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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

Scientists at Lobachevsky University have proved the possibility of using yellow-green light pulses to measure the photochemical reflectance index and to estimate the amount of light stress in agricultural plants

Precision farming, which relies on spatially heterogeneous application of fertilizers, biologically active compounds, pesticides, etc., is one of the leading trends in modern agricultural science.

A necessary condition for such farming is a quick and remote analysis of the state of plants in the fields and greenhouses. To solve this problem, various spectral indices based on measurements of reflected light in narrow spectral bands are widely used. One of these indices, currently in the focus of attention of Lobachevsky University researchers, is the photochemical reflectance index – PRI.

The photochemical reflectance index is determined by measuring reflected light at two wavelengths in the yellow-green spectral range, at 531 and 570 nm, which is carried out using special detectors or multispectral cameras.

“A unique feature of the photochemical reflectance index is its sensitivity even to weak stress-related changes in the state of the photosynthetic apparatus. This opens up the potential possibility of using the photochemical reflectance index for early and remote diagnosis of how adverse factors may affect plants. However, the use of PRI has a number of serious limitations, one of them being the high sensitivity of the index to the lighting conditions, which is especially important if the measurements take place under solar lighting conditions,” says Vladimir Sukhov, head of the UNN plant electrophysiology laboratory.

This problem is addressed in the research project carried out by Ekaterina Sukhova, graduate student at the Department of Biophysics Lobachevsky University. The project was supported by the Russian Science Foundation (project No. 17-76-20032, supervisor Vladimir Sukhov). Research results were published in one of the leading scientific journals in the field of remote monitoring – Remote Sensing, 2019, 11 (7): 810.

For this purpose, Lobachevsky University scientists proposed an idea that could potentially reduce the sensitivity of the photochemical reflectance index to lighting conditions. It is based on the use of periodic illumination of the plant by pulses of yellow-green measuring light from a source with known spectral characteristics.

The intensity of the reflected light is calculated as the difference between the reflected light during each pulse of yellow-green light and before such a pulse (Fig. 1), which allows one to eliminate the influence of other light sources on the measurement results. Ekaterina Sukhova’s research has proved that the use of yellow-green light pulses eliminates the distorting effects of other light sources on the measurement of the photochemical reflectance index, and therefore improves the accuracy of determining the PRI.

Further, the photochemical reflectance index was determined under conditions of stress-inducing light intensities in a number of agricultural plants and was compared with the generally accepted indicator of photosynthetic stress — non-photochemical quenching of chlorophyll fluorescence (Fig. 2).

“It appears that both indicators are closely related, which is confirmed by the use of the photochemical reflection index that was measured using yellow-green light pulses to assess the severity of photosynthetic stress of agricultural plants. The magnitude of the change in the photochemical reflectance index, which is linearly related to the intensity of stress on the plants under study, is a particularly effective indicator,” Ekaterina Sukhova comments.

On the whole, Lobachevsky University researchers obtained two significant results. First, it was shown that the use of periodic pulses of yellow-green light reduces the error in measuring the photochemical reflectance index and, secondly, scientists have found that the change of the PRI in the light is a more reliable indicator of the severity of photosynthetic stress in a plant than its absolute magnitude.

“These results provide the basis for a new approach to measuring the photochemical reflectance index, which involves pulsed illumination of the plant objects under study. The implementation of this approach opens up new prospects in remote monitoring of the state of agricultural plants. It means that this method will become an important tool in precision farming,” continues Ekaterina Sukhova.

Currently, scientists at Ekaterina Sukhova and their colleagues from the Institute of Applied Physics of the Russian Academy of Sciences are working to further develop the proposed method and to adapt it for measuring the spatial distribution of the photochemical reflectance index.

“In particular, a PRI imaging system based on the illumination of objects under study with pulses of yellow-green light has already been developed and is being tested. It is expected that the prototype already developed will become the basis for a commercial system for assessing the state of plants based on measuring the spatial distribution of the photochemical reflectance index,” Ekaterina Sukhova concludes.

Read the paper: Remote sensing

Article source: Lobachevsky University

Image: Lobachevsky University

Abortion of seeds with extra genomes is caused by the enzyme RNA Pol IV

In flowering plants, the embryo is surrounded by the endosperm. Endosperm tissue mediates nutrient transferbetween the growing embryo and the mother. The endosperm is distinct from the rest of the plant because it has onlyonecopy of the father’s genome and two copies of the mother’s. The ratio of maternal to paternal genomes is remarkable because of its importance to seed viability and development. Seeds with extra genomes that alter this critical ratio undergo a process known as interploidy seed abortion due to defective endosperm development. RNA Pol IV isan enzyme specific to plant genomes thatgeneratessmall RNA molecules thatsilence gene expression from transposons and repetitive DNA, playing a major role in defending the genome against viruses and transposable elements. The new work shows that RNA Pol IVplays akeyrole ininterploidy seed abortion.

This research, coauthored by P.R.V. Satyaki and Mary Gehring of the Whitehead Institute for Biomedical Research, focused on the following questions: How does the lack of RNA Pol IV prevent interploidy seed abortion? Where does RNA Pol IV act,in the endosperm or in the father,to influence gene expression in the endosperm? In what genetic pathway does RNA Pol IV function to cause seed abortion?Arabidopsis plants going to seed.

In this article, Satyaki and Gehring demonstratethat RNA Pol IV targetsgenes in the fatherviathe “canonical” RNA-directed DNA methylation pathway, a major gene-silencing pathway in Arabidopsis plants, resulting in interploidy seed abortion. The researchers compared gene transcription in the endosperm of aborted interploidy seeds with that of seedsthat were viable due tothe loss of paternal RNA Pol IV. The researchers found that transposons and thousands of genes, even imprinted ones, were misregulated in both living and dying seeds. Theresearchers learned that misregulation of a relatively small number of genes setsliving seeds apart from aborting ones.

This study is also important because it identified atranscriptional buffering system in the endosperm. This system counteractsthe effects of a higher dose of the paternal genome byreducingthe expression of the paternal copiesof some genes and increasingthe expression of maternal copies ofother genes.

First author P.R.V. Satyaki said: “The next steps are to unravel the mechanism underlying the transcriptional buffering system and to identify the genes responsible for interploidy seed abortion using the shortlist of candidate genes generated from our transcriptional studies.”

Read the paper: The Plant Cell

Article source: ASPB

Image: Conor Gearin/Whitehead Institute