Siberian Federal University: Karma of the oil palm: how to avoid disease in the trees

A team of researchers from Russia, the USA and Malaysia studied the fundamental principles of methylation (a biological process by which methyl groups are added to the DNA molecule) on oil palm, which is grown for industrial purposes in Malaysia.

The cultivation of oil palm (Elaeis guineensis) is an important part of the Malaysian economy. In 2020, Malaysia produced 19.14 million tonnes of palm oil for the food industry and 2.20 tonnes for various industrial purposes, and the country wants to increase oil production not by expanding the area of plantations, but by increasing the productivity of palm trees.

Back in 1941, scholars discovered shell (Sh) gene, and this was a real breakthrough that provided growth in the volume of oil produced. Thus, the heterozygous variant of tenera palm, obtained by crossing dura varieties with a very thick tough interlayer in the fruit and pisifera with a very thin interlayer, made it possible to increase the proportion of that part of the fruit (the so-called mesocarp) from which the oil is extracted. This hybrid produces 30% and 100% more oil than dura and pisifera, respectively.

The next step was cloning the palms, which increased productivity by another 30%. However, mass cloning has created new problems: one of them is the appearance of somaclonal variations, i.e. organisms with genetic alterations. In such trees, the degree of pathology could vary from a partially modified palm fruit to a completely sterile fruit.

Since this sign turned out to be reversible and manifested itself only partially, the scientists suggested a hypothesis about the epigenetic nature of this pathology. Epigenetics is a science that studies the functioning of the genome: which parts of it are active and which are not. Epigenetic regulation is the main mechanism of cell differentiation when it is necessary to turn on some genes and turn off others at different periods of the organism’s development.

Epigenetics is difficult, if even impossible, to fix. Nevertheless, it is possible to identify some epigenetic factors in the early stages of fetal development, thus filtering out pathologically forming palms. This problem is being solved by the joint efforts of Russian, US and Malaysian scientists.

“We performed genome–wide bisulfite sequencing (WGBS) on three palm samples: a mother sample and two clones, normal and pathological. Methylation analysis revealed a general decrease in the level of methylation throughout the palm genome, and areas of a significant decrease in the level of methylation,” explained Elizaveta Taranenko, research engineer of the Forest Genomics Laboratory, PhD student of Siberian Federal University.

The researcher said that during the work, they studies EgDEF1 gene, previously described in connection with the development of pathological palm fruit. Inside EgDEF1, there is a retroelement called Karma. The methylation level in this gene was significantly lower in the case of the pathological sample compared to the maternal sample and another normal clone.

“We believe that the found chromosomal regions, including EgDEF1 gene, are the main candidates for epigenetic analysis for the selection of young palms. However, the exact mechanism for reducing methylation in abnormal fruit has not yet been established. The work on the project continues: we are trying to improve the assembly of the genome and studying other epigenetic mechanisms that can affect the quality of oil palms through small RNAs. In addition, our group is investigating the influence of the genetic and epigenetic profile on the presence of fatty acids and other molecules in the oil,” summed up Elizaveta Taranenko.