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Transcriptional profiling of epigenetic regulators in somatic embryos during temperature induced formation of an epigenetic memory in Norway spruce

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Abstract

Main Conclusion

A significant number of epigenetic regulators were differentially expressed during embryogenesis at different epitype-inducing conditions. Our results support that methylation of DNA and histones, as well as sRNAs, are pivotal for the establishment of the epigenetic memory.

As a forest tree species with long generation times, Norway spruce is remarkably well adapted to local environmental conditions despite having recently, from an evolutionary perspective, recolonized large areas following the last glaciation. In this species, there is an enigmatic epigenetic memory of the temperature conditions during embryogenesis that allows rapid adaptation to changing environment. We used a transcriptomic approach to investigate the molecular mechanisms underlying the formation of the epigenetic memory during somatic embryogenesis in Norway spruce. Nine mRNA libraries were prepared from three epitypes of the same genotype resulting from exposure to epitype-inducing temperatures of 18, 23 and 28 °C. RNA-Seq analysis revealed more than 10,000 differentially expressed genes (DEGs). The epitype-inducing conditions during SE were accompanied by marked transcriptomic changes for multiple gene models related to the epigenetic machinery. Out of 735 putative orthologs of epigenetic regulators, 329 were affected by the epitype-inducing temperatures and differentially expressed. The majority of DEGs among the epigenetic regulators was related to DNA and histone methylation, along with sRNA pathways and a range of putative thermosensing and signaling genes. These genes could be the main epigenetic regulators involved in formation of the epigenetic memory. We suggest considerable expansion of gene families of epigenetic regulators in Norway spruce compared to orthologous gene families in Populus and Arabidopsis. Obtained results provide a solid basis for further genome annotation and studies focusing on the importance of these candidate genes for the epigenetic memory formation.

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Abbreviations

DEG:

Differentially expressed gene

SE:

Somatic embryogenesis

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Acknowledgments

The authors would like to thank Ksenia Zakharova (St.-Petersburg State University, Russia) for assistance during library preparation and sequencing. This work was supported by the Norwegian Research Council (FRIBIO Grant#191455/V40 and FRIMEDBIO Grant#240766/F20) and the EU FP7 project ProCoGen. Elena Carneros was supported by a grant from Iceland, Liechtenstein and Norway through the EEA Financial Mechanism, operated by Universidad Complutense de Madrid.

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Authors and Affiliations

  1. Norwegian Institute of Bioeconomy Research, 1431, Ås, Norway

    Igor A. Yakovlev, Elena Carneros & Carl Gunnar Fossdal

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

    YeonKyeong Lee & Jorunn E. Olsen

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  1. Igor A. Yakovlev
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  2. Elena Carneros
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  3. YeonKyeong Lee
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  4. Jorunn E. Olsen
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Correspondence to Igor A. Yakovlev.

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Data archiving statement

Unique transcripts from 9 libraries sequenced using Ion Torrent PGM™ Sequencer were deposited to the SRA (Short Read Archive, NCBI) and got the following accessions: submission ID SUB916697; BioProject ID PRJNA281286 and accession IDs: SAMN03486972—SAMN03486992.

Electronic supplementary material

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425_2016_2484_MOESM1_ESM.xlsx

List of candidate genes and description of primers used for qRT-PCR-analyses of transcripts in somatic embryos of Norway spruce (XLSX 3065 kb)

425_2016_2484_MOESM2_ESM.docx

Summary of RNA-Seq libraries and read mappings for Norway spruce somatic embryos of genotype B10W for three different embryogenesis stages (E1 – E2 – E3) at three epitype-inducing temperatures (18°C – 23°C – 28°C) (DOCX 23 kb)

425_2016_2484_MOESM3_ESM.docx

Characterization of epigenetic regulators in the somatic embryos of Norway spruce developing under different epitype-inducing temperatures (18, 23 and 28°C) (DOCX 18 kb)

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Yakovlev, I.A., Carneros, E., Lee, Y. et al. Transcriptional profiling of epigenetic regulators in somatic embryos during temperature induced formation of an epigenetic memory in Norway spruce. Planta 243, 1237–1249 (2016). https://doi.org/10.1007/s00425-016-2484-8

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