leaves and (2) assessment of variation in gene expression among genets collected from distinct latitudes but reared in a common garden. We also report a large single nucleotide polymorphism dataset that provides the groundwork for future studies of aspen evolution and ecology, and we identify a set of differentially expressed genes across individuals and population boundaries for the leaf transcriptome of P. tremuloides.


Trembling aspen Quaking aspen RNA-Seq Differential expression SNP (single nucleotide polymorphism) Populus trichocarpa