Soil Increasingly Salty: New Discovery Can Help Make Crops More Resilient

Salinization causes major crop losses worldwide. Plants die or their growth is severely limited. Researchers from Wageningen University & Research (WUR) have discovered that a local regulator protein promotes root growth in saline soil, allowing a plant to develop. The findings have been published in the scientific journal Plant Cell and form an important basis for further research into the development of more resilient crops.

Nearly a quarter of the world's irrigated agricultural land suffers from salinization. This problem is increasing due to rising sea levels, increasing drought and higher temperatures. A saline soil mainly has a negative influence on the development of lateral roots, says Professor of Plant Physiology Christa Testerink. “Plants need lateral roots to absorb water and nutrients. The growth of these roots is regulated by the hormone auxin. Salt causes the plant to pick up signals from that hormone less well, causing the development of lateral roots to lag behind. And the fewer lateral roots a plant has, the worse the condition of the plant is in general.”

Switch between hormone and lateral root formation
But how is it possible that some plant species are less affected by salt stress than others? To find the answer to this question, researchers delved into the molecular mechanism of lateral root formation in the model plant Arabidopsis , popularly known as thale cress. Testerink: “It was already known from previous research that the protein LBD16 acts as a switch between auxin and the actual formation of lateral roots. LBD16 turns on the genes involved in making lateral roots. In a salinized soil you would expect that not only the function of auxin is disrupted, but that the amount of the protein LBD16 in the plant also decreases.”

Alternative route discovered
Remarkably, when studying Arabidopsis, it turned out that although the effect of auxin in a salty environment decreased sharply, the amount of LBD16 actually increased. Testerink: “So there had to be an alternative route that controls the protein, so that the plant also produces lateral roots in a salty environment - albeit fewer, but still. We found that route with the discovery of another activator, the ZAT6 protein. This protein takes over the role as regulator of auxin. This discovery provides an important basis for further research into comparable local molecular networks in lateral roots that ensure that plants can function in stress situations. Not only during salinization, but also during drought and heat. This can help breeders to change the root growth of plants to create more resilient varieties.”

Machine learning lends a helping hand
In the search for the activator for LBD16, the researchers used machine learning. Aalt-Jan van Dijk, researcher at the Bioinformatics department, explains the role this computational method played: “In a plant there are tens of thousands of possible candidates that can regulate LBD16. So you have to look for a needle in a haystack. To search more specifically, it helps to make predictions. We have put data from all kinds of transcription factors from experiments into a machine learning model. This model then used patterns to predict whether or not a particular transcription factor regulates another. This leaves you with only a small list of possible candidates. By conducting experimental tests, we ultimately found ZAT6 as an important new regulator for LBD16.”

Further development in CropXR
According to Van Dijk, the combination of the use of experimental data and machine learning is new in the world of plant research. This approach will be continued in the CropXR research project . “In CropXR we will continue to work together with the universities of Utrecht, Delft and Amsterdam (UvA) over the next ten years on the development of fundamental knowledge and methods for developing more resilient crops. We do this, among other things, by combining machine learning with mechanistic models. These are models that contain knowledge about underlying physiological and cellular processes and cause-effect relationships. Predictions from those models can then be tested with targeted experiments.”

Drought and higher temperatures
In CropXR, the focus is not so much on salinization, but mainly on other climate-related challenges, such as drought and high temperatures, says Testerink. “In another paper – which is currently only available as a pre-print – we looked at the root growth of plants in a combination of heat and water shortage. We have uncovered a number of molecular factors that play a role in this. But predicting how plants cope with a combination of stressful conditions requires a larger-scale approach. In the first five years of CropXR we will still focus on Arabidopsis, in the second five years we will translate the knowledge gained into food crops. In this way, we ultimately hope to develop practical solutions together with partners from the field.”