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Temperature-dependent differential transcriptomes during formation of an epigenetic memory in Norway spruce embryogenesis

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Abstract

Embryogenesis is the initial stage of plant life, when the basics of body plan and the post-embryonic development are laid down. Epigenetic memory formed in the Norway spruce embryos permanently affect the timing of bud burst and bud set in progenies, vitally important adaptive traits in this long-lived forest species. The epigenetic memory marks are established in response to the temperature conditions prevailing during zygotic and somatic embryogenesis; the epitype is fixed by the time the embryo is fully developed and is mitotically propagated throughout the tree’s life span. Somatic embryogenesis closely mimics the natural zygotic embryo formation and results in epigenetically different plants in a predictable temperature-dependent manner with respect to altered phenology. Using Illumina-based Massive Analysis of cDNA Ends, the transcriptome changes were monitored in somatic embryos during morphogenesis stage under two different temperatures (18 vs. 30 °C). We found distinct differences in transcriptomes between the genetically identical embryogenic tissues grown under the two epitype-inducing temperatures suggesting temperature-dependent canalizing of gene expression during embryo formation, putatively based on chromatin modifications. From 448 transcripts of genes coding for proteins involved in epigenetic machinery, we found 35 of these to be differentially expressed at high level under the epitype-inducing conditions. Therefore, temperature conditions during embryogenesis significantly alter transcriptional profiles including numerous orthologs of transcriptional regulators, epigenetic-related genes, and large sets of unknown and uncharacterized transcripts.

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Abbreviations

MACE:

Massive Analysis of cDNA Ends

DE:

Differentially expressed

CE:

“Cold” embryogenesis environment (18 °C or C in libraries definitions)

WE:

“Warm” embryogenesis environment (30 °C or W in libraries definitions)

RT-PCR:

Real-time reverse transcription polymerase chain reaction

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Acknowledgments

The authors would like to thank Tone I. Melby (Norwegian University of Life Sciences) for assistance in RNA extraction and Anne E. Nilsen (Norwegian Forest and Landscape Institute) for valuable help during in vitro culturing. In addition, we would like to thank Ruth Jüngling and Nico Krezdorn (GenXPro GmbH) for conducting the sequencing and the initial bioinformatics processing of data. We express additional gratitude to Damien Vaisettes (Institut National Des Sciences Appliquees, France) for valuable technical help with primer testing and running qRT-PCRs. This work was supported by the Norwegian Research Council (FRIBIO Grant #191455/V40) and the EU FP7 project ProCoGen.

Data Archiving Statement

Unique transcripts from four libraries using Illumina-based MACE analysis were deposited to the SRA (Short Read Archive, NCBI) and got the following accession: PRJNA184229 and ID: 184229.

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Authors and Affiliations

  1. Norwegian Forest and Landscape Institute, P.O. Box 115, 1431, Ås, Norway

    Igor A. Yakovlev, Tore Skrøppa & Carl Gunnar Fossdal

  2. Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, 1432, Ås, Norway

    YeonKyeong Lee, Jorunn E. Olsen & Øystein Johnsen

  3. GenXPro GmbH, Frankfurter Innovationszentrum (FIZ), Altenhöferallee 3, 060438, Frankfurt am Main, Germany

    Björn Rotter

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  1. Igor A. Yakovlev
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  2. YeonKyeong Lee
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  4. Jorunn E. Olsen
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  5. Tore Skrøppa
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  6. Øystein Johnsen
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Correspondence to Igor A. Yakovlev.

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Communicated by J. Dean

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Yakovlev, I.A., Lee, Y., Rotter, B. et al. Temperature-dependent differential transcriptomes during formation of an epigenetic memory in Norway spruce embryogenesis. Tree Genetics & Genomes 10, 355–366 (2014). https://doi.org/10.1007/s11295-013-0691-z

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