Genetic influence on root growth discovered

Researchers in the United State have found the gene that influences whether roots need to grow deep or shallow

While flowers and leaves define a plant, of equal importance is its network of underground roots drawing up nutrients and water from the soil.

But missing from the knowledge of plant roots are the mechanisms that dictate which parts of the soil the roots actually explore.

Researchers at the Salk Institute for Biological Studies in La Jolla, California, have discovered a gene that influences whether roots need to grow deep or shallow.

As part of Salk’s Harnessing Plants Initiative, the discovery of the gene, which it named EXO70A3, is expected to help researchers develop plants that can grow deeper, stronger roots that will sequester more atmospheric carbon underground.

“When we initiated this project, we were mainly interested in understanding which genetic and molecular mechanisms led to the different root characteristics in natural strains of thale cress (Arabidopsis thaliana),” said Wolfgang Busch, associate professor at the Plant Molecular and Cellular Biology Laboratory.

“Over the course of our work, the clear effect on rooting depth became apparent. This was very exciting and one of the reasons we started thinking about developing plants that can fight climate change by enhancing their root system for optimizing carbon sequestration.”

Auxin is a hormone that plays a key part in controlling how the root system works. One of the goals was to identify the genes that regulate auxin and which factors determine a root system’s actual architecture.

“The flow of auxin in the root tip determines whether roots grow downwards or more horizontally,” said Busch. “When the root corrects its course (for instance when the root is not growing as downward as it should), the direction of the auxin flow needs to change. The gene that we found affects how fast this change of the auxin flow occurs. If the gene is too active or too inactive, roots correct their course slowly and less predictably. Over time, these small changes in the flow of auxin result in a changed root system depth.”

He said numerous factors determine how roots grow by sensing their environment and responding to nutrients, water, gravity and a variety of other molecules.

“We and other groups try to understand how such signals are integrated and impact root growth,” he said. “The response to gravity and the root growth direction are the best predictors for how deep root systems grow. Mechanisms such as the one we have found are key to predicting and engineering changes to root depth.”

He said that the gene regulates auxin distribution by regulating the distribution of a protein called PIN4 that transports auxin. When the researchers altered the gene, they found the root system changed its orientation and more roots grew deeper into the soil. They discovered that there are natural variants of the gene that determine how deep the root systems grow and they were able to make changes to the gene that led to deeper roots.

Making EXO70A3 more active or, alternatively, inactivating the gene both led to deeper roots. Busch said they believe that disturbing the natural balance of the gene’s function in shallow-rooted strains of the plant will actually trigger deeper rooting.

Going forward, the combination of climate change and an increasing global population will require crops to be produced with high yields, and more robust roots will aid this.

“To provide enough food for 11 billion people by the end of the century, we will need crops that will produce high yields under (future) climate conditions,” he said. “This is an enormous challenge. We have to understand which mechanisms will enable crop plants to produce yields in the climates that will exist in the coming decades. We are currently in the early process of starting a project addressing this by studying the naturally occurring variation in two model species that have genetically adapted to grow in a large variety of climates.”

The feedback from farmers and breeders on research results has been very positive. Some farmers have offered land for trial testing.

“There is definitely anticipation driven by a desire to help fight climate change via carbon sequestration in soils,” said Busch. “We have recently started the next phase of the Salk Harnessing Plants Initiative. We want to enhance root depth, root mass and suberin content. Suberin is a natural carbon-rich molecule that can store carbon in the soil much longer than other plant-made molecules in crop plants. For this we will survey existing crop varieties for these characteristics and leverage breeding approaches. We will also use genetic engineering that enhance these characteristics.”

By understanding the auxin pathway, they hope to uncover more components related to the rooting architecture. They expect to be able to create more adaptable crops, such as soybeans and corn.

The Salk Harnessing Plants Initiative will receive more than $35 million from organizations and individuals for further research.

The study was published in July 2019 in the journal Cell.

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