Plant Photoperception

The purpose of this thread is to provide Future4200 users with a better understanding of plant photoperception. My approach is to (1) add posts that serve as an educational resource for this community, and (2) answer relevant questions (when I am able to) that are posted in the thread.

Let’s start here:
Because plants are sessile organisms, their evolution includes an impressive array of mechanisms for detecting and responding to the continuous environmental changes that all plants encounter throughout their life cycle. From a plants perspective, these real-time changes in its micro-climate occur 24/7, 365 days a year, regardless of whether they are grown indoors or outdoors. It is important to note that these mechanisms for perceiving real-time changes in a plants micro-climate exist in wild plant species and in all cultivated crop species (e.g., cannabis).

To the best of our knowledge, humans have been cultivating different crop species for ~10,000 years. My guess is that farmers have suffered headaches and frustration for an equally-long period of time, when their crops exhibit variable yields and product quality due to the ever-changing micro-environments that all crops encounter year after year.

Greenhouses and indoor farms are nothing less than an attempt to minimize changes in a crop’s micro-climate and thereby achieve more reproducible crop yields and product quality. That said, plants are far more in tune with their environments than humans often appreciate, such that virtually EVERYTHING a human does in a greenhouse or indoor grow room perturbs these highly-controlled environments in ways that plants will perceive and respond to. Yield and terpene profiles from plants grown indoors are particularly relevant examples.

For reasons I may never understand, I have always viewed a plant’s hyper-sensitivity to its micro-climate as an opportunity (instead of a headache). Along these lines, I have always thought that understanding how plants perceive and respond to micro-climates provides us with the opportunity to manipulate a plant’s micro-climate in ways that increase that crop’s yield and/or product quality (hence this new thread). To put this another way, knowledge is power.

Your plants sense very small changes in temperature, soil moisture, day length, stress factors, humidity, wind speed, vibrations, pressure/altitude, light intensity (e.g., shading), light quality (i.e, the spectrum of incident light), the direction of incident light, overwatering, herbivore abundance/predation, soil bacteria populations, and likely every other environmental variable you can think of.

Because nearly all plants rely on light to make their energy (via photosynthesis), it should not surprise us that plants are exquisitely and continuously (24/7, 365) sensitive to surprisingly small changes in their ever-changing light environment. Along these lines, I have always enjoyed sharing the fact that an extremely small light pulse - equivalent to one-tenth of one flash from one firefly - is able induce changes in the biochemical processes in some plant cells.

I hope you are now asking yourself two questions:

  1. How is it that plants continuously monitor and respond to their ever-changing light environment?

  2. How can we leverage different light environments at different times in the cannabis plant’s life cycle to improve yield and/or product quality without adversely impacting other cannabis traits that determine cannabis crop value?

The answer to the first question is photoperception via three, and perhaps four, classes of proteinaceous plant photoreceptors, which appear to exist in all plant cells. Yes, root cells too. This is quite different from photoperception in animals. Generally speaking, animals (including humans) have a localized photoperception system, with their photoreceptors localized to an ocular system, i.e. eyes, which are a direct extension of the animal brain. Plant photoperception is very different. Instead of a localized vision system like animals, plants have a completely decentralized system of photoperception. In other words, virtually every cell in a plant can “see” and all of these plant cells monitor and respond to changes in their incident light in real time.

Three classes of plant photoreceptors have been well-documented in the scientific literature, and they allow plants to continually monitor changes in red/far-red light, blue light, and UV light (tangentially, humans are completely unable to see UV light). A possible fourth class of green-light photoreceptors might also exist in plants; it has become increasingly clear that plants have some green-light responses. That said, the protein photoreceptors - if they exist at all - and the gene/genes that encode these proposed green-light receptors remain poorly understood.

The purpose of this post was to set the stage for the thread. Mostly, it contains what I refer to as background material for this topic. Future posts will be shorter… much shorter.

Next up: The phytochrome photoreceptors, which plants use to detect changes in red and far-red light.

Why start with the phytochrome photoreceptors? Because plant phytochromes have long been known to control seasonal flowering (aka photoperiodic flowering). In addition, photoperception by plant phytochromes is known to be a key determinant of resource allocation in plants and resource allocation in plants is a key factor in driving higher yields in all crops (including cannabis).


Because that’s where we first had all the knockouts characterized in Arabidopsis?


There’s a couple transcriptome studies which have been performed, one could look at expression of certain genes to see what is happening on the molecular level. An even easier method would be PCR if you knew which genes you want to measure


I usually start with the red/far-red light receptors (i.e., the phytochrome photoreceptors) for two reasons. First, this class of photoreceptors have been the subject of intensive and continuous research for 100 years and it is this class of plant photoreceptors that we know the most about. In fact, phytochome-related plant processes are one of the most intensively studied processes in all of plant science. Second, it is the class of plant photoreceptors that I know the most about; I conducted research on the molecular genetics and molecular mechanisms of phytochrome-regulated physiology in tomato from 1994 through 2010.

To your point @cyclopath:
The very last plant science seminar I attended (May 1990) before graduating from UC-Santa Cruz (Go Slugs!) was a research seminar presented by a distinguished faculty member from Berkeley (Peter Quail). In that seminar Peter reported that his team at Berkeley was the first team to identify and clone the small gene family of five different phytochrome genes from the Arabidopsis genome. Among other things, they had discovered that plants contain more than one type of phytochrome photoreceptor. Five Arabidopsis lines containing DNA mutations that abolish the function of each one of these five Arabidosis phytochomes were soon to follow.

To your point, single-gene mutants such as these five Arabidopsis phytochrome mutants are an incredibly powerful research tool in the biological sciences, because they allow one to dissect which biochemical, physiological, and developmental processes are controlled by a mutated gene of interest. As a hypothetical example: if a A-type phytochrome mutants never flower in Arabidopsis, then you know that A-type phytochromes are somehow required for Arabidopsis flowering. (To be clear, A-type phytochrome mutants in Arabidopsis still flower, but you see my point.)

An aside about Arabidopsis:
Arabidopsis is a small mustard weed that occurs naturally around the globe.
Since the early- to mid-'80s, this little mustard weed has been considered “the fruit fly of modern plant genetics” and the majority of what we know about plant molecular genetics has been learned from this single plant species. The reasons that Arabidopsis became so widely used in plant science is because this plant species is highly ammenable to rapid experimentation (i.e., it is very easy to work with, and one can learn alot from Arabidopsis very very quickly). This is true for various reasons, including its very short life cycle (seed-to-seed in ~6 weeks), very small stature and “footprint”, its very small genome, and the fact that it is a self pollinator that also allows for facile hand-pollination to conducted genetic crosses of interest. The best way to explain why Arabidopsis is such an informative plant research “model” is to point out why we know so little about the reproductive processes in pine trees. Most pine species require ~30 years to become reproductively mature (i.e., fertile). Once pollination does occur in a pine species, it requires three years for the pollen tubes to deposit sperm nuclei in an unfertilized egg. In other words, it simply takes way too long to conduct experiments on reproductive processes in pine, so we do not know much about these processes in this species. Moreover, size alone prevents one from growing a large number of a pine species in an environmentally-controlled experimental greenhouse. Moreover, pine species have very large and complex genomes, which means identifying a gene of interest in pine is like searching through a whole state full of haystacks, whereas locating a gene of interest in the very small genome of Arabidopsis is akin to just searching through a field of haystacks (which is still difficult, but at least it is a tractable problem). For all of these reasons, the first plant genome ever to be DNA sequenced from end-to-end was Arabidopsis (early 2000s) and that complete DNA sequence serves as a high-resolution genetic map that has since been used to easily identify, clone, and/or mutate genes of interests. But I digress.

In the mid- to late-90s, I was part of a research team at the University of Georgia (where I attended graduate school) that characterized the phytochrome gene family in a second plant species - tomato. My research demonstrated that the tomato genome also contained five phytochrome genes, and the five tomato phytochrome genes fell into the same four sub-familes that Peter Quail’s team had previously discovered in Arabidopsis. Both species had one A-type phytochrome gene, two B-type phytochrome genes, one C-type phytochrome genes, and one E-type phytochrome gene. (Peter’s team originally named the five genes A-, B-, C-, D-, and E-types, but they quickly realized that the B- and D-type phytochrome genes were so closely related in DNA sequence that they should be classified as two members of the B-type subfamily.

So what’s my point?

  1. Most of what we know about plants has been learned from the single plant species Arabidopsis. This is also true for most of what we know about plant photoperception via phytochrome proteins.

  2. All plants studied to date contain a small family of different phytochrome photoreceptors, each of which is encoded by a different phytochrome gene. Generally speaking, dicotyledonous plant species (i.e., broad-leaf flowering plants) usually have five phytochrome genes that fall into four sub-families (the A-, B-, C-, and E subfamilies). Whereas, monocotyledonous plant species (i.e., grasses, including corn, rice, and sorghum) typically have three phytochrome subfamilies. For example, the corn genome contains two A-type phytochrome genes (A1 and A2), two B-type phytochrome genes (B1 and B2), and two C-type phytochrome genes (C1 and C2).

Why do flowering plants have multiple genes that encode what appear to be very similar photoreceptors?

Functional diversification.

In other words, different phytochrome genes encode slightly different phytochrome photoreceptors in different plant tissues/organs. This allows plants like cannabis to perceive and respond to different types of red/far-light signals in different tissues/organs, which then allows this small family of red/far-red light photoreceptos to regulate different biochemical, physiologicial, and developmental processes in these different plant tissues/organs (such as flowering in shoot tissues and growing away from the light in root tissues).

Next up:
What does the list of plant processes (i.e., biochemical, physiological, and developmental processes) that are controlled by phytochrome photoreceptors look like for flowering plants such as cannabis?


yep. preaching to the choir.
Peter was on my thesis committee.


Did you know Elena Monte from Peter’s lab? She was a good friend of mine, back in the day. She and I both worked in Lee Pratt’s lab at UGA, before she worked in Peter’s lab at the Plant Gene Expression Center.

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Thank you for the simplification of what you’ve stated so far at the end of each of your posts.

I’m a layman and you have been able to explain things at a level I can clearly understand.

This is super interesting and I am looking forward to more!


The Plant gene expression center is off-campus. I did a three month stint (included my first rotation) in Shelia McCormick’s (tomato) lab at the PGEC in 1991…right down the hall from Peter, I got to see a lot of work out of Peter’s lab over the years, but have to admit that I can’t remember the names of any of his grad students or postdocs at this point.


Phytochromes control many genetic, biochemical, physiological, and developmental processes, throughout the life cycle of plants.

These processes include:
Gene expression
Seed germination
Seedling development
Seedling elongation
Chlorophyll biosynthesis
Anthocyanin biosynthesis
Carotenoid biosynthesis
Ethylene biosynthesis
Flavonoid biosynthesis
Terpene biosynthesis
Glutamate metabolism
Chloroplast movements
Stem elongation
Leaf development
Leaf anatomy and size
Leaf number
Leaf positioning
Stomatal aperture
Plant architecture
Root architecture
Sensing beginning of the day
Sensing the end of the day
Shade avoidance
Resource allocation
Seasonal flowering (flowering time)
Fruit ripening
Crop yield

Note that flowing time, crop yield, and terpene biosynthesis are included in the list above. As you know, these three traits are high-value traits in the cannabis industry.


So is that why some leaves grow weird like missing the spiked edges on the leaf for example 3 smooth petals instead of 5 spike edged on some indoor grows or shady outdoor areas. Their missing a certain light wavelenght source to stimulate either a,b,c,d or e?

I remember growing one plant inside a 2x2ft box using only cfls long time ago and all the leaves grew this werid shape but i was able to yield half oz at the end of the experiment


Great question.

The short answer is: I don’t know. (The answer to your question might be yes, it might be no, and it might be only partly so.)

The long answer is: What you observed is likely a combination of environmental and genetic factors, aka nature (genetics) and nurture (environment). Most plant phenotypes, like the leaf phenotype you describe, result from the plant’s integration of multiple environmental factors and multiple genetic factors.

Leaf development is definitely a function of multiple environmental factors, including stress status, water status, humidity, temperature, light intensity, light directionality, and the spectrum of incident light. Phytochromes collect information from light intensity and from the spectrum of incident light, and feed that information into a complex developmental response equation.