Molecular Plant Sciences

Blog - Shapeshifting plants: plants adapt their body plan to different light conditions

Researchers reveal that plants respond differently to shade depending on their development, and uncover the genetic programmes behind this.

(Author: Andrew Romanowski, Editor: Helen Feord)

Diagram of Shade Avoidance Syndrome
Image credit: Andrew Romanowski

You may not have noticed, but plants are incredibly plastic organisms - they can change their body plan in response to their surrounding environment. For example, plants undergo a dramatic shape change when shaded by neighbouring vegetation. The response to light changes depends on whether a plant is shade tolerant or intolerant. Tolerant species will not change much under shade. In contrast, shade-intolerant species undergo significant changes, collectively known as the ‘Shade Avoidance Syndrome’ (or SAS, for short). This syndrome is characterized by an increase in stem-like tissues (like hypocotyls or leaf petioles) in detriment of harvestable tissues (such as leaf blades), leading to a decrease in overall plant biomass. Understanding how this process works therefore has implications that reach far beyond the lab into potential applications for crop improvement and increased yields.

In the lab, we use thale cress (Arabidopsis thaliana) as a model to study shade intolerant plants’ responses to light changes. In these plants, shade due to encroaching vegetation is perceived mainly through a family of photoreceptors called phytochromes (phys). Arabidopsis has 5 of these, PhyA-PhyE. Phys can sense the red (R) to far-red (FR) ratio of  light in the plants’ environment. Shade causes a reduction in this R/FR ratio, and when Phys sense this, they trigger the changes that are typical of the SAS. Interestingly, if we mutate PhyB, the main sensor of shade, plants exhibit a SAS body program even if they grow under full light conditions. So, when PhyB is not functional we get the same reduction in leaf blade size as when a plant is under shade. You might be wondering… ok, but how does this happen? How does Arabidopsis make smaller leaf blades? Well, to make a smaller leaf blade, plants could: a) produce fewer cells, b) make smaller cells or, c) a combination of both strategies. Using microscopy (and lots of nail varnish) we were able to answer this question. We found that to reduce the size of their leaf blades, these PhyB defective plants reduce their overall number of cells but do not change cell size.

Next, we asked ourselves: what happens if plants do not receive shade early in their life, but rather shade starts in different moments throughout a plant’s life? Will the effect be the same? Will the leaves still be smaller? And if so, what strategy will the plants use? Here, we ran into a problem: we could not use the phyB mutants as they develop as plants that have been always under shade. To overcome this issue, we used a trick from the photobiologists’ playbook. We used a brief pulse of FR light at the end of the day, which inactivates Phys and simulates shade-like conditions. Armed with this trick, we made plants believe they were under shade at different developmental stages. So, what happened? Well, before you continue reading and I reveal the answer to you, try to guess how the plants responded…

Leaf development
Image credit: Andrew Romanowski

And now to lift the veil on this mystery and to make the story short, we found that if you give a plant shade early in leaf development, you get a small leaf blade due to reduced cell division with no changes in cell size. No surprises here, as this was what we expected from the experiments with the PhyB inactive plants. However, if the treatment started later in leaf development, we found that the leaves were still smaller, albeit due to reductions in cell size and no changes in cell division! The plant had two alternative strategies to achieve the same outcome: smaller leaf blades.

To gain a deeper understanding of how plants controlled the two types of strategies mentioned above, we used a technology called mRNAseq that allows us to see all the genes expressed at a certain moment of a leaf’s life. Taking snapshots of gene expression at different developmental stages of leaves subjected to shade early in development, late in development, or not at all, we were able to create a ‘temporal map’ of how genes were changing over time. This allowed us to uncover that our ‘shade like treatment’ acts mainly by turning down gene expression. This was not known before, as many previous studies had focused mainly on genes that were turned on by this type of treatments. We also learned that this downregulation of genes led, quite logically, to turning off several biological processes (> 600, when considering all conditions!). Furthermore, the number of down-regulated processes were 10 times higher than those that were turned on by the treatment. This means that ‘shade’ acts mainly by repressing gene expression and biological processes.

Additionally, this map allowed us to uncover that to stop cells from dividing plants subjected to shade apply a coordinated strategy to turn off several processes. Not only was cell division turned off in earlier treatments, but also cytokinesis (cell division), DNA repair and replication. Also, our gene expression map revealed some unexpected but welcome surprises. For example, we found that processes related to translation (the process through which proteins are built) were only downregulated at later timepoints. Could this be a new avenue through which shade and Phys are controlling overall organ growth? Mmmhh… good question!  We now have lots of new questions to ask to uncover the mechanism of how plants sense and respond to light. Stay tuned to hear our future progress!

If you would like to find out more about how plants respond to light check out this blog:

And the orginal scientific paper here:

We are sad that the author of this blog, Andres, is leaving IMPS but excited for him too as he is moving on to new plant science adventures. From all of IMPS we wish you luck and hope to see you again soon Andres!

The Halliday Lab, where Andres did this work on light sensing, send this message:

“Dear Andres, 

These past years knowing you have been very fulfilling. We all can’t thank you enough for all your support, the chats, advice, the laughs at the lab and the fact that you always had time for every single one of us. You will truly be missed. We congratulate you and wish you all the best in your new position. We are sure you will succeed and will be hearing a lot from you!

Ammad, Ejaz, Matt, Marissa, Phil, Rist, Tara and KarenTus amigos from the Halliday lab