DIversité - Adaptation - DEveloppement des plantes


Estelle JALIGOT, F2F team - This email address is being protected from spambots. You need JavaScript enabled to view it.

An epigenetic variation with high economic impact.

The in vitro cloning of the oil palm through somatic embryogenesis is used as a way to multiply individuals with abundant production. This process enables breeders to free themselves from the constraints of classical selection methods when applied to plant species with long life cycles and to produce regenerant plants that are theoretically identical, both genetically and phenotypically, to the mother plant.

However, it has been observed that all protocols known to date result in the emergence in clonal progenies of a malformation of flowers and fruits, called the mantled abnormality. It can display variable degrees of severity, from a defect in oil accumulation in the fruit to flower sterility. If its average incidence rate of 2-5% may seem quite low, this should not hide the fact that it is highly variable according to the process and the genetic origins that are used, which makes it unpredictable. It is therefore necessary to design tools allowing the detection of this variation well before it becomes in adult palms in the field, at the end of a long and costly production process. Moreover, enabling the early detection of the potential for mantled abnormality as it is induced during the in vitro stages will enable the quality control of clonal fidelity in the course of the process.

In the absence of any ploidy defect or genetic polymorphism between the mother plant and the regenerant palms, both the heterogeneity and the spontaneous time-dependent reversibility of the mantled abnormality have lead us to investigate epigenetic mechanisms, as early as 1998. We have thus used a biochemical approach (HPLC) to demonstrate the occurrence, in all tissues that either carry or are affected by the abnormality in both adult palms and in vitro material, of a genome-wide deficit in DNA methylation. More recently, we have established that genomic methylation increases in embryogenic suspensions with the duration of the in vitro propagation phase. Currently, we are attempting to determine whether there is an interaction between the duration effect and the generation of abnormal palms. Also, the possible reactivation of Transposable Elements as a result of the micropropagation process needs to be explored. To this aim, a catalogue of full-length LTR retrotransposons of the oil palm genome has been created.  

Meanwhile, we have developed a "candidate gene" approach in order to directly target functions that are potentially affected in the mantled variation context. Looking for the origin of the genome-wide hypomethylation, we have found that neither the coding sequence nor the transcription of the three main DNA-methyltransferases display alterations that might suggest a regulatory dysfunction. By contrast, we have shown that transcripts generated by one of the genes involved in stamen emergence in the flower undergo alternative splicing. This discovery was the first step towards the demonstration of a functional relationship between the DNA methylation deficit and the malformation of floral organs in mantled palms. Today, we are setting out to better understanding when and how this phenotypic defect takes root into the in vitro multiplication process.


Partnerships (past and current)

CSIRO-Plant Industry, Australia

FELDA Global Ventures, Malaysia

PalmElit SAS, France


Further reading

  • Beulé T, Agbessi MDT, Dussert S, Jaligot E, Guyot R. 2015. Genome-wide analysis of LTR-retrotransposons in oil palm. BMC Genomics 16: 795.
  • Etienne H, Guyot R, Beulé T, Breitler J-C, Jaligot E. 2016. Plant Fidelity in Somatic Embryogenesis-Regenerated Plants. In: Loyola-Vargas VM, Ochoa-Alejo N, eds. Somatic Embryogenesis: Fundamental Aspects and Applications. Springer International Publishing, 121‑150.
  • Jaligot E. 2018. Advances in understanding oil palm reproductive development. In: Rival A, ed. Burleigh Dodds Series in Agricultural Science. Achieving sustainable cultivation of oil palm. Burleigh Dodds Science Publishing, 75‑91.
  • Jaligot E, Adler S, Debladis E, Beulé T, Richaud F, Ilbert P, Finnegan EJ, Rival A. 2011. Epigenetic imbalance and the floral developmental abnormality of the in vitro-regenerated oil palm Elaeis guineensis. Annals of Botany 108: 1463‑1475.
  • Jaligot E, Hooi WY, Debladis E, Richaud F, Beulé T, Collin M, Agbessi MDT, Sabot F, Garsmeur O, D’Hont A, Alwee SSRS, Rival A. 2014. DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm. PLoS ONE 9: e91896.
  • Jaligot E, Rival A, Beulé T, Dussert S, Verdeil JL. 2000. Somaclonal variation in oil palm (Elaeis guineensis Jacq.): the DNA methylation hypothesis. Plant Cell Reports 19: 684–690.
  • Rival A, Ilbert P, Labeyrie A, Torres E, Doulbeau S, Personne A, Dussert S, Beulé T, Durand-Gasselin T, Tregear JW, Jaligot E. 2013. Variations in genomic DNA methylation during the long-term in vitro proliferation of oil palm embryogenic suspension cultures. Plant Cell Reports 32: 359‑368.
  • Rival A, Jaligot E, Beulé T, Finnegan EJ. 2008. Isolation and expression analysis of genes encoding MET, CMT, and DRM methyltransferases in oil palm (Elaeis guineensis Jacq.) in relation to the « mantled » somaclonal variation. Journal of Experimental Botany 59: 3271‑3281.