On leaves and ligules

Guest post by Siva Chudalayandi (@sianj)

I love plants and a walk through the woods never fails to refresh my mind. I have been fortunate to have spent the last several years researching aspects of plant genetics and development. The cells of the plant leaves house many compartments called chloroplasts, which are the factories that make organic matter using just sunlight, water and carbon dioxide in a process called photosynthesis. Through this blog I’d like to pay tribute to this unique organ of plants.

Leaves occur in myriad shapes and forms. Sometimes they are large (e.g. banana leaves) or serrated (tomato leaves), or are needle-like, as seen on pine trees. However, like many other structural forms in biology they are made up of distinct substructures that are found in many different groups of plants. I live in the USA in the state of Iowa, an area that is flush with corn fields. Corn (maize) is a fascinating model to study how the leaves of the grasses and other monocot plants develop. The flat and wide portion of the leaf is called the leaf blade, while the part of the leaf that hugs the stem is called the sheath. The blade and sheath are separated by an outgrowth called the ligule and a loosely defined region called the auricle (Figure 1). This sheath and blade pattern is repeated in every leaf.

Maize Leaf

Figure 1: Maize shoot. Image credit: Chudalayandi et al. (1).

Over the years many researchers have proposed varied explanations for the existence of a ligule in grasses, including that it protects the interior of the plant from water and insects. However, a more plausible explanation for ligules and auricles is that they might act as a pivot to help position the leaf blade at the correct angle to receive appropriate amounts of solar radiation. Using tools in genetics and molecular biology, scientists have uncovered many of the cellular aspects of maize leaf and ligule development.

Leaves emerge from a structure called the shoot apical meristem. Researchers at Cornell University (2) used a technique called laser microdissection on developing maize shoots to precisely isolate the emerging ligule/auricle, leaf blade and sheath. Then they examined which genes were active in both maize plants with normal ligules and mutants that lacked ligules. The scientists found that gene networks involved in specifying initiation of various lateral organs (leaf, branches etc.) in plants are also involved in the formation of ligules. To briefly elaborate, in the shoot apical meristem, KNOX proteins (3) accumulate at the base while a plant hormone called auxin accumulates in regions marking where a leaf will form. This pattern is repeated in each emerging leaf and lateral organ that develops from the meristem. The same network of genes also specifies the blade sheath boundaries and where the ligule will form.

Along with producing auxin, the gene networks control the production of another plant hormone called cytokinin. The interplay between auxin and cytokinin is partly responsible for maintaining the pattern of leaf growth. Many researchers have studied this pathway in different plants over the years and this has been the subject of many fine review articles (4,5). These and other studies show that during evolution, a similar network of genes is often slightly modified and redeployed to make a newer organ that offers an organism another way to adapt to changes in its environment.



1: Chudalayandi, Sivanandan; Cahill, James; Scanlon, Michael; Muszynski, Michael. Cytokinin hypersignaling reprograms maize proximal-distal leaf patterning. Short talk abstract (T-20), 57th Annual Maize Genetics Conference, St. Charles, IL, USA (Mar 12-Mar 15, 2015).

2: Johnston R, Wang M, Sun Q, Sylvester AW, Hake S, Scanlon MJ. Transcriptomic analyses indicate that maize ligule development recapitulates gene expression patterns that occur during lateral organ initiation. Plant Cell. 2014 Dec; 26 (12):4718-32. (http://www.ncbi.nlm.nih.gov/pubmed/25516601)

3: Hay A, Tsiantis M. A KNOX family TALE. Curr Opin Plant Biol. 2009 Oct; 12(5):593-8. (http://www.ncbi.nlm.nih.gov/pubmed/19632142

4: Koenig D, Sinha N. Evolution of leaf shape: A pattern emerges. Curr Top Dev Biol. 2010;91:169-83. (http://www.ncbi.nlm.nih.gov/pubmed/20705182)

5: Lewis MW, Hake S. Keep on growing: building and patterning leaves in the grasses. Curr Opin Plant Biol. 2016 Jan 2;29:80-86. (http://www.ncbi.nlm.nih.gov/pubmed/26751036)


About the author: Siva Chudalyandi is a post-doctoral research associate at the Iowa State University. Siva studies maize genetics and genomics, and loves working at the intersection of biology and big data. Follow him on twitter (@sianj).

River cane, an American bamboo

Guest post by Alex Rajewski (@Rajewski)

When you picture a forest of bamboo, the last place you might think to find it is in the southeastern United States. Although the majority of bamboo species are found in Asia, River cane (Arundinaria gigantea) is the only* species of bamboo native to the United States. During my master’s degree research at the University of Georgia, I studied the propagation and genetics of this species, so I’m more than a little enamored with River cane.

Alex Rajewski River Cane.jpg

Alex by a small canebrake of River cane in Athens, Georgia

As the name suggests, River cane likes to hang out along riverbanks and streams, where it can form very large and very dense bamboo forests called ‘canebrakes’. When Europeans first surveyed North America, they often found these dense canebrakes running for several kilometers along rivers. Ecologically, these canebrakes are very important. Canebrakes have dense roots that make them very effective at controlling erosion, and they also work to absorb nitrogen fertilizer runoff before it can enter and pollute streams. There is also some evidence that canebrakes form a unique habitat for many birds and insects.1

Beyond its ecological value, River cane is botanically fascinating! Unlike many other plants, River cane takes an extremely long time to flower. Some observations suggest 30-40 years between flowerings. When River cane does flower though, it does it with style. Often the entire canebrake will flower simultaneously, produce hundreds of thousands of seeds, and then die off. The seeds look like green rice, but unlike rice, they must germinate immediately or die. After the flowering, birds consume many of the seeds, but the sheer number of seeds ensures that enough will germinate and restore the canebrake.

What exactly triggers the plants to flower after decades of growth is not yet clear, but researchers do have some insights into how the plants coordinate their flowering en masse. Each seed that germinates not only grows a leafy aboveground shoot but also many underground stems called rhizomes. These rhizomes spread out and send up new shoots along their length. This means that many (or even most2) of the shoots in a canebrake are from one individual plant. Additionally, all the seeds produced by a flowering event are the same age and are closely related. This combination of having very a few dominant individuals, who are related and of similar age makes flowering together easier, though no less interesting.

Of course it can’t be all milk and honey, River cane is critically endangered, though not yet federally protected in the US. Many scientists and private citizens are currently rising to the challenge by working to increase awareness, promote ornamental use of River cane, and enact conservation of canebrakes.

*The exact number of US bamboo species is (surprisingly) hotly debated, and numbers between one and three depending on how you define a species. River cane is almost always the primary species in the genus, but Hill cane (Arundinaria appalachiana) and Switch cane (Arundinaria tecta) are commonly mentioned.3


  1. Platt, S. G., Rainwater, T. R., Elsey, R. M. & Brantley, C. G. Canebrake fauna revisited: additional records of species diversity in a critically endangered ecosystem. Bamboo Science & Culture 26, 1-12 (2013).
  2. Kitamura, K. & Kawahara, T. Clonal identification by microsatellite loci in sporadic flowering of a dwarf bamboo species, Sasa cernua. Journal of plant research 122, 299-304, doi:10.1007/s10265-009-0220-1 (2009).
  3. Triplett, J. K., A.S. Weakley, and L. G. Clark. Hill Cane (Arundinaria appalachiana), a New Species of Bamboo from the Southern Appalachian Mountains. SIDA, Contributions to Botany 22, 79-95 (2006).


About the author: Alex Rajewski is a recent transplant to the University of California, Riverside, where he is pursuing his PhD. His current research focuses on the evolutionary and genetic forces that created fleshy fruits in the nightshade family. Follow him on twitter: @Rajewski.

Yucca aloifolia, the plant that’s found a reverse gear

Guest post by Alun Salt

If you’re a plant, then having a pollinator you can rely on seems like a good idea. Yucca plants have a partnership with Yucca moths. Yucca plants have flowers that are specialised for Yucca moths. The payback is that Yucca moths can’t find food so easily anywhere else, because they’re now adapted to access Yucca flowers. A Yucca plant can provide food, knowing its pollen won’t be wasted by a pollinator that visits other species of plant. It sounds like a good deal, but it’s also a dead end.

When plants and pollinators become dependent, a threat to one can wipe out the other. For example, if a new blight hit Yucca plants, the Yucca moth would find its food source had disappeared, and it would starve to extinction itself. Once a species has specialised it’s very hard to dismantle adaptations and build new ones.

However, sometimes Nature can provide a species with help reversing out of a dead end. Rentsch and Leebens-Mack have an Open Access paper in AmJBot, Yucca aloifolia (Asparagaceae) opts out of an obligate pollination mutualism, that finds a change in the ecosystem could be help one species of Yucca become a generalist.


Yucca aloifolia (public domain/Flickr)

The paper is based on two species of Yucca plant, Y. filamentosa (Adam’s Needle) and Y. aloifolia (Spanish Bayonet). The species are sympatric, meaning that they live in the same areas, so they’re a good match if you want to see if one species is doing something that the other isn’t.

What Rentsch and Leebens-Mack wanted to find out was, do Yucca plants need Yucca moths to be pollinated? Can they use another insect? There’s an obvious problem with this experiment: How do you exclude just Yucca moths, while letting other insects through? Do you need hundreds of dedicated volunteers standing over the flowers, with a keen eye and a swatter?

What they did was bag the flowers in a mesh, and block access to flowers between an hour before dusk till dawn – the period when the Yucca moth would be active. They also ran some other tests. On other flowers there was no blocking, so they could be sure Yucca moths were around and feeding. On other flowers there was a complete block of pollinators, to see if the flowers were setting fruit themselves. Finally, they also looked at blocking daytime pollinators, to be sure it was the Yucca moths doing the pollinating.

What they found was that Y. filamentosa was reliant on the Yucca moth to set fruit, but that Y. aloifolia was getting pollinated during the day. So who was the unexpected visitor?

The answer was found using some fluorescent dye added to the stamens of target flowers. Apis mellifera, the European Honey Bee was caught red-handed – or rather orange-legged where the dye had been collected. Like the European bit of the name suggests, A. mellifera is not native to the USA, but was introduced by European settlers. It’s spread, and its generalist foraging can mean it pushes into settled relationships elsewhere. In the case of the Yucca plants, Y. aloifolia has a larger opening on its stigmas, and this was enough for the bees to exploit.

Rentsch and Leebens-Mack suggest that while bees explain fruit set in Y. aloifolia, other species may use other species, for example they note Lapping flies visit Y. glauca (Soapweed Yucca). So, when there’s a lot of competition among pollinators, plants might be able to adapt to take advantage of a wide range of pollinators after all – despite specialisms.

I have simplified the paper, so I recommend reading it for yourself if you’re looking for more detail, but the experiments are themselves actually simple ideas executed elegantly. The core question is does a Yucca plant need a Yucca moth, and the bagging is a simple and effective way of excluding one set of pollinators in favour of another.

It also neatly questions something that “everybody knows”. Everybody knows that Yucca plants are obligate mutualists with Yucca moths. Rentsch and Leebens-Mack show that’s not actually so.


J. D. Rentsch, J. Leebens-Mack, 2014, ‘Yucca aloifolia (Asparagaceae) opts out of an obligate pollination mutualism’, American Journal of Botany, vol. 101, no. 12, pp. 2062-2067 http://dx.doi.org/10.3732/ajb.1400351

About the author: When he’s not the web developer for AoB Blog, Alun Salt researches something that could be mistaken for the archaeology of science. His current research is about whether there’s such a thing as scientific heritage and if there is, how would you recognise it?

Plant Scientist needs you!

Ever wanted to try your hand at blogging? Plant Scientist blog is looking for guest posts while I take a short break from writing.

I was just about to write my first article of the year when my oldest and best friend died suddenly. She was a very important part of my life and I will need some time to come to terms with her death before I will be able to return to writing regularly on this blog.

While I take this break, I am looking for 400-800 word guest articles on plants, microbes, science communication or life in science more generally. I would like to hear from anyone with an interest in any of these topics, regardless of whether you work in research or another science-related profession, or not. If you would like to write something please contact me using this contact form.

In the meantime, to get your fix of plant and microbial science, I recommend reading this article by Mary Williams, which includes a load of links to other plant science blogs out there.

And, in case you missed them, here are the 5 most popular articles published on Plant Scientist in 2015:

Thank you for all your support during 2015, I will be back soon.

Clove: A spice with many uses


Image by Franz Eugen Koehler, Koehler’s Medizinal-Pflanzen (Public domain)

Yesterday was the shortest day of the year in the Northern Hemisphere (also known as the Winter Solstice). At my home in the UK we received less than 8 hours of daylight today before the night closed in again, and the weather at this time of year is generally rather grey and damp. The gloom outside makes December my least favourite time of year, but I must confess that the food, drink and other traditions that accompany this period do help to make up for it.

Lots of the winter/Christmas themed foods eaten in the UK and other European countries are traditionally flavoured with spices. One of my favourite of these spices is the clove. Cloves are the dried flower buds of a medium-sized tree called Syzygium aromaticum, which is native to the ‘Spice Islands’ of Indonesia. It is one of the most valuable spices in the world and has been used for centuries as a flavouring, preservative and in medicinal remedies.

Cloves were so valuable in the 17th Century that when the Dutch seized control of the Maluku Islands in Indonesia, they guarded the production of cloves very carefully and made the unauthorized trading of this spice a crime punishable by death. The Dutch monopoly on clove allowed them to keep the price of the spice artificially high, but clove trees were common enough on the Maluku Islands that the French managed to smuggle some off the island in 1772. Today clove is grown in a variety of tropical countries around the globe including: Indonesia, Zanzibar, Sri Lanka, the Caribbean and Brazil.

Clove has many uses in both traditional and modern medicine. It acts as an antioxidant, and also has activity against some bacteria, fungi and viruses. It also has pain killing properties and research suggests that particular molecules in cloves may have the potential to be used to treat cancer. Many of these properties appear to be due to the presence of an oil called eugenol. Clove represents one of the richest sources of this oil, which is also used in perfumes and manufacturing.

The tasty seasonal foods may be healthier than I previously thought…



  1. Kew Science: Syzygium aromaticum (clove) http://www.kew.org/science-conservation/plants-fungi/syzygium-aromaticum-clove
  2. Cortés-Rojas DF, de Souza CRF, Oliveira WP. Clove (Syzygium aromaticum): a precious spice. Asian Pacific Journal of Tropical Biomedicine. 2014;4(2):90-96. doi:10.1016/S2221-1691(14)60215-X. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819475/

Sex change by fungus


White campion infected with anther smut fungus. Image by Martin C. Fischer (CC BY 4.0)

Fungi reproduce by releasing spores that lie dormant in the environment until conditions are right for them to grow. The spores of fungi that infect plants are often released from fungal structures that develop on the surface of their hosts’ leaves or stems. However, the anther smut fungus (Micobrotryum lychnidis-dioicae) employs a more unusual strategy. Its spores are displayed on its host’s flowers so that they can be carried to other plants by insect pollinators.

Anther smut fungus can infect a small flowering plant called white campion (Silene latifolia). White campion is dioecious, meaning that each plant can only produce either male or female flowers. In the flowers of the male plants, pollen is produced by structures called stamens. When the fungus infects a male plant, it manipulates the plant so that the stamens no longer produce pollen and display fungal spores instead.

The flowers of the female plants do not have stamens, so infecting a female would appear to be a dead end for the fungus. However, the fungus has another trick up its sleeve: it induces a partial sex change in female white campion plants so that they do produce stamens (albeit primitive ones).

Like us, white campion has sex chromosomes (X and Y) that determine whether a plant will be male or female. Some of the genes on the sex chromosomes regulate the activity (or expression) of genes on other chromosomes. Therefore, certain genes are more active in a male plant than a female plant, and vice versa. This sex-biased gene expression contributes to the physical differences between the males and females. To better understand how anther smut fungus causes the female plants to develop male characteristics, Niklaus Zemp and colleagues used a technique called RNA-seq to study gene expression in white campion (Zemp et al., 2015).

They found that the fungus causes different changes in gene activity in the male and female plants. The biggest differences were in genes that are more highly expressed in healthy male plants than healthy female plants (male-biased genes). Zemp et al. show that fungal infection decreases the expression of many of these genes in male plants, but has the opposite effect on these genes in female plants. The fungus also altered the expression of female-biased genes differently in males and females, but to a lesser extent.

The up-shot to these changes in gene expression is that the male plants become a bit more feminine when anther smut fungus infects, while the female plants become more masculine. How the fungus achieves this is still a mystery, but it is not the only microbe to cause sex changes in its host. Wolbachia bacteria can cause some male insects to become more female, and a parasite called Nosema granulosis also feminizes some crustaceans. So, in the natural world, gender is a more fluid concept than you might think.

Anther smut fungus is the Organism of the Month here at Plant Scientist.


Zemp N, Tavares R, Widmer A (2015) Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia. PLoS Genet 11(10): e1005536. doi:10.1371/journal.pgen.1005536

The helpful onion

Field of onions in Ismaning, Germany. Image by Rainer Haessner (CC BY SA 3.0 via Wikimedia Commons)

Field of onions in Ismaning, Germany. Image by Rainer Haessner (CC BY SA 3.0 via Wikimedia Commons)

This month it was all change in my vegetable patch as I harvested the last of the crops I planted in the spring and planted new things to grow over the winter. On a bit of whim I decided to plant some onion sets (mini bulbs) at one end of the patch, which should be ready to eat in early summer next year.

Onion is one of the oldest known cultivated plants and the earliest archaeological evidence of onions in human settlements dates back to around 5000 BC (Bronze age). It is grown all over the world where it features as a staple vegetable in a variety of dishes. It is not clear where they originated from, but there is some evidence that they may have come from southwestern Asia. Most cultivated onions are varieties of the common onion (Allium cepa L.) but some other onion species are cultivated too.

If you have ever cooked with onions you will know that when the bulbs are wounded they release a chemical that stings our eyes and can make us cry. This chemical – which has the catchy name syn-propanethial-S-oxide – doesn’t tend to put us off eating onions, but it does help them to defend themselves against herbivores and other pests. Charles Darwin hypothesized that tears triggered by cutting onions are the same as tears of sadness (2). However, he was later proved wrong because tears of sadness actually release extra “waste” proteins that aren’t found in onion tears.

Onions may also help to protect other plants from disease. Intercropping is a farming practice in which two or more crop species are grown in alternating rows. It has been used for a long time to increase crop productivity and to help control disease. Intercropping may help to protect plants against diseases by decreasing the number of attacks by the microbes that cause them, or by boosting the resistance of the host plant. Most studies so far have focused on investigating the first possibility, but little is known about whether plants release signals that can boost defense in their intercropping companion.

In Northeast China, a variety of A. cepa L called the potato onion is often the preferred companion plant to tomatoes. Tomatoes (but not onions) are susceptible to infection by a fungus called Verticillium dahlia, which causes a disease called tomato Verticillium wilt. A group of researchers recently investigated whether intercropping tomato with the potato onion is an effective way to control this disease (Fu et al. 2015).

Fu et al. found that when tomato and potato onion plants were grown together, molecules secreted from the tomato plants (but not the onion plants) inhibited the germination of fungus spores and also inhibited the growth of the fungus. This effect is due to the presence of the onion plants because molecules secreted from tomato and onion plants that were grown separately did not limit the growth of the fungus. Further experiments show that the onion plants trigger the expression of defense genes in the tomato plants.

These results indicate that intercropping tomatoes and potato onions may help to reduce the number and severity of outbreaks of Verticillium wilt. However, since these experiments were carried out under controlled conditions and the tomato plants were deliberately exposed to the fungus, large scale field trials would be needed to find out whether this effect is actually relevant in the field.

Onion is the (long-awaited!) Organism of October (apologies for the delay).


  1. Wikipedia: Onion  (retrieved 21/10/15)
  2. Law, B (2010) Fifty plants that changed the course of history. David and Charles.
  3. Fu X, Wu X, Zhou X, Liu S, Shen Y and Wu F (2015) Companion cropping with potato onion enhances the disease resisitance of tomato against Verticillium dahlia. Frontiers in Plant Science 6:726 doi: 10.3389/fpls.2015.00726