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Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development

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Abstract

With the aim of understanding the molecular mechanisms underlying somatic embryogenesis (SE) in oil palm, we examined transcriptome changes that occur when embryogenic suspension cells are initiated to develop somatic embryos. Two reciprocal suppression subtractive hybridization (SSH) libraries were constructed from oil palm embryogenic cell suspensions: one in which embryo development was blocked by the presence of the synthetic auxin analogue 2,4-dichlorophenoxyacetic acid (2,4-d) in the medium (proliferation library); and another in which cells were stimulated to form embryos by the removal of 2,4-d from the medium (initiation library). A total of 1867 Expressed Sequence Tags (ESTs) consisting of 1567 potential unigenes were assembled from the two libraries. Functional annotation indicated that 928 of the ESTs correspond to proteins that have either no similarity to sequences in public databases or are of unknown function. Gene Ontology (GO) terms assigned to the two EST populations give clues to the underlying molecular functions, biological processes and cellular components involved in the initiation of embryo development. Macroarrays were used for transcript profiling the ESTs during SE. Hierarchical cluster analysis of differential transcript accumulation revealed 4 distinct profiles containing a total of 192 statistically significant developmentally regulated transcripts. Similarities and differences between the global results obtained with in vitro systems from dicots, monocots and gymnosperms will be discussed.

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Abbreviations

2,4-d :

2,4-Dichlorophenoxyacetic acid

ARF:

ADP-ribosylation factor

EST:

Expressed sequence tag

GO:

Gene Ontology

GST:

Glutathione S-transferases

HCA:

Hierarchical cluster analysis

PR:

Pathogenesis-related

STM-like:

Shootmeristemless-like

SEm:

Somatic embryo

SE:

Somatic embryogenesis

SSH:

Suppression subtractive hybridization

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Acknowledgments

We would like to thank Xavier Sabau for the expertise in cDNA arraying at the Robotics and DNA Sequencing Platform CIRAD, Montpellier Languedoc-Roussillon Genopole (http://www.genopole-montpellier-lr.org), Thierry Beule for helpful technical advice on macroarray methodology, and Ivanna Fuentes for excellent technical assistance with handling the PCR amplification of the EST plasmid inserts. This work was financed by institutional funds from IRD and CIRAD.

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  1. Hsiang-Chun Lin

    Present address: ETH Zurich, Institute of Plant Science, LFW D 36.1, Universitätstrasse 2, 8092, Zurich, Switzerland

Authors and Affiliations

  1. IRD, UMR DIAPC, IRD/CIRAD Palm Development Group, 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France

    Hsiang-Chun Lin, James W. Tregear & Timothy John Tranbarger

  2. CIRAD, UMR DIAPC, IRD/CIRAD Palm Development Group, 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France

    Fabienne Morcillo

  3. IRD, UMR DIAPC, 911 Avenue Agropolis, 34394, Montpellier Cedex 5, France

    Stéphane Dussert & Christine Tranchant-Dubreuil

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  1. Hsiang-Chun Lin
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  2. Fabienne Morcillo
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Correspondence to Timothy John Tranbarger.

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Hsiang-Chun Lin and Fabienne Morcillo contributed equally to this work and a portion was originally presented at the 2006 Congress of the Federation of European Societies of Plant Biology Lyon, France.

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Lin, HC., Morcillo, F., Dussert, S. et al. Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development. Plant Mol Biol 70, 173–192 (2009). https://doi.org/10.1007/s11103-009-9464-3

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