Compiling the range of gene expression in plants may help study how plants cope with variable environmental conditions
Parents of identical twins will often tell you that, even though their twins are genetically the same and obviously raised under the same conditions, they still have varying behaviours. The same holds true for twin plants.
Plants that are genetically identical and grown in the same soil under the same environmental conditions can also have a range of behaviours.
Scientists studying the range of plant responses refer to that range as a level of noise (variability) in gene expression (behaviour).
This is the first time that levels of noise in gene expression have been measured in plants, and the information has now been documented in an open-access atlas (AraNoisy) available to plant scientists around the world to study gene expression variability influences in plant survival. The hope is that the new information will lead to more research on plant conservation and crop development.
“Several studies have shown that plants that are genetically identical, and growing in the same conditions, can behave differently,” said Sandra Cortijo, research associate with Cambridge University’s Sainsbury Laboratory in the United Kingdom.
“However, there was no information about which genes were the ones that were behaving variably. The dataset that we generated identifies the level of noise (variability) in gene expression (behaviour) for all genes between genetically identical plants. This information is of high value to other plant scientists who are studying how plants cope with variable environmental conditions and is why we decided to make it publicly available in an easy and open-access way.”
But what are “noisy” genes?
A gene is normally identified as a piece of code that programs a particular outcome, but when it doesn’t behave in a predictable way, scientists call this unexpected gene expression “noise.”
“(It’s) a bit like the background noise in a room that might be picked up by a microphone when recording music,” said Cortijo.
“It has an effect on the resulting recording but was not part of the composition. Scientists have found that gene expression is actually quite noisy, and previous studies in unicellular organisms have shown that this noise has a significant contribution to differences in the resulting physical characteristics (phenotype).”
For their study, the researchers used seedlings from thale cress, a small flowering plant considered a weed and a relative of wild brassica. They performed RNA-sequencing on each seedling every two hours over a 24-hour period and determined that nine percent of all the 15,646 genes in the plant are highly variable. Some showed more variability during the day, while some showed variable behaviour at night.
“These highly variable genes are often associated with how the plant responds to its environment like temperature and salinity,” she said.
“We studied one species of plant, Arabidopsis thaliana, a relative of brassica, but many of the genes that we measured are also seen in other plant species. While we did not estimate how much each individual plant would deviate from other genetically identical plants, scientists can use our data to conduct further research on specific genes to measure what impact this variability might be having.”
Cortijo said that the most studied example of variability between genetically identical plants is how long seeds need to germinate. If plants have a high level of variability in the timing of germination, it could potentially help a population of plants survive unexpected conditions such as drought. Variability between twin plants could be advantageous in other conditions such as heat, cold and nutrient availability.
“It has been shown in plants that some physical characteristics are more robust than others between genetically identical plants,” she said.
“For example, it has been observed that the plant height is less variable than the total number of flowers between genetically identical Arabidopsis thaliana plants.”
The study not only provides important information on gene expression in plants but also how they are intricately connected with their environment. Plants can’t move, so a community of plants needs a level of variability in order to individually respond to all the changing conditions that confront them and consequently ensure the species’ survival, especially in the face of more frequent weather extremes due to climate change.
However, uniformity in growth and maturity is important for farmers when it comes to harvest, and research is still ongoing to understand more about twin crop plants.
“We currently lack information and understanding about the scope and role of gene expression variability in crop plants, so while this is an important initial step, there is much more work that needs to be done to learn about gene expression noise and how it could be used to breed crops that are more adaptable to environmental fluctuations,” said Cortijo.
“A key part of future research would be to see whether the domestication process of crop plants affects gene expression variability. The first step would be to replicate this work in crops. We also need to better understand how gene expression variability between genetically identical plants is controlled and what are its phenotypic consequences. Answering these questions would be important to translate the main findings of this work in crops. Our work proposes hypothesis to both questions, and we are now working on addressing them.”
The research study, called Widespread inter-individual gene expression variability in Arabidopsis thaliana, was published in the journal Molecular Systems Biology.