Scientists have made a key breakthrough in understanding how epigenetic variation can be used to improve crop breeding.
Like genetic variation, epigenetic variation can be inherited and influence traits across generations — but without altering the underlying DNA sequence. Instead, it involves modifications, such as chemical markers, that affect how genes are expressed. These markers can switch genes on or off in response to environmental cues, functioning like punctuation in a sentence to shape meaning.
By tapping into this layer of genetic control, researchers hope to expand the range of traits available to breeders, particularly those linked to climate resilience and disease resistance, according to a press release.
Earlier studies identified DNA methylation as a heritable epigenetic mechanism in plants and pointed to the MET1-1 gene as a key player. However, studying the gene has been difficult because removing it entirely through genetic engineering typically causes plants to die.
To overcome this, Dr. Philippa Borrill’s team at the John Innes Centre turned to wheat, a crop with a complex genome containing three copies of the MET1-1 gene. In a study published in Experimental Botany, the researchers used mutagenesis to selectively knock out one or two copies of the gene — enough to study the effects without killing the plant.
The resulting “partial epigenetic mutants” showed altered DNA methylation and developed heritable traits relevant to breeding. Notably, the team identified a mutant with a different flowering time, a trait critical for adapting wheat to various climates.
They also found that knocking out different combinations of the gene copies led to different trait changes, though removing all three remained lethal. Interestingly, changes in DNA methylation did not affect the plants’ pollen count or fertility.
While epigenetic mutants have been proposed as a way to boost genetic diversity, the lack of viable examples has held back progress. This research brings that possibility closer to real-world application.
“These are the first epigenetic mutants in wheat,” observes Dr Borrill, group leader. “Our study demonstrates that the complicated wheat genome, so often an obstacle in the past, can be beneficial. Because it has multiple copies of the MET1 gene we can grow partial mutants which give us a happy medium, – with partial alterations within healthy plants. This has not been possible in other crops with less complicated diploid genomes.”
The Borrill group’s success with partial mutants offers a promising new approach for studying other genes that are typically lethal when fully knocked out—potentially across a range of crop species.
As an emerging and increasingly important field in the life sciences, epigenetics holds significant potential for agriculture. Applying epigenetic principles to crop breeding could unlock new types of variation — similar to how genetic variation has been harnessed for thousands of years — to support the development of improved, more resilient crops.
“We can think about genetic variation in the genome as analogous to altering specific words in a book chapter. In contrast, epigenetic variation does not change the words themselves. Instead, it is more like highlighting specific words or adding a bookmark in the chapter. This gives us additional flexibility to alter the genome and eventually plant characteristics,” explained Dr Borrill.
The team is now exploring the underlying causes of the novel traits seen in the MET1 mutants — specifically, whether these traits stem from the gene deletions themselves or are directly driven by changes in DNA methylation.
They are also investigating whether these traits remain stable across generations, a crucial factor in determining their viability for use in long-term crop breeding programs.
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