Molecular Aspects of Conifer Zygotic and Somatic Embryo Development: A Review of Genome-Wide Approaches and Recent Insights

Abstract

Genome-wide profiling (transcriptomics, proteomics, metabolomics) is providing unprecedented opportunities to unravel the complexity of coordinated gene expression during embryo development in trees, especially conifer species harboring "giga-genome." This knowledge should be critical for the efficient delivery of improved varieties through seeds and/or somatic embryos in fluctuating markets and to cope with climate change. We reviewed "omics" as well as targeted gene expression studies during both somatic and zygotic embryo development in conifers and tentatively puzzled over the critical processes and genes involved at the specific developmental and transition stages. Current limitations to the interpretation of these large datasets are going to be lifted through the ongoing development of comprehensive genome resources in conifers. Nevertheless omics already confirmed that master regulators (e.g., transcription and epigenetic factors) play central roles. As in model angiosperms, the molecular regulation from early to late embryogenesis may mainly arise from spatiotemporal modulation of auxin-, gibberellin-, and abscisic acid-mediated responses. Omics also showed the potential for the development of tools to assess the progress of embryo development or to build genotype-independent, predictive models of embryogenesis-specific characteristics.

Somatic Embryogenesis. An Overview

“…Cotton is the species most studied, but the number of species investigated by this technique is growing every day. The pattern that is emerging from these studies suggests a predominant role of auxins during the induction of SE, as well as for genes like LEC, WUS, FUS, and a set of transcription factors (Shi et al 2016;Tao et al 2016;Trontin et al 2016). The Next Generation Sequencing platforms of nucleic acids can be used together with techniques that allow the isolation of a specific cellular type, such as laser-assisted microdissection.…”

Somatic Embryogenesis for More Effective Breeding and Deployment of Improved Varieties in Pinus spp.: Bottlenecks and Recent Advances

“…Moreover, embryogenic lines were apparently genetically unstable as various mutations were detected at several microsatellite loci. In other species, a few initiated cell aggregates were shown to have embryogenic-like micromorphology (P. pinaster, Trontin et al 2016c) or to express putative embryogenesis-related genes (reviewed in Trontin et al 2016b;Miguel et al 2016), such as LEC1 in P. radiata (Garcia-Mendiguren et al 2015) or WOX2 in P. contorta (Park et al 2010). However, those cell aggregates could not be sustainably propagated.…”

“…This fundamental knowledge is important to achieve and/or further optimize all stages of SE, from induction to se maturation and ss regeneration (Miguel et al 2016). With these goals in mind, several approaches and methodologies targeting different layers of molecular information have been applied in conifers (Trontin et al 2016b). Genes, transcripts, proteins, metabolites and epigenetic mechanisms have been analyzed.…”

Forest tree genomics: 10 achievements from the past 10 years and future prospects

“…Transcriptomic profiling is generating a growing body of information about coordinated gene expression during conifer embryo development (ESM_2B.doc, reviewed in Trontin et al 2015). The number of transcribed genes appears to be 30 to 40 % larger than in any other tissue (Cairney and Pullman 2007;Yakovlev et al 2014) with high relevance to the gene network in A. thaliana (300-450 genes, Cairney and Pullman 2007;Zhang et al 2012a).…”

“…It should be possible to model embryo development, by interpreting and integrating the large transcript, protein, and metabolite datasets (Kell et al 2005;Vanderschuren et al 2013;Wolfender et al 2013). However, proteomic and metabolomic studies are currently scarce for conifers (ESM_2B.doc, reviewed in Trontin et al 2015). There are still many limitations, at both experimental (Abril et al 2011) and interpretational levels (Lippert et al 2005;Saghatelian and Cravatt 2005;Teyssier et al 2011Teyssier et al , 2014.…”