When it comes to crop diseases, insects, viruses, and fungi may get the media limelight but in certain regions it is actually other plants which are a farmer’s greatest enemy. In sub-Saharan Africa, one weed in particular – Striga hermonthica – is an almost unstoppable scourge and one of the main limiting factors for food security.
Striga is a parasitic plant; it attaches to and feeds off a host plant. For most of us, parasitic plants are simply harmless curiosities. Over 4,000 plants are known to have adopted a parasitic mode of life, including the seasonal favorite mistletoe (a stem parasite of conifers) and Rafflesia arnoldii, nicknamed the “corpse flower” for its huge, smelly blooms. Although the latter produces the world’s largest flower, it has no true roots – only thread-like structures that infect tropical vines.
When parasitic plants infect food crops, they can turn very nasty indeed. Strigahermonthica is particularly notorious because it infects almost every cereal crop, including rice, maize, and sorghum. Striga is a hemiparasite, meaning that it mainly withdraws water from the host (parasitic plants can also be holoparasites, which withdraw both water and carbon sugars from the host). However, Striga also causes a severe stunting effect on the host crop (see Figure 1), reducing their yield to practically nothing. Little wonder then, that the common name for Striga is ‘witchweed’.
Figure 1:Striga-infected sorghum. Note the withered, shrunken appearance of the infected plants. Image credit: Joel Ransom.
Several features of the Striga lifecycle make it especially difficult to control. The seeds can remain dormant for decades and only germinate in response to signals produced by the host root (called strigolactones) (Figure 2). Once farmland becomes infested with Striga seed, it becomes virtually useless for crop production. Germination and attachment takes place underground, so the farmer can’t tell if the land is infected until the parasite sends up shoots (with ironically beautiful purple flowers). Some chemical treatments can be effective but these remain too expensive for the subsistence farmers who are mostly affected by the weed. Many resort to simply pulling the shoots out as they appear; a time-consuming and labor-intensive process. It is estimated that Striga spp. cause crop losses of around US $10 billion each year .
Certain crop cultivars and their wild relatives show natural resistance to Striga. Here at the University of Sheffield, our lab group (headed by Professor Julie Scholes) is working to identify resistance genes in rice and maize, with the eventual aim of breeding these into high-yielding cultivars. To do this, we grow the host plants in rhizotrons (root observation chambers) which allow us to observe the process of Striga attachment and infection (see Figure 3). Already this has been successful in identifying rice cultivars that have broad-spectrum resistance to Striga, and which are now being used by farmers across Africa.
Figure 2: Life cycle of Striga spp. A single plant produces up to 100,000 seeds, which can remain viable in the soil for 20 years. Following a warm, moist conditioning phase, parasite seeds become responsive to chemical cues produced by the roots of suitable hosts, which cause them to germinate and attach to the host root. The parasite then develops a haustorium: an absorptive organ which penetrates the root and connects to the xylem vessels in the host’s vascular system. This fuels the development of the Striga shoots, which eventually emerge above ground and flower. Figure from .
But many fundamental aspects of the infection process remain almost a complete mystery, particularly how the parasite overcomes the host’s intrinsic defense systems. It is possible that Striga deliberately triggers certain host signaling pathways; a strategy used by other root pathogens such as the fungus Fusarium oxysporum. This is the focus of my project: to identify the key defense pathways that determine the level of host resistance to Striga. It would be very difficult to investigate this in crop plants, which typically have incredibly large genomes, so my model organism is Arabidopsis thaliana, the workhorse of the plant science world, whose genome has been fully sequenced and mapped. Arabidopsis cannot be infected by Striga hermonthica but it is susceptible to the related species, Striga gesnerioides, which normally infects cowpea. I am currently working through a range of different Arabidopsis mutants, each affected in a certain defense pathway, to test whether these have an altered resistance to the parasite. Once I have an idea of which plant defense hormones may be involved (such as salicylic acid or jasmonic acid), I plant to test the expression of candidate genes to decipher what is happening at the molecular level.
Figure 3: One of my Arabidopsis plants growing in a rhizotron. Preconditioned Striga seeds were applied to the roots three weeks ago with a paintbrush. Those that successfully attached and infected the host have now developed into haustoria. The number of haustoria indicates the level of resistance in the host. Image credit: Caroline Wood.
It’s early days yet, but I am excited by the prospect of shedding light on how these devastating weeds are so effective in breaking into their hosts. Ultimately this could lead to new ways of ‘priming’ host plants so that they are armed and ready when Striga attacks. It’s an ambitious challenge, and one that will certainly keep me going for the remaining two years of my PhD!
Could you begin by telling us a little about your research?
I am a plant physiologist specializing in seed biology. I have a long research record on various aspects of seeds, including the mechanisms and regulation of germination and dormancy, desiccation tolerance, as well as issues in seed technology. Being six years from retirement now, I decided to extend my desiccation tolerance studies from seeds to resurrection plants, which display vegetative desiccation tolerance. I strongly believe that unveiling of the mechanism of vegetative desiccation tolerance may help us create crops that are truly tolerant to severe drought, rather than (temporarily) resistant.
How did you become interested in this field of study, and how has your career progressed?
As with many things in life, it was coincidence. I majored in plant biochemistry and applied for a PhD position in seed biology. After obtaining the degree I was offered a tenure track position in seed physiology by the Laboratory of Plant Physiology at Wageningen University, where I still work as a faculty member. My career has progressed nicely and I am an authority in the field of seed science, editor-in-chief of the journal Seed Science Research, and will become the President of the International Society for Seed Science in September of this year.
I see my current work on vegetative desiccation tolerance as a highlight in my professional life. I have always been more interested in the desiccation tolerance of seeds until about five years ago, when my current collaborator Prof Jill Farrant of the University of Cape Town, South-Africa, made me enthusiastic about these wonderful resurrection plants. We started to work together and published our first study recently in Nature Plants.
In your recent paper, you sequenced the genome of the resurrection plant, Xerophyta viscosa, which can survive with less than a 5% relative water content. How is it possible for a plant to lose so much of its water and still survive?
These plants have a lot of characteristics that we’ve seen in seeds. They display protective desiccation tolerance mechanisms in their leaves, including anti-oxidants, protective proteins, and even dismantle their photosynthetic machinery during periods of drought. Even the cell wall structure and composition of resurrection plants resemble those of seeds. We are currently working on a paper describing the striking similarities between seeds and resurrection plants.
What was the most interesting discovery you made upon sequencing the genome of the resurrection plant?
First, the similarities between resurrection plants and seeds listed above were also apparent at the molecular level. For example, previous work suggested that the “ABI3 regulon”, consisting of about 100 genes regulated by the transcription factor ABI3, is specific to seeds, but we found that it is almost completely present (and active) in the leaves of Xerophyta viscosa too!
Secondly, we found “islands” or clusters of genes specific for desiccation tolerance that aren’t found in other species. Many of these regulate secondary metabolite pathways.
How challenging was it to sequence the genome of this plant? How did you overcome any difficulties?
It was very challenging. First, the species is an octoploid, meaning it has eight copies of each chromosome. This meant that we had to sequence its genome at very high coverage and employing the most advanced sequencing facilities, e.g. PacBio. Getting funding for this complex analysis was another challenge. We then took almost a year to assemble the genome and annotate it at the desired quality.
Xerophyta viscosa before and after the rains. Image credit: Prof. Henk Hilhorst.
You identified some of the most important genes involved in desiccation tolerance. Is it possible to translate this work into other species, such as crops that may be threatened by drought as the climate changes?
That will be our ultimate goal. It’s important to remember that desiccation-sensitive plants, including all our major crops, produce seeds that are desiccation tolerant. This implies that the information for desiccation tolerance is present in the genomes of these crops but that it is only turned on in the seeds. We are trying to determine how this is localized, in order to find a method to turn on the desiccation tolerance mechanism in vegetative parts of the (crop) plant too. In parallel we are expressing some of the key transcription factors from Xerophyta viscosa in some important crops to see how this affects them.
Are there any other interesting aspects of Xerophyta viscosa biology?
Contrary to plants that wilt and ultimately die because of (severe) drought, leaves of resurrection species do not show such stress-related senescence. This is related to the engagement of active anti-senescence genes during the drying of the leaves of resurrection species. We are currently investigating these senescence-related mechanisms too.
The rose of Jericho (Anastatica hierochuntica) is another resurrection plant. Image credit: FloraTrek. Used under license: CC BY-SA 3.0.
Do you expect to find that different types of desiccation-tolerant plants use the same subset of genes to survive drought, or could they have developed other pathways to resilience?
We expect that the core mechanism is very similar among the resurrection species but that each species may have adapted to its specific environment.
Funding permitting, we will sequence the genomes of at least another ten resurrection species to further clarify the various evolutionary pathways to desiccation tolerance and, importantly, to discriminate between species-specific and desiccation tolerance-specific genes.
What advice do you have for early career researchers?
Stick to what you believe in, even if you have to (temporarily) be involved in research that you appreciate less, e.g., because of better funding opportunities.
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.
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.
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.
Sales of quinoa (Chenopodium quinoa) have exploded in the last decade, with prices more than tripling between 2008 and 2014. The popularity of this pseudocereal comes from its highly nutritious seeds, which resemble grains and contain a good balance of protein, vitamins, and minerals. The nourishing nature of quinoa meant it was prized by the Incas, who called it the “Mother grain”.
Quinoa is a popular ‘grain’, but it is more closely related to spinach and beetroot than cereals like wheat or barley. Image credit: Flickr user. Used under license: CC BY 2.0.
Quinoa is native to the Andes of South America, where it thrives in a range of conditions from coastal regions to alpine regions of up to 4000 m above sea level. Its resilience and nutritious seeds means that quinoa has been identified as a key crop for enhancing food security, but there are currently very few breeding programs targeting this species.
The challenge of improving the efficiency and sustainability of quinoa production has so far been restricted by the lack of a reference genome. This week, a team of researchers led by Professor Mark Tester (King Abdullah University of Science & Technology; KAUST) addressed this issue, publishing a high-quality genome sequence for quinoa in Nature. They compared the genome with that of related species to characterize the evolution and domestication of the crop, and investigated the genetic diversity of economically important traits.
The evolution of quinoa
Tester and colleagues used an array of genomics techniques to assemble 1.39 Gb of the estimated 1.45-1.50 Gb full length of quinoa’s genome. Quinoa is a tetraploid, meaning it has four copies of each chromosome. The researchers shed light on the evolutionary history of this crop by sequencing descendants of the two diploid species (each containing two sets of chromosomes) that hybridized to generate quinoa; kañiwa (Chenopodium pallidicaule) and Swedish goosefoot (Chenopodium suecicum). Comparing these sequences to quinoa and other relatives, the team showed that the hybridization event likely occurred between 3.3 and 6.3 million years ago. A comparison with other closely related Chenopodium species also suggested that, contrary to previous predictions, quinoa may have been domesticated twice, both in highland and coastal environments.
Quinoa seeds are coated with soap-like chemicals called saponins, which have a bitter taste that deters herbivores. Saponins can disrupt the cell membranes of red blood cells, so they have to be removed before human consumption, but this process is costly, so quinoa breeders are always looking for varieties that produce lower levels of saponins.
Sweet (low-saponin) quinoa strains do occur naturally, but the genes that regulate this phenotype were previously unknown. Tester and colleagues investigated sweet and bitter quinoa strains and discovered that a single gene (TRITERPENE SAPONIN BIOSYNTHESIS ACTIVATING REGULATOR-LIKE 1 [TSARL1]) controls the amount of saponins produced in the seeds. The low-saponin quinoa strains contained mutations in TSARL1 that prevented it from functioning properly. This is a key target for the improvement of quinoa in the future, although farmers will have to find new ways to protect their crops from birds and other seed predators!
The high-quality reference genome for quinoa generated by Tester and colleagues is likely to be vital for allowing many exciting improvements in the future. Breeders hoping to improve the yield, ease of harvest, stress tolerance, and saponin content of quinoa can develop genetic markers to speed up breeding for these key traits, improving the productivity of quinoa varieties and enhancing future food security.
Read the paper in Nature: Jarvis et al., 2017. The genome of Chenopodium quinoa. Nature. DOI: 10.1038/nature21370
Thank you to Professor Mark Tester (KAUST) for providing information used in this post!
I am a post-doctoral research scientist within Rothamsted Research’s BBSRC-funded 20:20 Wheat® program, which aims to provide the knowledge base and tools to increase the UK wheat yield potential from 8.4 to 20 tons of wheat per hectare within the next 20 years. Field phenotyping is one component of this program and facilitates the non-destructive monitoring of field-grown crops. Traditional methods of field phenotyping require huge human effort, which consequently limits the accuracy, frequency, and number of different measurements that can be taken at one time. Fortunately, Rothamsted has an exciting solution to this problem.
The Field Scanalyzer
Dr Kasra Sabermanesh shows off the Field Scanalyzer. Image credit: Rothamsted Research
Our field phenotyping platform, the Field Scanalyzer (constructed by LemnaTec GmbH and being further developed by ourselves), supports a motorized measuring platform with multiple sensors that can be accurately positioned anywhere within a dedicated field. The sensor array comprises a high-definition RGB camera, two hyperspectral cameras, a thermal infrared camera, a system for imaging chlorophyll fluorescence and twin scanning lasers for 3D information capture. Together, these sensors generate a wealth of data about crop growth, architecture, performance, and health. The Field Scanalyzer operates autonomously and in high-throughput, meaning it can take a lot of non-destructive measurements without human supervision, throughout the crops lifecycle, with high-accuracy and reproducibility. (You can read more about the Field Scanalyzer in our recent paper: http://www.publish.csiro.au/FP/pdf/FP16163).
We are currently using the Field Scanalyzer to identify new characteristics of crops that relate to performance, as well as identifying new genetic diversity for existing traits. Outputs from either of these research components can be delivered to breeders. We are screening approximately 400 wheat varieties, but also imaging some oilseed rape and oat plants.
The scanalyzer. Image credit: Rothamsted Research
The big data problem
The Field Scanalyzer at Rothamsted is a world first, so we initially had to develop all the necessary image acquisition protocols and image processing tools, in order to exploit its full capabilities. A number of image processing tools are available; however, they are not suitable for field-grown crops, as they were not developed for complex canopies consisting of hundreds of plants in highly dynamic ambient conditions. The platform can generate up to 100 TB data with a year’s continuous operation (using all of the sensors). That’s why I work with two other post-docs to develop robust computer vision tools to automate the way we extracting quantitative image datasets. We are also validating the accuracy of the values extracted from our images by comparing them with measurements obtained manually.
Approximately 1.5 years have passed since we first began operating the Field Scanalyzer, and we have now optimized all of our image acquisition protocols and have collected a full seasonal dataset. With the good quality images stored in our database, we have developed some robust tools to automatically extract the information about some key growth stages (ear emergence and flowering), as well as quantifying height and the number of some plant organs. We are still just scraping the surface though, and have a list of traits for which we want to develop computer vision tools, in order to automatically analyze them.
Take to the skies: Drones for data collection
Some of my colleagues work with drones (UAVs) to capture information about crop height, plant density (Normalized Difference Vegetation Index), and canopy temperature from large-scale field trials containing 5000 plots. They also fly the UAVs over our Field Scanalyzer site, so we can compare data collected from the higher flying UAV with those collected from the Field Scanalyzer at close proximity. The way we see it, UAVs can image large fields in a very short time (15 min), so if we notice something interesting using the UAV at the large plot-scale, we can put the material under the Field Scanalyzer for high-resolution phenotyping. On the other hand, with the Field Scanalyzer, once we gain a better understanding of which trait/s we need to focus on, when we should be looking at them, and exactly which sensor/s are required to quantify the trait, we can deploy drones with the necessary sensors (once the sensors are portable enough) to collect this information at field-scale and at the appropriate time.
Taking to the skies: Drones are used for large-scale phenotyping at Rothamsted. Credit: Rothamsted Research.
The future of phenotyping
I envision that the future of phenotyping technology will focus on reducing the cost and size of cameras/sensors, ultimately increasing their portability and accessibility. This will result in more sophisticated cameras being attached to UAVs (as many of sensors we currently use far out-weigh a UAV’s payload). Parallel to this, research efforts are focusing on developing image processing systems that efficiently extract quantitative information about the crops from acquired images. Together, phenotyping systems such as low-flying UAVs that generate easily interpreted data outputs could be developed, which may be more widely adopted by breeders and farmers to get a deeper insight into their crop’s health and performance.
Another fantastic year of discovery is over – read on for our 2016 plant science top picks!
A Zostera marina meadow in the Archipelago Sea, southwest Finland. Image credit: Christoffer Boström (Olsen et al., 2016. Nature).
The year began with the publication of the fascinating eelgrass (Zostera marina) genome by an international team of researchers. This marine monocot descended from land-dwelling ancestors, but went through a dramatic adaptation to life in the ocean, in what the lead author Professor Jeanine Olsen described as, “arguably the most extreme adaptation a terrestrial… species can undergo”.
One of the most interesting revelations was that eelgrass cannot make stomatal pores because it has completely lost the genes responsible for regulating their development. It also ditched genes involved in perceiving UV light, which does not penetrate well through its deep water habitat.
Plants are known to form new organs throughout their lifecycle, but it was not previously clear how they organized their cell development to form the right shapes. In February, researchers in Germany used an exciting new type of high-resolution fluorescence microscope to observe every individual cell in a developing lateral root, following the complex arrangement of their cell division over time.
Using this new four-dimensional cell lineage map of lateral root development in combination with computer modelling, the team revealed that, while the contribution of each cell is not pre-determined, the cells self-organize to regulate the overall development of the root in a predictable manner.
Watch the mesmerizing cell division in lateral root development in the video below, which accompanied the paper:
In March, a Spanish team of researchers revealed how the anti-wilting molecular machinery involved in preserving cell turgor assembles in response to drought. They found that a family of small proteins, the CARs, act in clusters to guide proteins to the cell membrane, in what author Dr. Pedro Luis Rodriguez described as “a kind of landing strip, acting as molecular antennas that call out to other proteins as and when necessary to orchestrate the required cellular response”.
In April, we received an amazing insight into the ‘decision-making ability’ of plants when a Swiss team discovered that plants can punish mutualist fungi that try to cheat them. In a clever experiment, the researchers provided a plant with two mutualistic partners; a ‘generous’ fungus that provides the plant with a lot of phosphates in return for carbohydrates, and a ‘meaner’ fungus that attempts to reduce the amount of phosphate it ‘pays’. They revealed that the plants can starve the meaner fungus, providing fewer carbohydrates until it pays its phosphate bill.
Author Professor Andres Wiemskenexplains: “The plant exploits the competitive situation of the two fungi in a targeted manner, triggering what is essentially a market-based process determined by cost and performance”.
The transition of ancient plants from water onto land was one of the most important events in our planet’s evolution, but required a massive change in plant biology. Suddenly plants risked drying out, so had to develop new ways to survive drought.
In May, an international team discovered a key gene in moss (Physcomitrella patens) that allows it to tolerate dehydration. This gene, ANR, was an ancient adaptation of an algal gene that allowed the early plants to respond to the drought-signaling hormone ABA. Its evolution is still a mystery, though, as author Dr. Sean Stevensonexplains: “What’s interesting is that aquatic algae can’t respond to ABA: the next challenge is to discover how this hormone signaling process arose.”
Sometimes revisiting old ideas can pay off, as a US team revealed in June. In 1930, Ernst Münch hypothesized that transport through the phloem sieve tubes in the plant vascular tissue is driven by pressure gradients, but no-one really knew how this would account for the massive pressure required to move nutrients through something as large as a tree.
Professor Michael Knoblauch and colleagues spent decades devising new methods to investigate pressures and flow within phloem without disrupting the system. He eventually developed a suite of techniques, including a picogauge with the help of his son, Jan, to measure tiny pressure differences in the plants. They found that plants can alter the shape of their phloem vessels to change the pressure within them, allowing them to transport sugars over varying distances, which provided strong support for Münch flow.
BLOG: We featured similar work (including an amazing video of the wound response in sieve tubes) by Knoblauch’s collaborator, Dr. Winfried Peters, on the blog – read it here!
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.
In July, an international and highly multidisciplinary team published the genome of 6,000-year-old barley grains excavated from a cave in Israel, the oldest plant genome reconstructed to date. The grains were visually and genetically very similar to modern barley, showing that this crop was domesticated very early on in our agricultural history. With more analysis ongoing, author Dr. Verena Schünemannpredicts that “DNA-analysis of archaeological remains of prehistoric plants will provide us with novel insights into the origin, domestication and spread of crop plants”.
BLOG: We interviewed Dr. Nils Stein about this fascinating work on the blog – click here to read more!
Another exciting cereal paper was published in August, when an Australian team revealed that C4 photosynthesis occurs in wheat seeds. Like many important crops, wheat leaves perform C3 photosynthesis, which is a less efficient process, so many researchers are attempting to engineer the complex C4 photosynthesis pathway into C3 crops.
This discovery was completely unexpected, as throughout its evolution wheat has been a C3 plant. Author Professor Robert Henrysuggested: “One theory is that as [atmospheric] carbon dioxide began to decline, [wheat’s] seeds evolved a C4 pathway to capture more sunlight to convert to energy.”
Professor Stefan Jansson cooks up “Tagliatelle with CRISPRy fried vegetables”. Image credit: Stefan Jansson.
September marked an historic event. Professor Stefan Jansson cooked up the world’s first CRISPR meal, tagliatelle with CRISPRy fried vegetables (genome-edited cabbage). Jansson has paved the way for CRISPR in Europe; while the EU is yet to make a decision about how CRISPR-edited plants will be regulated, Jansson successfully convinced the Swedish Board of Agriculture to rule that plants edited in a manner that could have been achieved by traditional breeding (i.e. the deletion or minor mutation of a gene, but not the insertion of a gene from another species) cannot be treated as a GMO.
Phytochromes help plants detect day length by sensing differences in red and far-red light, but a UK-Germany research collaboration revealed that these receptors switch roles at night to become thermometers, helping plants to respond to seasonal changes in temperature.
Dr Philip Wiggeexplains: “Just as mercury rises in a thermometer, the rate at which phytochromes revert to their inactive state during the night is a direct measure of temperature. The lower the temperature, the slower phytochromes revert to inactivity, so the molecules spend more time in their active, growth-suppressing state. This is why plants are slower to grow in winter”.
A fossil ginkgo (Ginkgo biloba) leaf with its modern counterpart. Image credit: Gigascience.
In November, a Chinese team published the genome of Ginkgo biloba¸ the oldest extant tree species. Its large (10.6 Gb) genome has previously impeded our understanding of this living fossil, but researchers will now be able to investigate its ~42,000 genes to understand its interesting characteristics, such as resistance to stress and dioecious reproduction, and how it remained almost unchanged in the 270 million years it has existed.
Author Professor Yunpeng Zhaosaid, “Such a genome fills a major phylogenetic gap of land plants, and provides key genetic resources to address evolutionary questions [such as the] phylogenetic relationships of gymnosperm lineages, [and the] evolution of genome and genes in land plants”.
The year ended with another fascinating discovery from a Danish team, who used fluorescent tags and microscopy to confirm the existence of metabolons, clusters of metabolic enzymes that have never been detected in cells before. These metabolons can assemble rapidly in response to a stimulus, working as a metabolic production line to efficiently produce the required compounds. Scientists have been looking for metabolons for 40 years, and this discovery could be crucial for improving our ability to harness the production power of plants.