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.
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
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.
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.
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.
A nano-sized bio-degradable clay-comprising double stranded ribonucleic acid (dsRNA) could offer a cost-effective, clean and green alternative to chemical-based plant pesticides.
Australian researchers from the University of Queensland have successfully used a gene-silencing spray, named BioClay, a combination of biomolecules and clay, to protect tobacco plants from a virus for 20 days with a single application. Their study has been published in Nature Plants.
“When BioClay is sprayed onto a plant, the virus-specific dsRNA is slowly released from the clay nanosheets into the plant. This activates a pathway in the plant that is a natural defence mechanism. The dsRNA is chopped up into small bits of RNA by enzymes of this pathway. These small bits attack the virus when it infects the plant without altering the plant genome,” explains lead researcher, Neena Mitter.
“Even with current pesticides, we lose up to 40 per cent of our crop productivity because of pests and pathogens. We are hoping that having BioClay in the mix as an environmentally friendly, sustainable crop protection measure will reduce crop losses,” Mitter adds.
“The clay-based delivery technology could represent a positive inflection point in the progress towards commercialisation of topical RNAi. This is a non-GM, environmentally benign and very specific technology.”
John Killmer, APSE
While chemical-based pesticides kill the targeted insect, they can also affect a range of other insects that are beneficial. Mitter says, “BioClay is specific and it only kills the pathogen being targeted. Currently farmers use insecticides to kill the vector that comes with the viruses, but with BioClay we can target the virus itself.”
BioClay field trials may begin in Australia by year-end. “The first test will be on a virus that infects vegetable crops — capsicum, tomato, chilli,” Mitter tells SciDev.Net.
Farmers can use the existing equipment to deliver BioClay and the researchers are hopeful that it will be a commercially viable product for farmers everywhere. The clay component is cheap to make, but not the RNA.
Several companies like APSE, a US based startup, are working on the mass production of RNAs. APSE is developing RNA manufacturing technology for RNA interference (RNAi) or gene silencing applications.
“Our technology for RNA production should be ready in 2-3 years. We are targeting US$2 per gram,” APSE’s John Killmer tells SciDev.Net.
Killmer says, “The clay-based delivery technology could represent a positive inflection point in the progress towards commercialisation of topical RNAi. This is a non-GM, environmentally benign and very specific technology.”
RNAi technology is being used by many in the agriculture industry including the biotech firm Monsanto. The company’s BioDirect technology is focused on applications of RNAi directly onto the leaves of a plant.
Monsanto’s spokesperson John Combest tells SciDev.Net, “As insects develop resistance to certain classes of pesticides, giving farmers another option to control these pests is critical. The idea is not to replace any given system of farming, whether modern GM systems or others — it’s to provide farmers with products that can complement or replace agricultural chemical products.”
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.
Edith, you have put a huge amount of work into uncovering the history of plant physiology research in Argentina. Why did you decide to do it and how did you undertake this challenge?
The current president of the SAFV, Pedro Sansberro, asked Alberto Golberg and myself if we would be willing to document the history of the society. Unaware of the tremendous task ahead, we agreed.
The information was scattered, so the first thing we did was try to collect as many SAFV conference books as possible. Sending requests through the SAFV mailing did not work, so it was essentially through personal contacts that we were able to put together the whole collection of conference books. It is now deposited in the library of CIAP (Centro de Investigaciones Agropecuarias – contact: email@example.com). People also sent the minutes of past meetings and pictures.
Initially we were only going to analyze the conference books and interview some plant scientists that were among the first disciples of the “founding fathers” of Argentinian experimental plant biology, but as we worked, our book grew and diversified.
What was the most interesting thing you discovered while writing the book?
It’s hard to narrow down which discovery was most exciting!
Victorio Trippi, one of the disciples of the “founding fathers”, told us that many researchers initially published in the journal Phyton, which was founded in Argentina in 1951. Our inspection of the archives of this publication yielded a lot of valuable information, and was an enlightening experience. We traced great names in Argentine plant science to the very beginning of their careers, looking at their topics of interest, how they moved from one job to another, and who their co-authors were. Even earlier than this though, we managed to trace the first mention of plant hormones in Argentina to a paper written by Guillermo Covas in 1939.
Writing the book was rewarding too, because we realized that plant physiology research has steadily grown in Argentina, judging by the participation in the conferences and the amount of research groups all over the country. It was very good to reveal the significant contributions that Argentine experimental plant science has made to many topics, such as photobiology, crop ecophysiology, germination physiology, senescence, mineral nutrition and carbohydrate metabolism, among others.
Why did you decide to include essays from the many groups researching plant physiology in Argentina?
We included them to reflect how much plant physiology has grown and diversified in Argentina. In the book we also invite those that did not have a chance to join this edition to contribute to a future one.
What words of wisdom did the researchers who were interviewed want to share with early career researchers for the future?
Most of them emphasized the need for team work, with people from different background joining forces to tackle a specific problem. The SAFV, they point out, has provided a friendly environment that has promoted collaboration and exchange of ideas among its members, and they hope this spirit will persist. They are moderately optimistic about the future, underscoring the need for new research paradigms both in the public and private sectors.
Carlos Ballaré underscored the human aspect of the history of the SAFV in his description of your book, printed on the cover. Could you elaborate on this?
Carlos meant that the book includes personal accounts from the people that have devoted their professional lives to plant physiology and ecophysiology, anecdotes of how the research groups developed and grew, and tales of how researchers replaced the lack of equipment with clever ideas. He highlights that the book has an emphasis on human endeavor, rather than being just a review of numbers, places, and dates.
Beyond the analysis of numbers and growth, the book reveals how early researchers worked on problems that largely sprang from their environment, attempting to understand the causes of issues that had an impact on crop productivity. Thus, those in Tucumán initially worked on sugar cane, those in Mendoza researched grapevines, and the focus in Buenos Aires was potatoes. As groups grew and diversified, this initial link was often blurred; young researchers joining ongoing work never realized what the initial question had been.
In a country where agricultural products or their derivatives still make a significant contribution to GDP, it is sensible to resume the link to local agricultural problems. For this task, it will be essential to adopt a systemic collaborative approach.
The authors of the book, Edith Taleisnik and Alberto Golberg.
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.
Genome editing technologies comprise a diverse set of molecular tools that allow the targeted modification of a DNA sequence within a genome. Unlike “traditional” breeding, genome editing does not rely on random DNA recombination; instead it allows the precise targeting of specific DNA sequences of interest. Genome editing approaches induce a double strand break (DSB) of the DNA molecule at specific sites, activating the cell’s DNA repair system. This process could be either error-prone, thus used by scientists to deactivate “undesired” genes, or error-free, enabling target DNA sequences to be “re-written” or the insertion of DNA fragments in a specific genomic position.
The most promising among the genome editing technologies, CRISPR/Cas9, was chosen as Science’s 2015 Breakthrough of the Year. Cas9 is an enzyme able to target a specific position of a genome thanks to a small RNA molecule called guide RNA (gRNA). gRNAs are easy to design and can be delivered to cells along with the gene encoding Cas9, or as a pre-assembled Cas9-gRNA protein-RNA complex. Once inside the cell, Cas9 cuts the target DNA sequence homologous to the gRNAs, producing DSBs.
The guide RNA (sgRNA) directs Cas9 to a specific region of the genome, where it induces a double-strand break in the DNA. On the left, the break is repaired by non-homologous-end joining, which can result in insertion/deletion (indel) mutations. On the right, the homologous-directed recombination pathway creates precise changes using a supplied template DNA. Credit: Ran et al. (2013). Nature Protocols.
Genome editing in crops
Together with the increased data availability on crop genomes, genome editing techniques such as CRISPR are allowing scientists to carry out ambitious research on crop plants directly, building on the knowledge obtained during decades of investigation in model plants.
The concept of CRISPR was first tested in crops by generating cultivars that are resistant to herbicides, as this is an easy trait to screen for and identify. One of the first genome-edited crops, a herbicide-resistant oilseed rape produced by Cibus, has already been grown and harvested in the USA in 2015.
Researchers used CRISPR to engineer a wheat variety resistant to powdery mildew (shown here), a major disease of this crop. Image credit: NY State IPM Program. Used under license: CC BY 2.0.
Genome editing could also revolutionize the management of viral plant disease. The CRISPR/Cas9 system was originally discovered in bacteria, where it provided them with molecular immunity against viruses, but it can also be moved into plants. Scientists can transform plants to produce the Cas9 and gRNAs that target viral DNA, reducing virus accumulation; alternatively, they can suppress those plant genes that are hijacked by the virus to mediate its own diffusion in the plants. Since most plants are defenseless against viruses and there are no chemical controls available for plant viruses, the main method to stop the spread of these diseases is still the destruction of the infected plant. For the first time in history, scientists have an effective weapon to fight back against plant viruses.
The cassava brown streak disease virus can destroy cassava crops, threatening the food security of the 300 million people who rely on this crop in Africa. Image credit: Katie Tomlinson (for more on this topic, read her blog here).
Genome editing will be particularly useful in the genetic improvement of many crops that are propagated mainly by vegetative reproduction, and so very difficult to improve by traditional breeding methods involving crossing (e.g. cassava, banana, grape, potato). For example, using TALENs, scientists from Cellectisedited a potato line to minimize the accumulation of reducing sugars that may be converted into acrylamide (a possible carcinogen) during cooking.
Concerns about off-targets
One of the hypothesized risks of using CRISPR/Cas9 is the potential targeting of undesired DNA regions, called off-targets. It is possible to limit the potential for off-targets by designing very specific gRNAs, and all of the work published so far either did not detect any off-targets or, if detected, they occurred at a very low frequency. The number of off-target mutations produced by CRISPR/Cas9 is therefore minimal, especially if compared with the widely accepted random mutagenesis of crops used in plant breeding since the 1950s.
GM or not-GM
Genome editing is interesting from a regulatory point of view too. After obtaining the desired heritable mutation using CRISPR/Cas9, it is possible to remove the CRISPR/Cas9 integrated vectors from the genome using simple genetic segregation, leaving no trace of the genome modification other than the mutation itself. This means that some countries (including the USA, Canada, and Argentina) consider the products of genome editing on a case-by-case basis, ruling that a crop is non-GM when it contains gene combinations that could have been obtained through crossing or random mutation. Many other countries are yet to issue an official statement on CRISPR, however.
Recently, scientists showed that is possible to edit the genome of plants without adding any foreign DNA and without the need for bacteria- or virus-mediated plant transformation. Instead, a pre-assembled Cas9-gRNA ribonucleoprotein (RNP) is delivered to plant cells in vitro, which can edit the desired region of the genome before being rapidly degraded by the plant endogenous proteases and nucleases. This non-GM approach can also reduce the potential of off-target editing, because of the minimal time that the RNP is present inside the cell before being degraded. RNP-based genome editing has been already applied to tobacco plants, rice, and lettuce, as well as very recently to maize.
In conclusion, genome editing techniques, and CRISPR/Cas9 in particular, offers scientists and plant breeders a flexible and relatively easy approach to accelerate breeding practices in a wide variety of crop species, providing another tool that we can use to improve food security in the future.
For more on CRISPR, check out this recent TED Talk from Ellen Jorgensen:
About the author
Dr Damiano Martignago is a plant molecular biologist who graduated from Padua University, Italy, with a degree in Food Biotechnology in 2009. He obtained his PhD in Biology at Roma Tre University in 2014. His experience with CRISPR/Cas9 began in the lab of Prof. Fabio Fornara (University of Milan), where he used CRISPR/Cas9 to target photoperiod genes of interest in rice and generate mutants that were not previously available. He recently moved to Rothamsted Research, UK, where he works as Genome Editing Specialist, transferring CRISPR/Cas9 technology to hexaploid bread wheat with the aim of improving the efficiency of genome editing in this crop. He is actively involved with AIRIcerca (International Association of Italian Scientists), disseminating and promoting scientific news.
Aquaporins are water-channel proteins that move water molecules through cell membranes. They are found in every kingdom of life. Cell membranes are semi-permeable to water, but often require more rapid movements of water across membranes; cells achieve this using aquaporins.
Aquaporins play key roles in your kidneys, which typically filter each of the three liters of plasma in your body 60 times per day – that’s 180 liters of plasma each day! Around three times your body weight in water passes through your own aquaporins each day.
Around 50% of global rainfall passes through plants, and half of this moves through the aquaporins. Image credit: Dennis Seiffert. Used under license: CC BY-ND 2.0.
Have you got on the scales recently? Nearly 70% of your body weight is water. Water is the major component of cells in all of your tissues and this is the same for plants. Around 50% of global precipitation passes through plants, and half of this moves through aquaporins, so aquaporins account for the largest movement of mass for any protein on earth.
Often, in cell membranes, four aquaporin proteins will come together to form a tetramer to assist with the transportation of water across the cell membrane. There are types of aquaporins that only transport water, and others that transport glycerol, neutral acids or gasses. Historically, plant science literature has reported that the molecular structure of aquaporins prevents any charged particles, such as ions, from permeating. This is different in the animal world where there are reports of aquaporins that are permeable to ions. For example, in humans one of the most highly expressed aquaporins, AQP1, can function as a dual water and ion channel.
Testing plant aquaporins in frog cells
Recently, we observed that one of the most highly expressed plant aquaporins is permeable to ions when expressed in heterologous systems such as Xenopus laevis (frog) oocyte (egg) cells or yeast cells. This indicates that plants may also have types of aquaporins that can function as a dual water:ion channels.
The function of plant aquaporins can be studied by expressing them in different systems such as the Xenopus laevis oocyte cells pictured here. Photo credit: Dr Caitlin Byrt.
If you want to know if a particular plant aquaporin can function as a water channel you can test it by expressing the aquaporin in a laboratory oocyte expression system. We use a tiny needle to inject RNA coding for plant aquaporins of interest into the oocyte, and for control oocytes we inject the same amount of water. The oocytes are kept in a saline solution and we usually study them one or two days after injecting the RNA to allow time for them to synthesize the protein.
If you place oocytes expressing an aquaporin into water alongside control oocytes, then the aquaporin-expressing oocytes will burst much quicker than the controls because water rushes in through the aquaporin and causes the cell to swell rapidly. To explore whether a protein conducts ions, we use electrodes to measure the currents generated when charged ions pass across the oocyte membrane. We can also use ion-specific electrodes to explore which ions are transported.
AtPIP2;1 can transport water and ions
The plant aquaporin we studied is coded in the genome of the model plant Arabidopsis; it is a plasma membrane-located protein called AtPIP2;1. The AtPIP2;1 protein is known to be highly prevalent in root epidermal cell membranes, and it also functions in the guard cells of leaves, which act like tiny valves to regulate the uptake of carbon dioxide for photosynthesis and the release of water vapor.
The model plant Arabidopsis has an aquaporin, AtPIP2;1, that can function as a dual water:ion channel. Photo credit: Dr. Jiaen Qiu.
We observed that AtPIP2;1 expression induces both water and ion (salt) movement across the cell membrane of oocytes. We know that the ionic conductance can be carried in part by sodium ions and that it is inhibited by calcium, cadmium and protons. This means AtPIP2;1 is a candidate for a previously reported calcium-sensitive non-selective cation channel responsible for sodium ion entry into Arabidopsis roots in saline conditions.
We are investigating the physiological role of ion permeable aquaporins in plants, and exploring how plants regulate the coupling of ion and water flow across key membranes. The regulation of ion permeability through plant aquaporins could be important in the control of water flow and regulation of cell volume. There is increasing discussion around the hypothesis that plants could drive water transport in the absence of water potential differences using salt and water co-transport, and this makes us wonder whether ion-permeable aquaporins may be involved. Testing whether ion-permeable aquaporins can function as an ‘all-in-one’ osmotic system in plants is an exciting new direction for research in this field.
Dr. Caitlin Byrt, Professor Steve Tyerman and colleagues are investigating whether aquaporins permeable to ions are present in a range of different plant species. Photo credit: Wendy Sullivan
Plant samples in the genebank at the International Center for Tropical Agriculture’s Genetic Resources Unit, at the institution’s headquarters in Colombia. Credit: Neil Palmer / CIAT. Used under license: CC BY-SA 2.0.
It was too dry in the Australian region of Wimmera to produce crops last summer. This year, floods are set to wipe out yields again. Like a number of other regions across the planet, climate change is starting to be felt.
For Norton and many of her colleagues in agricultural genetics, the picture is increasingly clear: The variety of crops used today are not able to withstand the changing conditions and changes expected in the future.
Australia’s biodiversity may offer some help, according to discussions at the recent International Genebank Managers Annual General Meeting held in Horsham, Victoria. The gathering, which brings together 11 countries, focused on how to better conserve seeds, build databases to manage collections, boost capacity across the world and fill gaps in genebanks.
Researchers are particularly interested in crop wilds, “the ancestors of our domesticated crops,” Marie Haga, executive director of the The Crop Trust, explained to Devex. Australia is one of the richest sources of these seeds. “It’s like the wolf being the ancestor to our domesticated dogs. Crop wild relatives have traits that we have lost in the domestication process — they might need less water, might live in unfriendly conditions, may be resistant to pests and diseases.”
As climate change continues to batter agricultural yields, crop wild relatives could provide resilience. The seeds give breeders and farmers new options of plant varieties with traits to withstand a variety of conditions based on the harsh climates they are found — drought, fire, flood, poor soil, high salinity.
For Haga, crop wild relatives are a solution for food security. “The challenge is that many of the varieties widely used in modern agriculture are very vulnerable, because we have been breeding on the same line and they are adapted to very specific environment,” Haga said. Varieties that flourish today, she said, could wither as the climate fluctuates.
“Utilization of the natural diversity of crops is key to the future,” she said. “The climate is rapidly changing and we need to feed a growing population with more nutritious food. It is very hard to see how we can do this unless we go back to the building blocks of agriculture.”
Norton agreed: “Crop wild relatives have an amazing adaptability to changing conditions,” she told Devex. “When we talk about food security, we are talking about getting varieties in farm paddocks that have greater resilience to extreme conditions. It may not be the highest yield, but you are going to get something from this crop.”
Why have they been overlooked?
Crop wild relatives have so far been underutilized in the research and breeding process of crops.
“We have this fabulous natural diversity out there including 125,000 varieties of wheat and 200,000 varieties of rice.” Haga said. “We have not at all unlocked the potential of these crops.”
One reason is a dearth of research. “Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives,” a 10-year project led by Haga to ensure long-term conservation of crop wild relatives, conducted a global survey of distribution and conservation and found that of 1,076 known wild relatives for 81 crops, more than 95 percent are insufficiently represented in genebanks and 29 percent are completely missing. They are missing purely due to the fact that they have yet to be collected.
“Genebank managers are generally open to include crop wild relatives in their collections.” Haga said. “It’s just quite simply that not enough work has been done in this area and the full potential is yet to be realized,” she said.
At the moment, seeds are being collected in 25 countries around the world as part of the crop wild relative project, but it is Australia that has been identified as one of the richest sources for crop wild relatives in the world. Because of the continent’s low population density and vast, undisturbed natural environment, a wide variety of species have been conserved, said Norton.
Australia holds significant diversity of wild relatives of rice, sorghum, pigeon pea, banana, sweet potato and eggplant currently missing from global collections, according to research by the Australian Seed Bank Partnership. Forty species have been prioritized for collection with high hopes that they will enable crops to withstand the harsh environmental conditions in which Australian species are found.
There are still many areas of Australia yet to be surveyed, and the full extent of its agricultural riches may yet to be tapped.
Australian researchers will play an important role in pre-breeding local species of wild relatives to improve their use in breeding programs. Crop wild relatives have historically been used in a variety of crops including synthetic wheat, but Australian native wild relatives have been harder to include in the breeding process.
“In the next 10 to 15 years it would be surprising if there is not something coming out that hasn’t got a component of Australian native wild relative in it,” Norton said who is currently involved in the collection of Australian crop wild relatives.
Collection of crop wild relatives is time sensitive
There is an urgency to collect crop wild relatives. Not only are wild species needed now to support changing environmental conditions affecting crops and farming, urbanization is putting crop wild relatives at risk of disappearing.
“We need to collect these sooner rather than later,” Norton told Devex. “Urbanization has a big impact on any native environment, let alone crop wild relatives. We know what species on our target list are more threatened than others — urbanization, flooding and fire are all risks to their security. We certainly have a priority list of species to collect and we need to make sure we target the ones that are under threat first.”
Once the varieties are conserved, breeders and farmers will need to be convinced to start using crop wild relatives. Many are already on board. “Most breeders understand these wild relatives have great potential,” Haga said.
Still, wild relatives can be difficult to work with and produce a lower yield. Haga expects there to be some reluctance, though limited.
“The understanding of the need is increasing and we feel very confident that this material will be used and some of them may be the game changer we are looking for,” she said.
The plans for crop wild relatives
Haga’s 10-year project on crop wild relatives is halfway complete. They are nearing the end of the collection phase and entering the pre-breeding process, before they are able to breed and deliver new species to farmers.
Australian support for the program includes an agreement for additional amount of $5 million. That comes on top of previous support of $21.2 million to the Crop Diversity Endowment Fund, which supports crop diversity globally and with a focus on the Indo-Pacific. Brazil, Chile, Germany, Japan, New Zealand, Norway, Switzerland and the United States are among other supporters of the endowment fund that hopes to reach $850 million. In Australia, further resources are still required to fund and support better seed collection at home.
Globally, plans for crop wild relatives includes raising greater awareness of their potential and importance.
“We have a big job to do to create awareness of the important of crop diversity generally and crop wild relatives specifically,” Haga said. “We have been speaking for years about biodiversity in birds and fish and a range of other animals, but we have talked very little about conserving the diversity of crops. I will fight for all types of diversity, but especially plants.”
As popular British botanist (and GPC blog guest) James Wong wrote in the UK’s Guardian newspaper earlier this year: “gardening is good for you”. Ask most people how they can benefit from gardening, and they might suggest improved physical activity or stress relief, but this is only scratching the surface.
The People Plant Council (PPC) is an international group of researchers and other industrial and not-for-profit partners, which aims to understand the effects plants have on our well-being. By communicating its findings to affiliates and the public, the PPC encourages the translation of these findings into health-enhancing programs. The PPC was established after a 1990 symposium entitled, “The Role of Horticulture in Human Well-Being and Social Development”, which identified a need for scientific research into the influence of horticulture on human health and quality of life.
The benefits of plants
The earliest reports of horticulture being used to improve human health come from ancient Egypt, where members of royalty were prescribed walks through the palace gardens as a treatment for mental illness (1). Today, research from the PPC and others has identified wide-ranging psychological, physiological, and sociological benefits from plants.
Gardening is good for both physical and mental health. Credit: Shyn Darkly. Used under license: CC BY 2.0.
The physiological benefits of gardening include an increase in physical activity (and the resulting improvements in cardiovascular fitness, muscle strength and aerobic capacity), but there are also some less obvious benefits, including better hand-eye coordination, balance, and an improvement in some chronic diseases. In one PPC-led study, elderly women took part in 50-minute gardening sessions twice a week, which led to significant improvements in their dexterity, muscle mass and cognitive ability compared to a control group (2).
There are also significant psychophysiological benefits to horticulture. Two interesting studies found that exposure to soil – or more precisely, to a common bacterium in soil (Mycobacterium vaccae) – improved the quality of life for both human cancer patients and mice by inducing the production of the brain’s “happy chemical”, seratonin (3,4). Contact with nature has also been shown to improve memory, concentration and stress.
People connect with each other around plants; whether it’s admiring a friend’s garden, giving a partner some flowers, or sharing a picnic at the local park, most of us have experienced the sociological benefits of plants. A PPC-led study found that horticulture was brilliant for improving peer relationships in schools too; a collaborative gardening program for small groups of 12–13 year-olds led to meaningful friendships that persisted after the class ended. The gardening students were also more law-abiding and social than the control group.
People bond over the experience of enjoying nature together. Credit: Amelia Wells. Used under license: CC BY 2.0.
At the IPPS meetings, delegates address the inherent impacts of nature on every aspect of our lives, including physical and mental health, and education. Dr Park elaborated, “The IPPS is attended by researchers, practitioners (such as horticultural therapists), and educators in various fields such as horticultural science, ethnobotany, psychology, nursing, occupational therapy, etc. The International Society for Horticultural Science supports the PPC, and enables us to publish the IPPS proceedings in their journal, Acta Horticulturae”.