Estelle Jaligot

Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis

BACKGROUND The large-scale clonal propagation of oil palm (Elaeis guineensis) is being stalled by the occurrence of the mantled somaclonal variation. Indeed, this abnormality which presents a homeotic-like conversion of male floral organs into carpelloid structures, hampers oil production since the supernumerary female organs are either sterile or produce fruits with poor oil yields. SCOPE In the last 15 years, the prevailing point of view on the origin of the mantled floral phenotype has evolved from a random mutation event triggered by in vitro culture to a hormone-dependent dysfunction of gene regulation processes. In this review, we retrace the history of the research on the mantled variation in the light of the parallel advances made in the understanding of plant development regulation in model systems and more specifically in the role of epigenetic mechanisms. An overview of the current state of oil palm genomic and transcriptomic resources, which are key to any comparison with model organisms, is given. We show that, while displaying original characteristics, the mantled phenotype of oil palm is morphologically, and possibly molecularly, related to MADS-box genes mutants described in model plants. We also discuss the occurrence of comparable floral phenotypes in other palm species. CONCLUSIONS Beyond its primary interest in the search for discriminating markers against an economically crippling phenotype, the study of the mantled abnormality also provides a unique opportunity to investigate the regulation of reproductive development in a perennial tropical palm. On the basis of recent results, we propose that future efforts should concentrate on the epigenetic regulation targeting MADS-box genes and transposable elements of oil palm, since both types of sequences are most likely to be involved in the mantled variant phenotype.

Genome-wide analysis of LTR-retrotransposons in oil palm

BackgroundThe oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world’s largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. The recent publication of both the African oil palm genome assembly and the first draft sequence of its Latin American relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences.MethodsIn this study, we identified, annotated and compared Transposable Elements (TE) from the African and Latin American oil palms. In a first step, Transposable Element databases were built through de novo detection in both genome sequences then the TE content of both genomes was estimated. Then putative full-length retrotransposons with Long Terminal Repeats (LTRs) were further identified in the E. guineensis genome for characterization of their structural diversity, copy number and chromosomal distribution. Finally, their relative expression in several tissues was determined through in silico analysis of publicly available transcriptome data.ResultsOur results reveal a congruence in the transpositional history of LTR retrotransposons between E. oleifera and E. guineensis, especially the Sto-4 family. Also, we have identified and described 583 full-length LTR-retrotransposons in the Elaeis guineensis genome. Our work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred. Moreover, the analysis of chromosomal distribution suggests a preferential insertion of Copia elements in gene-rich regions, whereas Gypsy elements appear to be evenly distributed throughout the genome.ConclusionsConsidering the high proportion of LTR retrotransposon in the oil palm genome, our work will contribute to a greater understanding of their impact on genome organization and evolution. Moreover, the knowledge gained from this study constitutes a valuable resource for both the improvement of genome annotation and the investigation of the evolutionary history of palms.

Plant Fidelity in Somatic Embryogenesis-Regenerated Plants

This chapter reviews the literature on somaclonal variation affecting the micropropagation through somatic embryogenesis. The first part covers the following aspects: (i) principle, protocols, and applications of somatic embryogenesis and (ii) epigenetic reprogramming and changes in cell fate that underlie somatic embryogenesis. The second part addresses the problem of somaclonal variation in somatic embryogenesis by first (i) assessing their impact on somatic embryo-derived plant production and (ii) describing the multiple origins of somaclonal variation (chromosomal aberrations, genetic alterations, epigenetic regulations, and transposable elements). The last part focuses on how to manage somaclonal variation in commercial productions of SE-derived plants by covering different aspects: (i) detection of undesirable phenotypes: screening out the variants, (ii) strategies of avoidance and incidence limitation, (iii) generation and exploitation of desirable phenotypes in plant breeding, (iv) beyond the induction of stress-tolerant somaclonal variants: a plant breeder’s perspective.

Applying Epigenetics in Plant Breeding: Balancing Genome Stability and Phenotypic Plasticity

The correct implementation of epigenetic mechanisms is often a prerequisite for the timely regulation of genome expression and structure and ultimately for the development of higher plants. Developmental regulation is thus playing a paramount role in the elaboration of yields in agricultural crops. However, numerous studies have shown that this tight control includes a certain degree of freedom as epigenetic regulations can be loosened in the course of the reproductive development, after hybridization or as part of the response to environmental constraints – both in vitro and in vivo – whereas genome stability is globally maintained. As a result, several modified epigenetic marks and associated altered gene or transposable element expression can eventually give rise to qualitative or quantitative phenotypic changes on the long term. The present chapter is intended to present the main concepts governing epigenetic regulation of gene expression in higher plants and to review its potential applications for the selection of heritable phenotypes. It illustrates how epigenetic variations can be smartly used in breeding schemes and which questions remain to be addressed in order to make such integration successful. The Next Generation Sequencing revolution has also impacted our approach of plant epigenetics as more genomes, epigenomes and transcriptomes and are made available for crop plants and the simplistic Arabidopsis model is being questioned.