Eragrostis tef: About orphan crops, spill-overs and a gluten-free alternative

By Stephan Kamrad

In my last article I discussed why our diets are based on so few plant species. Wheat, rice, potatoes and maize are the major carbohydrate sources for almost the entire planet. This makes it all the more exciting when a new player enters the game or at least gets due recognition.

Eragrostis tef (commonly known as tef) is a grass that produces an extremely small seed (less than one millimetre in diameter). It is rich in iron and calcium and gluten-free which makes it suitable for people with celiac disease. It contains over 10% protein and is, unlike other cereals, rich in the essential amino acid lysine.
Tef is not a new cereal crop, it has been grown in the Horn of Africa for at least 3000 years and still makes up a quarter of Ethiopia’s carbohydrate production where tef flour is used to bake the traditional injera flatbread. In modern tef farming, it serves as both an orphan crop in Ethiopia and Eritrea and as a fodder crop and gluten-free cereal in the “Western World”.

Eragrotis tef (credit Rasbak)

Eragrotis tef (credit Rasbak)

Orphan crop is a term used for minor crops that are produced at much lower quantities than the big players and are not traded on international markets. However, they can be of great importance as part of the local culinary and agricultural tradition. They are also commonly well adapted to their specific habitats: Tef, for example, is resistant to many pests and pathogens as well as to drought and excess water. Sadly, orphan crops have been receiving almost no attention from crop improvement and breeding programmes. Advanced techniques like marker-assisted selection or the molecular tools to engineer these organisms genetically have simply not been developed/adapted for these plants. In Africa, orphan crops are especially common which means that our current efforts to improve food security partly miss exactly those who suffer most from hunger and poverty. Aiming to address this, a group of Swiss researchers have founded the Tef Improvement Project and recently published the genome of Eragrostis tef which will massively facilitate future breeding efforts. With help of the genomic sequence, many insights obtained from research on the model plant Arabidopsis and other major crop plants can probably be applied to tef. These “spill-overs” only require relatively small investments but have the potential to impact positively on the life of many millions.

Tef’s exceptional nutritional profile also attracted the attention of western consumers, especially since David William’s bestseller Wheat Belly convinced many Americans that a gluten-free diet is healthier even for people not suffering from celiac disease (for which there is no convincing evidence at all). Since the 1980s, tef has been grown in Idaho, US by a group of farmers around Wayne Carlson who brought the idea of growing tef back from Ethiopia. Due to increasing demands, tef production is rising and the flour is traded internationally with the biggest trader being Prograin International bv based in the Netherlands. Tef is a fast growing C4-grass that can be harvested multiple times within one growing season. High yields and its high protein content make a great fodder for livestock (a luxury that most Ethiopians do not have) and it is now grown in many of the warmer parts of the US as hay and forage crop.

Long ignored by international science and economics, tef couldn’t keep up with the intensively bred and fertilised major crop plants. Now that its importance for the people in its indigenous habitat and its potential for the “Western World” have been noticed, Ethiopian food security has a chance to improve in an effective and sustainable way and Eragrostis tef might turn out to be a valuable addition to our repertoire of crop plants.

 Interested and want to read more? Check out these papers about orphan crops and the TEF genome project.

Citizen Science in Botany: An Interview with Oliver Ellingham

By Nathan Smith

As we entrench ourselves firmly into the computational age, science is increasingly looking towards the general public for help with research. With the world just a click away, games and surveys have become common tools for engaging with the non-scientific community. Indeed, citizen science (as it is more formally known), has become a popular throughout all areas of science, including botany, and looks set to stay as a rewarding area for research in many disciplines. With this in mind, I interviewed Oliver Ellingham, a PhD student from the University of Reading, who has incorporated citizen science into his research of powdery mildew fungi.

What is the research you’re doing?

My PhD project at the University of Reading aims to develop molecular markers to aid in accurate and efficient identification of the approximate 800 powdery mildew species. When applying for funding, most research projects tend to include ‘avenues to impact’. However these are rarely followed through on. To achieve this small element in my project I have started the ‘Powdery Mildew Survey’: a citizen science scheme aiming to increase public knowledge and awareness in my research topic, but also biology, pathology, and horticulture in general. 

What is powdery mildew and why is research into it important?

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Powdery mildew on an oak leaf (credit Oliver Ellingham)

Powdery mildew is a fungal plant disease. It is termed ‘biotrophic’, meaning that is relies upon its plant host to live, survive, reproduce, and thrive. It will therefore not kill the plant, but greatly reduce its vigour, beauty, and fruit production.There are currently many research projects into varying aspects of this fungus, concerning disease spread and management (using both biological and chemical controls), as well as, like mine, ways to differentiate between the many species using varying parts of its DNA.This is important as being able to tell the difference between different species enables us to track them and know which are new to our island and which have always been here. In this way we can help to limit spread of pathogens between geographically separate areas.

 

What is the economic impact of powdery mildew?

Powdery mildew costs global agricultural industries millions of pounds per year in control and/or reduction in crop yields. As examples, up to 100% of a grape crop and 20% of a pepper or tomato crop can be lost if left untreated with fungicides.

Less precise figures are available in the horticultural industry, however there have been interesting developments in grand-scale flower production. Roses produced en masse in the Netherlands are treated with fungicides to prevent distortion of the flower via powdery mildew infection. However in recent years, large-scale growers have turned to a new, significantly more expensive, biological control: the plants are treated with another fungus, called Pseudozyma flocculosa. This is antagonistic to the powdery mildew, and strangles it, but not the plant.

What does the citizen science scheme entail?

I offer an identification service. Members of the public can send me their powdery mildew infected plant material, and by identifying the host plant, analysing the fungus’ microscopic, morphological features, and finally extracting and amplifying its DNA I can identify the single species of powdery mildew present. As a by-product of this the sampling number for my project is greatly improved, as well as the distribution and diversity.

 

What struggles have you had getting the public engaged in the scheme?

The hardest thing in this first year of the project has been spreading awareness. I believe this to be significantly easier in the present-day, due to the internet and social media. However contacting like-minded, enthusiastic people, willing to spread the word is difficult when just sitting at my computer. Networking at flower shows and various conferences has helped this hugely, and I am very grateful to the people who have showed an interest and shared contacts with me.

 

What do the initial results from you research show?

Firstly, that powdery mildew is extremely common in the UK and that identification of its presence is possible by anyone. Also, that species identification is possible using microscopic, morphological analysis combined with molecular data. It has also shown that certain species are more common than others: those of the Erysipheae tribe, which have been shown to possess certain proteins to increase their ability to adapt and infect new hosts, are most abundant; while Phyllactineae are less common, potentially due to the adaptation of many of their features to warmer, Mediterranean climates.

For more information on Oliver Ellingham’s research and to get involved in the citizen science scheme, please visit his blog at http://blogs.reading.ac.uk/crg/author/oliellingham/ or follow him on Twitter at @PowderyM 

Bumbling Along

By Sarah Wiseman

My third week began as the second had finished; with more RNA extractions (a task left over from the week before). I have to take samples from 24 different plants of different varieties, at different stages of maturity and have learnt the hard way that it’s a bad idea to tackle more than 4 at once, as the pipetting takes too long and the quality of RNA extracted starts to degrade.

PCRSarahMore excitingly, though with little success, I ran my first polymerase chain reaction (PCR) of the project. This is an important technique used throughout modern biology to amplify small quantities of DNA into quantities which are large enough to run tests with. However, you can’t just shove random fragments of DNA into the machine and hope that the right bits will be copied. Instead, we need primers which specify the regions to be amplified by the enzymes. Primers are short fragments of nucleotides, about 20 bases (the general term for the 4 different letters of DNA – A,T,G and C) long and bind to specific sections of DNA which complement their sequence. Primers must be well-designed, to amplify only the DNA you are interested in; so some work better than others. Whilst they can bind to DNA that they don’t perfectly match (and still allow the enzymes to make more DNA), the worse the match is, the less likely binding is to happen. Additionally, if the sequence is too general, non-targeted sections of the genome might be amplified leading to a confusing result.

PCR also often acts as a confirmation stage where we can check that things are working as expected – this is very useful when most of the time you are working with colourless and anonymous liquids! Before we designed our own primers, we trialed a set which targeted the rice version of the CKP gene to see if they matched up with the gene in wheat. These primers were already available to us and if successful, we wouldn’t need to go through the primer design process ourselves. Unfortunately, whilst some genetic material was amplified, sequencing showed us that the rice primers had amplified other random sections of the wheat genome instead of accurately copying the CKP gene as hoped. With no chance of other primers working, we spent a long morning working out which short sequences of bases would best amplify the CKP gene in wheat and have placed an order for their creation by Invitrogen – a specialist biotech company (other primer design companies are available…).

Since the primers were due to arrive in the next week, all PCR work was put on hold and I spent more time in the PGF. I felt rather cruel sorting through the Arabidopsis with my supervisor, weeding out the smallest plants for binning – those which were clearly not going to be ready for use in the experiments a couple of weeks later. We even composed a song from the perspective of the imperiled plants [to the tune of Bring Me Sunshine]:

“Give me sunlight, and some soil,

Lots of nutrients and water.

A little time, a lot of air.

Give me sunlight, give me soil, give me love!”

… you don’t have to be mad to work here but it helps!

On a more plant friendly note, I spent a happy afternoon helping my supervisor repot her wheat plants. They needed more root space and had to be prepared for their move into the glasshouse around the corner which can better accommodate the plants as they grow taller. Sadly, we only managed to re-pot about 200 out of 1000 plants, so we still have a long way to go….

Vegan Mayonnaise: The Future of Food?

By Stephan Kamrad

Our diet, even today in the globalised age, is made up of surprisingly few plant species: Wheat, rice, potatoes and maize are the major carbohydrate sources for almost the entire planet. When it comes to livestock fodder, fruit and veg, the range is a bit broader but still limited to maybe a few hundred plant species and that although there are estimated to be over 400,000 plant species living on this planet!

So why is that? The reason for this is historical or at least traditional. Since the beginning of agricultural farming (~12,000 years ago) plants have been selected for productivity, palatability and resistance to pests, disease and environmental stresses. The plants we eat today are a reflection of our history, culture and tradition: the exploration of America marked a turning point in world history as well as European diets since it was the Spanish conquistadores who brought the potato plant back from their travels. Today in our globalised world, exotic fruits are flown around the planet so that we can enjoy kiwi, peaches, and strawberries, all year around. Still, rice and wheat remain the main food crops in Asia and Europe respectively as they have been for millennia.

Credit Jennifer Barry

Credit Jennifer Barry

But are we not missing out on the other 99.9% of plant species? Who can imagine what delicacies remain forever out in the wild because they have not been traditionally bred as crop plants or are simply unusual and scary to us? (Would you just eat a random berry you find in the wild?)

A company that has picked up on that is Hampton Creek, a food company based in San Francisco. They have developed a vegan mayonnaise substitute called Just Mayo. The key in developing this product was finding a substitute for the egg (yolk) traditionally used in mayonnaise. Just Mayo instead uses “Pea Proteins” as they declare it on their ingredients list. The company has screened, according to their press releases and adverts, many thousand plants for their properties and potential to replace eggs and continue to do so. “Pea” usually refers to the seeds of the Fabaceae family but what species and variety is actually used and how the protein is being extracted from the pea remains the companies secret. Known is that the product has only 65% of the saturated fatty acids of conventional mayonnaise and is cholesterol free.

“So what?” may you ask. After all organic food stores and supermarkets have been stocking plant-based alternatives for a long time, especially soy-based dairy substitutes and tofu. But the general conception is that vegan food is for hippies and leads to vitamin and protein deficiencies although it is in principle a lot more sustainable and more or just as healthy (with animal welfare being a whole other issue in our intensive meat industry). So in a way, Hampton Creek took and old idea and turned it into something more: looking at their ads and website, Just Mayo almost appears to be a superior lifestyle product with supreme nutritional value. In a funding campaign in February, the company raised 23 million USD, they were in Bill Gates’ The Future of Food feature and recruited Chris Jones (contestant of an American cooking reality show), Joshua Klein (CalTech graduate who previously worked on HIV treatment discovery), and Dan Zigmond (formerly Lead Data Scientist at Google Maps). Up to now, Just Mayo was mostly sold at up-town organic food stores, but their products are now available in Walmart (the world’s largest retailer) which will surely bring production volumes up and prices down.

Hampton Creek’s success has shown that there is a growing market for vegan products. Will this be the future of food? Are we learning to use the plants around us so that our diet becomes healthier and more sustainable without actually losing variety, money or taste?

7 weeks in Sudbury

By Joanna Wolstenholme

Sudbury, on first inspection, is a rather bland, spread-out mining town, inhabited by many, many trucks (most of them blue). When I first arrived, to help out on a project run by Andrew Tanentzap, I have to say I was a little underwhelmed. However the more you explore, the more remarkable the town becomes. It is one of the few areas of the world where remediation has really worked, and the next generation will inherit a greener and cleaner city than the one that their parents inherited. This remarkable change, from a barren ‘moonscape’ caused by years of acid rain (Sudbury was once the largest point source of sulphuric oxide fumes in the world, thanks to the extraction of large amounts of nickel from many mines in the area), to an area with burgeoning first generation forest cover, and recovering lakes, is a great success story that the area can be immensely proud of.

A hard day at work...

A hard day’s work…

With its industrial heritage, Sudbury, with its 330 lakes, makes an idea experimental location for a research group dealing in ecosystems and global change. Our test lake, Daisy Lake, is perfectly set up for studying the effects of terrestrial influences on aquatic ecosystems, as along its length the shores and wetlands have been remediated to various degrees. One section has been limed (spread with calcium carbonate, neutralising the otherwise very acidic soils) and so the growth is relatively lush, and the trees, although young, are not stunted. Other areas, closer to the smelter at the far end of the lake, are far more barren; bare, stained rock predominates, with a few stunted trees.

In Daisy, we were studying eight stream deltas, each with very different personalities. At each site Andrew’s post-doc Erik and I collected algae samples (through a variety of fairly low tech contraptions, more of which later), sediment samples, water samples, and used the Floroprobe and BenthoTorch (two very expensive, high tech contraptions) to characterise the algal species found in the littoral zone (water near the edge of the lake) and benthic layer (the area at the top of the sediment) respectively. This all sounds very easy in theory, but in practice (as with any fieldwork, as I came to learn) things were far harder and more complicated… and often involved some rather novel solutions. If nothing else, this placement has certainly given me plenty of opportunities to stretch my problem solving skills!

My first job was to build umpteen algae-collectors, which were incredibly scientific looking plastic tubes with cut up swim floats attached, from which 6 microscope-slides dangled from fluorescent string. These floated on the surface, but we also sank clay pot holders tied to bricks, as another surface for algae to grow on. We left these in the lake (on a beautiful sunny day) at each of the deltas and then returned to collect them 3 weeks later. After those three weeks had passed, We set out early, trying to avoid a storm that was due around lunchtime, only to find that between two boats we only had one working fuel cable. Great. So we towed each other around the lake, with our little motor struggling along at a snail’s pace. Whilst the clay pot holders had proven attractive to algae at most of the sites, trying to scrape the algae off the pot and into a rather narrow-necked falcon tube proved difficult. However, these still looked like our best bet, as the microscope-slide contraptions had only a thin layer of algae on each slide – we may actually have just built elaborate feeding platforms for the algae-eating zooplankton! The rain set in in earnest after we had got through just half the sites, and the wind got up – heavy rain whilst trying to scrape algae off clay plates tends to complicate things somewhat! Eventually though, we made it around all the sites, collected all the contraptions, and the rain stopped. Fieldwork is great fun, but the weather makes such a difference, especially when you are out on a very exposed lake!

Busy collecting algae

Busy collecting algae

On a more high-tech note, we also made use of two fancy algae-counting probes – the Fluoroprobe (which detects the level of various algal species in the water column) and the BenthoTorch (which, as the name suggests, measures benthic algae growing on the top of the sediment). Both were a little baffling to start with; their comprehensive manuals detailing many things, but not necessarily the answers to what we actually needed to know! After several dry runs measuring the amount of algae on Erik’s office floor, we took them out to the lake, and used them at each of the deltas three times between when we deployed the contraptions and when we scooped them up. The unseasonal amount of rain that Sudbury was experiencing, however, complicated things, and meant that in some sites Erik had to swim down to the sediment with the Benthotorch, as we couldn’t reach it from the boat. Holding the boat still enough to steady the Benthotorch whilst it was measuring was also a challenge, especially on windy days – we often resorted to having one person standing on submerged logs holding the boat still, whilst the other measured! Again, something which sounds easy in theory, but when you are out on a lake, at the mercy of the elements, often proves more complicated…

Fieldwork in the Muskokas

Fieldwork in the Muskokas

As well as working on Daisy with Erik, I also helped Andrew collect additional data for a project looking at the interplay between terrestrial and lake ecosystems. This meant going out to 6 other lakes around Sudbury, and six down in the Muskokas, to collect water samples, use the fluroprobe, and deploy and collect the microscope slide contraptions. Key to the project was collecting clean leaf and algal samples, to go off for stable isotope analysis, to allow Andrew to calculate the influence of the terrestrial systems surrounding the lakes were having on the lake ecosystems. In order to grow clean algal samples without the influence of terrestrial DOM, we collected water from each of the lakes, then filtered it into jars and re-inoculated each jar with a small amount of unfiltered lake water, from which wehoped the algae would regrow. Again, simple in theory, but in practice involved hours and hours of standing by a vacuum pump, watching water drip, drip, drip through a filter. One night, on a field trip down to the Muskokas, we actually ended up filtering outside a Best Western hotel, so as not to set the fire alarms off! Safe to say we got many odd looks. However, the field trip down to the Muskokas was one of the best perks of the summer. We went down in September, almost at the peak of the colours changing, and had two lovely dry but crisp days. Driving down dirt tracks through beautiful forest, to find beautiful lakes to paddle out into was great fun, and a real adventure! It definitely offset the tedium of filtering.

At the end of my seven weeks here I am very sad to be leaving. It was a great experience, with plenty of messing about on boats, and exploring new places. I have learnt a lot about the complications of fieldwork, how to solve problems on the fly with limited supplies, and just what really goes on behind those dry-sounding ‘Materials and Methods’.