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

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.

Histological analysis and transcription profiles on somatic embryogenesis in interspecific hybrids of <i>Elaeis guineensis × E. oleifera</i>

“…The presence of ESTs homologous to TRANSPO-SASE was exclusively associated with the occurrence of embryogenesis in E. guineensis [19] but transposons were detected in tissues of tenera collected in and ex vitro with no remarkable differences in distribution/localization [44].…”

“…However, the expression rates of these two last genes diverged among callus lines with different genotypes and it was concluded that transcription had been modulated principally by stress [18]. At last, a TRANS-POSASE was among the ESTs expressed exclusively in actively proliferating E. guineensis embryogenic cell cultures and was not expressed in nonmultiplying cultures [19].…”

Transcriptome analysis for discovering candidate genes involve in embryogenesis in coconut (Cocos nucifera L.) through 454 pyrosequencing

“…Nonetheless, specific allocation of certain GO categories into a particular library might have a relationship with the function of that particular tissue at that time. For example oxygen binding sub category, which is represented only in 9ME has been previously reported in the oil palm initiation library but not in the proliferation library (Lin et al, 2009), suggesting the GO terms associated with early stages of embryogenesis. When the biological process ontology is considered, cellular process and metabolic process were the main subcategories bearing higher number of GO terms in all four libraries.…”

AN SNP MARKER POTENTIALLY LINKED TO SOMATIC EMBRYOGENESIS OF OIL PALM (Elaeis guineensis)

“…A total of 19,471 embryogenesis related ESTs were obtained from Low et al (2008) and Lin et al (2009). The ESTs libraries were assembled using CAP3 program resulting to 13,020 sequences of contigs and singletons (Table 1).…”

“…Target genes were derived from Expressed Sequence Tags (ESTs) from Low et al (2008), and Lin et al (2009) which were deposited in GenBank database EY396120-EY413718 and GH635901-GH637767. ESTs were subsequently assembled using CAP3 program (Huang & Madan 1999).…”