Salinization leads to crop failures worldwide, resulting in plant death or stunted growth, according to research from Wageningen and Research. Scientists from Wageningen University & Research (WUR) have identified a local regulator protein that promotes root growth in saline soil, enabling plants to thrive under such challenging circumstances. Published in the esteemed scientific journal, The Plant Cell, these findings serve as a pivotal foundation for ongoing investigations aimed at cultivating more resilient crop varieties.
Approximately 25% of irrigated farmlands are affected by salination, which are further intensified by rising sea levels, escalating droughts, and higher temperatures. According to Professor Christa Testerink, a plant physiology expert, saline soil adversely affects the formation of lateral roots crucial for water and nutrient absorption in plants. “The hormone that regulates the growth of lateral roots is called auxin. Salt hampers the plant’s ability to recognise the signals this hormone emits, causing the development of lateral roots to fall short. And fewer lateral roots mean the plant’s general health suffers.”
Switch Between Hormone and Lateral Root Growth
How is it that some plant species are less affected by salinity stress than others? To answer this question, researchers delved into the molecular mechanism that drives root development in the model plant Arabidopsis, commonly known as thale cress.
“Previous research already revealed that the protein LBD16 serves as a switch between the plant hormone auxin and the development of lateral roots. LBD16 activates the genes responsible for the development of lateral roots,” said Testerink. “In saline soil, you would expect auxin’s functioning to become impaired, but you would also expect the levels of the LBD16 protein to drop.”
Alternative Route Discovered
Surprisingly, research showed that the functioning of auxin was severely reduced in thale cress in a saline environment, while the levels of LBD16 rose. Testerink said that this suggests an alternative route driving the protein, which enables the plant to still produce, albeit fewer, lateral roots in saline conditions.
“We succeeded in finding this route by uncovering another activator, the ZAT6 protein. This protein takes over auxin’s role as regulator. This discovery provides a critical basis for further studies into similar local molecular networks in lateral roots that help plants function in stressful situations. Not just under saline conditions but also in times of drought or heat. This could help plant breeders to alter the plants’ root growth to create more resilient varieties.”
Help From Machine-Learning
The researchers used machine learning in their search for the LBD16 activator.
Aalt-Jan van Dijk, a researcher with the Bioinformatics group, explains how this computational method contributed.
“There are tens of thousands of possible candidates that could regulate LBD16 in a plant. You are looking for a needle in a haystack. A more targeted search is made possible by predictions.” He said they fed a machine-learning model with data from transcription factors from experiments. The model then used patterns to predict whether a particular transcription factor regulates another or not. This narrows down the list of possible candidates. Conducting experimental tests enabled us to identify ZAT6 as the new regulator for LBD16.
Further Development in CropXR
Van Dijk mentions that integrating experimental data with machine learning represents a novel approach in the realm of plant research. This methodology will be further explored and implemented in the ongoing CropXR research project.
“In CropXR, we will join forces with the universities of Utrecht, Delft and Amsterdam (UvA) in the coming decade on fundamental knowledge and methods for the development of more resilient crops,” said van Dijk. “We will use, among other methods, machine learning combined with mechanistic models. These are models containing knowledge of underlying physiological and cellular processes and cause and effect. Predictions made by these models can then be tested with targeted experiments.”
Drought and Rising Temperatures
According to Testerink, CropXR shifts its attention away from salination towards other climate change-related challenges like heat and drought. She explains that an upcoming paper, currently in pre-print stage, delves into the investigation of root growth in plants facing both warm temperatures and water deficit. This study has unveiled several molecular factors at play. However, a more comprehensive investigation is necessary to accurately predict plant responses to this combination of stressors.
“The first five years of the CropXR project, we will focus on Arabidopsis,” said Testerink. “During the next five years, we will apply the knowledge gained to food crops. We hope this will enable us to develop practicable solutions in collaboration with partners in the field.”
