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.


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.


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.


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.