Seed Abortion and the Role of RNA Pol IV in Seed Development

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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

Climate extremes explain 18%-43% of global crop yield variations

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Researchers from Australia, Germany, Switzerland and the US have quantified the effect of climate extremes, such as droughts or heatwaves, on the yield variability of staple crops around the world.

Overall, year-to-year changes in climate factors during the growing season of maize, rice, soy and spring wheat accounted for 20%-49% of yield fluctuations, according to research published in Environmental Research Letters.

Climate extremes, such as hot and cold temperature extremes, drought and heavy precipitation, by themselves accounted for 18%-43% of these interannual variations in crop yield.

To get to the bottom of the impacts of climate extremes on agricultural yields, the researchers used a global agricultural database at high spatial resolution, and near-global coverage climate and climate extremes datasets. They applied a machine-learning algorithm, Random Forests, to tease out which climate factors played the greatest role in influencing crop yields.

“Interestingly, we found that the most important climate factors for yield anomalies were related to temperature, not precipitation, as one could expect, with the average growing season temperature and temperature extremes playing a dominant role in predicting crop yields,” said lead author Dr. Elisabeth Vogel from the Centre of Excellence for Climate Extremes and Climate & Energy College at the University of Melbourne.

The research also revealed global hotspots – areas that produce a large proportion of the world’s crop production, yet are most susceptible to climate variability and extremes.

“We found that most of these hotspots – regions that are critical for overall production and at the same time strongly influenced by climate variability and climate extremes – appear to be in industrialised crop production regions, such as North America and Europe.”

For climate extremes specifically, the researchers identified North America for soy and spring wheat production, Europe for spring wheat and Asia for rice and maize production as hotspots.

But, as the researchers point out, global markets are not the only concern. Outside of these major regions, in regions where communities are highly dependent on agriculture for their livelihoods, the failure of these staple crops can be devastating.

“In our study, we found that maize yields in Africa showed one of the strongest relationships with growing season climate variability. In fact, it was the second highest explained variance for crop yields of any crop/continent combination, suggesting that it is highly dependent on climate conditions,” Dr Vogel said.

“While Africa’s share of global maize production may be small, the largest part of that production goes to human consumption – compared to just 3% in North America – making it critical for food security in the region.”

“With climate change predicted to change the variability of climate and increasing the likelihood and severity of climate extremes in most regions, our research highlights the importance of adapting food production to these changes,” Dr Vogel said.

“Increasing the resilience to climate extremes requires a concerted effort at local, regional and international levels to reduce negative impacts for farmers and communities depending on agriculture for their living.”

Read the paper: Environmental Research Letters

Article source: University of New South Wales

Image: Hans Braxmeier / Pixabay

The hunger gaps: how flowering times affect farmland bees

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For the very first time, researchers from the University of Bristol have measured farmland nectar supplies throughout the whole year and revealed hungry gaps when food supply is not meeting pollinator demand. This novel finding reveals new ways of making farmland better for pollinators, benefitting the many crop plants and wildflowers that depend on them.

Planting wildflower strips is a common strategy for providing pollinators with more food on farmland. These can provide plenty of pollen and nectar for bees to feed on, but most of this food supply is limited to the late spring and early summer when there is already plenty to eat. A new study published in the Journal of Applied Ecology found that early spring (March) and late summer (August-September) are periods of great nectar deficit on UK farmland.

Jane Memmott, Professor of Ecology from Bristol’s School of Biological Sciences and principal investigator, explained: “It’s not just how much nectar there is that matters, but what time of year that nectar is available.

“If a bumblebee queen comes out of hibernation in March and finds nothing to eat, it doesn’t matter how much nectar there is in summer, because she won’t be alive.”

Pollinators such as bees, flies and wasps require a constant supply of nectar throughout the year to stay alive, fly around and pollinate important crops and wild plants.

Tom Timberlake, PhD researcher at the University of Bristol and lead author, added: “By identifying these hungry gaps and finding plants to fill them, we could create a more consistent supply of pollen and nectar, allowing more pollinators to survive through the year.

“Early-flowering plants like willows and dandelions, or late-flowering red clover and ivy could all help to fill the hungry gaps, if we allow them to survive and flower on farmland.”

Pollinators such as bees are critical for the reproduction of most crop plants, including many of our favourites such as strawberries and coffee. Their services are worth up to $500 billion US each year but are under increasing threat as pollinators face worldwide declines. Providing more pollen and nectar rich flowers on farmland is certainly part of the solution. But this new research shows that if we want to be most effective, we must consider the timing of both food supply and pollinator demand.

Read the paper: Journal of Applied Ecology

Article source: University of Bristol

Image: Tom Timberlake

Scientists see fingerprint of warming climate on droughts going back to 1900

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In an unusual new study, scientists say they have detected the fingerprint of human-driven global warming on patterns of drought and moisture across the world as far back as 1900. Rising temperatures are well documented back at least that far, but this is the first time researchers have identified resulting long-term global effects on the water supplies that feed crops and cities. Among the observations, the researchers documented drying of soils across much of populous North America, central America, Eurasia and the Mediterranean. Other areas, including the Indian subcontinent, have become wetter. They say the trends will continue, with severe consequences for humans. The study appears in the leading journal Nature.

In general, scientists agree that as global warming progresses, many now dry regions will become drier, and wet ones will become wetter. Some recent studies suggest that human-induced warming has intensified droughts in particular regions, including a now near 20-year ongoing drought in the southwestern United States. However, the last report by the Intergovernmental Panel on Climate Change says confidence in attributing specific ongoing events directly to humans is still chancy.

The new study combines computer models with long-term observations to suggest that systemic changes in what scientists call the hydroclimate are already underway across the world, and have been for some time. The researchers looked not simply at precipitation, but rather soil moisture, a more subtle measure that balances precipitation against evaporation, and is the quality most directly relevant to farming and forestry. They used tree rings going back 600 to 900 years to estimate soil moisture trends before human-produced greenhouse gases started rising, then compared this data with 20th-century tree rings and modern instrumental observations, to see if they could pick out drought patterns matching those predicted by computer models, amid the noise of natural yearly or decadal regional weather variations.

“We asked, does the real world look like what the models tell us to expect?” said study coauthor Benjamin Cook of the NASA Goddard Institute for Space Studies and Columbia University’s Lamont-Doherty Earth Observatory. “The answer is yes. The big thing we learned is that climate change started affecting global patterns of drought in the early 20th century. We expect this pattern to keep emerging as climate change continues.”

Lead author Kate Marvel, a climate modeler at Goddard and Columbia University, said, “It’s mind boggling. There is a really clear signal of the effects of human greenhouse gases on the hydroclimate.”

Soil moisture is a complex issue, because precipitation and evaporation can work with each other, or against each other. Warmer air can carry more moisture, and thus more rain or snow. But warmer air can also evaporate more moisture from soil and carry it away, outweighing precipitation. That is probably the factor now at work in the drying western United States, and possibly other locations that have seen recent big droughts. “Precipitation is just the supply side,” said study coauthor Jason Smerdon, a Lamont-Doherty paleoclimatologist. “Temperature is on the demand side, the part that dries things out.” Which part predominates depends on complex factors including wind patterns, seasons, clouds, topography and proximity to the moisture-giving oceans.

The scientists identified three distinct periods in their study. The first was 1900 to 1949, when they say the global-warming fingerprint was the most obvious. During this time, as predicted by models, drying was seen in Australia, much of central America and North America, Europe, the Mediterranean, western Russia and southeast Asia. At the same time, it got wetter in western China, much of central Asia, the Indian subcontinent, Indonesia and central Canada.

From 1950 to 1975, the pattern scattered into seemingly random events. The scientists believe this might be related to enormous amounts of industrial aerosols then being poured into the air without modern pollution controls. These can affect regional cloud formation, rainfall and temperature, by, among other things, blocking solar radiation and providing nuclei for moisture droplets. The researchers believe that the complex effects of aerosols probably threw a monkey wrench into the weather in many places, masking the effects of greenhouse gases, even though those gases continued to rise.

Then, starting in the 1970s, many industrial countries including the United States started instituting progressively stricter clean-air laws. Even though industrial activities continued to grow, aerosols quickly leveled off or slightly declined in many places. But at the same time, greenhouse-gas emissions continued spiraling up, along with temperatures. As a result, the researchers say, the global-warming signature on hydroclimate began re-emerging around 1981. The signal is not yet as obvious as it was in the early 20th century, but it continues to rise, especially since around 2000.

“If we don’t see it coming in stronger in, say, the next 10 years, we might have to wonder whether we are right,” said Kate Marvel. “But all the models are projecting that you should see unprecedented drying soon, in a lot of places.”

Many of the areas expected to dry out are centers of agricultural production, and could become permanently arid. “The human consequences of this, particularly drying over large parts of North America and Eurasia, will likely be severe,” says the study.

Precipitation over much of central America, Mexico the central and western United States and Europe is projected to stay about the same, or even increase. But, according to both the new study and a separate 2018 paper, rising temperatures and resulting evaporation of moisture from soils in those regions will probably predominate. The Mediterranean region is expected to be hit with a double whammy of both less rainfall and more heat-driven evaporation. Adding to the drought dynamics of all the affected areas: populations are expected to continue increasing, adding to water demand. According to an earlier Lamont-Doherty study, a 2006-2010 drought leading up to the disastrous Syrian civil war was probably made more likely by warming climate, and the drought may have helped create the social and economic conditions that sparked the initial rebellion.

Some areas are expected to get wetter, but this may not necessarily be good. India and some surrounding nations are expected to get more rain, because they sit squarely in the path of monsoon winds that pick up moisture from the Pacific and Indian oceans, and those oceans are getting warmer. But the rain may come perhaps more often in overwhelming storms, and not necessarily at times when it is needed.

The new study was made possible in part by recently published atlases of tree-ring chronologies from thousands of sites around the world, going back as far as 2,000 years. These gave the researchers a baseline of how weather varied before humans started heavily affecting it. The atlases are largely the work of Lamont-Doherty scientist Edward Cook, father of study coauthor Benjamin Cook. The North American drought atlas came out in 2004, followed by a Monsoon Asia atlas in 2010, and compilations for Europe and the Mediterranean, Mexico and Australia/New Zealand in 2015. (One for South America is on the way; much of Africa still remains uncovered.)

“This important paper offers new insights into the link between increasing atmospheric greenhouse gases and regional droughts, both in the past and increasingly in the future,” said Peter Gleick, cofounder of California’s Pacific Institute, and expert on climate and water issues. “It also confirms the growing sophistication of our climate models and improves the tools available to detect and identify the fingerprint of human impacts on extreme hydrologic events.”

The study was coauthored also by Céline Bonfils and Paul Durack of Lawrence Livermore National Laboratory, and A. Park Williams of Lamont-Doherty.

Read the paper: Nature

Article source: Columbia University

Image: Kevin Krajick/Earth Institute

How plant viruses can be used to ward off pests and keep plants healthy

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Imagine a technology that could target pesticides to treat specific spots deep within the soil, making them more effective at controlling infestations while limiting their toxicity to the environment.

Researchers at the University of California San Diego and Case Western Reserve University have taken a step toward that goal. They discovered that a biological nanoparticle—a plant virus—is capable of delivering pesticide molecules deeper below the ground, to places that are normally beyond their reach.

The work could help farmers better manage difficult pests, like parasitic nematodes that wreak havoc on plant roots deep in the soil, with less pesticide. The work is published in the journal Nature Nanotechnology.

“It sounds counterintuitive that we can use a plant virus to treat plant health,” said Nicole Steinmetz, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering and senior author of the study. “This is an emerging field of research in nanotechnology showing that we can use plant viruses as pesticide delivery systems. It’s similar to how we’re using nanoparticles in medicine to target drugs towards sites of disease and reduce their side effects in patients.”

Pesticides are very sticky molecules when applied in the field, Steinmetz explained. They bind strongly to organic matter in the soil, making it difficult to get enough to penetrate deep down into the root level where pests like nematodes reside and cause damage.

To compensate, farmers end up applying large amounts of pesticides, which cause harmful residues to build up in the soil and leach into groundwater.

Steinmetz and her team are working to address this problem. In a new study, they discovered that a particular plant virus, Tobacco mild green mosaic virus, can transport small amounts of pesticide deep through the soil with ease.

A helpful virus

In lab tests, the researchers attached a model insecticide to different types of nanoparticles and watered them through columns of soil.

Tobacco mild green mosaic virus outperformed most of the other nanoparticles tested in the study. It carried its cargo down to 30 centimeters below the surface. PLGA and mesoporous silica nanoparticles, which researchers have studied for pesticide and fertilizer delivery, carried their payloads 8 and 12 centimeters deep, respectively.

Other plant viruses were also tested. Cowpea mosaic virus also carried its payload 30 centimeters deep below the surface, but it can only carry a fraction of the payload that Tobacco mild green mosaic virus can carry. Interestingly, Physalis mosaic virus only reached 4 centimeters below the surface.

The researchers hypothesize that nanoparticle geometry and surface chemistry could play a role in how it moves through the soil. For example, having a tubular structure might partly explain why Tobacco mild green mosaic virus travels farther than most of the other nanoparticles that are spherical in shape. Also, its surface chemistry is naturally more diverse than synthetic particles like PLGA and silica, which could cause it to interact with the soil differently. While these design rules may apply to Tobacco mild green mosaic virus, the researchers say more work is needed to better understand why other nanoparticles behave the way they do.

“We’re taking concepts we’ve learned from nanomedicine, where we’re developing nanoparticles for targeted drug delivery, and applying them to agriculture,” Steinmetz said. “In the medical setting, we also see that nanocarriers with skinny, tubular shapes and diverse surface chemistries can navigate the body better. It makes sense that a plant virus can more easily penetrate and move through the soil—probably because that’s where it naturally resides.”

In terms of safety, Tobacco mild green mosaic virus can infect plants of the Solanaceae (or nightshade) family like tomatoes, potatoes and eggplants, but is benign to thousands of other plant species. Also, the virus is only transmitted by mechanical contact between two plants, not through the air. That means if one field is being treated with this virus, nearby fields would not be at risk for contamination, researchers said.

Modeling pesticide delivery

The team also developed a computational model that can be used to predict how different pesticide nanocarriers behave in the soil—how deep they can travel; how much of them need to be applied to the soil; and how long they will take to release their load of pesticide.

“Researchers working with a different plant virus or nanomaterial could use our model to determine how well their particle would work as a pesticide delivery agent,” said first author Paul Chariou, a bioengineering PhD student in Steinmetz’s lab at UC San Diego.

“It also cuts down on experimental workload,” Chariou said. Testing just one nanoparticle for this study involves running hundreds of assays, collecting all the fractions from each column and analyzing them. “This all takes at least one month. But with the model, it only took us about 10 soil columns and 4 days to test a new nanoparticle,” he said.

As a next step, Steinmetz and her team are testing Tobacco mild green mosaic virus nanoparticles with pesticide loads. The goal is to test them in the field in the near future.

Read the paper: Nature Nanotechnology

Article source: UC San Diego Jacobs School of Engineering

Image: David Baillot/UC San Diego Jacobs School of Engineering

Plant discovery opens frontiers

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University of Adelaide researchers have discovered a biochemical mechanism fundamental to plant life that could have far-reaching implications for the multibillion dollar biomedical, pharmaceutical, chemical and biotechnology industries.

There are up to 80,000 fundamental-to-life enzymes working in plant or mammalian bodies, upon which almost all biochemical reactions depend. Enzymes carry out many chemical reactions, products of which can be used as building blocks or metabolites in a body, or they can serve as an energy source for every function in a body.

Researchers have discovered a new enzyme catalytic mechanism – catalysis being a process which speeds up chemical reactions – which they say could impact on work in biofuels production, in food and materials processing, and in drug discovery.

Their work has been published today in Nature Communication.

“The foundation for this was laid down in our earlier work but, at that time, we could not explain some fundamental processes at work in plants as these occur at immense rates,” said lead researcher Professor Maria Hrmova from the University of Adelaide’s School of Agriculture, Food and Wine.

“The solution to this came up only recently, when we combined high-resolution X-ray crystallography, enzyme kinetics, mass spectrometry, nuclear magnetic resonance spectroscopy, and multi-scale 3D molecular modelling tools to show those super-fast processes.

“Using computer simulations, we discovered a remarkable phenomenon during initial and final catalytic events near the surface of the plant glucose-processing enzyme. The enzyme formed a cavity which allowed the trapped glucose to escape to allow for the next round of catalysis,” Professor Hrmova said.

“Now that we can simulate these nanoscale movements we have opened the door to new knowledge on enzyme dynamics that was inaccessible before. These discoveries are made once in a generation.”

Professor Hrmova said the discovery of the catalytic mechanism involved specialists in plant and molecular biology, biochemistry, biophysics, bioinformatics and computer science from seven countries (Australia, France, Thailand, Spain, Chile, Slovak Republic and China).

“Being able to describe these minute and ultra-fast processes – unable to be captured via usual experimental techniques – means we can now work to improve enzyme catalytic rates, stability and product inhibition. This will have significance in biotechnologies to develop or manufacture products through novel forms of bioengineered enzymes that could be also used outside of biological systems.”

A movie describing the discovered catalytic mechanism can be seen here.

Read the paper: Nature Communication

Article source: University of Adelaide

Image: Designed by macrovector / Freepik

‘Exotic’ genes may improve cotton yield and quality

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Cotton breeders face a “Catch-22.” Yield from cotton crops is inversely related to fiber quality. In general, as yield improves, fiber quality decreases, and vice-versa. “This is one of the most significant challenges for cotton breeders,” says Peng Chee, a researcher at the University of Georgia.

To overcome the yield vs quality challenge, Chee and colleagues turned to obsolete cultivars – or strains – of cotton with ‘exotic’ genetic material. In a new study, they report findings that could help breeders improve cotton fiber quality while maintaining or even improving yield.

The study focused on the genetics of hybrid ‘Sealand’ cultivars. These cultivars were developed by breeding two different species of cotton – Upland and Sea Island. Sea Island cotton is the type generally also known as “Pima or Egyptian cotton” from the species Gossypium barbadense. Its fibers are found in the highest quality garments and linens, due to its long, strong and fine fibers.

About 97% of the cotton grown in the United States is Upland cotton from the species Gossypium hirsutum. Upland cotton has much higher yields and broader adaptation, but lower fiber quality compared to Pima cotton. “The breeding challenge lies in transferring Pima fiber quality to Upland,” says Chee.

Because they are two different species, there are significant genetic barriers between Upland and Pima. These differences can cause genetic abnormalities during and after breeding. Starting in the 1930s and 40s, breeders at the USDA successfully bred Upland with Sea Island cotton species. The results of these breeding efforts were the Sealand cotton cultivars, which has the appearance of Upland but with much improved fiber quality. In fact, a couple of Sealand cultivars were commercially grown briefly in parts of the US in the 1950s. “However, the genetic details of Sealand cultivars have remained largely unknown,” says Chee.

Until now. Chee and colleagues generated genetic ‘maps’ of two Sealand cultivars. They found that the superior fiber quality of Sealand cotton were in part due to genes inherited from the Sea Island cotton. Fiber length, for example, is one aspect of cotton fiber quality. The researchers found that two of the three genetic segments controlling fiber length in one of the Sealand cultivars was inherited from the Sea Island parent.

“These detailed genetic dissections help us better understand interspecies hybridization,” says Chee. “Now that we know which part of the genome controls fiber quality, we can now develop tools to select for these traits. We can also select desirable combinations of genes to improve multiple fiber quality traits.”

Improving cotton quality can have ramifications for international trade. The global cotton import-export market is estimated to be worth more than 12 billion dollars. The United States is the largest exporter of cotton.

In addition to improving fiber quality, there may be other benefits to combining Pima and Upland genetics. “Upland cotton has been domesticated from a very small set of wild relatives,” says Chee. “Selection for specific traits in the distant past led to the loss of other potentially useful traits.”

To address the issue of low genetic diversity, breeders turn to wild relatives or ‘cousins”, such as Pima. They search for useful genes influencing important traits, such fiber quality. They also look for genes connected to other traits, including drought tolerance and disease resistance.

Genetic segments from Pima cotton that have positive effects on fiber quality have been tagged with molecular markers. These markers make it easier for breeders to track genetic segments through generations. Cotton breeders can now use these genetic tools to guide their efforts in breeding new cultivars. For example, they can focus on the portions of the genome that improve fiber quality while maintaining or even increasing yields.

The researchers are testing a small subset of the Pima genetic segments they discovered in the study in different genetic backgrounds. “We want to confirm their desirable effects across a more diverse set of varieties,” says Chee. “Then they will be more useful in cotton breeding programs across the cotton belt.”

Read the paper: Crop Science

Article source: American Society of Agronomy

Image: Peng Chee

Excessive rainfall as damaging to corn yield as extreme heat, drought

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Recent flooding in the Midwest has brought attention to the complex agricultural problems associated with too much rain. Data from the past three decades suggest that excessive rainfall can affect crop yield as much as excessive heat and drought. In a new study, an interdisciplinary team from the University of Illinois linked crop insurance, climate, soil and corn yield data from 1981 through 2016.

The study found that during some years, excessive rainfall reduced U.S. corn yield by as much as 34% relative to the expected yield. Data suggest that drought and excessive heat caused a yield loss of up to 37% during some years. The findings are published in the journal Global Change Biology.

“We linked county-level U.S. Department of Agriculture insurance data for corn loss with historical weather data, letting us quantify the impact of excessive rainfall on yield loss at a continental scale,” said Kaiyu Guan, a natural resources and environmental sciences professor and the study’s principal investigator. “This was done using crop insurance indemnity data paired with rigorous statistical analysis – not modeled simulations – which let the numbers speak for themselves.”

The study found that the impact of excessive rainfall varies regionally.

“Heavy rainfall can decrease corn yield more in cooler areas and the effect is exacerbated even further in areas that have poor drainage,” said Yan Li, a former University of Illinois postdoctoral researcher and lead author of the study.

Excessive rainfall can affect crop productivity in various ways, including direct physical damage, delayed planting and harvesting, restricted root growth, oxygen deficiency and nutrient loss, the researchers said.

“It is challenging to simulate the effects of excessive rainfall because of the vast amount of seemingly minor details,” Li said. “It is difficult to create a model based on the processes that occur after heavy rainfall – poor drainage due to small surface features, water table depth and various soil properties can lead to ponding of water in a crop field. Even though the ponding may take place over a small area, it could have a large effect on crop damage.”

“This study shows that we have a lot of work to do to improve our models,” said Evan DeLucia, the director of the Institute for Sustainability, Energy and Environment, a professor of integrative biology and study co-author. “While drought and heat stress have been well dealt with in the existing models, excessive rainfall impacts on crop system are much less mature.”

Many climate change models predict that the U.S. Corn Belt region will continue to experience more intense rainfall events in the spring. Because of this, the researchers feel that it is urgent for the government and farmers to design better risk management plans to deal with the predicted climate scenarios.

“As rainfall becomes more extreme, crop insurance needs to evolve to better meet planting challenges faced by farmers,” said Gary Schnitkey, a professor of agricultural and consumer economics and study co-author.

Read the paper: Global Change Biology

Article source: University of Illinois

Image: L. Brian Stauffer

Scientists Reveal the Relationship Between Root Microbiome and Nitrogen Use Efficiency in Rice

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A collaborative team led by Prof. BAI Yang and Prof. CHU Chengcai from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), recently examined the variation in root microbiota within 68 indica and 27 japonica rice varieties grown in field conditions. They revealed that the indica and japonica varieties recruited distinct root microbiota.

In natural soil, plant roots provide an ecological niche for multiple soil microorganisms known as root microbiota. These microbes develop an intimate association with plants, enhancing plants’ nutrient uptake, growth and tolerance to pathogens.

Indica and japonica are the two major subspecies of cultivated rice (Oryza sativa L.). Indica varieties show better nitrogen use efficiency (NUE) compared with japonica varieties in the field; NRT1.1B contributes to this natural variation in rice. However, the effect of root microbiota on the NUE variation observed between the indica and japonica varieties is not yet clear.

The researchers established a model using a random-forest machine-learning approach. They found this model could accurately predict indica and japonica varieties in tested fields, suggesting that the root microbes can serve as a biomarker to distinguish indica and japonica varieties.

It is interesting that indica varieties had more bacteria associated with the function of nitrogen metabolism compared with japonica varieties, indicating that nitrogen transformation is more active in the root environment of indica rather than japonica varieties.

By comparing root-associated microbiota of wild-type varieties and the the nrt1.1b mutant, they found that NRT1.1B was associated with the recruitment of approximately half of the indica-enriched bacterial taxa.

Notably, wild-type varieties showed relative abundance of root bacteria that harbor key genes for the ammonification process; however, there was no such abundance in the root microbiome of the nrt1.1b mutant. This indicates that such root microbes may catalyze the formation of ammonium in the root environment.

Using an improved high-throughput protocol to cultivate and identify bacteria, the researchers successfully cultivated more than 70 percent of the bacterial species that were reproducibly detectable in the rice roots, and established the first systematic collection of rice root bacterial cultures.

They then used gnotobiotic experimental systems with a reconstructed synthetic community (SynCom) and found that indica-enriched SynCom showed a stronger ability to promote rice growth under a supply of organic nitrogen than japonica-enriched SynCom. This further suggests that indica-enriched bacteria may contribute to higher nitrogen-use efficiency in indica rice.

These results not only reveal the relationship between the root microbiome and NUE in rice subspecies, but demonstrate the role of NRT1.1B in the establishment of root microbiota. The bacterial culture collections provide a resource for functional research of root microbiota.

The research on the interaction between root microbes and rice has laid an important foundation for the application of beneficial microbes to the process of nitrogen utilization and provides a theoretical basis for reducing nitrogen fertilizer in sustainable agriculture.

Read the paper: Nature Biotechnology

Article source: Chinese Academy of Sciences (CAS)

Image: Trung Hieu Dang / Pixabay

New avenues for improving modern wheat

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Since the Agricultural Revolution about 12,000 years ago, humans have been selectively breeding plants with desirable traits such as high grain yield and disease resistance. Over time, Triticum aestivum, otherwise known as bread wheat, has emerged as one of the world’s most important crops. Together with the growing human population and the changing climate, the demand for wheat with a higher yield and additional resilience is increasing.

However, for a few years now the average yield increase of wheat is stagnating. In a new international study, the genetic diversity of 487 wheat genotypes originating from large parts of the world has been catalogued and contextualised with agronomic traits. The map of this rich pool of genetic diversity in bread wheat highlights our current knowledge of the ancestry of wheat and opens new avenues within modern selective wheat breeding.

The evolution of wheat is a complex history of hybridisation and gene flow events, which led to the allohexaploid (with six sets of chromosomes) Triticum aestivum, the species of wheat that we know nowadays as bread wheat. The modern bread wheat originated in the Fertile Crescent about 10,000 years ago and its genepool has been shaped by humans as a result of domestication and cultivation. Today, high-yielding varieties of Triticum aestivum can be found all over the world, each variety adapted to the particular environment it is being grown in, making wheat one of the world’s three most important crop species for human calories and protein supply.

The growing demand for wheat, the onset of global warming, and the transitioning of Western farming away from intensive agriculture, are exerting pressure on plant breeders to further adapt and improve modern bread wheat species. However, in order to select and breed new wheat cultivars with new and improved traits, plant breeders require plants with genetic variation for selection and combination during the breeding process. A new international study of bread wheat has now revealed knowledge of an extensive and rich gene pool for future breeding improvements of Triticum aestivum.

In this study, the exomes of 487 wheat genotypes from 68 countries around the world, including landraces, cultivars, as well as modern varieties, were sequenced. The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben) was able to contribute to this by providing wheat samples from the Federal Ex situ Gene Bank. Utilising the Refseqv1.0 reference sequence of the bread wheat landrace “Chinese Spring”, which had been published by the “International Wheat Genome Sequencing Consortium” (IWGSC) in 2017, the collaborating researchers were able to compile a comprehensive overview of wheat genomic diversity at the genic, chromosomal and subgenomic levels. This enabled them to refine and expand the model of wheat evolution and to decipher the genetic origins of modern day wheat species. As such, the durum wheat lineage was confirmed as the most likely ancestor of today’s bread wheat cultivated germplasm. Moreover, by investigating the selection footprints of wheat, the scientists showcased the effects of range expansion and allelic variants selected since the beginning of wheat domestication.

The reported data is another step towards the assembly of the “pan genome” of wheat – the description of all the genes and genetic variations within wheat, which will be a valuable resource for plant researchers and wheat breeders alike. However, the study as it stands already reveals a rich genetic data resource, which can be utilised for improving genetic traits in bread wheat, from environmental adaptation to improved yield and disease resistance. Moreover, the results illustrate our current knowledge of the ancestry of bread wheat, highlighting our cultural history as farmers and plant breeders.

Read the paper: Nature Genetics

Article source: Leibniz Institute of Plant Genetics and Crop Plant Research

Image: Julie Himpe/IPK