Rice gene response to water and nutrients discovered

Gloria Coruzzi of New York University’s Center for Genomics and Systems Biology studies gene regulatory networks controlling nitrogen use efficiency and root nutrient uptake. | New York University photo
Researchers at New York University have discovered how each gene in the rice genome senses and responds to combinations of water and nutrients. The finding could lead to ways to engineer rice crops to grow in various soils that now may be marginal, too dry, or lack the necessary nutrients to sustain rice growth.
Rice is a major food staple. Developing countries account for 95 percent of the total world production.
According to Joseph Swift, a doctoral candidate in NYU’s Center for Genomics and Systems Biology and the study’s lead author, changes in the nutrient dose can have dramatic effects on rice gene expression, or behaviour, and the plant’s growth.

“Fertilizer and irrigation are the two major inputs for agriculture,” said Swift. But rarely have scientists looked at how a plant’s biology allows it to respond to combinations of nutrients and water. This is important because, around the world, low nutrient soils often co-localize with dry soils. As climate change progresses, soils will become drier. Additionally, the globe needs to become less dependent on inorganic fertilizers that are big contributors to carbon pollution.”
Nutrients that plants absorb from the soil are dissolved in some level of moisture, but past studies were unable to determine whether organisms could sense the total amount of nutrient available or only the relative amount that was dissolved in water.
The research team wanted to know whether plants responded to changes in absolute nutrient amount compared to their concentrations in water.
Rice seedlings were exposed to an experimental matrix of varying nitrogen and water conditions, which showed the different effects they had on plant growth. Then, through computer analyses of the responses of more than 50,000 genes, they found that while some genes were controlled in response to either the amount of nitrogen or water, other genes responded specifically to combinations of both.
Taking the results into the field, the team collaborated with researchers in the Philippines and conducted trials over two growing seasons.
“I did field research at the International Rice Research Institute (IRRI), working closely with Dr. Amelia Henry, who is based there,” said Swift.
They found that the genes responding to combinations of both nitrogen and water were associated with the amount of grain produced by the rice crop.
“Our work indicates which rice genes could be important for growth under low nutrient, dry conditions. One option would be to genetically modify these genes to see if they produce rice varieties that require less water and nutrients to grow.”
However, he said that more conventional approaches are also on the table and he referred to the ability of breeders to focus on these genes when breeding climate-ready crops.
“These genes may assist in developing crops that require not only fewer nutrients to grow, but less water,” said professor Gloria Coruzzi in the university’s press release and the paper’s senior author. “This could potentially lead to allowing many marginal soils around the world — those that are too dry or nutrient poor for crop production — to be more agriculturally viable. Moreover, it is especially crucial to develop crops that produce grain yield in the face of global warming and climate change.”
The research findings were published recently in the journal Nature Communications.