Tag Archives: #crops

RNA Breakthrough Creates Crops That Can Grow 50% More Potatoes, Rice (Agriculture)

Manipulating RNA can allow plants to yield dramatically more crops, as well as increasing drought tolerance, announced a group of scientists from the University of Chicago, Peking University and Guizhou University.

In initial tests, adding a gene encoding for a protein called FTO to both rice and potato plants increased their yield by 50% in field tests. The plants grew significantly larger, produced longer root systems and were better able to tolerate drought stress. Analysis also showed that the plants had increased their rate of photosynthesis.

“The change really is dramatic,” said University of Chicago Prof. Chuan He, who together with Prof. Guifang Jia at Peking University, led the research. “What’s more, it worked with almost every type of plant we tried it with so far, and it’s a very simple modification to make.”

The researchers are hopeful about the potential of this breakthrough, especially in the face of climate change and other pressures on crop systems worldwide.

“This really provides the possibility of engineering plants to potentially improve the ecosystem as global warming proceeds,” said He, who is the John T. Wilson Distinguished Service Professor of Chemistry, Biochemistry and Molecular Biology. “We rely on plants for many, many things—everything from wood, food, and medicine, to flowers and oil—and this potentially offers a way to increase the stock material we can get from most plants.”

Rice nudged along

For decades, scientists have been working to boost crop production in the face of an increasingly unstable climate and a growing global population. But such processes are usually complicated, and often result only in incremental changes.

The way this discovery came about was quite different.

Many of us remember RNA from high school biology, where we were taught that the RNA molecule reads DNA, then makes proteins to carry out tasks. But in 2011, He’s lab opened an entire new field of research by discovering the keys to a different way that genes are expressed in mammals. It turns out that RNA doesn’t simply read the DNA blueprint and carry it out blindly; the cell itself can also regulate which parts of the blueprint get expressed. It does so by placing chemical markers onto RNA to modulate which proteins are made and how many.

He and his colleagues immediately realized that this had major implications for biology. Since then, his team and others around the world have been trying to flesh out our understanding of the process and what it affects in animals, plants and different human diseases; for example, He is a co-founder of a biotech company now developing new anti-cancer medicines based on targeting RNA modification proteins.

He and Guifang Jia, a former UChicago postdoctoral researcher who is now an associate professor at Peking University, began to wonder how it affected plant biology.

They focused on a protein called FTO, the first known protein that erases chemical marks on RNA, which Jia found as a postdoctoral researcher in He’s group at UChicago. The scientists knew it worked on RNA to affect cell growth in humans and other animals, so they tried inserting the gene for it into rice plants—and then watched in amazement as the plants took off.

“I think right then was when all of us realized we were doing something special,” He said.

The rice plants grew three times more rice under laboratory conditions. When they tried it out in real field tests, the plants grew 50% more mass and yielded 50% more rice. They grew longer roots, photosynthesized more efficiently, and could better withstand stress from drought.

The scientists repeated the experiments with potato plants, which are part of a completely different family. The results were the same.

“That suggested a degree of universality that was extremely exciting,” He said.

It took the scientists longer to begin to understand how this was happening. Further experiments showed that FTO started working early in the plant’s development, boosting the total amount of biomass it produced.

The scientists think that FTO controls a process known as m6A, which is a key modification of RNA. In this scenario, FTO works by erasing m6A RNA to muffle some of the signals that tell plants to slow down and reduce growth. Imagine a road with lots of stoplights; if scientists cover up the red lights and leave the green, more and more cars can move along the road.

Overall, the modified plants produced significantly more RNA than control plants.

Modifying the process

The process described in this paper involves using an animal FTO gene in a plant. But once scientists fully understand this growth mechanism, He thinks there could be alternate ways to get the same effect.

“It seems that plants already have this layer of regulation, and all we did is tap into it,” He said. “So the next step would be to discover how to do it using the plant’s existing genetics.”

He can imagine all sorts of uses down the road—and he’s working with the university and the Polsky Center for Entrepreneurship and Innovation to explore the possibilities.

“Even beyond food, there are other consequences of climate change,” said He. “Perhaps we could engineer grasses in threatened areas that can withstand drought. Perhaps we could teach a tree in the Midwest to grow longer roots, so that it’s less likely to be toppled during strong storms. There are so many potential applications.”

The study is published in Nature Biotechnology.

Featured image: Ripening heads of rice (Oryza sativa).© apisitwilaijit29/stock.adobe.com


Reference: Yu, Q., Liu, S., Yu, L. et al. RNA demethylation increases the yield and biomass of rice and potato plants in field trials. Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-00982-9


Provided by University of Chicago

Symbiotic Bacteria in Root Cells May Be Key To Producing Better Crops, Rutgers Study Finds (Agriculture)

A Rutgers study finds that symbiotic bacteria that colonize root cells may be managed to produce hardier crops that need less fertilizer.

The study appears in the journal Microorganisms.

Bacteria stimulate root hair growth in all plants that form root hairs, so the researchers examined the chemical interactions between bacteria inside root cells and the root cell.

They found that bacteria are carried in seeds and absorbed from soils, then taken into root cells where the bacteria produce ethylene, a plant growth hormone that makes root cells grow root hairs. When the root hair grows, it ejects some of the bacteria back into the soil, then the remaining bacteria in the root hairs replicate and trigger a growth spurt every 15 minutes until the hairs are fully developed.

Ethylene is also a stress hormone that causes plants to adapt and become more resistant to oxidative stresses, including heat, soil salt, heavy metals and stresses potentially caused by climate change.

The researchers found that ethylene triggers root cells to secrete superoxide onto bacteria in root cells, causing bacteria to produce nitric oxide that detoxifies the superoxide. Nitric oxide combines with superoxide to form nitrate that is absorbed by root cells. In this process, bacteria in root cells make root hairs grow and supply root cells with nitrogen and other nutrients.

“This matters because it shows that the microbiome of plants is important for plant cell development, particularly root cell development, and nutrient supply,” said study co-author James White, a professor in the Department of Plant Biology in the School of Environmental and Biological Sciences at Rutgers University-New Brunswick. “Use of bacteria in plants may enable us to grow better developed and stress resistant crops that require less fertilizers, and thus will reduce environmental damage due to excess fertilizer applications with consequent runoff. Further, with the correct bacteria in crop plants, we may produce crops that are resistant to oxidative stresses stemming from climate perturbations, thus we may produce hardier and more resilient crops.”

Featured image: A Rutgers study finds that symbiotic bacteria that colonize root cells may be managed to produce hardier crops that need less fertilizer. © Rutgers University-New Brunswick


Reference: Chang, X.; Kingsley, K.L.; White, J.F. Chemical Interactions at the Interface of Plant Root Hair Cells and Intracellular Bacteria. Microorganisms 2021, 9, 1041. https://doi.org/10.3390/microorganisms9051041


Provided by Rutgers University

Advancing the Green Transition: Fungi Strengthen Plants to Fend Off Aphids (Botany / Agriculture)

Researchers at the University of Copenhagen have demonstrated that unique fungi strengthen the “immune systems” of wheat and bean plants against aphids. Fungi enter and influence the amount of a plant’s own defences, resulting in fewer aphids. The results could serve to reduce agricultural insecticide use and bring Denmark a step further along the path towards its green transition.

Certain fungi are able to establish a close rapport with plants that results in fewer insect infestations and thereby less damage to crops. Until now, it was unclear how these fungi could be used to reduce insect infestations.

“In order for us to really use fungi to control agricultural pests in the future, we need to understand the mechanisms and processes behind their activity. So, it’s very exciting that we have managed to advance a step closer”, says Associate Professor Nicolai Vitt Meyling of UCPH’s Department of Plant and Environmental Sciences.

Fungi strengthen the “immune systems” of crops

The researchers studied three types of fungi to compare their effects against aphid infestations on wheat and bean plants:

“It turned out that two of these fungi were able to effectively reduce aphid infestations by establishing themselves in plant roots and tissues. By combining greenhouse-based experiments with advanced chemical analyses, we can see that the fungi cause plants to increase production of their own natural defences, thus strengthening plant “immune systems”. This translates into fewer aphids, which would otherwise weaken a plant”, says Nicolai Vitt Meyling, who explains:

 “When aphids suck up plant sap, plants lose energy, to the detriment of their root networks and overall growth. However, when fungi-treated plants were attacked by aphids, they were able to compensate by increasing root growth, so that they didn’t lose growth potential. Plants left untreated with the fungi couldn’t compensate for the attack,” says Nicolai Vitt Meyling.

The researchers “treated” wheat and bean plants by applying fungal spores to seed, from which the plants were then germinated and cultivated. They then added a few aphids and observed how many more aphids developed over two weeks in the greenhouse. Thereafter, plant leaves underwent chemical analysis in collaboration with researchers from Aarhus University’s Department of Agroecology.

“We see a clear correlation between an increased amount of defence substances in and fewer aphids on the plants treated with two of the fungi. Those plants left untreated with the fungi had lesser amounts of defence substances and more aphids. There is simply a marked upregulation of defence substances in a plant under aphid attack when these specific fungi are present. And, the same treatment produces the same result in both wheat and bean plants,” says Nicolai Vitt Meyling.

Thus, the researchers could see that the effect is related to the fungi and not the plant species. The same fungi had the same effect in both the wheat and bean plants, despite the two types of plants not being related and expressing different kinds of defence substances.

Swapping out insecticide for fungi coated seed

The fungi also have an effect on insects that attack the root systems of plants. And, in combination with other environmentally-friendly cultivation methods, could help to reduce insecticide use in agriculture.

“The fungi has the potential to reduce the need for insecticides because treated seeds result in fewer aphids in the field. If we can develop a large-scale method of pre-treating seed with Danish seed producers, to coat plant seeds with these fungi before planting, we may hardly need to spray with insecticides,” says Nicolai Vitt Meyling, who concludes:

“Limiting pesticide use is an important aspect of the green transition. This can be an effective and sustainable contribution towards such a reduction.”

The next step is to engage in longer term field trials of treated plants. This will allow researchers to gauge the longevity of effects under realistic growing conditions.

The research results have been published in the renowned scientific journal New Phytologist.

Reference: Rasool, S., Vidkjær, N.H., Hooshmand, K., Jensen, B., Fomsgaard, I.S. and Meyling, N.V. (2021), Seed inoculations with entomopathogenic fungi affect aphid populations coinciding with modulation of plant secondary metabolite profiles across plant families. New Phytol, 229: 1715-1727. https://doi.org/10.1111/nph.16979 https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.16979

Provided by University of Copenhagen

Hard to Crack Research Reveals How Crop Roots Penetrate Hard Soils (Botany)

Scientists have discovered a signal that causes roots to stop growing in hard soils which can be ‘switched off’ to allow them to punch through compacted soil – a discovery that could help plants to grow in even the most damaged soils.

Root Compaction © University of Nottingham

An international research team, led by scientists from the University of Nottingham’s Future Food Beacon and Shanghai Jiao Tong University has discovered how the plant signal ‘ethylene’ causes roots to stop growing in hard soils, but after this signal is disabled, roots are able to push through compacted soil. The research has been published in Science.

Hard (compacted) soils represent a major challenge facing modern agriculture that can reduce crop yields over 50% by reducing root growth, causing significant losses annually. Europe has over 33-million-hectares of soil prone to compaction which represents the highest in the world. Soil compaction triggers a reduction in root penetration and uptake of water and nutrients. Despite its clear importance for agriculture and global food security, the mechanism underpinning root compaction responses has been unclear until now.

Malcolm Bennett © University of Nottingham

Understanding how roots penetrate hard soils has huge implications for agriculture, as this knowledge will be crucial for breeding crops more resilient to soil compaction. Our team’s identification that the plant signal ethylene controls root responses to hard soil opens up new opportunities to select novel compaction resistant crops.Professor Malcolm Bennett, University of Nottingham, School of Biosciences

The research utilised X-ray Computed Tomography scanners available at the Hounsfield Facility at the University of Nottingham to visualise in situ how plant roots responded to compacted soil. Professor Sacha Mooney from the University of Nottingham and Director of the Hounsfield Facility explained: “Prior to this research we assumed that the hardness of the soil prevented roots growing deeper. By using our imaging approach, we were able to see that roots continued growing in very hard soils when the ethylene signal was switched off. The potential for new crops that can now go deeper in soils and capture previously unavailable resources is really exciting!”

The international team involved in this new Science paper includes researchers drawn from nine universities based in Europe, China and USA, integrating expertise spanning plant and soil sciences, bioimaging and mathematics. The team involves several early career researchers including Dr. Bipin Pandey and Dr. Rahul Bhosale who are funded by Royal Society Challenge Grant, BBSRC Discovery Fellowship and University of Nottingham Future Food Beacon awards.

Reference: Bipin K. Pandey, Guoqiang Huang, Rahul Bhosale, Sjon Hartman, Craig J. Sturrock, Lottie Jose, Olivier C. Martin, Michal Karady, Laurentius A. C. J. Voesenek, Karin Ljung, Jonathan P. Lynch, Kathleen M. Brown, William R. Whalley, Sacha J. Mooney, Dabing Zhang, Malcolm J. Bennett, “Plant roots sense soil compaction through restricted ethylene diffusion”, Science  15 Jan 2021: Vol. 371, Issue 6526, pp. 276-280
DOI: 10.1126/science.abf3013 https://science.sciencemag.org/content/371/6526/276/tab-article-info

Provided by University of Nottingham

Researchers Establish Molecular Link between Rice Clock Components and Salt Tolerance (Botany)

Excess sodium ion (Na+), the most widespread soluble cation in salinized soil, can damage plants by the sequential osmotic stress and oxidative stress, especially for glycophyte crops including rice. 

The model of core clock components regulating rice salt tolerance (Image by Dr. WANG Lei’s group)

The circadian clock, the endogenous time-keeping system in higher plants, has been demonstrated to function as an important integrator of multiple abiotic stresses signals, including salt stress in Arabidopsis. Nevertheless, whether rice core clock components participate in salt tolerance and the underlying mechanisms remain largely unclear.  

In a new study published in The EMBO Journal on December 21, a research group led by Prof. WANG Lei from the Institute of Botany of the Chinese Academy of Sciences has made great progress in indentifying a new molecular link between clock core components and salt stress tolerance in rice.  

By making use of CRISPR/Cas9 approach, the researchers systematically generated the loss-of-function mutants of OsPRRs, among which OsPRR73 is the unique member required for rice salt tolerance. Moreover, it was validated that OsPRR73 acts as a clock component in rice.  

Notably, the researchers found that the grain size and yield of osprr73 null mutants were significantly decreased in the presence of salt stress. And the osprr73 mutant plants are hypersensitive to Na+ treatment, suggesting that OsPRR73 is required for salt adaptation.  

Further, they identified OsHKT2;1, encoding a plasma membrane-localized Na+ influx transporter, as a direct transcriptional target of OsPRR73 in mediating salt tolerance.  

Thus, upon salt treatment, the increased OsPRR73 can efficiently repress the expression of OsHKT2;1 to reduce the accumulation of Na+.  

Immunoprecipitation-mass spectrometry assays further identified HDAC10 as nuclear interactor of OsPRR73 to repress OsHKT2;1 transcription. Furthermore, it was found that OsHKT2;1 is a major downstream component to mediate the salt hypersensitivity of osprr73 plants.  

“The OsPRR73-OsHKT2;1 transcriptional module confers the salt tolerance in rice via regulating Na+ homeostasis, which represents a novel molecular link between circadian clock and salt tolerance,” said Prof. WANG.  

These findings pave a way for further deciphering the regulatory networks of rice circadian clock-conferred abiotic stress responses in rice. The related genetic resources in this study may be useful for breeding the salt-tolerant rice varieties in the future. 

Reference: Hua Wei, Xiling Wang, Yuqing He, Hang Xu, Lei Wang, “Clock component OsPRR73 positively regulates rice salt tolerance by modulating OsHKT2;1‐mediated sodium homeostasis”, EMBO J (2020)e105086
https://doi.org/10.15252/embj.2020105086 https://www.embopress.org/doi/full/10.15252/embj.2020105086

Provided by Chinese Academy of Sciences

Glomalin Contributes to Multiple Soil Functions in Terrestrial Ecosystem (Botany)

Rising global population and anthropogenic activities increase tremendous pressure on soil for the production of crops and other kinds of biomass. Soil degradation are not only linked to agriculture intensification and over-exploitation of nutrients of soil but also caused by multiple pollutants from various anthropogenic sources discharge on land.

The role of glomalin in mitigation of multiple soil degradation problems (Image by Ashutosh Kumar Singh)

Glomalin, an arbuscular-mycorrhizal fungal soil protein, also contributes to the mitigation of soil degradation. However, to date, the role of glomalin in the amelioration of soil degradation problems and the underlying mechanisms are not well known and summarized.

In a study published in Critical Reviews in Environmental Science and Technology, researchers from the Xishuangbanna Tropical Botanical Garden (XTBG) systematically compiled and comprehensively literature reviewed each function of glomalin in the context of soil degradation.

Specifically, they covered the glomalin’s role in soil physical properties, nutrients cycling, soil carbon storage, microbial activity, remediation of pollutants, and ecological restoration.

The researchers highlighted that glomalin contributes to multiple soil functions, including conditioner of soil physical properties, nutrients supply, carbon storage, microbial substrate, biostabilize heavy metal and toxic organic pollutants, and catalyze ecological restoration.

According to the review, glomalin improves soil physical properties such as bulk density, porosity, water holding capacity, and control soil erosion by reducing soil runoff losses. By improving soil physical, chemical, and biological properties, glomalin can help restore degraded lands and possesses the ability to chelate toxic heavy metals and pollutants.

Glomalin production in soil relies on synergistic interaction among plant, soil, and arbuscular mycorrhizal fungi (AMF). Therefore, “specific or combined strategies are needed at the plant, soil, and AMF level to improve glomalin concentration in soil,” said Dr. Ashutosh Kumar Singh of XTBG.

To improve glomalin concentration, the researchers suggested developing genetically modified or hybrid plants for higher rhizodeposition and promoting soil microbial diversity through the inoculation of AMF and beneficial bacteria.

“This review can improve our understanding of glomalin, stimulate future research, and it is useful for the sustainable restoration of degraded lands,” said Prof. LIU Wenjie, principal investigator of the study.

This research got the fund from the National Natural Science Foundation of China (31570622), the CAS 135 Programme (2017XTBG-F01). This research was also funded by the China Postdoctoral Science Foundation (GRANT No. 2020M673317) and Yunnan Postdoctoral Research Project and postdoctoral Orientation Training Grant.

Reference: Ashutosh Kumar Singh , Xiai Zhu , Chunfeng Chen , Junen Wu , Bin Yang , Sissou Zakari , Xiao Jin Jiang , Nandita Singh & Wenjie Liu, “The role of glomalin in mitigation of multiple soil degradation problems”, Critical Reviews in Environmental Science and Technology, 2020. https://www.tandfonline.com/doi/citedby/10.1080/10643389.2020.1862561?scroll=top&needAccess=true https://doi.org/10.1080/10643389.2020.1862561

Provided by Chinese Academy of Sciences

Groups of Bacteria Can Work Together To Better Protect Crops and Improve Their Growth (Botany)

Certain bacteria, known as plant-growth-promoting bacteria (PGPB), can improve plant health or protect them from pathogens and are used commercially to help crops. To further improve agricultural yields, it is helpful to identify factors that can improve PGPB behavior.

Scientist Susanna Harris in the lab. © Noam Eckshtain-Levi, Susanna Leigh Harris, Reizo Quilat Roscios, and Elizabeth Anne Shank

Many PGPB form sticky communities of cells, known as biofilms, that help them adhere to plant roots. A group of scientists in North Carolina and Massachusetts were interested in finding other plant-associated bacteria that could help PGPB better adhere to plant roots, with the hope that increasing the number of PGPB cells attached to roots would increase their beneficial activities.

Using a liquid-growth-based method, they identified multiple bacterial strains that increased the adherence of PGPB to plant roots over time. These results indicate that the physical or chemical interactions between these different bacterial species result in better long-term maintenance of PGPB on roots.

“Our results highlight how bacteria can use each other for their own benefit. These findings could be used to create groups of bacteria that are able to work together to better protect crop plants and improve their growth,” said Elizabeth Shank, the senior scientist involved with this research. “The results of this research might also be used to better understand and design microbial treatments that could improve crop yields in agricultural settings.”

To conduct this research, Shank and her colleagues performed a high-throughput screen of bacteria originally obtained from the roots of wild-grown plants, ensuring that identified bacteria might naturally come into contact on the roots of plants in native soil environments. They also looked at how other native microbes might alter the behavior of each PGPB strain, emphasizing the importance of understanding how groups of plant-associated microbes affect plants.

This research specifically focused on a PGPB currently used in agricultural treatments so that their findings related to commercial interventions. According to Shank, “One important impact of our work may be further encouraging agricultural biotechnology companies to consider using groups of multiple bacteria (rather than a single isolate) in their search for better and longer-lasting biological treatments to improve crop yield and help increase food production.”

Their research also demonstrates how a reasonably fast and straightforward screen can identify important bacterial interactions and provides a starting point for future work studying the mechanisms of these cell-to-cell relationships. For more information, read “Bacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thaliana” in the Phytobiomes Journal. For supplemental information, including a 60-second video, visit: https://susannalharris.com/research/.

Reference: Noam Eckshtain-Levi, Susanna Leigh Harris, Reizo Quilat Roscios, and Elizabeth Anne Shank, “Bacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thaliana“, Phytobiomes Journal, 2020. https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-02-20-0019-R#

Provided by American Phytopathological Society

SMART Researchers Engineer a Plant-based Sensor to Monitor Arsenic Levels in Soil (Botany)

Nanoscale devices integrated into the leaves of living plants can detect the toxic heavy metal in real time.

Scientists from theDisruptive and Sustainable Technologies for Agricultural Precision (DiSTAP) research group at theSingapore-MIT Alliance for Research and Technology (SMART), MIT’s research enterprise in Singapore, have engineered a novel type of plant nanobionic optical sensor that can detect and monitor, in real time, levels of the highly toxic heavy metal arsenic in the underground environment. This development provides significant advantages over conventional methods used to measure arsenic in the environment and will be important for both environmental monitoring and agricultural applications to safeguard food safety, as arsenic is a contaminant in many common agricultural products such as rice, vegetables, and tea leaves.

A novel type of plant nanobionic optical sensor can detect and monitor, in real-time, levels of arsenic in the underground environment. Credits: Image courtesy of Singapore-MIT Alliance for Research and Technology; Christine Daniloff, MIT

This new approach is described in a paper titled “Plant Nanobionic Sensors for Arsenic Detection,” published recently in Advanced Materials. The paper was led by Tedrick Thomas Salim Lew, a recent graduate student of MIT, and co-authored by Michael Strano, co-lead principal investigator of DiSTAP and the Carbon P. Dubbs Professor at MIT, as well as Minkyung Park and Jianqiao Cui, both graduate students at MIT.

Arsenic and its compounds are a serious threat to humans and ecosystems. Long-term exposure to arsenic in humans can cause a wide range of detrimental health effects, includingcardiovascular disease such as heart attack, diabetes, birth defects, severe skin lesions, and numerous cancers including those of the skin, bladder, and lung. Elevated levels of soil arsenic as a result of anthropogenic activities such as mining and smelting are also harmful to plants, inhibiting growth and resulting in substantial crop losses.

Food crops can absorb arsenic from the soil, leading to contamination of food and produce consumed by humans. Arsenic in underground environments can also contaminate groundwater and other underground water sources, the long-term consumption of which can cause severe health issues. As such, developing accurate, effective, and easy-to-deploy arsenic sensors is important to protect both the agriculture industry and wider environmental safety.

The novel optical nanosensors exhibit changes in their fluorescence intensity upon detecting arsenic. Embedded in plant tissues, with no detrimental effects on the plant, these sensors provide a nondestructive way to monitor the internal dynamics of arsenic taken up by plants from the soil. This integration of optical nanosensors within living plants enables the conversion of plants into self-powered detectors of arsenic from their natural environment, marking a significant upgrade from the time- and equipment-intensive arsenic sampling methods of current conventional methods.

Novel optical nanosensors embedded in plant tissues exhibit changes in their fluorescence intensity upon the detection of arsenic. Credits: Image courtesy of Singapore-MIT Alliance for Research and Technology

“Our plant-based nanosensor is notable not only for being the first of its kind, but also for the significant advantages it confers over conventional methods of measuring arsenic levels in the below-ground environment, requiring less time, equipment, and manpower,” says Lew. “We envision that this innovation will eventually see wide use in the agriculture industry and beyond. I am grateful to SMART DiSTAP and the Temasek Life Sciences Laboratory (TLL), both of which were instrumental in idea generation and scientific discussion as well as research funding for this work.”

Besides detecting arsenic in rice and spinach, the team also used a species of fern, Pteris cretica, which can hyperaccumulate arsenic. This fern species can absorb and tolerate high levels of arsenic with no detrimental effect — engineering an ultrasensitive plant-based arsenic detector, capable of detecting very low concentrations of arsenic, as low as 0.2 parts per billion. In contrast, the regulatory limit for arsenic detectors is 10 parts per billion. Notably, the novel nanosensors can also be integrated into other species of plants. The researchers say this is the first successful demonstration of living plant-based sensors for arsenic and represents a groundbreaking advancement that could prove highly useful in both agricultural research (e.g., to monitor arsenic taken up by edible crops for food safety) and general environmental monitoring.

Previously, conventional methods of measuring arsenic levels included regular field sampling, plant tissue digestion, extraction, and analysis using mass spectrometry. These methods are time-consuming, require extensive sample treatment, and often involve the use of bulky and expensive instrumentation. The new approach couples nanoparticle sensors with plants’ natural ability to efficiently extract analytes via the roots and transport them. This allows for the detection of arsenic uptake in living plants in real time, with portable, inexpensive electronics such as a portable Raspberry Pi platform equipped with a charge-coupled device camera akin to a smartphone camera.

Co-author, DiSTAP co-lead principal investigator, and MIT Professor Michael Strano adds, “This is a hugely exciting development, as, for the first time, we have developed a nanobionic sensor that can detect arsenic — a serious environmental contaminant and potential public health threat. With its myriad advantages over older methods of arsenic detection, this novel sensor could be a game-changer, as it is not only more time-efficient, but also more accurate and easier to deploy than older methods. It will also help plant scientists in organizations such as TLL to further produce crops that resist uptake of toxic elements. Inspired by TLL’s recent efforts to create rice crops which take up less arsenic, this work is a parallel effort to further support SMART DiSTAP’s efforts in food security research, constantly innovating and developing new technological capabilities to improve Singapore’s food quality and safety.”

The research is carried out by SMART and supported by the National Research Foundation (NRF) Singapore under its Campus for Research Excellence And Technological Enterprise (CREATE) program.

Led by MIT’s Strano and Singapore co-lead principal investigator Professor Chua Nam Hai, DiSTAP is one of the five Interdisciplinary Research Groups (IRGs) in SMART. The DiSTAP program addresses deep problems in food production in Singapore and the world by developing a suite of impactful and novel analytical genetic and biosynthetic technologies. The goal is to fundamentally change how plant biosynthetic pathways are discovered, monitored, engineered, and ultimately translated to meet the global demand for food and nutrients. Scientists from MIT, TTL, Nanyang Technological University, and National University of Singapore are collaboratively developing new tools for the continuous measurement of important plant metabolites and hormones for novel discovery, deeper understanding and control of plant biosynthetic pathways in ways not yet possible, especially in the context of green leafy vegetables; leveraging these new techniques to engineer plants with highly desirable properties for global food security, including high yield density production, drought and pathogen resistance and biosynthesis of high-value commercial products; developing tools for producing hydrophobic food components in industry-relevant microbes; developing novel microbial and enzymatic technologies to produce volatile organic compounds that can protect and/or promote growth of leafy vegetables; and applying these technologies to improve urban farming.

SMART was founded by MIT in partnership with the NRF in 2007 and is the first entity in CREATE. SMART serves as an intellectual and innovation hub for cutting-edge research between MIT and Singapore, and currently comprises an Innovation Center and five IRGs: Antimicrobial Resistance, Critical Analytics for Manufacturing Personalized-Medicine, DiSTAP, Future Urban Mobility, and Low Energy Electronic Systems.

Provided by MIT

Novel Haplotype-led Approach to Increase the Precision of Wheat Breeding (Botany)

Wheat researchers at the John Innes Centre are pioneering a new technique that promises to improve gene discovery for the globally important crop.

Crop breeding involves assembling desired combinations of traits that are defined by underlying genetic variation. Part of this genetic variation often stays the same between generations, with certain genes being inherited together. These blocks of genes – very rarely broken up in genetic recombination – are called haplotype blocks. These haplotypes are the units that breeders switch and select between plants to create new crop lines.

Novel haplotype-led approach will increase the precision of wheat breeding. ©John Innes Centre

In the new study which appears in Communications Biology John Innes Centre researchers led by the group of Professor Cristobal Uauy show that current platforms used by breeders do not provide the resolution needed to distinguish between haplotypes, potentially leading to inaccurate breeding decisions.

They defined shared haplotype-blocks across the 15 bread wheat cultivars assembled in the 10+ Wheat Genome Project a major international collaboration published today in Nature.

To illustrate the application of this haplotype-led approach to support crop improvement, they focused on a specific region of the wheat genome on chromosome 6A.

Through detailed genetic studies and extensive field experiments, they showed that UK breeders are maintaining multiple genes as an intact chromosome 6A haplotype to maximise the expression of desirable traits including flowering time and yield.

Given the low diversity on chromosome 6A, they tested the haplotype approach to discover and introduce novel haplotypes from wheat landraces not subjected to modern breeding.

Combining haplotype knowledge, genetics and field studies, they identified three novel haplotypes in the landraces associated with improved productivity traits in UK environments.

As these haplotypes are not present in modern germplasm, they represent novel variations that could be targeted for yield improvement in elite cultivars, using modern genomic tools.

Lead author Dr Jemima Brinton says: “We used strict criteria to distinguish these shared haplotype blocks from near-identical sequences. We argue that this stringency is essential for crop improvement. The breeding process is poised to undergo an improvement in precision and efficiency through haplotype-led breeding.”

The knowledge generated in the study directly affect the breeding and discovery process by allowing scientists to:

  • Perform focused discovery of novel haplotypes and use breeding strategies to introduce this genetic diversity into modern germplasm.
  • Prioritise research targets to understand the biological functions of sequences selected by breeders
  • Perform more precise selection of parents to maximise genetic gains within breeding programmes
  • Intentionally assemble optimised haplotype combinations

To make the work more accessible to readers, scientists and breeders, the group developed a new haplotype visualisation interface at http://www.crop-haplotypes.com.

The findings are set out in the study: ‘A haplotype-led approach to increase the precision of wheat breeding’ for publication in Communications Biology. Communications Biology https://www.nature.com/articles/s42003-020-01413-2

Reference: Jemima Brinton, Ricardo H. Ramirez-Gonzalez, James Simmonds, Luzie Wingen, Simon Orford, Simon Griffiths, Georg Haberer, Manuel Spannagl, Sean Walkowiak, Curtis Pozniak, Cristobal Uauy. A haplotype-led approach to increase the precision of wheat breeding. Communications Biology, 2020; 3 (1) DOI: 10.1038/s42003-020-01413-2

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