Epigenetic Leadership: Preparing crops to face the worst

Excerpts
"There are two urgent needs in crop production—yield stability and resilience. We need crops to be more plastic, more able to recover from a week of drought without losing what was put into them," says Sally Mackenzie, genomics expert and director of the Penn State Plant Institute. The plant scientist has worked out how to significantly boost a plant's bounce-back power using epigenetic manipulation.

What is epigenetics?  

Epigenetics refers to the genomic neighborhood that surrounds genes and controls how they are expressed. This local process controls how genes respond to environmental change. It could be a plant that grows better in shade or a multi-generational northerner unbothered by subzero temperatures. Sometimes these changes are strong enough to confer a stable, heritable, expressed phenotype.

Mackenzie and her team have discovered how to stimulate a stronger epigenetic response to stress in plants. The result is crop genetic lines carrying epigenetic memory of stress and prompting future generations to express more resilience-based traits. This memory holds for around five generations, or indefinitely in vegetatively propagated plants, like strawberries.

These changes aren't the result of altered DNA or genetic combinations. Change occurs by merely opening pathways between existing genes. 

"When we think about crop genetics, we are only referring to gene combinations of a specific line. Breeders create new varieties by recombining those genes to give new features or traits," Mackenzie explains. "Epigenetic trait expression doesn't result from changing the gene combination, it's changing how the genes themselves are expressed."

Plants sense their environment and sense patterns of change, she says. This information triggers a cascade of events. The plant undergoes epigenetic reprogramming, changing the epigenetic roadmap to access its genetic bag of tricks for dealing with changing environments. Mackenzie and her team have studied these responses and discovered one key to triggering stress response—the MSH1 gene.

Thanks to genome mapping and CRISPR technology, it's become possible to observe genes and their interactions. They used this technology to home in on the MSH1 gene. The MSH1 gene is present in all plants, she explains. A plant under stress will suppress the MSH1 gene, which heightens stress responses. The plant then passes this information to its offspring, resulting in progeny with enhanced resilience and vigor traits.

"When I cross a plant with suppressed MSH1 to a normal variety with the same genetics, I find the progeny has enhanced resilience and vigor," Mackenzie says. In stressful conditions, such as heat at flowering, and drought, her trials produced yield advantages of 20-29% in tomatoes, 30-35% in sorghum and 8-11% in soybeans. "The interesting thing is it's just tinkering with what Mother Nature already uses for survival. It's not genetic engineering. It's not foreign DNA. Everything a breeder or grower puts into the variety stays the same. All we do is change the way the genes are expressed to allow the plant to be more hardy, more resilient and higher producing."

EPICROP TECHNOLOGIES INC
"Control of European corn borer or tolerance to glyphosate are very useful, but genetic engineering is one gene, one purpose. Epigenetics is the sum of many small effects," says Michael Fromm, Epicrop Technologies Inc., CEO. When it comes to making the plant work better—maybe using energy from the sun more effectively or growing a deeper, more robust root system—there are too many genes involved. Instead of one big change, epigenetics trait expression is the result of multiple connections of varying strength between genes.

Plant breeding has produced ever improving cultivars, hybrids and varieties. They test and develop these lines in diverse environments. However, using traditional breeding methods to produce plants tolerant to heat, drought, or nitrogen deficient environments is exceptionally difficult, says Fromm. His company is working in partnership with Penn State to transition tomatoes and soybeans with superior epigenetic trait expression from the academic world to seed companies and then fields.

"I believe epigenetics succeeds here. We can create more tolerance to a wider variety of environmental conditions," Fromm says. "Epigenetics is not a variable breeders have control over. They work with the genes and live with whatever epigenetic expression happens. We intentionally change the epigenetics."

Mackenzie knows—and has proven—that her technology works.

"The technology works in every crop we've tried: sorghum, soybeans, canola, tomatoes, all are more-or-less successful to a commercial level," she says.