New Method Boosts Crop Yield And Drought Resistance Using Plants' Own Genes

UChicago tests lifted rice harvests up using plants’ own protein, with implications for other crops

The way to make a plant grow more may be to take something away.

Trimming a section off a plant gene raised rice harvests up to 25% in new tests by University of Chicago scientists, with better tolerance for drought and heat.

The research builds on a striking finding five years ago, when the group showed that they could insert a gene into plants like rice or potatoes that resulted in a substantial increase in crop yield—but it required using an animal gene in a plant. He and his lab wanted to find a way to create a similar effect, using only genes that come from plants themselves.

The new study, published July 23 in Nature Genetics, lays out the path to do just that. It also reveals a new wrinkle in our understanding of the way that plants regulate their genes.

“My hope is that we are laying a scientific foundation for a new strategy to develop plants that not only offer higher yields, but are resilient to a variety of stresses, from drought to heat to salt,” said He, who is the John T. Wilson Distinguished Service Professor in the Department of Chemistry and the Department of Biochemistry and Molecular Biology.

The root of the question
He’s lab specializes in understanding the fundamental ways that living things grow. Genetics is extraordinarily complex; three-quarters of a century after the discovery of DNA itself, humans are still untangling the ways that organisms get from DNA to what we see before us.

In 2011, He’s lab made a surprising discovery. They found that RNA—long thought to simply be a middleman between DNA instructions and protein makers—actually had a much more substantial role in which genes get expressed, by placing and removing markers.

That led to the lab’s huge finding in 2021, when the team inserted a common gene from animals known as FTO into plants. This turned out to loosen the RNA-associated reins that restrict plant growth, so plants with this gene grew larger crops and sent out longer roots—making them more resistant to drought.

But He wanted to find a way to do the same thing without inserting a foreign gene, which would be less concerning to consumers worried about genetically modified organisms. Nature often evolves multiple ways to do the same task, so the scientists hoped to find a mechanism in plants themselves that does the same thing.

They did—but it took years of research, and a new wrinkle in our understanding of genetics.

Intrinsic disorder
Virtually all life forms make proteins that carry out the basic functions of cells, such as processing nutrients, carrying signals and removing waste.

But a substantial chunk of the proteins most animals make are called intrinsically disordered regions. Instead of a “typical” protein, which assembles itself into a 3-D structure, these proteins instead exist as flexible segments. At first, scientists thought these segments simply served as links for larger proteins or unimportant tails to proteins, but they have come to understand these intrinsically disordered regions have a much larger and more active role in what happens in a cell.

He and his team encountered these regions during their search for a way to boost growth in plant cells.

Plants don’t have a direct equivalent of the FTO gene found in mammals, but they do have variants of another gene with a similar function, known as ALKBH5; the plant versions are ALKBH9 and ALKBH10.

While trying to understand how these variants worked, the scientists discovered that the intrinsically disordered regions restrict these plant proteins from acting on the packaged DNA in the cell, known as the chromatin.

But if the scientists removed the intrinsically disordered region from the end (known as the C-terminus) of ALKBH9 or 10, they found it instead would spread out around the cell and perform a similar function as the mammal gene FTO—affecting the chromatin and removing the brakes on growth.

He’s lab specializes in understanding the fundamental ways that living things grow.

The group tested the strategy in rice plants and saw boosts in yield of about 20 to 25%, as well as increased stress resistance.

Removing the C-terminus is a relatively small change. “We show that the growth benefit can be gained by simply expressing the plant’s own ALKBH9 or 10 with deletion of the C-terminus segments,” He said.

“This strategy promoted plant growth and improved rice yield, pointing to a new way of reprogramming chromatin dynamics to boost agricultural productivity using engineered plant proteins” said Liudan Jiang, the first author of the study.

“In principle, we could just perform base-editing of the plant genome to remove the C-terminus of the plant’s intrinsic ALKBH9 or 10,” said He. “That is, we’re not introducing foreign genes, just changing one or a few base pairs in a plant’s existing genome.”

The group is still working to untangle precisely how this change promotes growth and makes the plants so much more resilient to stresses. They are also testing the strategy in other crops, because the ALKBH9 or 10 genes appear in many plants.

Additional authors on the study were Long Zhao, Jiangbo Wei, Bochen Jiang, Yu Xiao, Fan Yang, and Xiaolin Zeng.