Nigerian Researcher Sheds New Light on DNA Methylation Patterns in Plants

Fadekemi Ajakaiye

A study by Nigerian researcher Laide Abbas Rasaki is offering deeper insight into how DNA methylation, the chemical modification that regulates gene expression, can influence traits like disease resistance and other traits in economically important crops.

Laide, a PhD student in the Crop and Soil Science department specializing in Plant Breeding, Genetics, and Genomics at North Carolina State University, conducted the research as part of his graduate thesis, focusing on a comparative analysis of two modern DNA sequencing approaches: (Enzymatic Methyl Sequencing)EM-seq and PacBio sequencing. His work was on table beet (Beta vulgaris), a globally cultivated crop prized for its deep red roots and nutritional value.

Speaking with Thisday about the study, Laide explained, “DNA methylation doesn’t change the DNA sequence itself, but it influences how genes behave. My research looked at how this plays out in table beet trait expression, especially in genes responsible for the red coloration and resistance to Rhizomania, a devastating disease affecting sugar beet and related crops.”

Traditionally, bisulfite sequencing has been the method of choice for analyzing methylation in plant genomes. However, this technique often damages DNA, especially in plants with large and complex genomes. Laide’s study explored the use of newer, less damaging methods. EM-seq uses enzymes, while PacBio detects methylation marks by measuring the speed of DNA copying.

The study revealed that the PacBio sequencing approach not only detected more methylation sites overall, particularly in CG sequence contexts, but also offered a broader utility by allowing researchers to study both genetic structure and methylation patterns in a single run. This dual capability makes it especially valuable for breeding programs aiming to integrate genomic and epigenomic information.
One of the key findings from the project was that the genes involved in betalain production, the pigment responsible for the beet’s red root coloration, showed very low levels of methylation in their promoter regions. According to Laide, “This sparse methylation likely allows those genes to be expressed freely, which explains the strong pigmentation we see in the roots.”

In contrast, genes related to disease resistance, such as those involved in controlling Rhizomania, were found to be highly methylated in their gene bodies but sparsely methylated in their promoter regions. “This supports the idea that promoter methylation plays a more critical role in gene expression than gene body methylation. Even if the gene is methylated internally, as long as the promoter remains open, it may still be active,” he said.

The study also explored methylation patterns in transposable elements (TE), which are segments of DNA that can move around the genome and potentially disrupt normal gene function. Class 1 TE, including Copia and Gypsy types, showed higher methylation levels compared to Class 2 TE, DNA transposons, suggesting a possible mechanism for keeping these mobile elements in check.

Laide’s research not only demonstrates the reliability of these newer sequencing methods for methylation analysis but also sets the stage for more targeted use of these tools in plant improvement programs. He is now applying a similar approach in his ongoing doctoral research on cotton, where he is studying the epigenetic differences between Upland and Pima cotton varieties using PacBio sequencing data.

“The goal is to understand why some cotton varieties are regenerable and others aren’t in tissue culture media, which is a key step in modern plant breeding and genetic transformation,” Laide explained. “If we can pinpoint the methylation patterns linked to these genes that control plant regeneration in cotton, it could help us breed cotton more efficiently.”

With a dual master’s degree in Agricultural Biotechnology and molecular plant breeding from universities in Hungary and Austria, respectively, Laide brings a global perspective to his work. He is currently a research assistant at the Hulse-Kemp Lab at NC State, where he continues to explore the interface between genomics, epigenetics, and plant breeding.

His work adds to a growing body of research highlighting the role of epigenetic modifications in shaping how plants grow, adapt, and defend themselves. It is a promising area that could unlock new advances in sustainable agriculture and food security, particularly across developing regions like sub-Saharan Africa.