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Jan 05
0

2016 Plant Science Round Up

By | Blog, Research

Another fantastic year of discovery is over – read on for our 2016 plant science top picks!

January

Zostera marina

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.

Read the paper in Nature: The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.

BLOG: You can find out more about the secrets of seagrass in our blog post.

 

February 

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:


Read the paper in Current Biology: Rules and self-organizing properties of post-embryonic plant organ cell division patterns.

 

March

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”.

Read the paper in PNAS: Calcium-dependent oligomerization of CAR proteins at cell membrane modulates ABA signaling.

*If you’d like to read more about stress resilience in plants, check out the meeting report from the Stress Resilience Forum run by the GPC in coalition with the Society for Experimental Biology.*

 

April

Arbuscular mycorrhizal fungi.

This plant root is infected with arbuscular mycorrhizal fungi. Image credit: University of Zurich.

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 Wiemsken explains: “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”.

Read the paper in Ecology Letters: Options of partners improve carbon for phosphorus trade in the arbuscular mycorrhizal mutualism.

 

May

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 Stevenson explains: “What’s interesting is that aquatic algae can’t respond to ABA: the next challenge is to discover how this hormone signaling process arose.”

Read the paper in The Plant Cell: Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE, a regulator of ABA responses unique to basal land plants and required for desiccation tolerance.

 

June

Knoblauch with phloem

Professor Michael Knoblauch shows off a microscope image of phloem tubes. Image credit: Washington State University.

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.

Read the paper in eLife: Testing the Münch hypothesis of long distance phloem transport in plants.

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!

 

July

Ancient barley grain

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 Schünemann predicts that “DNA-analysis of archaeological remains of prehistoric plants will provide us with novel insights into the origin, domestication and spread of crop plants”.

Read the paper in Nature Genetics: Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley.

BLOG: We interviewed Dr. Nils Stein about this fascinating work on the blog – click here to read more!

 

August

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 Henry suggested: “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.”

Read the paper in Scientific Reports: New evidence for grain specific C4 photosynthesis in wheat.

 

September

CRISPR lunch

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.

Read more in the Umeå University press release: Umeå researcher served a world first (?) CRISPR meal.

BLOG: We interviewed Professor Stefan Jansson about his prominent role in the CRISPR/GM debate earlier in 2016 – check out his post here.

*You may also be interested in the upcoming meeting, ‘New Breeding Technologies in the Plant Sciences’, which will be held at the University of Gothenburg, Sweden, on 7-8 July 2017. The workshop has been organized by Professor Jansson, along with the GPC’s Executive Director Ruth Bastow and Professor Barry Pogson (Australian National University/GPC Chair). For more info, click here.*

 

October

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 Wigge explains: “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”.

Read the paper in Science: Phytochromes function as thermosensors in Arabidopsis.

 

November

Ginkgo

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 Zhao said, “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”.

Read the paper in GigaScience: Draft genome of the living fossil Ginkgo biloba.

 

December

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.

Read the paper in Science: Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum.

 

Another amazing year of science! We’re looking forward to seeing what 2017 will bring!

 

P.S. Check out 2015 Plant Science Round Up to see last year’s top picks!

Dec 27
0

Genome editing: an introduction to CRISPR/Cas9

By | Blog, Future Directions
Damiano Martignago

Dr Damiano Martignago, Rothamsted Research

This week’s blog post was written by Dr Damiano Martignago, a genome editing specialist at Rothamsted Research.

 

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.

CRISPR/Cas9

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.

Wheat powdery mildew

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.

 

Using CRISPR, scientists from the Chinese Academy of Sciences produced a wheat variety resistant to powdery mildew, one of the major diseases in wheat. Similarly, another Chinese research group exploited CRISPR to produce a rice line with enhanced rice blast resistance that will help to reduce the amount of fungicides used in rice farming. CRISPR/Cas9 has also been already applied to maize, tomato, potato, orange, lettuce, soybean and other legumes.

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.

Cassava brown streak disease

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 Cellectis edited 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.

Dec 20
0

Please consider making a donation to the Global Plant Council

By | Blog, Future Directions, GPC Community

As a reader of our blog, we know that you are passionate about the power of plant science to tackle global challenges, such as food security, climate change, and human health.

The Global Plant Council is dedicated to promoting plant science collaborations across borders to address global challenges in a sustainable way. We are a strong voice for science, but as a not-for-profit organization we need your support.

Help us to keep supporting researchers and plant science by making a single or monthly donation today, via our secure PayPal system.

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Dec 19
0

Aquaporins capable of functioning as all-in-one osmotic systems

By | Blog, GPC Community
Caitlin Byrt

Dr Caitlin Byrt, University of Adelaide

This week’s post was written by Dr Caitlin Byrt, University of Adelaide, whose research focuses the roles of water-channeling proteins – aquaporins – and ion transport in plants.

 

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.

Water on leaf

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.

Aquaporin function

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.

 

Xenopus oocytes

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.

 

AtPIP2 Arabidopsis

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.

 

Caitlin Byrt and Steve Tyerman

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

 

More information:

Byrt, C.S., Zhao, M., Kourghi, M., Bose, J., Henderson, S.W., Qiu, J., Gilliham, M., Schultz, C., Schwarz, M., Ramesh, S.A., Yool, A., and Tyerman, S.D., 2016. Non‐selective cation channel activity of aquaporin AtPIP2; 1 regulated by Ca2+ and pH. Plant, Cell & Environment.

Yool, Andrea J., and Alan M. Weinstein. New roles for old holes: ion channel function in aquaporin-1. Physiology 17.2 (2002): 68-72.

Dec 12
0

Battening down the hatches: priming plant defense

By | Blog, Future Directions

This week’s blog post was written by Dr. Mike Roberts (Lancaster University, UK).

Dr. Mike Roberts

Dr. Mike Roberts, Lancaster University, UK, Mike with an experiment to test the effects of parental herbivory on defense priming in the next generation of Arabidopsis plants. (Photo credit: Lancaster University)

It is widely accepted that achieving agricultural sustainability means reducing our reliance on synthetic agrochemicals. One major group of agrochemicals is pesticides, which include the insecticides and fungicides that protect crop plants against pests and diseases. Pests and diseases aren’t going to go away, so reducing pesticide usage means that alternative crop protection approaches are needed. EU Directive 2009/128/EC (Sustainable Use of Pesticides) recommends the use of integrated pest and disease management (IPM) – the combined use of multiple approaches that together provide sufficient protection.

Our contribution to this challenge has been to identify ways in which we might enhance a plant’s own natural defense mechanisms. Plants have a wide array of structural and chemical defenses that they can employ to fight off enemies. Many of these are inducible, meaning that they are only activated in response to attack, which allows plants to balance the costs and benefits of defense. For crop plants, these costs can often translate into reduced yields. Spraying with compounds that switch on inducible defenses, such as the plant hormones jasmonic acid (JA) and salicylic acid (SA), can make plants more resistant, but this approach also risks unwanted growth reductions.

The JA team

(Left to right) Jane Taylor, Mike Roberts and Nigel Paul, who led the research on defense priming using seed treatments, in the glasshouse at the Lancaster Environment Center. (Photo credit: Lancaster University)

Fortunately, evolution has produced another way of regulating inducible defenses that we can take advantage of: the phenomenon we refer to as ‘priming’. When we ourselves get infected with something like a virus, our immune system generates antibodies to quickly fight it off, but it also produces memory cells that can respond to the same infection many months, or even years, in the future, with a more rapid and effective immune response. This is the basis of the familiar concept of vaccination. While plants don’t make antibodies, they are nevertheless able to alter future patterns of defense activation in response to previous infection by disease or feeding by herbivorous insects; thus, priming results in a faster and stronger activation of future inducible defense responses.

 

Benefits of plant defense priming

Transgenerational immune priming enhances disease resistance in Arabidopsis. All the plants in the photograph were inoculated by spraying the whole tray with a suspension of Pseudomonas syringae bacteria. The plants on the right side of the photo are from seed collected from parent plants that were infected with the same P. syringae bacteria, whilst those on the left come from healthy parents. (Photo credit: Belinda Ameyaw)

 

If we can find ways to prime defenses in crop plants, we might be able to improve pest and disease resistance with minimal impacts on yield. One way to do this is through seed treatments. We found that treating seeds with the defense hormone JA provides long-term enhanced resistance against herbivory and some fungal diseases, without affecting growth and development. We were able to patent this discovery, and the approach has since been successfully commercialized. The same approach can also be used to prime defenses against other forms of biotic and abiotic stress.

Seed treatment

Tomato seeds being treated with jasmonic acid solution. (Photo credit: Lancaster University)

How and why seed treatments provide long-term defense priming can be explained by the phenomenon of transgenerational immune priming, which my lab has also been investigating. After our success with the seed treatment, we wondered, “What if seeds were exposed to hormones like JA during the course of their development on the parent plant?” We tested this by infecting plants with bacteria or exposing them to herbivores, and then examined defense in their offspring. Remarkably, we saw that priming responses established in the parent were passed on to the offspring; something we refer to as transgenerational immune priming.

The evidence we have at present suggests that the mechanism for this heritable stress memory is epigenetic, meaning the genes that control priming are chemically tagged to alter their activity. These epigenetic modifications don’t involve changes in the DNA sequence and are reversible, allowing rapid, flexible responses to environmental stress. Understanding the nature of these epigenetic changes may provide another way to exploit priming for crop protection. Introducing the right epigenetic marks onto genes in elite crop varieties may enable the priming of defense without altering their genetic make-up. Given the difficulty of introducing new chemical and biological methods of crop protection, which require time-consuming and costly regulatory approval before they can be brought to market, this could prove an especially attractive option in the future.

Dec 05
0

Does Australia hold the key to food security?

By | Blog, Future Directions

This article is reposted from the Devex blog with kind permission from the author, Lisa Cornish.

CIAT research

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.

“It’s like this every year somewhere,” said Sally Norton, head of the Australian Grains Genebank, which stores diverse genetic material for plant breeding and research.

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.”

 

This article is reposted from the Devex blog with kind permission from the author, Lisa Cornish.

Nov 28
0

Temperate matters in agriculture

By | Blog, Future Directions, GPC Community

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Most of the world’s food is produced in temperate zones. The Global Food Security program’s Evangelia Kougioumoutzi reports on the TempAg network.

Agricultural production in temperate regions is highly productive with a significant proportion of global output originating from temperate (i.e. non-tropical) countries – 21% of global meat production and 20% of global cereal production [link opens PDF] originate from Europe alone. This proportion is very likely to increase in light of climate change.

Temperature zones

Little fluffy clouds: temperate zones are well suited to agricultural production. Image credit: connect11/Thinkstock

TempAg is an international research collaboration network that was established to increase the impact of agricultural research and inform policy making in the world’s temperate regions. Its work does not solely focus on research, but also provides insights into current thinking through mapping existing scientific findings and outstanding knowledge gaps. In this way, the network aspires to become a platform for the alignment of national agricultural research and food partnership programs (such as Global Food Security) that will enable the development of more effective agricultural policies with a long-term vision.

Since its official inauguration in Paris in April 2015, TempAg has been leading a series of on-going workstreams around:

  • Boosting resilience of agricultural production systems at multiple scales and levels
  • Optimising land management for ecosystem services and food production
  • Improving sustainability of food productivity in the farms & enterprise level

You can read more about these themes on the TempAg website: http://tempag.net/themes/.

Future foresights

After 18 months of existence, TempAg held a foresight workshop in London on 5–7 October to determine its future priorities.

Forty delegates took part in the workshop, coming from the 14 different countries in the temperate region, and from academia, policy, industry, and professionals at the science–policy interface. Through a series of presentations and interactive sessions, participants were invited to consider what the current and future challenges are in temperate agriculture, taking into account the needs of policy makers and industry in helping them to improve sustainable agriculture practices.

 

Temperate zones

Temperate zones cover much of the world’s major food-growing areas. Image from Wikipedia/CIA-Factbook

 

To tackle sustainability in temperate agriculture, there is a need to better manage risks and stresses (both biotic and abiotic), as well as finding ways to manage the restoration of natural capital, ecosystem services, and soils. During the workshop, it was noted that utilizing the diversity within different agricultural systems, via identifying the best practice and using the appropriate technological mix, may be a way forward in making production systems more sustainable.

Participants stressed the importance of taking a holistic view of the sustainability agenda within agriculture, without just focusing on environmental aspects. This means also taking into consideration socioeconomic factors, such as making food value chains (like turning milk into cheese), more equitable by identifying who gets the equity from the food commodities’ prices, or identifying what the optimum legal framework for sharing data might be.

The group also considered sustainable agriculture issues from a policy and industry needs angle. It was interesting to see that dealing with shocks (environmental, socioeconomic, and technological) featured highly in this discussion as well. It was suggested that increasing resilience to these shocks could be facilitated via the widespread diffusion of existing technologies. Engaging with farmers during this time would be necessary to identify technology uptake barriers.

Forward moves

Future-proofing agricultural resilience and enhancing the capacity to respond to shocks was deemed an urgent priority, so the development of a comprehensive map identifying the multiple shocks that could impact on farm resilience in temperate zones might be a future workstream for TempAg. Work in this area could help develop models to assess the flexibility within agricultural production systems.

 

What we eat is largely based on the types of food we produce. Therefore, healthy diets are intrinsically linked with our production systems. Another area of interest for TempAg could be to explore what the nutritional value of crops should be for better health, and what a nutritional diet will look like for sustainable temperate agriculture. Developing frameworks in this area could further inform future farming practices in temperate areas.

Since TempAg’s initiation, two major global policy agendas have been adopted by the international community: the Sustainable Development Goals and the Paris COP21 agreement. Identifying what types of data and scientific evidence policy makers will need to achieve the agriculture-relevant targets was another area where TempAg could focus its activity moving forward.

Finally, delegates highlighted areas of work that could help to build more effective policies with a longer-term vision. These included developing economic tools for valuing natural capital and ecosystem services, as well as integrated assessment tools to monitor the performance and impact (environmental cost) of existing policies.

This article is cross-posted with the Global Food Security blog.

About Evangelia Kougioumoutzi

Evangelia is International Coordinator & Programme Manager for the Global Food Security program (GFS). Before joining GFS, Evangelia worked as an Innovation Manager for GFS partners BBSRC. She holds a PhD in plant development and genetics from the University of Oxford.

 

Nov 16
0

Flipping the symposium

By | Blog, GPC Community, Scientific Meetings
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Answers to the question: “Which crop species are most critical with regard to stress resilience?”

Lisa Martin, GPC Outreach & Communications Manager

GPC Executive Director Ruth Bastow and I recently travelled to Australia to hold the GPC’s annual general meeting – but we didn’t go all that way for a one-day meeting! We also took the opportunity to attend ComBio 2016, a large conference jointly hosted by the Australian Society for Biochemistry and Molecular Biology, the Australia and New Zealand Society for Cell and Developmental Biology, and GPC Member Organization the Australian Society of Plant Scientists.

Sadly, one person was conspicuous by his absence – GPC President Bill Davies, who had been due to give more than one talk at the conference, was unable to fly out to Australia at very short notice. While Ruth and our Chair Professor Barry Pogson could cover his talk during the GPC’s own lunchtime symposium, this left Dr Rainer Hofmann’s ‘Abiotic Stress and Climate Change’ session one speaker short at the last minute!

Answers to the question, "Which challenges do these crops face?"

Answers to the question, “Which challenges do these crops face?”

Fortunately Rainer, who happens to be a representative to the GPC for the New Zealand Society of Plant Biology, found a quick solution to the hole in his program: it was time for a bit of audience participation!

The ‘flipped classroom’ is an approach I’d heard of, but was not overly familiar with – however, according to Rainer it is used quite extensively in New Zealand, where plant biologists can be geographically isolated. Unlike the traditional university lecture, in which the teacher gives a presentation and the students go away to consolidate what they have learned with revision notes or problems to solve, the flipped classroom turns this model on its head. Instead, students are given the subject content to learn in advance, then bring their own questions to the lecture.

Arguably, this approach makes better use of students’ contact time and the lecturer’s expertise, and provides a richer and more independent learning experience. This model also works very well in distance learning: topic notes and presentation slides can be emailed out in advance, then a video-linked webinar can be used to connect students and teachers, and a web-tool like Socrative Student can be used to ask and answer questions online.

Answers to the question, "What are key solutions to address these challenges, in the next 3 years and in the longer term?"

Answers to the question, “What are key solutions to address these challenges, in the next 3 years and in the longer term?”

Rainer used this idea to fill the gap in his symposium – and it was great! He asked three important questions, and members of the audience were invited to provide short answers via the Socrative Student platform using their computers, cell phones or tablets – answers were then displayed on a screen in real time. Thank goodness for WiFi! The questions and answers can be seen in the word clouds we’ve created here – the size of the word provides an indication of the frequency of that particular response, so it’s easy to see which were the most and least popular answers. These responses provided useful, engaging stimuli for audience-led discussion – I’d really like to see this model used at other meetings!

The three questions asked were:

  1. Which crop species are most critical with regard to stress resilience?
  2. Which challenges do these crops face?
  3. What are key solutions to address these challenges, a) in the next three years, and b) in the longer term?

What would your answers have been? Leave us a comment below!

Nov 09
0

Down Under: the Global Plant Council’s 2016 AGM

By | Blog, GPC Community, Scientific Meetings

img_20161006_075356Lisa Martin, GPC Outreach & Communications Manager

As a truly global organization, the Global Plant Council hosts its annual general meeting (AGM) on a different continent each year, to give our members from far-flung corners of the globe the opportunity to come together to celebrate progress and discuss future strategies to develop plant science for global challenges.

With our current Chair Professor Barry Pogson hailing from ‘down under’, this year’s AGM was held in Brisbane, Australia, which made for a warm, sunny change from autumnal London for Ruth and I!

Starting bright and early at 8 am on Monday 3rd October, representatives from the GPC’s member societies joined the GPC’s Executive Board at a hotel in Brisbane’s central business district. After a welcome from the Chair, and a minute’s respectful silence to remember our former Board Member Professor Carl Douglas, who sadly passed away earlier this year, introductions were made and we got down to business. Ruth and myself first provided introductions to, and updates on, the main GPC initiatives and activities.

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While waiting for our Stress Resilience white paper to be published, why not read our Nutritional Security report? (Link opens PDF – right-click and save-as to download a copy to your computer!)

The DivSeek initiative continues to grow in strength and numbers, with 67 partner organizations now committed to working together to address genomic and phenomic data challenges in plant science. With funding from the UK’s Biotechnology and Biological Sciences Research Council Ruth has been providing essential coordination services specifically for this project, and with DivSeek Chair (Professor Susan McCouch) and a Steering Committee in place, the initiative is making real progress; a number of working groups have been launched to actively engage DivSeek partners and help the initiative advance its mission and aims.

Our other major, current initiative is in the area of Stress Resilience. As you may have read around this time last year, the GPC held a workshop and discussion forum on the subject of ‘Stress Resilient Cropping Systems for the Future’, in conjunction with our 2015 AGM in Brazil. This successful two-day event brought together experts in this area to share and showcase new research, tools and techniques. We are now turning our discussions from this meeting into a forthcoming white paper, and hopefully a commentary or two for publication in a high impact journal – we’ll let you know when these have been launched!

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Lisa talked to the Global Plant Council about our successful outreach and communications activities. Do you follow us on Twitter or Facebook?

Then it was my turn to speak on the subject of outreach and communication. With much help from our New Media Fellow (NMF) Sarah Jose (and our former NMF Amelia-Frizell Armitage, who left the GPC for a new job earlier this year), the GPC’s social media efforts have been tremendously successful this year. We now have nearly 3000 followers on Twitter, hundreds of ‘fans’ on Facebook, and over 1200 subscribers to our monthly e-Bulletin (though readership is much wider, thanks to many of our Member Organizations who also distribute this newsletter!). We were also pleased to welcome Current Plant Biology to our journal supporters; they join Journal of Experimental Botany, Nature Plants and New Phytologist in providing some financial sponsorship to support our outreach efforts.

In other activity updates, we discussed Plantae, the social media-cum-knowledge hub that the GPC has been working on developing with the American Society of Plant Biologists. Plantae is in beta testing mode to capture feedback on the design and user experience, but is growing and evolving all the time. We encourage you to register an account and sign up, if you haven’t already done so!

Sadly our President Bill Davies was unable to attend the AGM, but Ruth and Barry explained the premise of a new GPC Knowledge Exchange initiative that Bill is working hard to get off the ground. If successful in securing funding to progress this project, we hope to be involved with the development of an online training platform to transfer knowledge from the laboratory to the field – an exciting idea that will, we hope, be of invaluable benefit to communities in developing regions.

screen-shot-2016-11-09-at-14-37-18As with many research networks and non-profit organizations, securing long term funding for the GPC is a continual challenge. The GPC’s main source of income is its member organizations; a revised membership fee structure was agreed at last year’s AGM, but further refinement and additional sources of funding will be required to ensure the continued sustainability of the GPC. As such we are actively seeking donations to help us continue the work of GPC so if you would like to make a contribution to support our efforts, you can do so via our PayPal giving link here: https://globalplantcouncil.org/donate.

Happily, we are pleased to welcome three new affiliate members to our ranks – the Center for Plant Aging Research in Korea, the Max Planck Institute for Molecular Plant Physiology in Germany, and the ARC Centre of Excellence in Plant Energy Biology in Australia.

Before discussing the GPC’s vision for the future, we took the opportunity to hear from our Member Organizations about what they would like the GPC to do for them, and what they can do for us. Lots of excellent suggestions for cross-collaborations, outreach, and novel funding sources were made, and we will be eagerly following up on these in the coming months – watch this space!

Aside from plant science, we found some time to familiarize ourselves with the local wildlife!

Aside from plant science, we found some time to familiarize ourselves with the local wildlife!

In addition to the AGM GPC also hosted a lunchtime symposium during the ComBio 2016 meeting, entitled, “Addressing Global Challenges in Plant Science: the Importance of Co-operation beyond National Boundaries”. During this session, we showcased exemplar projects involving multi-national stakeholders, stressing that global challenges need global solutions, and highlighting the unique and essential role that GPC plays.

Ruth spoke about DivSeek, GPC Treasurer Vicky Buchanan-Wollaston spoke about our Stress Resilience initiative, and Barry provided an overview of the Nutritional Security Initiative and also filled in for Bill by talking about our proposed plans for the knowledge exchange platform mentioned above. Professor Andy Borrell from the University of Queensland also gave an engaging and insightful talk about why a transnational approach to plant, crop and agricultural science is needed, highlighting some of the real-world scenarios where the GPC might offer practical, proactive support for research across borders.

It was fantastic to see over 70 plant scientists who gave up their lunchtime to attend our symposium – there were plenty of questions and very positive feedback at the end that we hope this will spark new ideas, interactions and collaborations. We felt very encouraged by the interest in and support for the GPC and its initiatives, and look forward to being able to continue serving the global plant science community.