Targeted genome engineering has been described as a “game-changing technology” for fields as diverse as human genetics and plant biotechnology. Novel techniques such as CRISPR-Cas9, Science’s 2015 Breakthrough of the Year, are revolutionizing scientific research, allowing the targeted and precise editing of genomes in ways that were not previously possible.
Used alongside other tools and strategies, gene-editing technologies have the potential to help combat food and nutritional insecurity and assist in the transition to more sustainable food production systems. The application and use of these technologies is therefore a hot topic for a wide range of stakeholders including scientists, funders, regulators, policy makers and the public. Despite its potential, there are a number of challenges in the adoption and uptake of genome editing, which we propose to highlight during this SEB satellite meeting.
One of the challenges that scientists face in applying technologies such as CRISPR-Cas9 to their research is the technique itself. Although the theoretical framework for using these techniques is easy to follow, the reality is often not so simple. This meeting will therefore explain the principles of applying CRISPR-Cas9 from experts who have successfully used this system in a variety of plant species. We will explore the challenges they encountered as well as some of the solutions and systems they adopted to achieve stably transformed gene-edited plants.
The second challenge for these transformative technologies is how regulatory bodies will treat and asses them. In many countries gene editing technologies do not fit within current policies and guidelines regarding the genetic modification and breeding of plants, as it possible to generate phenotypic variation that is indistinguishable from that generated by traditional breeding methods. Dealing with the ambiguities that techniques such as CRISPR-Cas9 have generated will be critical for the uptake and future use of new breeding technologies. This workshop will therefore outline the current regulatory environment in Europe surrounding gene editing, as well as the approaches being taken in other countries, and will discuss the potential implications and impacts of the use of genome engineering for crop improvement.
Overall this meeting will be of great interest to plant and crop scientists who are invested in the future of gene editing both on a practical and regulatory level. We will provide a forum for debate around the broader policy issues whilst include opportunities for in-depth discussion regarding the techniques required to make this technology work in your own research.
One of the biggest modern myths about agriculture is that organic farming is inherently sustainable. It can be, but it isn’t necessarily. After all, soil erosion from chemical-free tilled fields undermined the Roman Empire and other ancient societies around the world. Other agricultural myths hinder recognizing the potential to restore degraded soils to feed the world using fewer agrochemicals.
When I embarked on a six-month trip to visit farms around the world to research my forthcoming book, “Growing a Revolution: Bringing Our Soil Back to Life,” the innovative farmers I met showed me that regenerative farming practices can restore the world’s agricultural soils. In both the developed and developing worlds, these farmers rapidly rebuilt the fertility of their degraded soil, which then allowed them to maintain high yields using far less fertilizer and fewer pesticides.
Their experiences, and the results that I saw on their farms in North and South Dakota, Ohio, Pennsylvania, Ghana and Costa Rica, offer compelling evidence that the key to sustaining highly productive agriculture lies in rebuilding healthy, fertile soil. This journey also led me to question three pillars of conventional wisdom about today’s industrialized agrochemical agriculture: that it feeds the world, is a more efficient way to produce food and will be necessary to feed the future.
Myth 1: Large-scale agriculture feeds the world today
According to a recent U.N. Food and Agriculture Organization (FAO) report, family farms produce over three-quarters of the world’s food. The FAO also estimates that almost three-quarters of all farms worldwide are smaller than one hectare – about 2.5 acres, or the size of a typical city block.
Only about 1 percent of Americans are farmers today. Yet most of the world’s farmers work the land to feed themselves and their families. So while conventional industrialized agriculture feeds the developed world, most of the world’s farmers work small family farms. A 2016 Environmental Working Group report found that almost 90 percent of U.S. agricultural exports went to developed countries with few hungry people.
Of course the world needs commercial agriculture, unless we all want to live on and work our own farms. But are large industrial farms really the best, let alone the only, way forward? This question leads us to a second myth.
Myth 2: Large farms are more efficient
Many high-volume industrial processes exhibit efficiencies at large scale that decrease inputs per unit of production. The more widgets you make, the more efficiently you can make each one. But agriculture is different. A 1989 National Research Council study concluded that “well-managed alternative farming systems nearly always use less synthetic chemical pesticides, fertilizers, and antibiotics per unit of production than conventional farms.”
And while mechanization can provide cost and labor efficiencies on large farms, bigger farms do not necessarily produce more food. According to a 1992 agricultural census report, small, diversified farms produce more than twice as much food per acre than large farms do.
Even the World Bank endorses small farms as the way to increase agricultural output in developing nations where food security remains a pressing issue. While large farms excel at producing a lot of a particular crop – like corn or wheat – small diversified farms produce more food and more kinds of food per hectare overall.
Myth 3: Conventional farming is necessary to feed the world
We’ve all heard proponents of conventional agriculture claim that organic farming is a recipe for global starvation because it produces lower yields. The most extensive yield comparison to date, a 2015 meta-analysis of 115 studies, found that organic production averaged almost 20 percent less than conventionally grown crops, a finding similar to those of prior studies.
But the study went a step further, comparing crop yields on conventional farms to those on organic farms where cover crops were planted and crops were rotated to build soil health. These techniques shrank the yield gap to below 10 percent.
Consider too that about a quarter of all food produced worldwide is never eaten. Each year the United States alone throws out 133 billion pounds of food, more than enough to feed the nearly 50 million Americans who regularly face hunger. So even taken at face value, the oft-cited yield gap between conventional and organic farming is smaller than the amount of food we routinely throw away.
Building healthy soil
Conventional farming practices that degrade soil health undermine humanity’s ability to continue feeding everyone over the long run. Regenerative practices like those used on the farms and ranches I visited show that we can readily improve soil fertility on both large farms in the U.S. and on small subsistence farms in the tropics.
I no longer see debates about the future of agriculture as simply conventional versus organic. In my view, we’ve oversimplified the complexity of the land and underutilized the ingenuity of farmers. I now see adopting farming practices that build soil health as the key to a stable and resilient agriculture. And the farmers I visited had cracked this code, adapting no-till methods, cover cropping and complex rotations to their particular soil, environmental and socioeconomic conditions.
Whether they were organic or still used some fertilizers and pesticides, the farms I visited that adopted this transformational suite of practices all reported harvests that consistently matched or exceeded those from neighboring conventional farms after a short transition period. Another message was as simple as it was clear: Farmers who restored their soil used fewer inputs to produce higher yields, which translated into higher profits.
No matter how one looks at it, we can be certain that agriculture will soon face another revolution. For agriculture today runs on abundant, cheap oil for fuel and to make fertilizer – and our supply of cheap oil will not last forever. There are already enough people on the planet that we have less than a year’s supply of food for the global population on hand at any one time. This simple fact has critical implications for society.
So how do we speed the adoption of a more resilient agriculture? Creating demonstration farms would help, as would carrying out system-scale research to evaluate what works best to adapt specific practices to general principles in different settings.
We also need to reframe our agricultural policies and subsidies. It makes no sense to continue incentivizing conventional practices that degrade soil fertility. We must begin supporting and rewarding farmers who adopt regenerative practices.
Once we see through myths of modern agriculture, practices that build soil health become the lens through which to assess strategies for feeding us all over the long haul. Why am I so confident that regenerative farming practices can prove both productive and economical? The farmers I met showed me they already are.
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 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.
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.
[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. CIMMYTs 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 landracestraditional, 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.
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 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.
Have you ever wanted a free, on-line textbook written by experts and regularly updated?
Plants in Action is an on-line resource for students and academics teaching plant function to undergrads, published by the Australian and New Zealand societies of plant science. Each chapter has up to 100 illustrations suitable for Powerpoint presentations. It is also ideal for graduate students and post-docs in molecular biology looking for the whole-plant context for their work. Of the original 20 chapters, ten have been fully revised.
Could you begin by describing the Plants in Action (PiA) textbook and how the idea first came about?
The original editors and contributors produced a textbook on plant function that used examples from the southern hemisphere, with view of adaptations in nature to performance in cultivation. They were motived to communicate the strong plant science in Australia and New Zealand. PiA was born as a textbook in 1999, and ten years later went open-access and free online.
Who are your target audience?
Undergraduate students, educators, practitioners and researchers, and others interested in plants and how they function. PiA gets thousands of hits per day from around the globe, including developing countries.
What topics do you cover?
To the best of my knowledge, PiA is the only comprehensive plant science textbook with a southern hemisphere perspective. It covers molecular, cellular, and whole-plant function, in ecophysiology and vegetation-environment interactions, from Antarctica to the tropics. PiA features plants that are some of the best studied genetic models and crops, as well as wild plants.
The topics covered in Chapter 4: Nutrient uptake by plants involving beneficial microorganisms. Image credit: Scott Buckley, The University of Queensland.
Who has contributed to the textbook, and how did you enlist potential collaborators?
PiA was written by Australian and New Zealand plant scientists from a range of institutions, many of whom have worked on both editions. Chief Editor Dr Rana Munns and the chapter editors find new contributors if the original authors are not available, although occasionally authors volunteer contributions
What changes have you made in the second edition, and how are the revisions coming along?
PiA2 is being updated to reflect recent advances in plant science, and has a new look as software enables ever more attractive layouts, with no limit for images and illustrations. PiA can be read online and is easily printed, which is important for internet-challenged regions and for students wanting to add notes. Ten chapters are fully updated with several chapters expanded.
Revisions can be made instantly (as a wiki) but take a little longer if the expert skills of our IT assistants are required. Complete revisions of chapters are slower to come on board.
Encouragingly, some excellent contributions have recently been made by junior scientists who see a strong value in developing an open-access resource to share their expertise widely.
You mentioned the text can be translated into different languages. How might users go about getting a textbook in their native language?
Are you looking to expand on the work in the future? How can potential contributors get involved?
It would be marvelous to have a person with time and expertise to develop further materials to add to PiA2 in collaboration with editors, authors, educational designers, and students. This could include material specifically designed for schools and interactive learning tools for students of all levels. We welcome all contributors (irrespective of their connections to the plant societies), and they can contact Rana or any chapter editor.
Without plants, Earth would not give us habitat, food and materials. But with 25% of the global flora threatened with extinction, we need more people to understand plants, and what we need to do protect them and their habitats.
This week we spoke to Dr. Anil Day, a synthetic biologist at the University of Manchester who has developed an impressive array of tools and techniques to transform chloroplast genomes.
Could you begin by giving our readers a brief overview of synthetic biology?
Synthetic biology involves the application of engineering principles to biological systems. One approach to understanding a biological system is to break it down into smaller parts, which can be used to design new properties. These redesigned pieces can be reassembled into a new system, tested experimentally, and refined in an iterative process. Synthetic biology projects that are underway in our lab include designing plastids such as chloroplasts with new metabolic functions, and in the longer term the design and assembly of synthetic chloroplast genomes.
Dr. Anil Day examines a cabinet of transformed plants. Credit: Dr. Anil Day.
Why do you use chloroplasts for synthetic biology systems?
Chloroplasts have a relatively small genome, coding for about 100 genes. Importantly, exogenous (foreign) genes coding for new functions can be precisely introduced into the chloroplast genome. All of the plastids within a plant contain the same genome so, once established, the user-designed reprogrammed plastids will be present throughout the plant. Chloroplasts can also produce very high levels of protein; researchers have achieved expression levels where over 70% of the total soluble protein in the leaves is the engineered protein. Expression in tomato fruit is also possible.
Multiple genes can be introduced into chloroplasts and expressed coordinately, allowing the metabolic engineering of more complex processes. The upper size limit for insertions is not known but is likely to be above the 50,000 nucleotide insertion achieved to date. Furthermore, chloroplasts and other plastids are important metabolic hubs and contain a wide variety of chemical substrates useful for metabolic engineering.
Plants have several types of plastids, including green photosynthetic chloroplasts, pigment-containing chromoplasts, and starch-containing amyloplasts. Credit: Dr. Anil Day.
Could you describe the current state of our ability to engineer chloroplasts?
Chloroplast engineering is routine in many labs around the globe. Although there are multiple chloroplasts in every cell, the process of converting all the chloroplasts to a single population of engineered genomes is not an issue. Most researchers use the tobacco plant because it is easily transformed, but other crops are amenable to transformation, including oilseed rape, soybean, tomato, and potato (cereals such as rice and wheat are more problematic). There has been progress with developing the inducible expression of exogenous genes in chloroplasts too.
What challenges/differences do you face when transforming chloroplast genomes when compared to the nuclear genome?
Typical genetic modification of the DNA in the nucleus is performed by introducing exogenous genes in T-DNA. T-DNA is transferred to the plant using the bacterium Agrobacterium tumefaciens, which is an efficient process, but the T-DNA integrates ‘randomly’ at many sites within chromosomes and different lines can have variable expression levels due to positional effects and gene silencing.
A. tumefaciens-mediated gene delivery systems do not work for chloroplast transformation. Most chloroplast transformation labs introduce genes into plastids by blasting cells with gold or tungsten particles coated with DNA. Because chloroplast genomes are present in multiple copies per cell, the process of converting all resident chloroplasts to the transgenic genome requires a continued period of selection. This means that the isolation of chloroplast transformants can take slightly longer than nuclear transformation. In our lab, we speed up this process by using restoration of photosynthesis to select chloroplasts with exogenous genes. Once plants with a uniform population of transgenic plastid genomes have been isolated, the transgenes are stable and inherited through the maternal line.
For the novice, I would say nuclear transformation using A. tumefaciens is easier to accomplish than chloroplast transformation.
A tobacco plant containing leaf areas with edited (pale green) and normal (darker green) chloroplasts. Credit: Dr. Anil Day.
Chloroplasts are inherited from the female parent in wheat. This is useful because it restricts the pollen-mediated spread of chloroplast-localized transgenes into the environment. Previously, no-one had studied the mechanism of maternal chloroplast inheritance in wheat using modern cell biology tools. With our collaborators Lucia Primavesi, Huixia Wu, and Huw Jones at Rothamsted Research, we developed an efficient method to observe small non-green plastids in wheat pollen in real time. We found that the plastids were destroyed during the maturation of sperm cells, which explained the absence of paternal plastids in the offspring.
This discovery has applications in crop breeding. Anther culture is a powerful technique where new homozygous plants can be produced by doubling the chromosome numbers of haploid plants regenerated from pollen. This technique has been challenging in cereals, as chloroplast degradation in pollen leads to a high percentage of albino plants (in some cases 100% albinos). Understanding how to prevent the destruction of plastids in pollen sperm cells will improve this technique in cereals, which could speed up crop breeding in the future.
Transformed plantlets are selected by their ability to survive on a herbicide-containing agar plate, and can then be grown up into mature plants. Credit: Dr. Anil Day.
What sorts of processes have you successfully transformed into chloroplasts, and what kinds of results have you achieved?
We have expressed a variety of exogenous genes in chloroplasts, from those conferring resistance to herbicides to vaccine epitopes and pharmaceutical proteins:
Plants expressing the bar gene in chloroplasts were resistant to the herbicide glufosinate (also known as phosphinothricin).
A chloroplast-expressed viral epitope was used to identify samples of human blood infected with the hepatitis C virus.
Human transforming growth factor 3 (hTGFβ3), a potential wound healing drug, accumulated to high concentrations in chloroplasts, and could be processed to a pure active form resembling clinical grade hTGFβ3.
In collaboration with Ray Dixon, Cheng Qi, and Mandy Dowson-Day at the John Innes Centre, we investigated the feasibility of introducing nitrogen-fixing genes into chloroplasts. This work was initiated in a unicellular green alga with the bacterial nifH gene.
What is the cutting edge of chloroplast transformation research?
Chloroplast genes are important for plant growth and development but they are difficult to improve by conventional breeding methods. We recently developed a method to edit plastid genomes, which allows beneficial single point mutations to be introduced into chloroplast genes. This is important because the resulting plants have an identical genome to the original cultivar apart the single base substitution, potentially leading to a new class of biotech crop.
In two short videos, New Phytologist Editor-in-Chief Prof Alistair Hetherington provides a step by step guide for early career researchers, intending to publish their work in New Phytologist.
“One of my top tips would be: get the author list decided very early on.”
Alistair talks through the process of working out whether research is within the scope of the journal, deciding the author list, and submitting a presubmission enquiry.
“Remember, the Editor will use the covering letter to help him or her decide whether or not to send your work out for review. You need to put your work in context, and describe how your findings are novel, and exciting.”
In part two, Alistair explains the submission process, including what should be included in the covering letter. He then describes the peer review process at New Phytologist and what to do after you’ve received a decision on your manuscript.
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.