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

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Abstract

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.

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Acknowledgments

Thanks to Tim Benedict, Mary Lou Fairweather, and E. Pfalzer for sample collections. Thanks to Tara Jennings for laboratory assistance and Chris Sullivan for biocomputing assistance. This research was funded by the USDA Forest Service Western Forest Transcriptome Survey and National Fire Plan (2012-NFP-GSD-1).

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Authors and Affiliations

  1. Ecology Center and Department of Wildland Resources, Utah State University, 5230 Old Main Hill, Logan, UT, 84322, USA

    Hardeep S. Rai & Karen E. Mock

  2. Rocky Mountain Research Station, USDA Forest Service, Provo, UT, 84606, USA

    Bryce A. Richardson

  3. Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR, 97331, USA

    Richard C. Cronn & Brian J. Knaus

  4. Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA

    Katherine J. Hayden

  5. Pacific Southwest Research Station, USDA- Forest Service, 1731 Research Park Drive, Davis, CA, 95618, USA

    Jessica W. Wright

  6. Ecology Center and Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT, 84322, USA

    Paul G. Wolf

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  1. Hardeep S. Rai
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  2. Karen E. Mock
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  3. Bryce A. Richardson
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Correspondence to Paul G. Wolf.

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Communicated by P. Ingvarsson

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Rai, H.S., Mock, K.E., Richardson, B.A. et al. Transcriptome characterization and detection of gene expression differences in aspen (Populus tremuloides). Tree Genetics & Genomes 9, 1031–1041 (2013). https://doi.org/10.1007/s11295-013-0615-y

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  • DOI: https://doi.org/10.1007/s11295-013-0615-y

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