Cassava brown streak: lessons from the field

This week’s post was written by Katie Tomlinson, a PhD student at the University of Bristol, UK, who spent three months as an intern at the National Crops Resource Research Institute in Uganda. She fills us in on the important research underway at the Institute, and how they communicate their important results to local farmers and benefit rural communities.  

Over the summer, I had a great time at the National Crops Resources Research Institute (NaCRRI) in Uganda. I’m currently in the second year of my PhD at the University of Bristol, UK, where I’m researching how the cassava brown streak disease (CBSD) viruses are able to cause symptoms, replicate and move inside plants. I was lucky enough to be given a placement at NaCRRI as part of the South West Doctoral Training Partnership Professional Internship for PhD Students (PIPS) scheme, to experience the problem for myself, see the disease in the field, meet the farmers affected and investigate the possible solutions.

 

Cassava brown streak disease

Cassava brown streak disease symptoms on tubers. Image credit: Katie Tomlinson.

 

Cassava is a staple food crop for approximately 300 million people in Africa. It is resilient to seasonal drought, can be grown on poor soils and harvested when needed. However, cassava production is seriously threatened by CBSD, which causes yellow patches (chlorosis) to form on leaves and areas of tubers to die (necrosis), rot and become inedible.

Despite being identified in coastal Tanzania 80 years ago, CBSD has only been a serious problem for Uganda in the last 10 years, where it was the most important crop disease in 2014–2015. The disease has since spread across East Africa and threatens the food security of millions of people.

NaCRRI is a government institute, which carries out research to protect and improve the production of key crops, including cassava. The focus is on involving farmers in this process so that the best possible crop varieties and practices are available to them. Communication between researchers and farmers is therefore vital, and it was this that I wanted to assist with.

 

Scoring cassava brown streak disease

Scoring cassava plants for Cassava brown streak symptoms. Image credit: Katie Tomlinson.

 

When I arrived I was welcomed warmly into the root crop team by the team leader Dr Titus Alicai, who came up with a whole series of activities to give me a real insight into CBSD. I was invited to field sites across Uganda, where I got to see CBSD symptoms in the flesh! I helped to collect data for the 5CP project, which is screening different cassava varieties from five East and Southern African countries for CBSD and cassava mosaic disease (CMD) resistance. I helped to score plants for symptoms and was fascinated by the variability of disease severity in different varieties. The main insight I gained is that the situation is both complex and dynamic, with some plants appearing to be disease-free while others were heavily infected. There are also different viral strains found across different areas, and viral populations are also continually adapting. The symptoms also depend on environmental conditions, which are unpredictable.

I also got to see super-abundant whiteflies, which transmit viruses, and understand how their populations are affected by environmental conditions. These vectors are also complex; they are expanding into new areas and responding to changing environmental conditions.

It has been fascinating to learn how NaCRRI is tackling the CBSD problem through screening different varieties in the 5CP project, breeding new varieties in the NEXTGEN cassava project, providing clean planting material and developing GM cassava.

 

Tagging cassava plants

Tagging cassava plants free from Cassava brown streak disease for breeding. Image credit: Katie Tomlinson.

 

And there’s the human element…

In each of these projects, communication with local farmers is crucial. I’ve had the opportunity to meet farmers directly affected, some of whom have all but given up on growing cassava.

 

Challenging communications

Communicating has not been easy, as there are over 40 local languages. I had to adapt and learn from those around me. For example, in the UK we have a habit of emailing everything, whereas in Uganda I had to talk to people to hear about what was going on. This is all part of the experience and something I’ll definitely be brining back to the UK! I’ve had some funny moments too… during harvesting the Ugandans couldn’t believe how weak I was; I couldn’t even cut one cassava open!

 

Real world reflections

I’m going to treasure my experiences at NaCRRI. The insights into CBSD are already helping me to plan experiments, with more real-world applications. I can now see how all the different elements (plant–virus–vector–environment–human) interact, which is something you can’t learn from reading papers alone!

Working with the NaCRRI team has given me the desire and confidence to collaborate with an international team. I’ve formed some very strong connections and hope to have discussions about CBSD with them throughout my PhD and beyond. It’s really helped to strengthen collaborations between our lab work in Bristol and researchers working in the field on the disease frontline. This will help our research to be relevant to the current situation and what is happening in the field.

 

Some of the NaCRRI team

Saying goodbye to new friends: Dr. Titus Alicai (NaCRRI root crops team leader), Phillip Abidrabo (CBSD MSc student) and Dr. Esuma Williams (cassava breeder). Image credit: Katie Tomlinson.

 

In Nature Plants: Come together

This post is republished with permission from Nature Plants.

Science is not a solo endeavour but a social one, and the most social part is conference attendance. Regardless of their other strengths and weaknesses, scientific meetings are critical for encouraging researchers early in their careers.

Conference

Image credit: Dion Hinchcliffe. Used under license: CC BY-SA 2.0.

Unquestionably, one of the most enjoyable aspects of being a journal editor is the opportunity to attend conferences. While the average scientist may get to one or two scientific meetings a year, we try to get to many more — and so are in a good position to compare the different styles of meeting, and to try to understand what makes a conference not just good, but great.

Mainly, it is the people who are attending. Meetings are exactly what the name implies: an opportunity to meet colleagues and discuss science. But there are many factors that determine who will attend a conference, and whether they will get to talk constructively while they are there. Location is important. Many scientific conferences are held in places well worth visiting in their own right. Last year’s International Plant Molecular Biology Congress, for example, was held near Iguazú Falls, Brazil; the XIV Cell Wall Meeting was held this year on the Greek island of Crete; and, next year, the Plant Biology 2017 conference of the American Society of Plant Biology (ASPB) will be in Honolulu, Hawaii. However, as much as exotic locations may be a draw for participants, the long and expensive journeys can be a deterrent.

Conference

Image credit: Dimitris Kalogeropoylos. Used under license: CC BY-SA 2.0.

An additional factor is the breadth, or narrowness, of focus of a meeting, which affects both its size and atmosphere. Larger meetings with a broad range of topics guarantee that there will be something of interest to everyone. These can be superb at giving a broad view of the important questions currently being addressed in a field, and usually have presentations by impressive well-known and well-practiced speakers. However, it can be difficult to meet all the people with whom you want to chat without considerable dedication and forward planning.

You often see a reluctance in speakers to present new and unpublished work at larger meetings. For that, smaller meetings come into their own, where a more tightly defined community makes it more appealing to share confidences in a room perceived to be full of ‘friends’. If the location is remote, so much the better, as it forces that community closer together. The summertime masters of such meetings are the Gordon Research Conferences, which are often (though not exclusively) held in out-of-season New England boarding schools — two of which, this year, are the Plant Molecular Biology and Plant & Microbial Cytoskeleton meetings. In the winter, there are the Keystone Symposia, which have the added attraction of afternoons left free for skiing. In fact, the conversations had while trapped on a ski lift can often be the most scientifically productive of the whole event.

Presentation

Image credit: NASA Goddard Space Flight Center. Used under license: CC BY 2.0.

More focused meetings will usually give attendees the opportunity to attend every talk, but larger conferences frequently host parallel sessions to allow many more topics to be discussed. Successfully presenting parallel sessions is hard. Ideally the topics covered should overlap so little that every attendee would wish to attend one session, and one session only — a goal never fully achieved, and rarely even approached. Instead, attendees must pick the talks that they most want to see, which are often presented in different sessions, leading to a lot of distracting crowd movement between talks. For sessions to remain synchronized, speakers must keep strictly to their allotted time — again something so difficult to achieve that it rarely, if ever, happens.

At its heart, the main point of a scientific conference is not to visit interesting places, to catch up with old friends, to party with colleagues (although much partying does occur), or even to listen to high-profile scientists lecture on their work. All these are important aspects of a successful conference, but its central function is to bring people together to discuss their own studies. Where this happens most is at the poster sessions — the great equalizer of any scientific conference..

Poster

GPC New Media Fellow Sarah Jose presents a poster at a conference

However lofty the professor or junior the student, with a poster everyone can present their work on an equal level, open to the criticism of all. They are the soul of any good conference, but they are the most difficult aspect to organize successfully. Ideally the posters should all be in one place rather than spread out over a number of rooms, to avoid some groups getting ignored. The posters need to be arranged close enough together that when the session is in full swing there is a throng and hubbub of chatter, but not so closely packed that posters are blocked by people reading the next one over. It is also vital that there is enough space to move freely between posters without having to squeeze past huddles of scientists talking with the presenters. Above all, posters must be available for long enough that conference-goers can read all that are relevant to them. Therefore poster rooms need to be open throughout the conference, not just during designated sessions, and all posters should be available for the whole conference, not taken down halfway through to make way for a second batch.

Posters provide some of the first opportunities that early-career scientists have to present their research. It is therefore always good to see conferences enhancing their status in some way. The simplest is the awarding of prizes for the ‘best’ posters, judged as much for the clarity of presentation as for the story being told. Some conferences have started to schedule ‘flash talks’, selecting presenters to give a short description of their work, and serving as an advert for their posters. This commonly takes the format of five-minute presentations with no more than three slides — but ‘slam’ sessions are also possible, where a single minute is allocated to each speaker. A variation of this occurred at the recent ASPB Plant Biology 2016 meeting in Austin, Texas: early-stage researchers were helped to video ‘elevator pitches’ about their work, which can now be seen on the Plantae YouTube channel. It is also encouraging to see that the New Phytologist Trust will again be holding a Next Generation Scientists symposium next year, following on from the successful inaugural meeting in 2014.

The planning, organization and execution of a scientific meeting requires as much skill, enthusiasm and innovation as any other part of the scientific endeavour. After all, a good conference brings scientists together to discuss ideas, initiate collaborations and forge friendships that can last for entire careers, and sometimes longer.

Interview with Dr. Winfried Peters: Bringing forgotten ideas on plant biomechanics into the 21st century

This week we spoke to Dr. Winfried S. Peters from Indiana University/Purdue University Fort Wayne (IPFW). His research mainly focuses on the biomechanics of plant cells, which led him to take a second look at some of the ideas of botanists in the 19th and early 20th century and use modern techniques to make exciting new discoveries.

Winfried Peters

Dr Winfried S. Peters, Indiana University/Purdue University Fort Wayne (IPFW), next to several tons of land-plant sieve elements!

 

Could you begin by describing your research interests?
I am interested in the biophysical aspects of the physiology of plants and animals. In plants, my research focuses on the mechanics of growth and morphogenesis, and on the cell biology of long-distance transport in the phloem. For both topics, a solid background in the history of the field can be quite helpful – I love studying the old literature to reconstruct the ideas botanists had a century or two ago regarding the functioning of plants.

At the recent New Phytologist Symposium, entitled “Colonization of the terrestrial environment 2016”, you presented fascinating work on the sieve tubes of kelp, which resemble the phloem tubes of vascular plants. What is the purpose of these tubes?
In large photosynthetic organisms, not all parts of the body are truly autototrophic. Some tissues produce more material by photosynthesis than they need, while others produce less than they require or none at all– think of green leaves and growing root tips. Over-producing tissues can act as sources and export photoassimilates to needy sink tissues. Sieve tubes are arrays of tubular cells that mediate this exchange, enabling the rapid movement of photosynthate-rich cytoplasm between sources and sinks.

What techniques did you utilize to investigate the function of these tubes, and what did this reveal?
During my recent sabbatical, I became involved in this project in the lab of my friend and long-term collaborator, Professor Michael Knoblauch. Michael heads the Franceschi Microscopy and Imaging Center at Washington State University, where we studied sieve tubes of the Bull Kelp (Nereocystis luetkeana) using a variety of state-of-the-art microscopy techniques. Most importantly, we employed fluorescent dyes to visualize transport in sieve tube networks. To do this, one needs to work with intact kelp, which is demanding given a thallus size of 12 meters and more. So we moved to Bamfield Marine Sciences Centre on Vancouver Island, where Bull Kelp is a ‘common weed’.

A particularly important result was the pressure-induced reversal of the flow direction in sieve tubes and across sieve plates. This was in line with Ernst Münch’s (1876-1946) theory, who suggested that sieve tube transport was driven by osmotically generated pressure gradients.

 

Nereocystis wounding

An intact Nereocystis luetkeana is kept in a tank (right) while sieve tube transport is studied using a fluorescence microscope. Photo credit: Michael Knoblauch.

How do the biomechanics of the kelp sieve tubes differ from the phloem tubes of higher plants?
Regarding cytoplasmic translocation, there doesn’t seem to be a difference – in higher plants as in kelps, the contents of the sieve tubes move in bulk flow – but wounding responses differ drastically. After wounding, we found that kelps have a massive swelling of the walls, which reduced the sieve tube diameter by more than 70%. By injecting silicon oil into severed kelp sieve tubes we demonstrated that wall swelling was fully reversible, and that the swelling state of the walls depended on intracellular pressure.

Wounding response in kelp

Sieve wall tubes swell after wounding due to changes in intracellular pressure. (Images taken from video below).

Have reversible wall-swelling reactions been observed in other species, and what are the implications of this finding?
We have observed the wall-swelling response in all kelp species examined. Ironically, there is no shortage of drawings and photographs of kelp sieve tubes with swollen walls in the literature over the last 130 years; however, the dynamics of cell behavior remained hidden in plain sight because fixed tissue samples rather than fully functional, whole organisms were studied. Consequently, sieve tubes with swollen walls were misinterpreted as senescent cells. There also are publications on turgor-dependent cell wall swelling in red and green algae, but these ceased around 1930.

Afterwards, wall swelling was completely forgotten, judging from the textbooks. This is remarkable, as Wilhelm Hofmeister (1824-1877), often celebrated as a founding father of plant biomechanics, denied a significant role for osmotic processes in the generation of turgor, the hydrostatic pressure within plant cells. Rather, he maintained that living cells were pressurized by the swelling of their walls. The example of the kelp sieve tube shows how easy it is to remain unaware of wall swelling when it happens right before our eyes. Maybe we should take Hofmeister’s idea seriously once again?

What are the evolutionary implications of your work?
Brown algae and vascular (land) plants are only remotely related, and their sieve tube networks certainly evolved independently of each other. It seems surprising that such sophisticated structures, which serve a complex function that integrates the physiology of the entire organism, have evolved at least twice, but think again. Real cells are not embedded in a totally homogeneous environment, and neither is the cytoplasm within the cell a homogeneous solution. Thus every cell experiences gradients of solute concentrations along its inner and/or outer surface. As a consequence, differential water fluxes across the plasma membrane will occur, resulting in movements of the cell contents. In other words, Münch flow, the cytoplasmic bulk flow driven by osmotically generated pressure gradients, is not a peculiar process operating specifically in sieve tubes, but a ubiquitous phenomenon. Sieve tubes consist of cells that simply do the things cells do, just a little more efficiently as usual. In this view, the repeated convergent evolution of sieve tube networks is not really unexpected.

But kelps resemble land plants in other ways too. As in land plants, kelp cell walls are made of cellulose (at least partly), kelp cells are connected through plasmodesmata, and the kelp life-cycle is a sporophyte-dominated alternation of generations. Evidently, none of these features represents a specific adaptation to life on dry land.


Wound responses including wall swelling in a sieve tube of Nereocystis luetkeana. (Watch for the rapid cell wall swelling between 11 and 14 seconds in!) This video was taken by Professor Michael Knoblauch in collaboration with Dr Winfried S. Peters.
 


If you’d like to know more about this fascinating work, it was been published in the following articles:

Knoblauch, J., Peters, W.S. and Knoblauch, M., 2016. The gelatinous extracellular matrix facilitates transport studies in kelp: visualization of pressure-induced flow reversal across sieve platesAnnals of Botany117(4), pp.599-606.

Knoblauch, J., Drobnitch, S.T., Peters, W.S. and Knoblauch, M., 2016. In situ microscopy reveals reversible cell wall swelling in kelp sieve tubes: one mechanism for turgor generation and flow control? Plant, Cell and Environment39(8), pp.1727-1736.

 

Feeding the world with virtual crops

This week’s blog comes from Rachel Shekar, the project manager for the “Crops in silico” project.

Researchers watch a field of soybean emerge, grow, and abruptly die in the span of one minute — on their computer screens. These virtual crops will help them understand how crops will respond to climate change – an ever-growing threat to worldwide food production – and could lead to overcoming its threat to global food security.

Food security

Image credit: Kate Holt. Used under license: CC BY 2.0.

It is estimated that, by 2050, food production will need to increase by 70% to meet the demands of a growing global population. According to the latest UN projections, the world’s population will rise from 6.8 billion today to 9.1 billion in 2050 – a third more mouths to feed than there are today. Nearly all of the population growth will occur in developing countries.

At the same time as demand for food is increasing, the world will also be facing fresh water scarcity and climate change.

Climate change is expected to bring warmer temperatures, changes to rainfall patterns, and increased frequency and severity of extreme weather events. Although projections vary, it is clear that crop yields will decrease as climate change increases. Furthermore, the countries that most need food – such as sub-Saharan Africa – are the very places that will be most severely affected by climate change. Growing water use and rising temperatures are expected to further increase water stress in many agricultural areas by 2025.

Soy field

Soy field. Image credit: Neil Palmer (CIAT). Used under license: CC BY-SA 2.0.

Can crop yields be increased in time?

The introduction of new crop varieties that produce higher and more stable yields in the face of drought, heat, diseases, and other stresses will allow farmers to grow crops that are adapted to climate change.

Plant models can be used to rapidly identify genes that will improve yields and utilize resources more efficiently, which will provide targets for developing productive varieties of food crops more quickly than ever before.

Because many traits, such as yield, are controlled by interactions between genetics, the environment, and the ecosystem, the most accurate results can be obtained by incorporating information across different biological scales—from molecular and cellular up to the organ, plant, and community levels.

Understanding the whole plant

Soy trials

Data for the system-level model was derived from soybean trials at University of Illinois South Farms. Image credit: Haley Ahlers.

The Crops in silico team at the University of Illinois and National Center for Supercomputing Applications is developing and linking models across different biological scales to more accurately simulate plant responses to a changing environment.

The team is developing models from the molecular to field, and root to leaf levels. Once the models are linked, an entire virtual crop canopy can be created and used to identify target genes for yield improvement under a range of environments. Other researchers can then use this information to develop crops that will thrive in tomorrow’s climate.

Crops in silico is currently focusing on soybean plants. The wealth of data from SoyFACE, an open-air experiment at the University of Illinois where soybean is grown in future climate conditions (e.g. elevated carbon dioxide, temperature, and drought), is facilitating model development and validation.

Soy render

Rendered plant- and canopy-level data from the system-level model. Image credit: Crops in silico.

Future work by Crops in silico will target staple food crops in developing countries including rice, legumes, and cassava.

Crops in silico aims to create an open-source teaching and training tool for students. A user-friendly web interface will allow non-modelers to visualize model outputs as easy-to-interpret graphs, tables, animated simulations of plant growth and ecosystem interactions.

Building a research community

Plants In Silico Meeting

Photograph from the Plants in silico Symposium & Workshop held in Urbana, Illinois in 2016. Image credit: Rachel Shekar (Crops in silico).

The success of this effort is dependent on a connected Crops in silico community that can take full advantage of advances in computational science, and our mechanistic understanding of plant processes and their responses to the environment. The first step in creating the community was taken this summer when a group of international scientists met at the first Plants in silico Symposium & Workshop in Illinois. Workshop participants identified specific challenges to integrative and multi-scale modeling in plants, and their solutions.

Together, this community will create the most complete models of staple food crops, to identify varieties that will ensure food security around the world in the face of climate change.


For more information on the Plants in silico project, read the recent paper in Plant, Cell and Environment (open access): Plants in silico: why, why now and what?—an integrative platform for plant systems biology research.

Plantwise – promoting and supporting plant health for the Sustainable Development Goals

Andrea Powell

Andrea Powell, CABI

Promoting and supporting plant health will be an important part of how we achieve the United Nations’ Sustainable Development Goals (SDGs). Andrea Powell, Chief Information Officer of the Centre for Agriculture and Biosciences International (CABI) looks at how the CABI-led Plantwise programme is helping to make a difference.

By Andrea Powell

 

On 26th and 27th July 2016, CABI held its 19th Review Conference. This important milestone in the CABI calendar saw our 48 member countries come together to agree a new medium-term strategy. As always, plant health was a key focus to our discussions, cutting across many of CABI’s objectives. For CABI, with 100 years of experience working in plant health, it has become one of our most important issues, upon which our flagship food security program, Plantwise, has been built.

Plant health can, quite simply, change the lives and livelihoods of millions of people living in rural communities, like smallholder farmers. Human and animal health make headlines, while plant health often falls under the radar, yet, it is crucial to tackling serious global challenges like food security. Promoting and supporting plant health will be an important way to achieve the Sustainable Development Goals (SDGs).

Plant health and the SDGs

Take, for example, SDG 1, which calls for ‘no poverty’. The UN states that one in five people in developing regions still lives on less than $1.25 a day. We know that many of these people are smallholder farmers. By breaking down the barriers to accessing plant health knowledge, millions of people in rural communities can learn how to grow produce to sell to profitable domestic, regional and international markets.

Plantwise ReportSDG 2 focuses on achieving ‘zero hunger’. Almost one billion people go hungry and are left malnourished every day – and many are children. Subsistence farmers, who grow food for their families to eat, can be left with nothing when their crops fail. Access to plant health knowledge can help prevent devastating crop losses and put food on the table.

Interestingly, SDG 17 considers ‘partnerships for the goals’ and is critical to the way in which we can harness and share plant health knowledge more widely to help address issues like hunger and poverty. By themselves, individual organizations cannot easily resolve the complicated and interconnected challenges the world faces today. This is why partnership is at the heart of CABI’s flagship plant health programme: Plantwise.

What is Plantwise?

Plantwise Report 2015

Since its launch in 2011, the goal of Plantwise has been to deliver plant health knowledge to smallholder farmers, ensuring they lose less of what they grow. This, in turn, provides food for their families and improves living conditions in rural communities. Plantwise provides support to governments, helping to make national plant health systems more effective for the farmers who depend on them. Already, Plantwise has reached nearly five million farmers. With additional funding, and by developing new partnerships, we aim to bring relevant plant health information to 30 million farmers by 2020, safeguarding food security for generations to come.

Plantwise ‘plant clinics’ are an important part of the fight against crop losses. Established in much the same way as clinics for human health, farmers visit the clinics with samples of their sick crops. Plant doctors diagnose the problem, making science-based recommendations on ways to manage it. The clinics are owned and operated by over 200 national partner organizations in over 30 countries. At the end of 2015, nearly five thousand plant doctors had been trained.

Plantwise

A Plantwise plant clinic in action. Credit: Plantwise

Harnessing technology for plant health

The Plantwise Knowledge Bank reinforces the plant clinics. Available in over 80 languages, it is an online and offline gateway to plant health information, providing the plant doctors with actionable information. It also collects data about the farmers, their crops and plant health problems. This enables in-country partner organizations to monitor the quality of plant doctor recommendations; to identify new plant health problems – often emerging due to trade or climate change issues; and develop new best-practice guidelines for managing crop losses.

Plantwise

The first ever e-plant clinic, held in Embu Market, Kenya. Credit: Plantwise

The Plantwise flow of information improves knowledge and helps the users involved: farmers can receive crop management advice, and researchers and governments can access data from the field. With a new strategy for 2017–19 agreed, CABI will continue to focus on building strong plant health systems. We are certain that plant health is of central importance to achieving the SDGs and, together in partnership, we look forward to growing the Plantwise program and making a concrete difference to the lives of smallholder farmers.

“A few years ago, I would make ZMW 5000 per year. Last year I got 15 000. I have never missed any plant clinic session. I’ve been very committed, very faithful, because I have seen the benefits.”––Kenny Mwansa, Farmer, Rufunsa District, Zambia.

Take a look at Plantwise in action in Zambia (YouTube):

Plantwise in Zambia

Meet Linda, a Zambian plant doctor

Meet Kenny, a Zambian farmer

 

Learn more about Plantwise at www.plantwise.org.

Uncovering the secrets of ancient barley

This week we speak to Dr Nils Stein, Group Leader of the Genomics of Genetic Resources group at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). We discuss his recent work on the genomes of 6000-year-old cultivated barley grains, published in Nature Genetics, which made the headlines around the world.

Nils Stein

Dr Nils Stein, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

Could you describe your work with the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)?

The major research focuses of my group, the Genomics of Genetic Resources, are to continue sequencing the genomes of barley and wheat, perform comparative genomics on the Triticeae tribe, isolate genes of agronomic interest, and investigate the genomics of wild barley relatives.

We are currently leading the work to generate the barley reference genome, and we are also partners in several wheat genome sequencing projects. We are genotyping-by-sequencing (GBS) all 20 000 barley accessions in the IPK Genebank, as well as 10 000 pepper accessions as part of a Horizon 2020 project (G2P-SOL) investigating the Solanaceae crop species.
Your recent collaborative paper on the genomic analysis of 6,000-year-old barley grains made headlines around the world. What did this study involve?

This was an interdisciplinary study to sequence the DNA of 6000-year-old barley grains. The grains were excavated by a team of Israeli archaeologists and archaeobotanists led by Prof. Ehud Weiss, Bar-Ilan University, the DNA was extracted and sequenced by ancient DNA specialists Prof. Johannes Krause and Dr. Verena Schünemann in Germany, and the data were analyzed by Dr. Martin Mascher in the context of our comprehensive barley genome diversity information. This allowed the resulting sequence information to be put into a population genetic and ecogeographic context.

Ancient barley

Preserved remains of rope, seeds, reeds and pellets (left), and a desiccated barley grain (right) found at Yoram Cave in the Judean Desert. Credit: Uri Davidovich and Ehud Weiss.

What led you to the realization that barley domestication occurred very early in our agricultural history?

The genome of the analyzed ancient samples was highly conserved with extant barley landraces of the Levant region, which look very similar to today’s high-yielding barley varieties. Although suggestive and tendentious, this told us that the barley crop 6000 years ago looked very similar to extant material. The physical appearance and the archaeobotanical characters of the analyzed seeds also very much resembled modern barley.

 

These barley grains contain the oldest plant genomes reconstructed to date. Did you find any differences between the samples that might give us an insight into the traits that were first selected in the early domestication of the crop?

We have only scratched the surface so far. The major domestication genes controlling dehiscence, brittleness or row-type of the main inflorescence had the same alleles in the ancient samples that are found in extant barley, confirming that these traits were selected for early in domestication. Additional analyses on other genes controlling different traits in barley are still ongoing – bear in mind that many of the genes controlling major traits in barley are still unknown, which complicates the selection of targets for analysis.

Modern barley

Modern barley cultivar. Credit: Christian Scheja. Used under license: CC BY 2.0.

 Do these grains have any genetic variation that we lack at key loci in modern barley lines, for example in stress or disease resistance?

This is matter of ongoing analysis. So far it is obvious that the most genetically similar extant landraces from the Levant region have accumulated natural mutations over the last 6000 years, resulting in additional variation that we don’t find in the ancient sample.

 

What can we expect from the barley genome projects in the future?

The International Barley Genome Sequencing Consortium is preparing a manuscript on the reference sequence of barley. This will allow further analysis of the ancient DNA data with a more complete, genome-wide view, including the consideration of a more complete gene set than has been available so far. Our Israeli collaborators (Professor Ehud Weiss and Professor Tzion Fahima) have more ancient samples of similar quality. We hope we will be able to generate a more comprehensive view of the ancient population genomics of barley in the future, to better address the question of novel ancient alleles and lost genetic diversity.

The Barley Pan-Genome analysis will soon give us a better understanding of the structural variation in the barley genome. Putting the ancient DNA information into this more comprehensive genomic context will be very exciting. We also hope to be able to compare a variety of ancient samples of different ages to more precisely date the event of barley domestication.


You can read the paper here: Genomic analysis of 6000-year-old cultivated grain illuminates the domestication history of barley ($).

Professor Stefan Jansson on what makes a GMO, and the Scandinavian Plant Physiology Society

This week we speak to Professor Stefan Jansson, Umeå University, Sweden, who is the President of one of the Global Plant Council member organizations, the Scandinavian Plant Physiology Society (SPPS). He tells us more about his fascinating work, his prominent role in the GM debate, and his thoughts on the work of the SPPS and GPC, both now and in the future.

Stefan_Jansson

Could you tell us a little about your areas of research interest?

I have worked on (too) many things within plant science, but now I am focused on two subjects: “How do trees know that it is autumn?”, and “How can spruce needles stay green in the winter?” We use several approaches to answer these questions, including genetics, genomics, bioinformatics, biochemistry and biophysics.

 

Your ground-breaking work on CRISPR led to you being awarded the Forest Biotechnologist of the Year award by the Institute of Forest Biosciences. Could you tell us more about this work, and the role you have played in the GM debate?

In our work on photosynthetic light harvesting, we have generated and/or analyzed different lines lacking an important regulatory protein; PsbS. PsbS mutants resulting from treatment with radiation or chemical mutagens can be grown anywhere without restriction, but those that are genetically modified by the insertion of disrupting ‘T-DNA’ are, in reality, forbidden to be grown. For years, I, and many other scientists, have pointed out that it does not make sense for plants with the same properties to be treated so differently by legislators. In science we treat such plants as equivalents; when we publish our results we could be required to confirm that the correct gene was investigated by using an additional T-DNA gene knock-out line or an RNAi plant (RNA interference, where inserted RNA blocks the production of a particular protein), but in the legislation they and the ‘traditionally mutated’ plants are opposites.

This has been the situation for many years, but it has been impossible to change. To challenge this, we set up an experiment using a targeted gene-editing approach called CRISPR/Cas9 to make a deletion in the PsbS gene, which resulted in a plant with a non-functional PsbS gene but no residual T-DNA. We asked the Swedish competent authority if this would be treated as a GM plant or not, arguing that it is impossible to know if it is a ‘traditional’ deletion mutant or a gene-edited mutant. In the end, the authority said that, according to their interpretation of the law, this cannot be treated as a GMO.

If this interpretation is also used in other countries, plant breeders will have access to gene-editing techniques to aid them in their work to generate new varieties, which would otherwise not be a possibility. The reason we did this was to provide the authorities with a concrete case, and one which was not linked to a company or commercial crop but rather something that everyone would realize could only be important for basic science. Therefore most of the arguments that are used against GMOs could not be used, and this should be a step forward in the debate.

 

Check out Stefan’s fantastic TEDxUmeå talk to hear more on the GM debate:

spps_logoYou are the President of the Scandinavian Plant Physiology Society, one of the Global Plant Council member organizations. Could you briefly outline the work of the SPPS?

We support plant scientists – not only plant physiologists – in the Nordic countries, organize meetings, publish a journal (Physiologia Plantarum), etc.

 

What are the most important benefits that SPPS members receive?

This is an issue that we discuss a lot in the society right now. Only a limited fraction of Nordic plant scientists are members – obviously are the benefits not large enough – and this is something that we intend to change in the coming years. We think, for example, that we need to be a better platform for networking between researchers and research centers, and have a lot of ideas that we would like to implement.

 

How does the GPC benefit the SPPS?

Although there are country- and region-specific issues important for plant scientists, the biggest issues are global. The arguments why we need plant science are basically the same whether you are a plant scientist in Umeå or Ouagadougou, therefore we all benefit from a global plant organization.

 

What do you see as important roles for the future of the GPC, both for SPPS and the wider community?

This is quite clear to me: we will contribute to saving the planet.

 

What advice would you give to early career researchers in plant science?

Your curiosity is your biggest asset, so take good care of it.

 

Is there anything else you’d like to add?

The challenge for the GPC is clearly to get enough resources to be able to fulfil its very worthwhile ambitions. GPC has made a good start: the vision is clear and the roadmap is there, which are two prerequisites, but additional resources are needed to employ people to realize these ambitions, build upon current successes, and perform the important activities. It is easy to say that if we all contribute with a small fraction of our time that would be sufficient, but we all have may other obligations and commitments, and a few dedicated people are needed in all organizations.

Interview with Laura Lagomarsino, winner of the Ernst Mayr award at Evolution 2016

This week’s post is reproduced with permission from the New Phytologist blog.

Written by Mike Whitfield

 

During Evolution 2016, I spoke to Laura LagomarsinoNew Phytologist author and one of the winners of the Ernst Mayr Award. Awarded each year by the Society of Systematic Biologists, the Ernst Mayr Award celebrates the quality and creativity of the research conducted by a PhD student in the field of systematic biology. Read more about Laura’s research career and the Ernst Mayr Award in the interview below.

 

Hi Laura, please introduce yourself and tell us a little bit about your career

I am an evolutionary biologist and botanist who studies the evolution and systematics of Neotropical bellflowers in the family Campanulaceae, and the Andean flora more broadly. I am currently an NSF postdoctoral fellow. I spend most my time at the Missouri Botanical Garden and University of Missouri- St. Louis, but am also affiliated with the University of Gothenburg in Sweden. Before that, I finished my Ph.D. at Harvard University, and next year I will begin my own lab as an assistant professor at Louisiana State University.

 

Burmeistera_Panama

Image courtesy of Laura Lagomarsino

Tell me a bit more about the Ernst Mayr Award

The Ernst Mayr Award is given by the Society of Systematic Biologists to graduate students and recent grads for the creativity and breadth of their doctoral research, as presented in a talk at the annual Evolution conference. This year there were two awardees: Michael Landis and myself. It’s an immense honour to receive the award, and it is one of the more important, humbling events of my professional life to date. Much of the research I presented was recently published in New Phytologist.

 

What inspired your interest in plant science?

I grew up camping in the redwood forests of northern California every summer. Being surrounded by such extraordinary plants — the tallest trees in the world — really jumpstarted my interest in the natural world. My very specific interest in Neotropical plant diversity was cultivated when I was an undergraduate at UC Berkeley, studying heliconias, a group of very colourful hummingbird pollinated plants that I fell in love with immediately. Since then I haven’t turned away from trying to understand relationships between species in large evolutionary radiations in Latin America.

 

What are the current hot topics and big questions in your field?

Phylogenetics is making huge strides in methodology right now. I’d say improved phylogenetic inference, especially via methods that incorporate gene tree-species tree incongruence on genomic-scale datasets, combined with advances in molecular dating are rapidly pushing the field forward. These methods and others coming on board increasingly allow us to really tackle the large questions in a more thorough, explicit manner than previously possible. These large questions are what motivate my own empirical research: What explains global biodiversity patterns, and, in particular, why are the Andes home to a disproportionately large number of species? Why are some groups (such as Neotropical bellflowers) so morphologically and ecologically diverse, while others seem to not vary nearly as much?

 

Sipho_retorsus_CDB241__COL_4141

Image courtesy of Laura Lagomarsino

How do you think your research benefits society?

As a systematist, I both describe new biodiversity via species description and attempt to explain biodiversity patterns. My research focuses on the tropical Andes, one of the world’s richest biodiversity hotspots, but also one of the most threatened by climate change and deforestation. In addition to uncovering basic information about poorly studied species, I hope that my research will provide insights in how to best protect this stunning biodiversity for generations to come. It helps that the group of plants that I study is attractive and has such charismatic pollinators (hummingbirds and nectar bats); it makes it that much easier to communicate my research to the general public.

 

Who (scientist or not) do you see as your role model(s)?

I was incredibly lucky to conduct undergraduate research with Dr. Chelsea Specht at UC Berkeley. Chelsea was a great mentor then — providing me with the tools necessary to independently conduct research and helping me apply to fellowships, grants, and eventually graduate school — and she continues to be a great mentor and role model today. I hope that I can remain as enthusiastic about my research and generate as many well-trained, passionate scientists as she has.

 

What’s your favourite thing about your job?

I love working in herbaria, where I can be transported to any part of the world by opening a cabinet and catching a glimpse of the flora of some faraway country in an herbarium specimen. There’s so much botanical diversity that most people, even many plant biologists, are unaware of — and it’s all at my fingertips in these collections! After years studying plant diversity, it’s so rewarding to see a plant, whether a specimen, a photo, or in real life, and think, “Hey, I know you!”

 

… and your least favourite?

It’s perhaps a cliché response, but it can be so challenging to put work aside as an early career scientist. There is the guilt when I shut down my laptop for the evening that I could have worked one more hour, or that I need to work weekends after returning from vacation. I’m not sure there’s an easy way to get around these feelings, but I do my best to regularly carve out unplugged time.

 

What advice would you give to early career researchers?

Be prepared for things to change quickly! It’s hard to predict where you’re going to be in a year until you land a permanent job. It’s also important to maintain your professional relationships with current and previous advisors and collaborators; they can provide insights into your next steps based on what they know about you and from their own hard-earned experiences. But of course, also continue to forge friendships with peers: it’s so important to have a wide social net as you manoeuvre this often-scary, but also very exciting career stage.

 

Aside from science, what other passions do you have?

I love traveling frequently with my husband, whether we’re visiting his family in Costa Rica, getting to know the Midwest a little better, or hopping on a plane to somewhere further afield. We are both botanists, so wherever we go, our hand lenses and portable plant press come along. But most calm weekends at home involve lots of cooking and baking, maybe a good Netflix binge, and at least one puzzle (usually jigsaw or crossword).

SantaTeresa_Peru

Image courtesy of Laura Lagomarsino

 

Follow Laura on Twitter: @lagomarsino_l.

Watch a video of the award presentation at Evolution 2016 here.

Read Laura’s recent New Phytologist paper, ‘The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)‘ and its associated Commentary by Colin E. Hughes: ‘The tropical Andean plant diversity powerhouse‘.

 

This article was originally posted on the New Phytologist blog. This material was republished with permission.

A postcard from the Spanish Society of Plant Physiology

SEFV logoThe Spanish Society of Plant Physiology (Sociedad Española de Fisiología Vegetal; SEFV) is a society for scientific professionals with an interest in how plant organs, tissues, cells, organelles, genes, and molecules function, not only individually but also through their interaction with the natural environment.

The society was founded in 1974, and currently has approximately 600 members distributed across the seven groups that constitute the SEFV, namely; Phytohormones, Maturation and Postharvest, Carbohydrates, Nitrogen Metabolism, Water Relations, Mineral Nutrition, and Biotechnology and Forestry Genomics.

One of the main objectives of the society is to organize meetings, which are held every two years in collaboration with fellow GPC Member Organization, the Portuguese Society of Plant Physiology (Sociedade Portuguesa de Fisiologia Vegetal; SPFV). In the alternate years between SEFV conferences, the different SEFV groups hold individual biannual meetings.

SEFV 2015 Biannual Meeting

XXI Reunión de la Sociedad Española de Fisiología Vegetal/ XIV Congreso Hispano-Luso de Fisiología Vegetal. Photograph from the combined biannual meeting of the SEFV and SPFV held in Toledo, Spain in 2015

 

Each week the SEFV distributes a newsletter to its members containing information on courses, conference announcements around the world, jobs, student scholarship opportunities, and some current news. Twice a year the SEFV issues a bulletin that comprises a scientific review, interviews with leading figures in plant physiology, information on different research groups, abstracts of doctoral theses presented in the last 6 months, as well as news on science policy.

The SEFV is a member of the Scientific Societies Confederation of Spain (Confederacíon de Sociedades Científica de España; COSCE), which aims to contribute to scientific and technological development, act as a qualified and unified interlocutor to represent government in matters affecting science, promote the role of science in society, and contribute to the dissemination of science as a necessary and indispensable cultural ingredient.

The SEFV is also part of another GPC Member Organization, the Federation of European Societies of Plant Biology (FESPB) and has links with the Argentine Society of Plant Physiology (SAFV). (You can read a Postcard from the SAFV here.)

We sponsor student attendance at the SEFV and FESPB conferences and encourage their active participation by awarding poster and oral presentation prizes. Additionally, the SEFV convenes biannually (coinciding with the SEFV Congress) to award the Sabater Prize for young researchers.

The SEFV website, Facebook page and Twitter (@NewsSEFV) account provide information to SEFV members and general readers with an interest in plant physiology.

How do you grow a plant scientist?

This week’s blog post is written by Sarah Blackford.

Plant scientists are generally very good at growing their plants, taking good care of them and making sure they’re well fed and watered. But what about their own development? Who’s growing them?

In a recent survey, Principal Investigators (PIs) were asked to rate areas of their work they perceived to be the most important. Research-related activities were valued the highest (Vitae, 2011), while conversely, “providing career development advice” and “continuing professional development” were rated as two of their lowest priorities, at around 5% (see figure). This, perhaps, is not surprising when you consider PIs need to prioritize a multitude of responsibilities on their ‘to do’ list.

PI Leaders report 2011

Figure reproduced from Principal investigators and research leaders survey, Vitae (2011) showing the importance of activities and functions for the development of research leaders, against their own confidence in those activities

 

From small shoots

Like the plant, overlooking the growth of the person could lead to plant scientists being held back from a flourishing career. So, taking responsibility for your own development is vital, especially since programs of professional and personal development are not always readily available to PhD students and researchers in many institutes and universities. Even if they are, the content and timing is not always relevant or convenient. I’ve been delivering bespoke career development workshops for bioscientists, including plant scientists, for over 10 years now and one of the main aims is to help people to help themselves. As well as providing practical information and advice on bioscience-related careers, job seeking strategies and career transition planning, I use interactive exercises and discussions to raise self-awareness. This involves recognizing the range of skills acquired through research, appreciating work values, linking interests with career choice and showing how personality plays a crucial role in effective communication and leadership. During the workshops, the participants complete a personal action plan identifying what they need to do to grow their own careers.

Firmly planted

Most people need to update and improve their CVs (even me!), hone their interview technique and perfect their self-presentation skills. But personal and professional development requires a range of different actions depending on career goals and intentions. Some PhD students want to continue on to do at least one postdoc and then decide whether to carry on after that. With quite a good number of posts available, and with some industry recruiters saying they prefer researchers with postdoc experience, this can be an excellent first step – but be careful to ensure you’re moving forward and building on your experience. Look at the career stories of early career researchers who were awarded this year’s prestigious SEB president’s medal – they relate strategies they have used to fill gaps in their expertise and to position themselves favorably to secure a permanent research leadership position. For researchers who are aspiring academics, their plans may include actions such as submitting an abstract to give a talk at a forthcoming conference, doing some strategic networking or finding a mentor to help them to apply for a fellowship.

Branching out

For those considering a non-academic career, their personal development will depend on which career sector they plan to move into. For example, arranging work shadowing or doing voluntary work can help shift your career towards your desired destination. I helped out at the career service during my job as assistant editor when I was based at Southampton University, giving me enough experience and a reference to break into this career. Internships can provide opportunities to spend time working in areas such as policy, outreach and publishing, and if you’re a budding science writer you can simply start up your own blog, or write on someone else’s – like this one! Everyone would benefit from setting up or improving their presence on social media, whether it’s Researchgate, LinkedIn or Twitter. These global networks help to raise your profile, provide information about companies and careers of interest, build relationships and even advertise jobs. Generic training in communication, networking, self-awareness and other personal effectiveness can help to improve everyone’s self-reliance and confidence.

A fertile future

So in answer to the question, “how do you grow a plant scientist?” I would say it depends on their field of interest and direction of growth. Never think of your PhD as the end of your learning – it’s another new beginning. Even PIs lack confidence in some important aspects of their work, such as securing research funding (see figure) and would likely benefit from training in this area, not to mention management and leadership. Growing plants is your business; without them you would make no progress, nor generate results on which to write your publications and build a career. Ignore your own personal growth and you might be in danger of going to seed!

This blog is a summary of the career workshop, organized and delivered by Sarah Blackford, at the recent FESPB/EPSO Congress 2016 in Prague.


Sarah Blackford

Dr Sarah Blackford

 

Sarah Blackford started her career in plant science research at York University, moved into journal publishing with the Journal of Experimental Botany and then trained to be a professional higher education careers adviser. She is currently the Head of Education and Public Affairs at the Society for Experimental Biology (SEB) and writes a regular blog for bioscience PhD students and postdocs: www.biosciencecareers.org