Plant Model Species: Who, What & Why?

Plant life: Model plant species: Who, what, and why?

Every sub-section of biology has a model species that every biologist loves (or loathes). A model species is a well characterised and easy to grow organism, often with a fully sequenced genome. This makes it way easier for biologists to understand, investigate, and uncover new information and translate. Once this new finding is discovered in one model species, more often than not, it’s also found in a close evolutionary partner. This then gives us insights into how a particular pathway, mechanism, or response is conserved across species, or even entirely different biological kingdoms. Model organisms are also chosen based on behavioural similarity. You may think human beings are a cut above the rest, but you’d be surprised how similar we are to our ‘distant’ cousins.

Mammalian genetics mostly revolves around two very unassuming heavyweights: the fruit fly and the zebra fish (AKA Drosophila melanogaster and Danio rerio) (and no, the second isn’t a Game of Thrones character). The fruit fly has a tiny genome, which means nearly every biological function is mapped, and characterised. Fruit flies are especially well suited to developmental biology: how an organism grows, from fertilisation through to a fully differentiated and functional fruit fly.

model organisms
A fruit fly (Drosophila melonogaster) and a zebra fish (Danio rerio), common model organisms used in developmental human genetics

What about zebra fish? They first made mainstream news headlines in 2003, when glow in the dark fish were introduced to US markets, based on the work of Singaporean scientist, Dr. Zhiyuan Gong. Initially, these fluorescing fishes were developed as a toxicity sensor for polluted rivers in the fish’s native India. But, the ingenious sensor was capitalised on, and you can now buy GloFish® in aquariums up and down the US.

Danio GloFish, harbouring a gene isolated from a jellyfish

Moving on from fish and flies, it’s time to look at plant science’s big guns: a weed, and a highly regulated addictive substance.

Arabidopsis thaliana (ara-bid-op-sis tha-lee-an-a) is commonly known as Thale cress. It’s a small, radial plant, with leaves growing flat to the ground, shooting flowers near vertically up. It can grow nearly anywhere, in a variety of harsh conditions. It’s also a global plant, so different accessions (the same species identified from a different location) allow plant scientists to unpick what makes these plants tick under a variety of different stressors.

Arabidopsis is dicotyledenous, meaning when it first germinates from a seed, two tiny ‘leaflets’ (not the kind the takeaway puts through the door) are produced. From there, two ‘true leaves’ are formed, and the plant continues to grow. Underground, a taproot system forms: think of a carrot. There’s a main root, with a series of lateral roots, which forage for nutrients and water in the soil, to ensure a healthy, happy plant. Arabidopsis plants grow fast, are hardy, and can be made to harbour specific genes of interest (yes, this includes glow in the dark proteins!)

So, what about this addictive substance? It’s tobacco! Most labs use either Nicotiana benthamiana or tabacum. Benth is standard tobacco’s smaller, more flimsy cousin, but both are frequently used in plant labs all over the world. So, why use tobacco? It’s no secret, for corporate tobacco companies, it made a lot of sense to get their best selling product sequenced. Before this, loads of information had already been accrued, given its importance socially, historically, and economically.

Model plant species
A: Arabidopsis thaliana (Thale cress) B: Nicotiana tabacum (Tobacco). 

Tobacco can be used as a model for crop species, as it’s more closely related to barley, wheat, and rice. N. benth is also used for virology studies; helping plant scientists understand the diseases that kill off our food supplies every year. Unlike Arabidopsis, tobacco has a fibrous network of roots.  It’s also useful for ‘transient’ studies, a gene or fluorescent tag can be introduced to quickly check that your experiment is going smoothly, before you ‘stably’ transform Arabidopsis. The downside to tobacco is it’s huge, in size and genome. This makes it much harder to ‘genetically’ navigate and characterise. To stably transform tobacco, it’s not nearly as easy as its weedy counterpart, it needs to be morphed back into a stem-cell-like blob (called a callous), before turning back into a fully functional tobacco plant. Cool, right?

This is just the tip of the botanical iceberg, as we all know. Check back soon for more insights into the weird world of plant science.

Interested in knowing more? Tweet me @emilyxarmstrong, or comment on this post.



So why study plants in the first place?

So why study plants in the first place? Climate change, crops, and crises.

It’s no secret that our fragile planet is changing at a rapid rate (unless you’re Donald Trump). Our population is booming, our cities are growing, and our fresh water supply is shrinking. All whilst our temperature and weather extremes become, well, increasingly extreme. Biologists, chemists, physicists, geologists, scientists, are rapidly trying to invent ingenious solutions to the problems that climate change is presenting.

As a plant scientist, my work focuses on improving plant species to cope with the challenges our climate will bring. These include, drought, flooding, heat, salinity, insect pests, temperature extremes and heavy metal contamination.

Rice, growing here in China, is especially susceptible to flooding risks

Plants are responsible for everything we see around us. Plants as we know them first evolved from microscopic photosynthetic algae around 450 million years ago. They began to produce oxygen, a by-product of photosynthesis, where plants use light to produce energy. This oxygen built up in the atmosphere, providing the perfect starting point for other life to flourish. Even now, plants are responsible for virtually every breath we take. They are also the building blocks of our diet: we can either eat the plants, or eat animals reared on them.  In fact, the whole of humanity is based around hunter-gatherers settling down to begin agriculture and farming.

Wheat growing in the UK

A plant scientist’s work stems from trying to stabilise food security and food sovereignty. Security focuses on four pillars: access to nutritious food (is the food supply chain robust?), availability of suitable food (do people have access to available food?), utilisation of food (is it safe to eat?), and finally food stability (is there enough food to last the winter?). These four fundamental questions guide a plant scientist’s journey into improving what we eat, and how we access it.

Encroaching desert in Africa

Food sovereignty asserts that those who “produce food, distribute, and consume food, should control the mechanisms of production and distribution, rather than market leaders”. This provides a conundrum to the plant scientist: a lot of our work is funded by so-called ‘market-leaders’, but we want to help people directly affected by climate change.

There are loads of ways for us to improve plant resilience; we can help the plant make more of a specific gene, which might improve how a plant copes with heat. We can help the plant make less of a different gene, which might improve how a plant copes with extra salt in water. We can even change entire networks of genes to improve a response to a stress. The possibilities are practically endless. But, as plant scientists, we also need to make sure that our work is ethically sound.

So there we have it, plants are the building block of our entire world and food supply. Without them, we would be nothing. Climate change destabilises our food supply, meaning we need to come up with creative solutions to help our plants, food, or otherwise, thrive.


Since I’ve started my PhD, I’ve found it difficult to tear myself away from the lab, the office, the mentality of ‘constantly-thinking’. I’m pretty sure nearly every other PhD student feels the same way, but it’s pretty hard  to work out how to stop. This weekend I decided to really challenge my body (& mind) by completely detaching myself (even just for half a day) by travelling to Finnich Glen, a beautiful gorge just north of Glasgow.

A quick ten minute walk from the road through woodland led us to the entrance, a steep 20 meter drop with some old stone steps, and lots of ropes.

We were greeted by stunning greens and reds, beautiful fern species, and perfectly clear water. There were a few other people there too, but not enough to disturb us.

Scrambling to the pulpit itself was a challenge for me, as I’ve only just gained enough confidence & muscle tone to really push myself. Shedding the shoes and heading in barefoot (up to my knees) across slippy rocks under water, it was well worth the struggle.

Even though it was a small escape, it’s left me feeling recharged, with a fresh perspective on my research. What seemed to be massive problems on the Friday had shrunk to small, manageable ones by Monday, and all it took was a slight change in perspective. I’d urge all PhD students to get out, escape, and immerse yourself in something different and new, even if it’s just for a day.