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Researchers make important breakthrough in unlocking the power of epigenetic variation in crop breeding

Epigenetic variation, like genetic variation, can be inherited and influence traits across generations. However, epigenetic variation does not involve changes to the genetic sequence that makes up DNA.

Instead, like punctuation and highlights in a text, these epigenetic markers and modifications in the genome can influence how the genetic sequence is expressed, for example, by switching genes on and off in response to environmental triggers.

If we can harness knowledge of this increasingly influential area of genetics, we can vastly increase the palette of diversity available to researchers and breeders as they seek new traits to make crops more climate resilient and disease resistant.

Previous studies had shown that DNA methylation, is a heritable epigenetic process in plants and that the gene MET1-1 is important to it.

However, the effects of this gene have been difficult to study in plants because using genetic engineering techniques to remove or "knock out" the gene results in the plants dying.

To solve this problem Dr. Philippa Borrill's group at the John Innes Centre turned to wheat's notoriously complex genome, because it has three copies of the gene.

In a available on the bioRxiv preprint server, they used a technique called mutagenesis to knock out some, but not all, of the copies of the gene and observe the effects.

They discovered that some of these partial epigenetic mutants showed altered DNA methylation which had interesting heritable traits which could be applied in plant breeding. For example, they identified a plant with altered flowering time which is an important trait for adapting wheat to different growing environments.

The team observed different traits depending on how many of the genes were knocked out, although knocking out all three copies of the gene was still lethal.

A surprising aspect was that the pollen count and fertility of the plants were not affected by the changes in DNA methylation.

Epigenetic mutants have been proposed as a new way to enhance genetic variation, but a lack of epigenetic mutants has prevented real-world application of the method.

"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 breakthrough in using partial mutants could be applied in other plant crops and for other genes for which gene-editing knockouts have proved lethal.

Epigenetics is an emerging and increasingly influential area of the life sciences. By applying it to crops, the door is open to creating variations in crops using epigenetic variation, the way we have for thousands of years by using genetic variation.

"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 group is now investigating exactly why novel traits emerge in the MET1 mutants—and to what extent these observable changes are influenced by deletions or directly caused by methylation changes.

Experiments will also examine if the changes are stable across the generations, which is essential for their use in crop breeding.