Putting Big Data to Work with ARPA-E’s TERRA Program

This week we spoke to Dr. Joe Cornelius, the Program Director at the Advanced Research Projects Agency – Energy (ARPA-E). His work focusses on bioenergy production and conversion as a renewable and sustainable energy source, transportation fuel, and chemical feedstock, applying innovations in biotechnology, genomics, metabolic engineering, molecular breeding, computational analytics, remote sensing, and precision robotics to improve biomass energy density, production intensity, and environmental impacts.

 

What is ARPA-E? How are programs created?

The Advanced Research Projects Agency-Energy (ARPA-E) is a young government agency in the U.S. Department of Energy. The agency is modeled on a successful Defense Department program, the Defense Advanced Research Projects Agency (DARPA). Both agencies target high-risk, high-reward research in early-stage technologies that are not yet ready for private-sector investment.

Program development is one of the unique characteristics of the agency. ARPA-E projects are in the hands of term-limited program directors, who develop a broad portfolio of concepts that could make a large impact in the agency’s three primary mission areas: energy security, energy efficiency, and emissions reductions. The agency motto is “Changing what’s possible”, and we are always asking ourselves, “if it works, will it matter?”. Getting a program approved is a lot like a doing a PhD; you survey the field, host a workshop, determine key points to research, define aggressive performance metrics, and finally defend the idea to the faculty. If the idea passes muster, the agency makes a targeted investment. This flexibility was recently noticed as one of the great aspects of ARPA-E culture and is an exciting part of the job.

 

What is TERRA and how is it new for agriculture?

TERRA stands for Transportation Energy Resources from Renewable Agriculture, and its impact mission is to accelerate genetic gains in plant breeding. This is an advanced analytics platform for plant breeding. Today, significant scientific progress is possible through the convergence of diverse technologies, and TERRA’s innovation for breeders comes through the integration of remote sensing, computer vision, analytics, and genetics. The teams are using robots to carry cameras to the field and then extracting phenotypes and performing gene linkages. It’s really awesome to see.

 

This is run by the U.S. Department of Energy. How does TERRA tie into energy?

The United States has a great potential to generate biomass for conversion to cellulosic ethanol, but the crops useful for producing this biomass have not seen the improvement that others, such as soybeans or maize, have had. TERRA is focused on sorghum, which is a productive and resilient crop with existing commercial infrastructure that can yield advanced biomass on marginal lands. In addition, sorghum is a key food and feed crop, and the rest of the world will benefit from these advancements.

 

How does TERRA address the challenge of phenotyping in the field?

The real challenges that remain are in calibrating the sensor output and generating biological insight. A colleague from the United Kingdom, Tony Pridmore, captured the thought well, saying “Photography is not phenotying.” It’s generally easy to take the pictures — unless it’s very windy, the aerial platforms can pass over any crop, and the ground platforms are based on proven agricultural equipment. To get biological insights however, each team requires an analytics component, and a team from IBM is contributing their analytics expertise in collaboration with Purdue University.

 

 

What is most exciting about the TERRA program?

We commissioned the world’s biggest agricultural field robot, which phenotypes year-round. The six teams have successfully built other lightweight platforms involving tractors, rovers, mini-bots, and fixed and rotary wing unmanned aerial vehicles. It’s exciting to see some of the most advanced technologies move so quickly into the hands of great geneticists. The amazing thing is how quickly the teams have started generating phenotyping data. I expected it to take years before we got to this point, but the teams are knocking it out of the park, and we are entering into full-blown breeding systems deployment.

 

Who’s on the TERRA teams? How did you build the program?

ARPA-E system teams include large businesses, startups, and university groups. The program was built to have a full portfolio of diverse sensor suites, robotic platform types (ground and aerial), analytics approaches, and geographic breadth. Because breeders are working for a particular target population of environments, different phenotypes are valued differently across the various geographies. For that reason, each group is collecting its own set of phenotypes. Beyond that, we’ve worked very hard to encourage collaboration across the teams and have an exciting GxE (genotype x environment) experiment running, where several teams plant the same germplasm across multiple geographies. By combining this with high-throughput phenotyping, the teams are in a good position to determine key environmental inputs to various traits.

 

Once we achieve rapid-fire field phenotyping, what’s next?

We’re going underground! ARPA-E has made another targeted investment, this time in root phenotyping. We’re really excited about this one. It’s a very similar concept, but the sensing is so much harder. The teams have collaborated with medical, mining, aerospace, and defense communities for technologies that can allow us to observe root and soil systems in the field to allow breeders to improve crops.  Ask us again next year—we will have some cool updates to both programs!

Taking the brakes off plant production: not so good after all

Reposted with kind permission from the MSU-DOE Plant Research Laboratory. Original article.

By: Igor Houwat, Atsuko Kanazawa, David Kramer

The need for speed: increasing plant yield is one way to increase food and fuel resources. But asking plants to simply do more of the usual is a strategy that can backfire. Photo by Romain Peli on Unsplash

When engineers want to speed something up, they look for the “pinch points”, the slowest steps in a system, and make them faster.

Say, you want more water to flow through your plumbing. You’d find the narrowest pipe and replace it with a bigger one.

Many labs are attempting this method with  photosynthesis, the process that plants and algae use to capture solar energy.

All of our food and most of our fuels have come from photosynthesis. As our population increases, we need more food and fuel, requiring that we improve the efficiency of photosynthesis.

But, Dr. Atsuko Kanazawa and the Kramer Lab are finding that, for biological systems, the “pinch point” method can potentially do more harm than good, because the pinch points are there for a reason!  So, how can this be done?

 

ATP synthase: an amazing biological nanomachine

Atsuko and her colleagues at the MSU-DOE Plant Research Laboratory (PRL) have been working on this problem for over 15 years. They have focused on a tiny machine in the  chloroplast called the  ATP synthase, a complex of proteins essential to storing solar energy in “high energy molecules” that power life on Earth.

That same ATP molecule and a very similar ATP synthase are both used by animals, including humans, to grow, maintain health, and move.

In plants, the ATP synthase happens to be one of the slowest process in photosynthesis, often limiting the amount of energy plants can store.

Photosynthetic systems trap sunlight energy that starts the reaction to move electrons forward in an assembly-line fashion to make useful energy compounds. The ATP synthase is one of the “pinch points” that slows the flow as needed, so plants stay healthy. In cfq, the absence of feedback leads to an electron pile up at PSI, and a crashed system. By MSU-DOE Plant Research Laboratory, except tornado graphic/CC0 Creative Commons

 

Kicking up the gears of plant production

Atsuko thought, if the ATP synthase is such an important pinch point, what happens if it were faster? Would it be better at photosynthesis and give us faster growing plants?

Years ago, she got her hands on a mutant plant, called cfq, from a colleague. “It had an ATP synthase that worked non-stop, without slowing down, which was a curious example to investigate. In fact, under controlled laboratory conditions – very mild and steady light, temperature, and water conditions – this mutant plant grew bigger than its wild cousin.”

But when the researchers grew the plant under the more varied conditions it experiences in real life, it suffered serious damage, nearly dying.

“In nature, light and temperature quality change all the time, whether through the passing hours, or the presence of cloud cover or winds that blow through the leaves,” she says.

 

Plants slow photosynthesis for a reason!

Recent innovations from the Kramer lab are enabling Atusko and her colleagues to probe into how real environmental conditions affect plant growth.

Atsuko’s research now shows that the slowness of the ATP synthase is not an accident; it’s an important braking mechanism that prevents photosynthesis from producing harmful chemicals, called reactive oxygen species, which can damage or kill the plant.

“It turns out that sunlight can be damaging to plants,” says Dave Kramer, Hannah Distinguished Professor and lead investigator in the Kramer lab.

“When plants cannot use the light energy they are capturing, photosynthesis backs up and toxic chemicals accumulate, potentially destroying parts of the photosynthetic system. It is especially dangerous when light and other conditions, like temperature, change rapidly.”

“We need to figure out how the plant presses on the brakes and tune it so that it responds faster…”

The ATP synthase senses these changes and slows down light capture to prevent damage. In that light, the cfqmutant’s fast ATP is a bad idea for the plant’s well-being.

“It’s as if I promised to make your car run faster by removing the brakes. In fact, it would work, but only for a short while. Then things go very wrong!” Dave says.

“In order to improve photosynthesis, what we need is not to remove the brakes completely, like in cfq, but to control them better,” Dave says. “Specifically, we need to figure out how the plant presses on the brakes and tune it so that it responds faster and more efficiently,” David says.

Atsuko adds: “Scientists are trying different methods to improve photosynthesis. Ultimately, we all want to tackle some long-term problems. Crucially, we need to continue feeding the Earth’s population, which is exploding in size.”

The study is published in the journal, Frontiers in Plant Science.

 

Potatoes, allies on Earth and on Mars

By
Zoraida Portillo (Perú)

[LIMA] A joint initiative between NASA and the International Potato Centre (CIP), which is based in Peru, offers scientific evidence that it is possible to grow at least four types of potatoes on Mars.

A scenario starring the root crop was portrayed in the movie “The Martian” (2015), in which a lost astronaut, played by Matt Damon, survives on potatoes he cultivates on the red planet while awaiting rescue.

But in addition to this interplanetary possibility, scientists also observed the crop is genetically suited to adapting to the changes creating more adverse environmental conditions on Earth.

So before turning fiction into reality, the tuber has a mission on Earth.

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In the movie “The Martian”, Matt Damon survives eating the potatoes he cultivates on Martian soil. Credit: 20th Century Fox.

The hardy potato quartet
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Scientists have studied 65 types of potatoes and have identified four that could grow successfully on Martian soil. Credit: International Potato Center / Mars Project

The study has identified four types of potatoes, out of 65 examined, which have shown resistance to high salinity conditions and were able to form tubers in a type of soil similar to that on Mars.
One of these is the Tacna variety, developed in Peru in 1993. It was introduced to China shortly afterwards, where it showed high tolerance to droughts and saline soils with hardly any need for irrigation.

This variety became so popular in China that it was ‘adopted’ in 2006 under the name of Jizhangshu 8. The same high tolerance was seen on the saline and arid soils of Uzbekistan, a country with high temperatures and water shortages, where the variety was also introduced and renamed as Pskom.

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In China, the Peruvian Tacna potato variety was renamed Jizhangshu 8. Credit: International Potato Center 

The second variety that passed the salinity test is being cultivated in coastal areas of Bangladesh that have high salinity soils and high temperatures. The other two types are promising clones — potatoes that are being tested for attributes that would make them candidates for becoming new varieties.

These four potato types were created as a result of the CIP’s breeding programme to encourage adaptation to conditions in subtropical lowlands, such as extreme temperatures, which are expected to be strongly affected by climate change.

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Women harvest resistant potatoes in saline soils in Bangladesh. Credit: International Potato Center

Down to Earth

In addition to these four potato ‘finalists’, other clones and varieties have shown promising results when tested in severe environmental conditions. The findings offer researchers new clues about the genetic traits that can help tubers cope with severe weather scenarios on Earth.

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Walter Amorós, CIP’s potato breeder is one of the five researchers involved in the project. Credit: Zoraida Portillo

“It was a pleasant surprise to see that the potatoes that we have improved to tolerate adverse conditions were able to produce tubers on this soil [soil similar to that on Mars],” says Walter Amorós, CIP potato breeder and one of the five researchers involved in the project, who has studied potatoes for more than 30 years.

According to Alberto García, adviser to the UN Food and Agriculture Organization in Peru who is in charge of food security programmes, this experiment “serves to verify that potato, a produce of great nutritional value, is a crop extremely adaptable to the worst conditions”, something that is very relevant for current climate scenarios.

García stresses that global temperatures are now rising at a rate higher than expected, affecting not only potatoes but also other crops. Many now need to be cultivated at higher altitudes — which, he says, is not always a disadvantage and may even be beneficial for crops that were previously cultivated in valleys.

papa-en-marte-7-by ZP.jpg

Credit: Zoraida Portillo

“But it can also have negative consequences that we have to anticipate,” adds García. Therefore, he says this experiment can inspire others to think about future scenarios and look for other crops than can adapt to extreme conditions that will have an impact on agriculture.

Similar to Mars

The project began with a search for soils similar to that found on Mars. Julio Valdivia-Silva, a Peruvian researcher who worked at NASA’s Ames Research Center, eventually concluded that the soil samples collected in the Pampas de la Joya region of southern Peru were the most similar to Martian soil.

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Julio Valdivia-Silva took soil samples at Pampa de La Joya, Peru. Credit: NASA/ International Potato Center

Arid, sterile and formed by volcanic rocks, these soil samples were extremely saline.

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Credit: Pampas de La Joya Official Site

 

Helped by engineers from the University of Engineering and Technology (UTEC) in Lima and based on designs by NASA’s Ames Research Center, the CIP built CubeSat — a miniature satellite that recreates, in a confined environment, a Martian-like atmosphere. This is where the potatoes were cultivated.

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The varieties were cultivated inside CubeSat, built by the CIP to recreate environmental conditions similar to those on Mars. Credit: International Potato Center / Mars Project

“If potatoes could tolerate the extreme conditions to which we exposed them in our CubeSat, they have a good opportunity to develop on Mars,” says Valdivia-Silva.

They then conducted several rounds of experiments to find out which varieties could better withstand the extreme conditions, and what minimum conditions each crop needed to survive.

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La Joya desert, Peru (left); Martian soil (right). Credits: Pampas de La Joya Official Site and NASA, respectively.

CubeSat, hermetically sealed, housed a container with La Joya soil, where each one of the tubers was cultivated. CubeSat itself supplied water and nutrients, controlled the temperature according to that expected at different times on Mars, and also regulated the planet’s pressure, oxygen and carbon dioxide levels.

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Connected to a computer, the CubeSat supplied water and nutrients, and imitated other environmental conditions that would be found on Mars. Credit: International Potato Center / Mars Project

 

Cameras were installed to record the process, broadcasting developments on the soil and making it possible to see the precise moment in which potatoes sprouted.

Based on the results, CIP scientists say that in order to grow potatoes on Mars, space missions will have to prepare the soil so it has a loose structure and contains nutrients that allow the tubers to obtain enough oxygen and water.

In a next phase of the project, the scientists hope to expose successful varieties to more extreme environmental conditions. This requires, among other things, developing a prototype satellite similar to CubeSat that can replicate more extreme conditions with greater precision, at a price tag of US$ 100,000.

This piece was produced by SciDev.Net’s Latin America and Caribbean desk.

This article was originally published on SciDev.Net. Read the original article.

Roots of a second green revolution

This week we spoke to Professor Jonathan Lynch, Penn State University, whose research on root traits has deepened our understanding of how plants adapt to drought and low soil fertility.

 

 

Could you begin by giving us a brief introduction to your research?

We are trying to understand how plants adapt to drought and low soil fertility. This is important because all plants in terrestrial ecosystems experience suboptimal water and nutrient availability, so in rich nations we maintain crop yields with irrigation and fertilizer, which is not sustainable in the long term. Furthermore, climate change is further degrading soil fertility and increasing plant stress. This topic is therefore both a central question in plant evolution and a key challenge for our civilization. We need to develop better ways to sustain so many people on this planet, and a big part of that will be developing more resilient, efficient crop plants.

 

Drought is devastating for crops

Drought and low soil fertility are devastating for crops. Image credit: CIAT. Used under license: CC BY-SA 2.0.

 

What got you interested in this field, and how has your career developed over time?

When I was 9 years old I became aware of a famine in Africa related to crop failure and resolved to do something about it. I studied soils and plant nutrition as an undergraduate, and in graduate school worked on plant adaptation to low phosphorus and salinity stress, moving to a research position at the CIAT headquarters in Colombia. Later I moved to Penn State, where I have maintained this focus, working to understand the stress tolerance of staple crops, and collaborating with crop breeders in the USA, Europe, Africa, Asia, and Latin America.

 

Your recent publications feature a variety of different crop plants. Could you talk about how you select a species to study?

We work with species that are important for food security, that grow in our field environments, and that I think are cool. We have devoted most of our efforts to the common bean – globally the most important food legume – and maize, which is the most important global crop. These species are often grown together in Africa and Latin America, and part of our work has been geared to understanding how maize/bean and maize/bean/squash polycultures perform under stress. These are fascinating, beautiful plants with huge cultural importance in human history. They are also supported by talented, cooperative research communities. One nice feature of working with food security crops is that their research communities share common goals of achieving impact to improve human welfare.

 

Common bean (Phaseolus vulgaris)

The common bean (Phaseolus vulgaris) is an important staple in many parts of the world. Image credit: Ervins Strauhmanis. Used under license: CC BY 2.0.

 

Many researchers use Arabidopsis thaliana for plant research, but are crops better suited for root research than the delicate roots of Arabidopsis? Are crop plants more or less difficult to work with in your research than Arabidopsis?

The best research system is entirely a function of your goals and questions. We have worked with Arabidopsis for some questions. Since we work with processes at multiple scales, including crop stands, whole organisms, organs, tissues, and cells, it has been useful to work with large plants such as maize, which are large enough to easily measure and to work with in the field. The most interesting stress adaptations for crop breeding are those that differ among genotypes of the same species, and at that level of organization there is a lot of biology that is specific to that species, that cannot readily be generalized from model organisms with very different life strategies. There has been considerable attention to model genomes and much less attention to model phenomes.

 

You have developed methodologies for the high-throughput phenotyping of crop plants. What does this technique involve and what challenges did you have to overcome to succeed?

We have developed multiple phenotyping approaches – too many to summarize readily here. Our overall approach is simply to develop a tool that helps us achieve our goals. For example, we have developed tools to quantify the root architecture of thousands of plants in the field, to measure anatomical phenotypes of thousands of samples from field-grown roots, to help us determine which root phenotypes might affect soil resource capture, etc. Working with geneticists and breeders, we are constantly asked to measure something meaningful on thousands of plants in a field, in many fields, every season. ARPA-E (the US Advanced Research Projects Agency for Energy) has recently funded us to develop phenotyping tools for root depth in the field, but this is the first time we have been funded to develop phenotyping tools – generally we just come up with things to help us do our work, which fortunately have been useful for other researchers as well.

 

Could you talk about some of the computational models you have developed for investigating plant growth and development?

The biological interactions between plants and their environment are so complex, we need computational (in silico) tools to help us evaluate them. Increasingly, in silico tools can integrate information across multiple scales, from gene expression to crop stands. These tools also allow us to evaluate things that are difficult to measure, such as phenotypes that do not yet exist, or future climates. In silico biology will be an essential tool in 21st Century biology, which will have access to huge amounts of data at multiple scales that can be used to try to understand incredibly complex systems, such as the human brain or roots interacting with living soil. Our main in silico tool is SimRoot, developed over the past 25 years to understand how root phenotypes affect soil resource capture.

Check out a SimRoot model below:


 

You have been working on breeding plants that have improved yield in soils with low fertility. What have you achieved in this work?

In collaboration with crop breeders and colleagues in various nations we have developed improved common bean lines with better yield under drought and low soil fertility that are being deployed in Africa and Latin America, improved soybean lines with better yield in soils with low phosphorus being deployed in Africa and Asia, and are now working with maize breeders in Africa to develop lines with better yield under drought and low nitrogen stress. Many crop breeders are using our methods for root phenotyping to target root phenotypes in their selection regimes in multiple crops.

 

What piece of advice do you have for early career researchers?

You are at the forefront of an unprecedented challenge we face as a species – how to sustain 10 billion people in a degrading environment. Plant biologists are an essential part of the effort to reshape how we live on this planet. Do not doubt the importance of your efforts. Do not lose sight of the very real human impact of your scientific choices. Do not be deterred by the gamesmanship and ‘primate politics’ of science. You can make a difference. We need you.

Creole maize reveals adaptation secrets

By Lucina Melesio

[MEXICO CITY] An international team of scientists identified a hundred genes that influence adaptation to the latitude, altitude, growing season and flowering time of nearly 4,500 native maize varieties in Mexico and in almost all Latin American and Caribbean countries.

Creole — or native — varieties of maize are derived from improvements made over thousands of years by local farmers, and contain genes that help them adapt to different environments.

“We are now using this analysis to find other genes that are of vital importance to breeders, such as those resistant to extreme heat, frost or drought — environmental conditions associated with climate change and that could affect maize production.”

Sarah Hearne, CIMMYT

“Latin American breeders will be able to use these results to identify native varieties that could contribute to improved adaptation”, Edward Buckler, a Cornell University researcher and co-author of the study published in Nature Genetics (February 6), told SciDev.Net.

The information on the genetic markers described in the study will be available online, said Sarah Hearne, a researcher at the International Maize and Wheat Improvement Center (CIMMYT) and co-author of the study. “Meanwhile, any breeder can contact us to request information”, she said.

“We are now using this analysis to find other genes that are of vital importance to breeders, such as those resistant to extreme heat, frost or drought — environmental conditions associated with climate change and that could affect maize production”, Hearne said.

Maize ears from CIMMYT’s collection, showing a wide variety of colors and shapes. CIMMYT’s germplasm bank contains about 28,000 unique samples of cultivated maize and its wild relatives, teosinte and Tripsacum. These include about 26,000 samples of farmer landraces—traditional, locally-adapted varieties that are rich in diversity. The bank both conserves this diversity and makes it available as a resource for breeding.
Photo credit: Xochiquetzal Fonseca/CIMMYT.

Studying native maize varieties is extremely difficult because of their genetic variation. Although domesticated, they are wilder than commercial varieties.

For this study, the researchers cultivated hybrid creole varieties in various environments in Latin America and identified regions of the genome that control growth rates. They looked into where the varieties came from and what genetic features contributed to their growth in that environment.

 In comments to SciDev.Net, James Holland, a researcher at North Carolina State University, Jeffrey Ross-Ibarra, a researcher at the University of California Davis, and Rodomiro Ortiz, a researcher at the Swedish University of Agricultural Sciences — who did not participate in the study — commended the magnitude of the study and the original method developed by the researchers to access the rich set of genetic information about native maize varieties.

Hearne added that the research team has initiated a “pre-breeding” programme with a small group of breeders in Mexico. As part of that programme, CIMMYT delivers to breeders materials from its germplasm bank of Creole maize; it also provides molecular information the breeders can use to generate new varieties.

This piece was produced by SciDev.Net’s Latin America and Carribean edition.

This article was originally published on SciDev.Net. Read the original article.

Global Plant Council stress resilience commentaries published in Food and Energy Security

In October 2015, researchers from around the world came together in Iguassu Falls, Brazil, for the Stress Resilience Symposium, organized by the Global Plant Council and the Society for Experimental Biology (SEB), to discuss the current research efforts in developing plants resistant to the changing climate. (See our blog by GPC’s Lisa Martin for more on this meeting!)

Building on the success of the meeting, the Global Plant Council team and attendees compiled a set of papers to provide a powerful call to action for stress resilience scientists around the world to come together to tackle some of the biggest challenges we will face in the future. These four papers were published in the Open Access journal Food and Energy Security alongside an editorial about the Global Plant Council.

In the editorial, the Global Plant Council team (Lisa Martin, Sarah Jose, and Ruth Bastow) introduce readers to the Global Plant Council mission, and describe the Stress Resilience initiative, the meeting, and introduce the papers that came from it.

In the first of the commentaries, Matthew Gilliham (University of Adelaide), Scott Chapman (CSIRO), Lisa Martin, Sarah Jose, and Ruth Bastow discuss ‘The case for evidence-based policy to support stress-resilient cropping systems‘, commenting on the important relationships between research and policy and how each must influence the other.

Global Plant Council President Bill Davies (Lancaster University) and CIMMYT‘s Jean-Marcel Ribaut outline the ways in which research can be translated into locally adapted agricultural best practices in their article, ‘Stress resilience in crop plants: strategic thinking to address local food production problems‘.

In the next paper, ‘Harnessing diversity from ecosystems to crops to genes‘, Vicky Buchanan-Wollaston (University of Warwick), Zoe Wilson (University of Nottingham), François Tardieu (INRA), Jim Beynon (University of Warwick), and Katherine Denby (University of York) describe the challenges that must be overcome to promote effective and efficient international research collaboration to develop new solutions and stress resilience plants to enhance food security in the future.

University of Queensland‘s Andrew Borrell and CIMMYT‘s Matthew Reynolds discuss how best to bring together researchers from different disciplines, highlighting great examples of this in their paper, ‘Integrating islands of knowledge for greater synergy and efficiency in crop research‘.

In all of these papers, the authors suggest practical short- and long-term action steps and highlight ways in which the Global Plant Council could help to bring researchers together to coordinate these changes most effectively.

Read the papers in Food and Energy Security here.

Lentils under the lens: Improving genetic diversity for sustainable food security

This week’s post comes to us from Crystal Chan, project manager of the Application of Genomic Innovation in the Lentil Economy project led by Dr. Kirstin Bett at the Department of Plant Sciences, University of Saskatchewan.

 

Could you begin with a brief introduction to your research?

Our research focuses on the smart use of diverse genetic materials and wild relatives in the lentil (Lens culinaris) breeding program.

Canada has become the world’s largest producer and exporter of lentils in recent years. Lentils are an introduced species to the northern hemisphere and, until recently, our breeding program at the University of Saskatchewan involved just a handful of germplasms adapted to our climatic condition. With dedicated breeding efforts we have achieved noteworthy genetic gains in the past decade, but we are missing out on the vast genetic diversity available within the Lens genus. This is a major dilemma faced by all plant breeders: do we want consistency (sacrificing genetic diversity and reducing genetic gains over time) or diversity (sacrificing some important fixed traits and spending lots of time and resources in “backcrossing/rescue efforts”)?

 

In our current research, we use genomic tools to understand the genetic variability found in different lentil genotypes and the basis of what makes lentils grow well in different global environments (North America vs. Mediterranean countries vs. South Asian countries). We will then develop molecular breeding tools that breeders can use to improve the diversity and productivity of Canadian lentils while maintaining their adaptation to the northern temperate climate.

 

What first led you to this research topic?

Dr. Albert (Bert) Vandenberg, professor and lentil breeder at the University of Saskatchewan, noticed one of the wild lentil species was resistant to several diseases that devastate the cultivated lentil. After years of dedicated breeding effort, he was able to transfer the resistance traits to the cultivated lentil, but it took a lot of time and resources. We began looking into other beneficial traits and became fascinated with the domestication and adaptation aspects of lentil – after all lentil is one of the oldest cultivated crops, domesticated by man around 11,000 BC! With the rapid advance in genomic technology, we can start to better understand the biology and develop tools to harness these valuable genetic resources.

 

You have been involved in the development of tools that assist researchers to build databases of genomics and genetics data. Could you tell us more about projects such as Tripal?

Over the past six years, Lacey Sanderson (bioinformaticist in our group) has developed a database for our pulse research program at the University (Knowpulse, http://knowpulse.usask.ca/portal/). The database is specifically designed to present data that is relevant to breeders, as our group has a strong focus on variety development for the Canadian pulse crop industry. Knowpulse houses genotypic information from past and on-going lentil genomics projects, and includes tools for looking up genotypes as well as comparing the current genome assembly (currently v1.2) and other sequenced legume genomes. The tools are being developed in Tripal, an open-source toolkit that provides an interface between the data and a Drupal web content management system, in collaboration with colleagues at Washington State University.

 

At the moment we are developing new functionalities that will allow us to store and present germplasm information as well as phenotypic data. We are also working with our colleagues at Washington State University (under the “Tripal Gateway Project” funded by the National Science Foundation) to enhance interconnectivity between Knowpulse and other legume databases, such as the Legume Information Service (LIS) and Soybase, to facilitate comparative genomic studies.

How challenging are pulse genomes to assemble? How closely related are the various crops?

We had the fortune to lead the lentil genome sequencing initiative thanks to the support from producer groups and governments across the globe.  The lentil genome is really challenging to assemble! We see nice synteny between lentil and the model legume, medicago, however the lentil genome is much bigger. We see a significant increase in genome size between chickpea and beans versus lentil (and pea for that matter), yet we have evidence to show that genome duplication is not the cause of the size increase. There are a lot of very long repetitive elements sprinkled around the genome, which makes its sequencing and proper assembly very challenging. Not to mention understanding the role of these long repetitive elements in biological functions…

 

What insights into crop domestication have you gained from these genomes?

That’s what we are working on right now under the AGILE (“Application of Genomics to Innovation in the Lentil Economy”) project. Stay tuned!

 

Do you work with breeders to develop new cultivars? What sorts of traits are most important? 

Breeding is at the core of our work – both Kirstin and Bert are breeders (Kirstin has an active dry bean breeding program when she’s not busy with genomic research). All our research aims to feed information to the breeders so that they can make better crossing and selection decisions. Our work in herbicide tolerance has led to the development and implementation of a molecular marker to screen for herbicide resistance. With that marker we save time (skipping a crossing cycle) and forego the herbicide spraying test for all of our early materials.

Disease resistance and drought tolerance are also important for the growers. Visual quality (seed shape, size, color) are very important too as our customers are very picky as to what sort of lentils they like to buy/eat.

What does the future of legume/lentil agriculture hold?

Lentils have been a staple food in many countries for centuries and have been gaining popularity in North America in recent years as people are looking for plant-based protein sources. Lentils are high in fibre, protein, and complex carbohydrates, while low in fat and calories, and have a low glycemic index. They are suitable for vegetarian/vegan, gluten-free, diabetic, and heart-smart diets. Lentils also provide essential micronutrients such as iron, zinc and folates. Lentils are widely recognized as nutrient-dense food that could serve as part of the solution to combat global food and nutritional insecurity.

In modern agriculture, adding lentil or other leguminous crops in the crop rotation helps improve soil structure, soil quality, and biotic diversity, as well as enhancing soil fertility through their ability to fix nitrogen. Because pulse crops require little to no nitrogen fertilizer, they use half of the non-renewable energy inputs of other crops, reducing greenhouse gas emissions.

2016 was marked by the United Nations as the International Year of Pulses, which was great as many people have become more aware of the benefits of pulse crops on the plate and in the field.

 

Follow us on twitter (@Wildlentils) for research updates!

 

All images are credited to Mr Derek Wright.

Sustainable, resilient, and nutritious food production with N8 AgriFood

This week we spoke with Dr Sally Howlett, a Knowledge Exchange Fellow with the N8 AgriFood Programme. (More on Sally at the end).

Sally, what is the N8 AgriFood Programme? When and why was it established?

The N8 Research Partnership is a collaboration of the eight most research-intensive universities in the North of England, namely Durham, Lancaster, Leeds, Liverpool, Manchester, Newcastle, Sheffield, and York. It is a not-for-profit organization with the aim of bringing together research, industry and society in joint initiatives. These partners have a strong track record of working together on large-scale, collaborative research projects, one of which is the N8 AgriFood Programme. This £16M multi-disciplinary initiative is funded by the N8 partners and HEFCE (The Higher Education Funding Council for England), and was launched in 2015 to address three key global challenges in Food Security: sustainable food production, resilient food supply chains, and improved nutrition and consumer behavior.

How does plant science research fit into the N8 AgriFood Programme?

There is a strong motivation to ‘think interdisciplinary’ when it comes to developing projects for the N8 AgriFood Programme; therefore, whilst the most obvious home for plant science may be within the theme of sustainable food production, e.g. crop improvement, we see no boundaries when it comes to integrating fundamental research in plant science with applications in all three of our research themes. The testing of research ideas in the ‘real world’ is supported by the five University farms within the N8, which include arable and livestock holdings.

We are launching a Crop Innovation Pipeline to assist with the translation of research into practical applications, with the first event taking place in Newcastle on 2nd-3rd May 2017. It is an opportunity for scientists from academia and industry and representatives from the farming community to discuss their ideas for the implementation of plant biology research into on-farm crop improvement strategies.

How is the work split between the different institutions? How is such a large-scale initiative managed?

Whilst there are many areas of shared expertise between the eight partner institutions, each also has its own areas of specialism within the agri-food arena. The strength of the N8 AgriFood Programme is in working collaboratively to identify complementary strengths and grow those areas in a synergistic way. In this way, we are collectively able to tackle research projects that would not be possible for a single university alone. Pump-priming funds are available at a local and strategic level to support this kick-starting of new multi-institution projects. The Programme itself is led out of the University of York, and each University has its own N8 AgriFood Chair in complementary areas across the Programme. Having both inward- and outward-facing roles, they work with the Knowledge Exchange Fellows and the Programme Lead for each theme to ensure activities at their own institute are connected with what is going on in the wider N8.

What does your work as a Knowledge Exchange Fellow entail?

As a Knowledge Exchange Fellow within the N8 AgriFood Programme, my initial contact with people usually begins with the question ‘What on earth does a Knowledge Exchange Fellow do?’ – and it can be quite difficult to answer! Although some form of knowledge transfer activity has been a defined output of research projects for some time now, knowledge exchange as an ongoing two-way dialogue between researchers and external stakeholders to enable a co-creation process has been less common until recently. Hence dedicated Knowledge Exchange Fellows with academic training are a relatively ‘new’, but growing, phenomenon.

My role is best described as acting as a bridge between the research community and non-academics with a vested interest in developing or using the findings of the research process. It is key to have a good understanding of the perspectives of all parties involved and be able to translate this into the appropriate language for a particular sector. Each of the N8 institutes has appointed Knowledge Exchange Fellow(s), and we work as a cohort to keep abreast of the latest developments in our fields in order to support the development of relationships and innovative projects. In such a huge undertaking, the phrase ‘there is strength in numbers’ is certainly apposite!

 

How does N8 AgriFood interact with companies?

N8 Agrifood engages with UK-based companies in many ways, including individual face-to-face meetings, attending and hosting networking events, participating in national exhibitions, and holding business-facing conferences. We also run a series of Industry Innovation Forums on various topics throughout the year. These provide a unique opportunity to discuss key challenges, identify problems and deliver new insights into innovation for agri-food, matching practical and technical industry challenges with the best research capabilities of the N8 universities.

 

How does N8 Agrifood interact with farmers?

As the engine of the agri-food industry, the views and collective experience of the farming community are vitally important in shaping the direction and content of the projects we develop. Co-hosting events with programs such as the ADAS Yield Enhancement Network (YEN), which involves over 100 farms, is one way that we connect with the sector. We are also working with agricultural societies to promote what we are doing and engage directly with their networks of farming members, e.g. the Yorkshire Agricultural Society’s Farmer Scientist Network. Last year we gave a series of seminars at the Great Yorkshire Show and are keen to encourage further collaboration with practicing farmers and growers across the UK.

 

Does N8 AgriFood collaborate with other research institutes around the world?

The N8 AgriFood Programme has strong international connections and actively welcomes working with international research institutes. Given the interconnectedness of our global food system, we feel that it is vital to link with overseas partners and that real impact can be had by bringing together top researchers from other countries to work together on problems. The value of N8 AgriFood as a one-stop shop is that we represent a large breadth and depth of expertise under a single umbrella, which greatly facilitates collaborating and finding suitable collaboration partners. Our pump-priming funds are a way for researchers to initiate new international partnerships, and we are also working to build links with global research organizations who have shared interests. For example, we recently visited Brazil and China to explore specific opportunities for collaboration and leveraging of research expertise and facilities, and are currently organizing a workshop in Argentina in March.

 

Where can readers get more information?

If you’d like to find out more, please visit our website: http://n8agrifood.ac.uk/, or consider attending one of our upcoming events:

 

All images are credited to the N8 Agrifood Programme.


Dr Sally Howlett is a Knowledge Exchange Fellow with the N8 AgriFood Programme. Her research background is in sustainable crop production and plant pest management.  After working on the control of invertebrate crop pests in New Zealand for several years, she returned to on-farm research in the UK and extended her focus to include the crops themselves taking a whole-systems view and comparing performance under conventional, organic and agroforestry management approaches. Sally’s role within N8 AgriFood provides a great opportunity to use her experience of agriculture and working with different actors across the sector to engage with external stakeholders, co-producing ideas and multi-disciplinary projects with applications throughout the agrifood chain.

Chickpea innovation: Revisiting the origins of crops to solve the challenges of modern agriculture

Doug Cook

Professor Doug Cook

This post was written by Professor Doug Cook (University of California, Davis), the Director of the Feed the Future Innovation Lab for Climate Resilient Chickpea. His current research spans both model and crop legume systems from a cellular to an ecosystem scale. 

 

The origins of modern human society derive, in large part, from the transition to an agrarian lifestyle that occurred in parallel at multiple locations around the world, including ~10,000 years ago in Mesopotamia*. Early agriculturalists wrought a revolution that would define human trajectory to the current day, domesticating wild plant and animal species into crops and livestock. The wild progenitors of chickpea, for example, were among a handful of Mesopotamian neo-crops, brought from hilly slopes into more fertile and cultivable plains and river valleys. In doing so, these farmers selected a small number of useful traits largely based on natural mutations that made wild forms amenable to agriculture, such as the consistency of flowering, upright growth, and seeds that remained attached to plants rather than dispersing.

Chickpea innovation

Doug Cook collecting chickpeas

Collecting wild chickpea plants, soil, and seed in southeastern Turkey. Image credit: Chickpea Innovation lab.

An unintended consequence of crop domestication was the loss of the vast majority of genetic diversity found in the wild populations. The Feed the Future Innovation Lab for Climate Resilient Chickpea at the University of California, Davis (Chickpea Innovation Lab) documented a ~95% loss of genetic variation from wild species to modern elite varieties. This reduction in genetic variation constrains our ability to adapt the chickpea crop to the range of challenges facing modern agriculture.

The Chickpea Innovation Lab is re-awakening the untapped potential of wild chickpea and directing that potential to solve global problems in agriculture, especially in the developing world.  Combining longstanding practices in ecology with the remarkable power of genomics and sophisticated computational methods, we have spanned the gap from the wild systems to cultivated crops. Beginning with the analysis of ~2,000 wild genomes, the simple technology of genetic crosses applied at massive scale has delivered a large and representative suite of wild variation into agricultural germplasm. These traits are now being actively used for phenotyping and breeding in the U.S., India, Ethiopia and Turkey, and our team is currently prospecting for tolerance to drought, heat and cold; increased pest and disease resistance; improved seed nutritional content; nitrogen fixation; plant architecture; and yield.

Characterizing wild germplasm

Sultan Mohammed Yimer

Visiting Ethiopian student, Sultan Mohammed Yimer investigating disease resistance in wild chickpea. Image credit: Chickpea Innovation lab.

Along the way, the Chickpea Innovation Lab has deposited wild germplasm into the multi-lateral system, providing open access to a treasure trove of genetic variation. The Chickpea Innovation Lab derives support from numerous sponsors whose funds enable the collection, characterization, and utilization of this vital germplasm resource.

International research

A unique strength of the lab is that our diverse sponsorship permits activities ranging from fundamental scientific investigation to applied agricultural research and product development.

An additional objective of the Lab is to train and educate students in the developing world. Towards that end, 18 international and nine domestic students, postdoctoral scientists and visiting faculty have received training in disciplines ranging from computational biology, plant pathology and entomology, to agricultural microbiology, and molecular genetics and breeding.

Chickpea breeding

Harvesting progeny derived by crossing wild and cultivated chickpea plants in Davis, California. Image credit: Chickpea Innovation lab.

* Mesopotamia, literally “between the rivers”, is the region of modern day southeastern Turkey, bounded by the Tigris and Euphrates rivers.