Epigenetic variation—like genetic variation—can be inherited and influence plant traits across generations. But unlike genetic variation, it doesn’t involve changes to the DNA sequence itself. Instead, it works more like punctuation or highlighting in a text, subtly guiding how genes are expressed—switching them on or off in response to environmental cues.

Harnessing this increasingly influential area of genetics could dramatically expand the diversity available to breeders, enabling the development of crops that are more resilient to climate change and disease.

Previous studies have shown that DNA methylation, a heritable epigenetic process, is crucial in plants—and that the MET1 gene plays a key role. However, studying MET1 has been challenging because completely removing or knocking out the gene through traditional genetic engineering typically kills the plant.

To overcome this, Dr. Philippa Borrill’s team at the John Innes Centre turned to wheat, a crop with a famously complex genome that contains three copies of the MET1 gene. In a study published in the Journal of Experimental Botany, the team used a method called mutagenesis to selectively knock out some—but not all—of these gene copies. This allowed them to observe the effects of partial gene disruption without harming the plant.

Their findings were striking. Some of these partial epigenetic mutants showed altered DNA methylation patterns that were associated with heritable traits relevant to breeding. Notably, they identified a mutant with altered flowering time—a key trait for adapting wheat to diverse growing environments.

The study revealed different traits depending on how many MET1 copies were knocked out. While knocking out all three remained lethal, partial knockouts led to viable plants with valuable trait variations. Surprisingly, these changes in DNA methylation did not affect the plants’ pollen count or fertility.

Although epigenetic mutants have been proposed as a way to enhance genetic diversity in crops, practical application has been limited due to the scarcity of such mutants. These are the first epigenetic mutants in wheat, says Dr. Borrill. Our work shows that wheat’s complex genome—usually seen as a barrier—can actually be an advantage. With multiple MET1 copies, we can create partial mutants that are both healthy and genetically interesting.

This breakthrough paves the way for applying similar approaches in other crops, particularly where full gene knockouts are lethal. It marks a turning point for applying epigenetics in plant breeding—unlocking a new dimension of crop variation.

Think of genetic variation as changing specific words in a book. Epigenetic variation, on the other hand, is like highlighting those words or placing a bookmark. The content stays the same, but the emphasis shifts—giving us more tools to shape plant traits.

The team is now investigating the underlying mechanisms behind these new traits—determining whether they result from methylation changes or gene deletions—and whether the traits remain stable across generations, a key factor for successful crop breeding.

Source: https://www.jic.ac.uk/news/does-this-breakthrough-mark-a-new-epigenetic-chapter-in-crop-breeding/