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Rice blast fungus (Magnaporthe oryzae) is a global food security threat due to its destruction of cultivated rice, the most widely consumed staple food in the world. Disease containment efforts using traditional breeding or chemical approaches have been unsuccessful as the fungus can rapidly adapt and mutate to develop resistance. Because of this, it is necessary to understand fungal infection-related development to formulate new, effective methods of blast control.

A group of scientists at Nanjing Agricultural University and Louisiana State University Health Sciences Center examined the fungal cell biology of rice blast fungus pathogenesis and recently published the first systematic and comprehensive report on the molecular mechanism of the actin-binding protein (MoAbp1) that plays a crucial role in the pathogenicity of the fungus.

Through ongoing research, these scientists found that rice blast fungus forms a specialized infection structure that applies mechanical force to rupture the rice leaf cuticle. Once inside the host, the infection proliferates by living off the plant’s nutrients. These two processes are enabled by the actin-binding protein (MoABp1) that links an actin-regulating kinase (MoArk1) and a cyclase-associated protein (MoCap1) to an actin protein (MoAct1). These processes are necessary for the growth and perseverance of the fungus.

On a large scale, these findings shed a new light on the eukaryotic cell biology and virulence mechanisms of plant pathogenic fungi. On a smaller scale, these findings could reveal novel approaches or targets for anti-blast fungus management.

Rye bread or porridge oats may not be everyone’s first choice of breakfast, but scientists say Europeans need to broaden their taste in cereals both to boost their own health and to protect the future of Europe’s farming.

Wheat makes up nearly half of all cereals grown in the EU. The rest is mainly maize and barley.

Although Europe’s strategy to focus on a few high-yielding plants has produced bumper harvests, the lack of genetic variation means the crops are more susceptible to disease, pests and drought, scientists say.

‘If we rely on only one crop we are very vulnerable,’ said Dr Dagmar Janovská, curator of minor crops at the Prague-based Crop Research Institute in the Czech Republic.

‘We should learn from our history and grow a lot of different crops,’ she added, referring to Ireland’s potato famine in the mid-19th century. At the time, most Irish farmers grew just potatoes. When disease wiped out the country’s crop, it led to widespread starvation.

Dr Janovská coordinated a Europe-wide project to help boost the breeding and popularity of minor cereals rye, oat, spelt, emmer and einkorn.

Researchers on the HealthyMinorCereals project evaluated more than 1,700 genotypes – sets of genes in a plant’s DNA – for specific traits including yield, nutritional quality and resistance to disease. They carried out field experiments in Estonia, the UK, the Czech Republic and Crete.

‘We would like to improve breeding programmes in Europe (of minor cereals),’ Dr Janovská said.

The project’s results should help breeders develop varieties of cereal – including common wheat – which are better suited to the changing climate and need fewer pesticides. For example, the researchers found one genotype of spelt that is resistant to a fungus called fusarium head blight.

Globally, more than 6,000 plant species have been cultivated for food, but just nine of these account for 66% of the world’s crop production, according to the UN’s Food and Agriculture Organization (FAO).

Growing a diverse range of crops and cutting the amount of chemical inputs is better for the environment, and the health of the soil. ‘If we harm (Europe’s) ecosystems … we can assume we will have a very big problem in producing any food. Everything is interconnected,’ Dr Janovská said.

‘We should learn from our history and grow a lot of different crops.’ said Dr Dagmar Janovská, Crop Research Institute, Prague, Czech Republic.

Health-boosting

Some of the minor cereals contain more health-boosting nutrients like iron, zinc and antioxidants compared to common wheat, the researchers found.

‘The more diverse our food, the better. And spelt, rye and oat are very beneficial for our health, for example in lowering cholesterol,’ said Dr Janovská.

They also need fewer chemical inputs and can grow in relatively poor soil.

Common wheat expanded with the mechanisation of farming in the last century. It is high yielding – it produces large quantities of grain per hectare of land – and easy to process into flour.

It has expanded even in countries like the Czech Republic where people traditionally eat rye bread. Wheat makes up more than 60% of cereals grown there now, up from 18% in 1920. Over the same period, rye production has fallen to just 2%, from 35% in 1920, according to Dr Janovská.

‘That change is mainly because wheat is easier to grow,’ said Dr Janovská.

Fears about the lack of diversity on farms are widespread, even affecting traditional farmers working on small farms high up in the Andes mountains in South America. Some of them are ditching a wide variety of crops in favour of quinoa, a lucrative ‘superfood’ which has become popular in Europe and North America.

Taste

Some scientists hope that Europeans – as well as Americans – will expand their taste for other foods from the mountains in Peru, Bolivia and Ecuador.

Many of them, like quinoa, are high in protein and good for vegetarians, diabetics and people with gluten allergies.

‘I think Europe is a great market … because (these kinds of foods are) what people are looking for and what the European market can pay for,’ said Dr Gabriela Alandia Robles, a researcher in high-protein crops at the University of Copenhagen, Denmark.

Europe is the second largest market for quinoa after the United States. Other comparable foods from the Andes could follow a similar trend, she said.

Dr Alandia Robles worked on a project called Latincrop which aimed to increase Andean crops’ production and consumption both locally and in Europe.

Hot on the heels of quinoa is amaranth. The tiny grain has a nutty flavour and can be cooked like risotto rice or made into popcorn.

‘It has the whole range of amino acids that your body needs,’ said Dr Alandia Robles. It also is good for diabetics and people allergic to gluten, and has important amounts of folic acid, calcium, phosphorous and iron, she added.

The Andean lupin also has potential. ‘Europe is looking for a high protein crop, and Andean lupin has as much protein as soya bean – 51%,’ said Dr Alandia Robles. Its beans can be made into a kind of hummus.

One chef promoting these foods in Europe is Simon Brammer who, together with his wife Janice Pelayo Hansen, cook Peruvian food for weddings and corporate events in Denmark. They are passionate about sharing the nutritious foods with as many people as possible.

‘When we started Panca (a food truck) in 2016, it was a totally new thing. Some people hadn’t even heard of Peru … They were surprised by the flavours,’ Pelayo Hansen said.

Their dishes include a spicy chicken dish served with biscuits made from arracacha roots grown around Titicaca lake, and a quinoa salad popular with their vegetarian customers.

Cookbook

If European demand is to grow for both Andean foods and locally grown cereals, people need to know how to cook them. To help with this, the Latincrop project produced a cookbook, and the HealthyMinorCereals project is planning one too.

Dr Janovská’s favourite cereal from the project is spelt. ‘At Christmas we make cookies out of spelt flour, because the taste is better,’ she said, adding that its fibre content makes it healthier.

‘We need to improve demand, and then we can ask our farmers to grow it … If you want to improve anything on the field, you have start with the fork,’ she said.

Article source: Horizon Magazine

Image: Pixabay

Topping the list of Australia’s major crops, wheat is grown on more than half the country’s cropland and is a key export commodity. With so much riding on wheat, accurate yield forecasting is necessary to predict regional and global food security and commodity markets. A new study published in Agricultural and Forest Meteorology shows machine-learning methods can accurately predict wheat yield for the country two months before the crop matures.

“We tested various machine-learning approaches and integrated large-scale climate and satellite data to come up with a reliable and accurate prediction of wheat production for the whole of Australia,” says Kaiyu Guan, assistant professor in the Department of Natural Resources and Environmental Sciences at the University of Illinois, Blue Waters professor at the National Center for Supercomputing Applications, and principal investigator on the study. “The incredible team of international collaborators contributing to this study has significantly advanced our ability to predict wheat yield for Australia.”

People have tried to predict crop yield almost as long as there have been crops. With increasing computational power and access to various sources of data, predictions continue to improve. In recent years, scientists have developed fairly accurate crop yield estimates using climate data, satellite data, or both, but Guan says it wasn’t clear whether one dataset was more useful than the other.

“In this study, we use a comprehensive analysis to identify the predictive power of climate and satellite data. We wanted to know what each contributes,” he says. “We found that climate data alone is pretty good, but satellite data provides extra information and brings yield prediction performance to the next level.”

Using both climate and satellite datasets, the researchers were able to predict wheat yield with approximately 75 percent accuracy two months before the end of the growing season.

“Specifically, we found that the satellite data can gradually capture crop yield variability, which also reflects the accumulated climate information. Climate information that cannot be captured by satellite data serves as a unique contribution to wheat yield prediction across the entire growing season,” says Yaping Cai, doctoral student and lead author on the study.

Co-author David Lobell of Stanford University adds, “We also compared the predictive power of a traditional statistical method with three machine-learning algorithms, and machine-learning algorithms outperformed the traditional method in every case.” Lobell initiated the project during a 2015 sabbatical in Australia.

The researchers say the results can be used to improve predictions about Australia’s wheat harvest going forward, with potential ripple effects on the Australian and regional economy. Furthermore, they are optimistic that the method itself can be translated to other crops in other parts of the world.

Read the paper: Agricultural and Forest Meteorology

Article source: University of Illinois

Image: Mylene2401 – Pixabay

Tomato breeders have traditionally emphasized traits that improve production, like larger fruits and more fruits per plant. As a result, some traits that improved other important qualities, such as flavor and disease resistance, were lost.

Researchers from Boyce Thompson Institute and colleagues from partnering institutions have created a pan-genome that captures all of the genetic information of 725 cultivated and closely related wild tomatoes, establishing a resource that promises to help breeders develop more flavorful and sustainable varieties.

As described in a paper published in Nature Genetics, the researchers found 4,873 new genes and identified a rare version of a gene that can make tomatoes tastier.

“The pan-genome essentially provides a reservoir of additional genes not present in the reference genome,” said Boyce Thompson Institute faculty member Zhangjun Fei. “Breeders can explore the pan-genome for genes of interest, and potentially select for them as they do further breeding to improve their tomatoes.”

The first tomato genome sequence was a large modern variety published in 2012, revealing approximately 35,000 genes and facilitating crop improvement efforts. Since then, several hundred additional tomato genotypes have been sequenced.

The current study is the first to mine all of these genome sequences—as well as another 166 new sequences generated by the researchers—to hunt for genes that were absent from the reference genome.

“During the domestication and improvement of the tomato, people mostly focused on traits that would increase production, like fruit size and shelf-life,” Fei said, “so some genes involved in other important fruit quality traits and stress tolerance were lost during this process.”

Indeed, the researchers found that genes involved in defense responses to different pathogens were the most common group of genes that were missing in the domesticated varieties of tomato.

“These new genes could enable plant breeders to develop elite varieties of tomatoes that have genetic resistance to diseases that we currently address by treating the plants with pesticides or other cost-intensive and environmentally unfriendly measures,” added James Giovannoni, a BTI faculty member and USDA scientist.

Giovannoni and Fei are co-corresponding authors on the paper and adjunct professors in Cornell University’s School of Integrative Plant Science.

In addition to recovering these “lost” genes, the researchers also analyzed the pan-genome to find genes and gene mutations that are rare among the modern cultivars.

This analysis identified a rare version of a gene, called TomLoxC, which contributes to a desirable tomato flavor. The rare version is present in 91.2% of wild tomatoes but only 2.2% of older domesticated tomatoes.

“The rare version of TomLoxC now has a frequency of 7% in modern tomato varieties, so clearly the breeders have started selecting for it, probably as they have focused more on flavor in the recent decades,” Giovannoni said.

The researchers also discovered a new role for the TomLoxC gene.

“TomLoxC appears, based on its sequence, to be involved in producing compounds from fats,” said Giovannoni. “We found it also produces flavor compounds from carotenoids, which are the pigments that make a tomato red. So it had an additional function beyond what we expected, and an outcome that is interesting to people who enjoy eating flavorful tomatoes.”

Ultimately, the tomato pan-genome could benefit the economy and the consumer, according to Clifford Weil, program director of the NSF’s Plant Genome Research Program, which supported the work.

“How many times do you hear someone say that tomatoes from the store just don’t quite measure up to heirloom varieties?” Weil asked. “This study gets to why that might be the case and shows that better tasting tomatoes appear to be on their way back.”

Tomatoes are one of the most consumed vegetables in the world—although technically we eat their fruit—with 182 million tons worth more than $60 billion produced each year. Tomatoes also are the second most-consumed vegetable in the U.S., with each American consuming an average of 20.3 pounds of fresh tomatoes and 73.3 pounds of processed tomatoes each year.

Researchers from the University of Florida, Cornell, the U.S. Department of Agriculture, the Pennsylvania State University, the Polytechnic University of Valencia, the University of Georgia and the Chinese Academy of Agricultural Sciences also participated in the study.

Read the paper: Nature Genetics

Article source: Boyce Thompson Institute

Image: Mike Carroll

A group of researchers from the University of Helsinki has found a groundbreaking new method to facilitate the observation of photosynthetic dynamics in vegetation. This finding brings us one step closer to remote sensing of terrestrial carbon sinks and vegetation health.

In 2017, the group from the Optics of Photosynthesis Lab (OPL) developed a new method to measure a small but important signal produced by all plants, and in this case trees. This signal is a called chlorophyll fluorescence and it is an emission of radiation at the visible and near-infrared wavelengths. Chlorophyll fluorescence relates to photosynthesis and the health status of plants, and it can be measured from a distance, for example from towers, drones, aircraft and satellites. Interpretation of the signal is, however, complicated and so far it has only been possible to measure it within discrete spectral bands from fully-grown trees in the field.

OPL devised a new technique that, for the first time, allowed them to observe from a distance the full spectrum (all colours) of fluorescence of mature trees growing in the forest. Measuring the whole spectrum of emission reveals information on both plant performance (how they photosynthesise) and the structure of the plants themselves.

The issue with conventional remote sensing methods used so far has been that during daytime, most of the fluorescence distribution remains hidden from view, as the signal is so weak compared to sunlight. Therefore measuring fluorescence during daytime, commonly referred to as Solar-Induced Fluorescence (SIF), requires extremely sensitive and specialised instrumentation. The new technique differs from these previous efforts by using commercially available LED technology, which literately lights up the forest at night to reveal the full spectrum of emission of whole trees.

“We realised we could use the night as a ‘natural light filter’, so we went into the forest at night and attached a strong wavelength-restricted light source (a commercial disco-type light) to a tower that excited the fluorescence. Next, we used specialist scientific instrumentation, a spectroradiometer, also mounted in the tower to observe the signal”, describes Jon Atherton, researcher from the University of Helsinki Optics of Photosynthesis Lab at the Institute for Atmospheric and Earth System Research (INAR) / Forest Sciences of the University of Helsinki.

Combining night and light simplifies things: measuring fluorescence at night can be done with potentially cheaper (less sensitive) instruments and it provides data that is easier to interpret.

The link between fluor­es­cence and ter­re­strial car­bon sinks

The researchers’ new contribution puts us one step closer to “observing photosynthesis” by looking at the light emitted by plants, both on smaller scales (greenhouse, crops, forest stand) but also globally using satellites. The European Space Agency is preparing the FLEX satellite mission, which aims to map fluorescence globally. The hope is that fluorescence will be used to routinely estimate plant photosynthesis from space, which is the process that drives the terrestrial carbon cycle.

The role of forests in the uptake and assimilation of atmospheric carbon is crucial and widely discussed in the media. Measuring the exchange of carbon dioxide between forests and the atmosphere is accomplished with expensive instrumentation in specific places (flux tower sites) which produce localised estimates of fluxes (carbon exchange) close to the sites. This is where fluorescence enters into play by providing a remote sensing friendly means of estimating photosynthesis across the landscape by filling in the coverage (gaps) between the stations. Interpreting the data is challenging, but with the Light Emitting Diode Induced Fluorescence (LEDIF) technique there should be a significant leap forward.

“It is the potential for measuring fluorescence from space that really motivated us to do this work, although our results could have other applications too such as phenotyping, precision farming or forest nurseries. We hope that our data can be used to inform algorithms used to ‘retrieve’ fluorescence from space. Such algorithms work in a slightly different way to our spectral technique as they exploit dark atmospheric ‘lines’ to estimate fluorescence. Hence, the full emission spectrum remains effectively hidden in satellite data, and that is what our data reveals”, Jon Atherton adds.

Read the paper: Remote Sensing of Environment

Article source: University of Helsinki

Image: Albert Porcar-Castell

Giving local communities in Nepal the opportunity to manage their forests has simultaneously reduced deforestation and poverty in the region, new research has shown.

In the largest study of its kind, an international team of experts led by The University of Manchester has found that community-forest management led to a 37% relative reduction in deforestation and a 4.3% relative reduction in poverty.

This is particularly significant in a low income country, where more than a third of the country’s forests are managed by a quarter of the country’s population.

The findings, published in Nature Sustainability, is the largest study on community-based forest management. It estimates the impacts of more than 18,000 community forest initiatives across Nepal, where community-forest management has actively been promoted for several decades.

Forests are critical to sustainable development: they regulate the world’s climate, sequester carbon from the atmosphere, harbour biodiversity, and contribute to the local livelihoods of millions of people worldwide.

Over the past four decades, governments and international organisations have actively promoted community-based forest initiatives as a way to merge natural resource conservation with human development. Local communities now legally manage approximately 13% of the world’s forests.

But evidence of the impact of community-based forest management has been largely limited to small-scale evaluations, or narrowly focused studies until now.

Lead author Dr Johan Oldekop, The University of Manchester said, “Our study demonstrates that community forest management has achieved a clear win-win for people and the environment across an entire country. Nepal proves that with secure rights to land, local communities can conserve resources and prevent environmental degradation.”

“Our study demonstrates that community forest management has achieved a clear win-win for people and the environment across an entire country. Nepal proves that with secure rights to land, local communities can conserve resources and prevent environmental degradation” Dr Johan Oldekop says.

Reductions in deforestation did not occur at a cost to local wellbeing. The study found that areas with community forest management were 51% more likely to witness simultaneous reductions in deforestation and poverty.

Co-author Professor Mark Whittingham, University of Manchester said, “It’s not easy to balance sustainable management of the environment against the needs, or wants, of mankind. These findings highlight one positive solution.”

The research, authored by an interdisciplinary team of ecologists, economists and political scientists, overcomes previous data limitations by using rigorous techniques to analyse publically available data on forests, people, and institutions. The team combined satellite image-based estimates of deforestation with data from Nepal’s national census of 1.36 million households, and information on more than 18,000 community forests.

Co-author author Professor Arun Agrawal, The University of Michigan said, “Identifying a mechanism – community forestry – that can credibly reduce carbon emissions at the same time as improving wellbeing of the poor is an important step forward in global efforts to combat climate change and protect the vulnerable.”

Mexico, Madagascar, and Tanzania have similar community-forest management programmes, with Indonesia and others developing them.

Co-author Katharine Sims, Amherst College, said, “We sought to learn from Nepal’s experience implementing an innovative conservation policy. We hope our methods will be useful for future study of community forestry in different contexts and compared to alternate governance structures.”

If other areas are able to replicate Nepal’s success, community-forest management could play an even greater role in achieving multiple Sustainable Development Goals.

Read the paper: Nature Sustainability

Article source: University of Manchester

Image: Pixabay

University of Cordoba research analyzes how changes in the structure of soil microbiota affect holm oak decline

Holm oak decline, which threatens dehesa sustainability, has got governments, farmers, civilians and the research community to join forces in protecting this ecosystem. Though the pseudofungus oomycete Phytophthora cinnamomisería is thought to be the main cause of holm oak decline, climate conditions have been shown to influence as well. Even so, this puzzle has yet to be solved.

In search of the last few pieces to help understand how the disease develops, University of Cordoba Forest Engineering researchers Francisco Ruiz and Rafael Mª Navarro, in collaboration with researcher Alejandro Pérez de Luque from IFAPA(Agricultural and Fishing Training Research Institute of Andalusia, Alameda del Obispo center), and international researchers, carried out a study on microorganism biodiversity in soil by means of using molecular techniques, in order to analyze if and how interactions among soil microorganisms influence the seriousness of the disease.

The study focused on fungi and oomycetes that live in soil, and the interactions that occur among them. In addition, it confirms that changes in microbiota structure and biodiversity are fundamental for woodland health in two ways: on the one hand, interactions among soil microorganisms directly influence pathogens that affect holm oak and on the other, the presence of some beneficial microorganisms helps to improve the trees’ health.

A well-known biocontrol agent, Trichoderma, appeared to be related to the absence or scarcity of oomycete pathogens. What is more, an abundance of mycorrhizae resulted in less defoliation of the woodland. These microorganisms are able to establish antagonistic relationships with the pathogens, increase a tree’s ability to absorb and stimulate an autoimmune response. In other words, a structure conducive to the fungi community and the presence of key beneficial species provide the oak with more resources to defend itself from the pathogen and improve the health of a woodland, even when root rot is present.

Turning the focus underground also unravels other mysteries. All of the lands that were studied had root rot (decline), and nevertheless, the pathogens that are considered to be the main causes of the disease were not relevant on many plots of land, despite them being teeming with dying holm oaks. The key to this mystery was the presence of a mixture of less aggressive individual species such as Alternaria and Fusarium among others. When these kinds of species synergize, they can cause the same symptomatology as do more aggressive species, even to the point that they cause the tree to die. So, UCO and IFAPA researchers concluded that a diagnosis of oak decline should not only be limited to the presence of one single pathogen, but rather a complete analysis of the present communities and the relationships among them is required in order to detect danger in a more precise way.

Advances in technology is what has allowed for solving the complexity of this study. The research group applied plant biotechnology methods to the study of forest pathology, which along with being able to access data from the Environmental Damage Tracking Network, part of the Andalusian Regional Government, allowed for understanding the role of soil microorganisms in the decline of Andalusian dehesas. The diversity and structure of microbiota is a key piece to this puzzle. Considering the soil microbiome within the comprehensive management of holm oak and cork oak root rot on the dehesa is bringing the research community closer to finding the solution that will most effectively protect this ecosystem.

Read the paper: Scientific Reports

Article source: University of Cordoba

Image: University of Cordoba

While the fate of most human cells is determined by their lineage—for example, renal stem cells go on to form the kidney while cardiac progenitor cells form the heart—plant cells are a little more flexible. Research shows that although they undergo orderly division during growth, the fate of plant cells is often determined by their location in the growing plant rather than how they started out. Intriguingly, this suggests that plant cells recognize where they are and can alter gene activity in response to their location.

To investigate position-dependent gene expression in plants, Hiroyuki Iida, Ayaka Yoshida, and Shinobu Takada from the Department of Biological Sciences at Japan’s Osaka University studied the differentiation of shoot epidermal cells in model plant Arabidopsis thaliana. Publishing in a recent issue of Development, the researchers showed that in plants, location really is everything.

“Many land plants have a single layer of epidermal cells to protect themselves from dehydration. However, it is not known how only the outermost cells are differentiated into the epidermis,” explains lead author Iida. To examine the differentiation process, the researchers focused on a protein called ATML1, which helps determine epidermal cell identity in the shoots of plants.

“We found that although the ATML1 gene was expressed in subepidermal cells, there was a much greater accumulation of ATML1 protein in the outermost cell layer, suggesting that protein accumulation was inhibited in the internal cell layers,” says Iida.

By tagging the proteins with a fluorescent dye, the researchers could also examine where ATML1 was located inside the cells. Interestingly, while the fluorescent protein was most frequently found in the nucleus of the outermost cells, nuclear accumulation of ATML1 was weak in the inner cells, meaning that it could not interact with genes necessary for epidermal cell differentiation.

Going one step further, the researchers were even able to show that a section of the ATML1 protein called the ZLZ domain was necessary, but not entirely responsible for, the reduced nuclear accumulation and activity of ATML1 in the inner cells.

“Our study shows that post-transcriptional regulation of ATML1 based on the location of the cells is likely to be responsible for the formation of the single epidermal layer seen in many seed plants,” says senior author of the study Dr Shinobu Takada. “These findings provide greater insight into plant morphogenesis and help us to understand the evolutionary processes by which land plants have acquired the epidermis.”

Read the paper: Development

Article source: Osaka University

Image: Osaka University