Unexpected discovery in cassava genome sheds light on epigenetic clues

20 June 2025

Science often throws us a curveball, and it came from cassava this time. Researchers have uncovered a massive, previously unknown chunk of DNA in a farmer-preferred cassava landrace, shedding new light on the crop’s genetic complexity.

While digging into the genome of TMEB117, researchers stumbled upon a previously uncharted 9.7 Mb chunk of DNA sitting quietly on chromosome 12. This huge insertion does not exist in the current cassava reference genomes. It is like finding a hidden attic in a house you have lived in for years.

So, what is in this genetic attic?

It is packed with transposable elements, those nomadic pieces of DNA that copy and paste themselves around the genome. One group, the MUDR-Mutator superfamily, was especially overrepresented by the rowdy guests of the genomic party.

However, here is where things get interesting: on the border of all this genetic clutter are two unique genes—HDA14 and SRT2. These genes are involved in epigenetic regulation through histone deacetylation (how the genome decides which genes to turn on or off). Their presence suggests that this mysterious insertion may play a role in shaping the cassava genome’s chromatin architecture and perhaps even its expression behavior.

A PhD student, Michael Landi, led the work with support from IITA scientists Trushar Shah, IITA Virologist Livia Stavolone, and IITA Bioinformatician Andreas Gisel. The project was carried out in collaboration with researchers at the Italian Research Council in Bari, Dr. Laurent Falquet from the University of Fribourg, and Dr Adnan Niazi from the Swedish University of Agricultural Sciences. The PhD research was conducted under the supervision of Professor Erik Bongcam-Rudloff, who was also at the Swedish University of Agricultural Sciences.

Michael’s findings also made waves at the First African Plant Genomics Symposium, where he presented a poster on the TMEB117 insertion and won the Best Poster Prize.

Now, the team is zooming in even further, looking at DNA methylation patterns across this mysterious region to determine its function. Could it be regulating stress responses or influencing important traits? Only time and more data will tell.

For a crop that feeds over 800 million people, every new insight into cassava’s genome is a step toward better varieties and smarter breeding. In addition, as this study shows, sometimes the most fascinating discoveries are hidden in plain sight.

Contributed by Rose-Harriet Okech