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The battle against viral diseases: Novel strategies for antiviral resistance in potatoes

on May 17, 2023

This article was written by Jorge Luis Alonso G., an information consultant specializing
in the potato crop.

Scientists at the Inner Mongolia Agricultural University in China recently published a review in the journal Plants describing the advancement of antiviral strategies in potatoes through the engineering of both viral and plant-derived genes.

The article below is a summary of the information presented in this scientific paper.

1. Introduction

Potatoes, as a nutritious and staple food crop, have the potential to address food insecurity in developing countries. However, a major impediment to this aptitude is the prevalence of viral diseases in potato production, which result in the destruction of seed potatoes and often cause yield losses of 20–30%. Major viruses, including Potato virus Y (PVY), Potato leafroll virus (PLRV), and Potato virus X (PVX), cause various damaging symptoms such as leaf curling, necrosis, and stunted growth.

Complicating disease prevention, these viruses enter the plant through various vectors and use plant resources to replicate. Although virus-free seed potato technology can limit disease damage, some viruses are persistent and can re-infect during the growing season.

In addition, the hetero-tetraploid nature of the plant limits conventional breeding methods in developing antiviral potato varieties. On the positive side, advances in molecular biology and plant genetic engineering have opened the door to creating virus-resistant crops. Promising strategies have emerged, such as RNA interference (RNAi)-mediated resistance, which targets the viral coat proteins of the major potato viruses.

Eventually, genetically modified (GM) potatoes, including virus-resistant varieties, are now being introduced and commercialized in certain countries. This progress represents a major step forward in the fight against potato virus diseases.

2. Engineering Virus-Derived Viral Resistance in Potato

Researchers have developed genetically engineered virus-resistant plants, including potatoes, by using the coat protein (CP) gene of viruses such as tobacco mosaic virus (TMV), PVY, PVX, and PLRV. CP has several functions, including protection of the viral nucleic acid and regulation of the host range of infection. However, CP-mediated resistance is often limited, providing protection only against the CP donor virus or related strains and only at low viral doses. Additional complications in virus transmission can arise when the plant is transformed with the CP of an insect-borne virus.

To overcome these challenges, investigators are attempting to combine different viral CPs in the same plant or to incorporate coat protein genes with satellite RNA for a broader antiviral spectrum. An alternative approach involves replicase, an RNA polymerase encoded by viral genes. This enzyme synthesizes the positive and negative strands of viral RNA during replication. Although researchers have shown that replicase-mediated resistance is stronger than CP-mediated resistance, its specificity limits its use in the field due to the rapid mutation rate of plant RNA viruses.

In addition, antisense RNAs (asRNAs), which are complementary to messenger RNA (mRNA), have also been used for viral resistance. Although some success has been achieved in acquiring antiviral infection ability and protecting plants, antisense RNA-directed resistance is generally weak due to insufficient expression, which limits its practical application. However, there are still ways to improve the expression level of antisense RNA, which keeps this avenue open for exploration.

3. Engineering Virus-Resistant Plants Using Plant Endogenous Genes in Potato

Scientists are increasingly focusing on creating virus-resistant plants by using the plant’s own genes. They have discovered antiviral genes in both wild and cultivated potato species. These can be categorized into two distinct groups: extreme resistance (ER) genes and hypersensitive resistance (HR) genes. ER genes are known to resist many viruses and thwart viral reproduction in the early stages of infection. On the other hand, HR genes resist various virus species, triggering cell necrosis after a virus infection to limit its spread.

In potatoes, the Ry genes confer ER to all PVY strains, including the Rysto, Ryadg, and Rychc genes. Breeders have incorporated these into potato breeding programs and have identified Rysto as recognizing the central 149 amino acids of the PVY coat protein domain, suggesting its potential utility in engineering virus resistance.

The Y-1 gene is unique in its action as it induces cell death without preventing the systemic spread of PVY, thus hinting at its possible use in potato breeding. The G-Ry gene, a Y-1 homolog, has been detected to enhance resistance to PVY. Meanwhile, Ny genes, such as Ny-1 and Ny-2, have demonstrated HR against PVY in many potato cultivars. The Nytbr gene exhibits hypersensitivity to PVY, showing necrosis symptoms upon infection. Interestingly, scientists have identified the HCPro cistron of PVY as influencing necrotic reactions and resistance in plants carrying certain resistance genes.

As for resistance to PVX, it is mediated by the Rx1 gene, which causes a rapid termination of viral replication. A transcription factor that interacts with Rx1 mediates antiviral immunity, thereby enabling the Rx1 gene to confer ER to PVX.

One major and two minor quantitative trait loci (QTL) for resistance to potato leaf roll virus (PLRV), a potato disease, have been identified. The major QTL has mapped to potato chromosome XI. These identified genes associated with potato virus resistance can be used for antiviral breeding and for the development of potato varieties resistant to a single virus or many viruses. However, further research is needed to use these resistance genes and to discover new ones.

4. RNAi-Mediated Viral Resistance in Potato

RNA silencing, a common gene regulation mechanism in eukaryotes, plays a central role in protecting against viruses. This mechanism involves the interaction of small interfering RNAs (siRNAs), Dicer-like (DCL) endonucleases, and AGO family proteins. Specifically, DCL4 and DCL2 are responsible for generating siRNAs that mount a defense against RNA viruses. Further amplifying this system, RNA-dependent RNA polymerases (RDRs) convert aberrant single-stranded RNA into double-stranded RNA precursors of secondary siRNAs. This strategy is particularly promising for the development of virus-resistant transgenic plants.

In the specific context of viroid infection in plants, RNA silencing plays an important role. For example, replication of potato spindle tuber viroid in tomato plants induces resistance to RNA silencing, suggesting the critical role of secondary structures in resistance to RNAi.

The process of RNAi silencing can be manipulated to change miRNA sequences, creating artificial miRNAs (amiRNAs) that can target specific sequences. This ingenious approach has been used to engineer virus-resistant plants by creating resistant plants by creating amiRNAs that can actively fight viral infections.

In nature, however, viruses often encode silencing suppressors to counteract host RNAi-based defenses. To improve viral resistance, research is focused on enhancing RNAi activity by increasing the efficiency of AGO proteins and modifying siRNAs.

Despite extensive studies on RNA silencing as a strategy in plant antiviral protection, the beneficial effect of RNA silencing in viral infection remains somewhat puzzling. In particular, the mechanism by which some components of RNA silencing systems contribute to viral infection is not well understood. A deeper understanding of this could open up new opportunities for engineering viral resistance in various crops, such as potato.

5. CRISPR/Cas9-Mediated Viral Resistance in Potato

CRISPR/Cas, a system created to provide immune protection against invading nucleic acids in bacteria, has been repurposed for efficient genome engineering and the development of antiviral immunity in plants. This was amply demonstrated by the ability of CRISPR/Cas systems to effectively control Beet Severe Curly Top Virus (BSCTV) in N. benthamiana and A. thaliana. In addition, the CRISPR/Cas9 system has been ingeniously used to mutate susceptibility genes in rice and tobacco to confer resistance to Rice Tungro Spherical Virus (RTSV) and Potato Virus Y (PVY), respectively.

Besides these applications, the CRISPR/LshCas13a system was used in potato crops to generate resistance to Potato Virus Y, further demonstrating the potential of CRISPR technology in crop protection. Taken together, these studies underscore the significant capacity of CRISPR/Cas9 to control plant RNA viruses in major crops such as potato.

6. Future Prospects and Conclusions

As the battle against genetically complex virus strains in potato varieties escalates, researchers are moving to strengthen virus resistance. They are gearing up for a multi-pronged strategy.

First and foremost, they aim to disrupt the virus-host interaction by editing the potato genome. Using the available potato genome sequences, their goal is to construct an effective shield to protect potato plants from viral invasion. In this regard, they’ve identified CRISPR editing technology as a possible powerhouse in the fight against plant virus infections, a tool that could outperform RNAi.

Second, they are embarking on a mission to discover resistance genes that are key to antiviral response. This discovery could provide a significant boost to potato breeding efforts. Once identified, these genes will be introduced into potato plants through genetic transformation.

Third, they are formulating plans to harness the power of inducible responses in naturally virus-resistant plants. Because these plant defenses have broad-spectrum capabilities, their goal is to identify viral components that activate plant immune mechanisms. This promising area of study could reveal resistance genes that control these protective mechanisms. This, in turn, would pave the way for the development of strategies to engineer the broad-spectrum components of natural defenses.

Fourth, armed with an increasing understanding of the molecular functions of viral proteins, they plan to manipulate these proteins to create cross-protection against further viral infection in potato plants.

Finally, they see the transgenic expression of antiviral proteins of non-plant origin, including antibodies, as a promising frontier in the search for increased resistance to specific potato viruses. This approach underscores the relentless pursuit of new strategies to strengthen potatoes against viral threats.

Source: Liu, J., Yue, J., Wang, H., Xie, L., Zhao, Y., Zhao, M., & Zhou, H. (2023). Strategies for Engineering Virus Resistance in Potato. Plants, 12(9), 1736. https://doi.org/10.3390/plants12091736
Photo: Potato leafroll virus causes stunted plants. Credit Government of Western Australia

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A ‘New Green Revolution’ is brewing — just in time, as the world population breaks past the 8 billion mark

Gurjeet Singh Mann | January 26, 2023

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Credit: CGTN
Credit: CGTN

You can mark the date on your calendar: On November 15, 2022, a mother [gave] birth to a baby who [was] the world’s 8 billionth person.

This milestone in human history comes to us from an estimate by demographers at the United Nations.

They also predict that next year, my country of India will pass China as the planet’s most populous nation, with about 1.4 billion people.

Credit: United Nations

This means the expanding population will need much more food than we ever had before. If we’re going to feed them, we need another Green Revolution and a lot more for

India as well as for the rest of the world. Farmers must enjoy access to the full power of modern technology so that we can do our part to meet the necessities of life.

The challenges of population growth are enormous. I’ve seen the effects in my region of northern India, where I’ve worked on my family farm for more than four decades and currently grow rice and wheat. Areas that once were devoted to agriculture now are dotted with dwellings to accommodate more families and people. The boundaries of cities and villages continue to expand, cutting into cropland. Everything feels more congested.

We’re losing arable land every day to urbanization and industrialization. Because we can’t make more of it, we must do more with what we have—and in a world of 8 billion people, that means growing more food on less land than ever before.

This is our task for the rest of the century, too. The UN predicts continued growth in global population, with 9.7 billion people in 2050 and 10.4 billion in 2100.

Prediction intervals (shaded area around a projected trend) were derived from a probabilistic assessment of projection uncertainty. Credit: United Nations

The problem is especially severe in India. Soon we’ll have more people than China, but China always will have more arable land.

China is also spending enormous resources to improve food security and production. Credit: Yuan Chai et al

Feeding our nation will involve one of history’s biggest tests.

This is a serious problem, but it can be transformed into an opportunity as well. The good news is that we know what to do, at least in principle, and that’s because we’ve done it before.

Back in the 1960’s, the global population topped 3 billion—and many experts worried about the ability of farmers to improve their production and keep up. Enter Norman Borlaug, the agronomist who made it his mission to find a solution. In India, he worked with M.S. Swaminathan and M.S. Randhawa to develop new seed varieties, which gave a big boost to the yield and total production of cereals, especially wheat in India.

At a time when pessimists were ready to surrender in the war on hunger, Borlaug showed the power of human ingenuity to solve problems with science and technology. He went on to win the Nobel Peace Prize for his achievements as an agronomist.

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This is the hidden benefit of population growth: For all the ways that additional people can present dilemmas, they also give us a better chance to create a new generation of innovators who will help us think our way to answers.

As they do, farmers like me stand ready to do our part. We are ready to innovate, too.

During my career as a farmer, I’ve watched technology transform everything. The advent of GMOs, for example, allowed cotton farmers finally to withstand the assaults of boll worms and other pests—and we enjoyed a massive boom in production. Although I’m now growing other kinds of crops, I was a full participant in this development and saw firsthand how much it helped farmers and consumers alike.

Sadly, our government has prevented us from adopting GM technology in edible produce. While much of the developed world has embraced this technology, India has hesitated, due mainly to the opposition of political activists. We have an amazing potential to grow more food. A couple of the most promising examples are mustard and brinjal (which is known as “eggplant” in other parts of the world). Today, we have a ray of hope as GM mustard recently received environmental clearance from the Government. Access to these GM seeds would immediately help farmers strengthen India’s food security.

Yet this is about more than just a single technology. The gene-editing technology called “CRISPR” gives us new abilities to grow crops in harsher conditions, including drought, heat, and frost. We should apply it to every crop—starting with wheat and rice, which may be the commodities that could gain the most from new technological approaches and farmer access needed to meet the worlds hunger challenge.

Credit: Somisetty V. Satheesh et. al.

Everything begins with having the best seeds, but we have other technological opportunities: Climate-smart farming requires better machinery, from large harvesters for big fields to small and micro size so a maximum number of farmers can adopt it to small drones for mapping and surveillance; micro-irrigation, for the efficient delivery of water in a time of climate change; improved weather forecasting, to help us make planting decisions; and crop-protection tools that fight weeds, pests, and disease.

These are the makings of a new Green Revolution—one that a world of 8 billion people and counting will need.

Gurjeet Singh Mann is a farmer who embraces new technology including GM crops, and he helps guide his fellow and young farmers with farm technologies. Gurjeet runs Mann Farms  out of Sirsa, India. 

A version of this article was posted at Global Farmer Network and is used here with permission. Check out Global Farmer Network on Twitter @GlobalFarmerNet

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Video: UNESCO examines the environmental and biodiversity impacts of gene-edited plants and animals

UNESCO | November 8, 2022

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Credit: UNESCO
Credit: UNESCO

Genome editing is a powerful tool. It allows us to modify genes not only to treat human diseases but also to change characteristics of animals and plants within a very short period of time at a much larger scale than any other methods that humans had ever used in the past. A technique called “gene drive” that uses genome editing to spread certain genes in the entire population of a target species could eradicate diseases caused by insects such as malaria and other vector borne diseases. Plants and animals could be more resistant to diseases and grow quicker. But is it safe? What would be the impact on the environment and biodiversity?

The third of the series of Ethics of Genome Editing “3. Impact of Genome editing on plants, animals and environment” is now available in English, French, Japanese, Spanish and other languages subtitles.

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CRISPR is on the cusp of revolutionizing food and farming. Here is a global regulatory primer

Kyle DiamantasOlga BezzubovaPatricia Campbell | JD Supra | August 26, 2022

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Credit: Varsity
Credit: Varsity

The ability to edit eukaryotic DNA entails an almost limitless ability to alter the genetic makeup of the plants that become our food. Recently, scientific attention has been directed to applying a class of new gene-editing techniques that utilize CRISPR to food crops for the introduction of commercially desirable traits. Gene-edited crops can have a positive impact on food productivity, quality, and environmental sustainability, and CRISPR is unique in its relative simplicity, robust flexibility, cost-effectiveness, and wide scope of use.

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In general, the EU subjects agricultural products edited with CRISPR technology to the full suite of genetically modified organism (“GMO”) premarket approval, safety, and labeling requirements.

In contrast to the EU approach, the United States does not currently regulate CRISPR-edited agricultural products as GMOs. The United States regulates biotechnology and genetic modification in food through a “Coordinated Framework” between the U.S. Department of Agriculture (“USDA”), Food and Drug Administration (“FDA”), and Environmental Protection Agency (“EPA”).

The regulation of CRISPR-edited agriculture is continuing to develop across the world, with notably different approaches and outcomes. While the European Union expressly considers CRISPR-edited agriculture to be “genetically modified” and subject to associated regulations, the United States generally does not currently consider CRISPR-edited agriculture to be “genetically modified.”

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omeCropsCotton Cotton gene-editing project aims to make plant more insect resistant

Cotton gene-editing project aims to make plant more insect resistant

Shelley E. Huguleybanner- swfp-shelley-huguley-eddie-eric-smith-jdcs770-20.jpg

Texas A&M AgriLife, USDA and Cotton Incorporated collaborate on the research project.

Farm Press Staff | Aug 24, 2022



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Aug 30, 2022 to Sep 01, 2022

Scieintists in the Texas A&M Department of Entomology have received a matching grant of almost $150,000 to conduct a three-year project to research novel pest management tools for cotton production. If successful, the project, Modifying Terpene Biosynthesis in Cotton to Enhance Insect Resistance Using a Transgene-free CRISPR/CAS9 Approach, could provide positive cost-benefit results that ripple through the economy and environment.

The project goal is to silence genes in cotton that produce monoterpenes, chemicals that produce an odor pest insects home in on, said Greg Sword, Texas A&M AgriLife Research scientist, Regents professor and Charles R. Parencia Endowed chair in the Department of Entomology. By removing odors that pests associate with a good place to feed and reproduce, scientists believe they can reduce infestations, which will in turn reduce pesticide use and improve profitability.


Research to improve a plant’s ability to tolerate or resist pest insects and diseases via breeding programs is nothing new, Sword said. But editing genomes in plants and pest insects is a relatively new and rapidly advancing methodology.

swfp-shelley-huguley-sam-stanley-cotton-drip-22.jpgA gene-editing project aims to expose and exploit simple but key ecological interactions between plants and insects that could help protect the plant. This is Sam Stanley’s 2022 drip-irrigated cotton near Levelland, Texas. (Photo by Shelley E. Huguley)

Sequencing genomes of interest and using the gene-editing tool CRISPR have become increasingly viable ways to identify and influence plant or animal characteristics. 

However, using gene-editing technology to remove a characteristic to make plants more resistant to pests is novel, Sword said. The research could be the genesis for a giant leap in new methodologies designed to protect plants from insects and other threats. 

Sword’s gene-editing project aims to expose and exploit simple but key ecological interactions between plants and insects that could help protect the plant.

“Insects are perpetually evolving resistance to whatever we throw at them,” Sword said. “So, it’s important that our tools continue to evolve.”

The matching grant is from both the U.S. Department of Agriculture National Institute of Food and Agriculture, NIFA, and the Cotton Board, a commodity group that represents thousands of growers across Texas and the U.S. The grant totals $294,000.

Critical seed funding 

Sword is collaborating with Anjel Helms, chemical ecologist and assistant professor in the Department of Entomology; Michael Thomson, AgriLife Research geneticist in the Department of Soil and Crop Sciences and the Crop Genome Editing Laboratory; and graduate student Mason Clark.

This research team is working on a project that was “seeded” by Cotton Incorporated, the industry’s not-for-profit company that supports research, marketing and promotion of cotton and cotton products.

The seed money allowed the AgriLife Research team to create a graduate position for Clark and produce preliminary data that laid the foundation for the NIFA grant proposal, Sword said. In addition, the terpene research is part of larger and parallel projects that began with direct support from Cotton Incorporated.    

“Cotton Incorporated’s support has been absolutely critical to jumpstart the project from the beginning,” he said. “From a scientific standpoint, industry support and collaboration are vital to project success, whether that’s leveraging money for research or identifying, focusing on and solving a problem, which actually helps producers.”

Industry collaborations strengthen the impact

Texas cotton production represents a $2.4 billion contribution to the state’s gross domestic product. From 2019 to 2021, Texas cotton producers averaged 6.2 million bales of cotton on 4.6 million harvested acres, generating $2.1 billion in production value. The Texas cotton industry supports more than 40,000 jobs statewide and $1.55 billion in annual labor income.

Research like Sword’s is augmented and sometimes directly funded by commodity groups representing producers and related industries.


Projects supported by the Cotton Board and Cotton Incorporated run the gamut of production, including reducing plant water demands, increasing pest and disease resistance, and improving seed and fiber quality. (Photo by Shelley E. Huguley)

Jeffrey W. Savell, vice chancellor and dean for Agriculture and Life Sciences, said collaborative projects help research dollars make the greatest impact for producers. Texas A&M AgriLife’s relationships with commodity groups that represent producers can jumpstart groundbreaking work and help established programs maintain forward momentum.

“Cotton Incorporated is one of our long-time partners, and that collaboration has made an enormous impact on individuals, farming operations, communities and the state,” Savell said. “This project is just one example of how we can do more by engaging with the producers we serve.”

The Cotton Board’s research investment

Bill Gillon, president and CEO of the Cotton Board, said projects supported by the Cotton Board and Cotton Incorporated have run the gamut of production, including reducing plant water demands, increasing pest and disease resistance, and improving seed and fiber quality.

Cotton Incorporated scientists typically identify a need or a vulnerability and create and prioritize topics for potential projects. These projects are developed in coordination with agricultural research programs that will either be directly funded by the group or could be submitted to funding agencies for competitive grants. The Cotton Board reviews project proposals and approves them for submission to NIFA for competitive grant dollars.

The Cotton Board’s Cotton Research and Promotion Program has generated more than $4 million in competitive cotton research grants from NIFA over the past three years, Gillon said. When coupled with $1.35 million from the Cotton Board, the program has generated $5.4 million in agricultural research funding for projects critical to improving productivity and sustainability for upland cotton growers in the U.S.

Gillon said funding-match grants represent a collaborative investment that maximizes financial support for science, ultimately impacting growers and local economies throughout Texas and the Cotton Belt.

swfp-shelley-huguley-21-cotton-harvest-sunset-vert.jpgPublic-private strategic support for research emphasizing sustainable practices across the agricultural spectrum has far-reaching benefits, says Phillip Kaufman, head of the Department of Entomology, Texas A&M University. (Photo by Shelley E. Huguley)

“We value our long-standing relationship with Texas A&M and other institutions across the Cotton Belt because the work would not be done without their expertise,” he said. “We certainly view this as a partnership and want to support their land-grant mission and help researchers maintain their capabilities, programs and labs that continue to produce results critical for cotton producers and agricultural production.” 

Industry buy-in 

Phillip Kaufman, head of the Department of Entomology, said an overarching goal for his department is addressing relevant topics or concerns, from public health to agricultural production. Whether research meets the immediate needs of producers or lays the foundation for breakthroughs in coming decades, many agricultural research projects’ relevance is guided by producer input.

Industry buy-in is critical to entomology research, he said. Topics relevant to commodities, in this case, cotton, and the public’s interest, in this case, NIFA, is a good representation of how the land-grant mission delivers for producers but can also ripple through communities, the economy and the environment.

Kaufman said public-private strategic support for research emphasizing sustainable practices across the agricultural spectrum has far-reaching benefits.

“This grant project is a good example of how cotton producers, the gins and other elements of their industry effectively tax themselves to fund campaigns and research that adds value to what they produce,” he said. “It also shows the motivation from a public dollar perspective to invest in research focused on providing pest control methods that reduce chemical use.”


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CRISPR gene-edited rice could help soil bacteria produce nitrogen fertilizer. Here’s how it works

Genetic Engineering & Biotechnology News | August 18, 2022

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Nitrogen fertilizers are very expensive, this innovation could make plants use them more efficiently. Credit: RusticWise
Nitrogen fertilizers are very expensive, this innovation could make plants use them more efficiently. Credit: RusticWise

Researchers have used CRISPR to engineer rice that encourages soil bacteria to fix nitrogen, which is required for their growth. The findings may reduce the amount of nitrogen fertilizers needed to grow cereal crops, save farmers in the United States billions of dollars annually, and benefit the environment by reducing nitrogen pollution.

“Plants are incredible chemical factories,” said Eduardo Blumwald, PhD, a distinguished professor of plant sciences from the University of California, Davis, who led the research. His team used CRISPR to enhance apigenin breakdown in rice. They found that apigenin and other compounds induced nitrogen fixation in bacteria.

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Then they identified the pathways generating the chemicals and used CRISPR gene editing technology to increase the production of compounds that stimulated the formation of biofilms. Those biofilms contain bacteria that enhanced nitrogen conversion. As a result, nitrogen-fixing activity of the bacteria increased, as did the amount of ammonium available for the plants.

Much of the fertilizer that is applied is lost, leaching into soils and groundwater. Blumwald’s discovery could help the environment by reducing nitrogen pollution. “What this could do is provide a sustainable alternative agricultural practice that reduces the use of excessive nitrogen fertilizers,” he said.

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A New Green Revolution Is in the Offing

Thanks to some amazing recent crop biotech breakthroughs

RONALD BAILEY | 8.10.2022 5:00 PM

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man stands in wheat field facing away from camera with outstretched arms

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A recent spate of crop biotech breakthroughs presage a New Green Revolution that will boost crop production, shrink agriculture’s environmental footprint, help us weather future climate change, and provide better nutrition for the world’s growing population.

The first Green Revolution was generated through the crop breeding successes pioneered by agronomist Norman Borlaug back in the 1960s. The high-yielding dwarf wheat varieties bred by Borlaug and his team more than doubled grain yields. The Green Revolution averted the global famines confidently predicted for the 1970s by population doomsters like Stanford entomologist Paul Ehrlich. Other crop breeders using Borlaug’s insights boosted yields for other staple grains. Since 1961, global cereal production has increased 400 percent while the world population grew by 260 percent. Borlaug was awarded the Nobel Peace Prize in 1970 for his accomplishments. Of course, the disruptions of the COVID-19 pandemic and Russia’s invasion of Ukraine are currently roiling grain and fertilizer supplies.

Borlaug needed 20 years of painstaking crossbreeding to develop his high-yield and disease-resistant wheat varieties. Today, crop breeders are taking advantage of the tools of modern biotechnology that can dramatically increase the rate at which yields increase and drought- and disease-resistance can be imbued in crops.

The Green Revolution’s crops required increased fertilizer applications to achieve their higher yields. However, fertilizers have some ecologically deleterious side effects. For example, the surface runoff of nitrogen and other fertilizers not absorbed by crops spurs the growth of harmful alga in rivers, lakes, and coastal areas. In addition, excess nitrogen fertilizer gets broken down by soil bacteria such that there are rising atmospheric concentrations of the greenhouse gas nitrous oxide, which, pound for pound, has 300 times the global warming potential of carbon dioxide.

The good news is that in the last month, two teams of modern plant breeders have made breakthroughs that will dramatically cut the amount of nitrogen fertilizers crops need for grain production. In July, Chinese researchers reported the development of “supercharged” rice and wheat crops, which they achieved by doubling the expression of a regulatory gene that increases nitrogen uptake by four- to fivefold and enhances photosynthesis. In field trials, the yields of the modified rice were 40 to 70 percent higher than those of the conventional varieties. One upshot is that farmers can grow more food on less land using fewer costly inputs.

Some crops like soybeans and alfalfa get most of the nitrogen fertilizer they need through their symbiotic relationship with nitrogen-fixing soil bacteria. Soybeans supply the bacteria living on their roots with sugars, and the bacteria in turn take nitrogen from the air and turn it into nitrate and ammonia fertilizers for the plants. However, nitrogen-fixing bacteria do not colonize the roots of cereal crops.

A team of researchers associated with the University of California Davis reported in July their success in gene editing rice varieties to make their roots hospitable to nitrogen-fixing bacteria. As a result, when grown under conditions of limited soil nitrogen, the yields of the gene-edited varieties were 20 to 35 percent higher than those of the conventional varieties. The researchers believe their gene-editing techniques can be applied to other cereal crops.

This new biotech-enabled Green Revolution promises a future in which more food from higher yields grown using less fertilizer means more farmland restored to nature, less water pollution, and reduced greenhouse gas emissions.

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Study: How GMOs and crop gene editing can increase genetic diversity and help contain climate change

Helen CurrySarah Garland | PLOS Biology | August 3, 2022

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Credit: kwest via Shutterstock
Credit: kwest via Shutterstock

As climate change increasingly threatens agricultural production, expanding genetic diversity in crops is an important strategy for climate resilience in many agricultural contexts. In this Essay, we explore the potential of crop biotechnology to contribute to this diversification, especially in industrialized systems, by using historical perspectives to frame the current dialogue surrounding recent innovations in gene editing. We unearth comments about the possibility of enhancing crop diversity made by ambitious scientists in the early days of recombinant DNA and follow the implementation of this technology, which has not generated the diversification some anticipated.

We then turn to recent claims about the promise of gene editing tools with respect to this same goal. We encourage researchers and other stakeholders to engage in activities beyond the laboratory if they hope to see what is technologically possible translated into practice at this critical point in agricultural transformation.

A new hope: Gene editing for crop diversity

Leading plant scientists today praise innovative gene editing techniques as game-changing methods destined to fulfill aspirations for expanding crop genetic diversity through biotechnology. This fanfare sounds familiar, as scientists throughout the history of crop breeding have heralded various innovations in similar ways, most recently with the expectation that recombinant DNA would create paradigm-shifting possibilities. What, if anything, is different about the potential of gene editing technologies with respect to genetic diversity?

Gene editing …  offers opportunities to radically rethink the breeding process in ways that enhance genetic diversity by “restarting” crop domestication. Crop domestication relies upon a combination of spontaneously occurring genetic mutations and artificial selection by humans. In wild rice, for example, grains shatter in order to widely disperse the seed. During rice domestication, a mutation arose that caused non-shattering grains, a trait beneficial for early agricultural societies and therefore selected for cultivation. Rice wild relatives today carry beneficial traits like adaptation to diverse growth environments but their grains still shatter.

…Using biotechnology to expand crop genetic diversity will also require that researchers understand the many junctures in crop variety development and dissemination, especially those linked to seed commercialization, that work against such expansion. Addressing these obstacles will involve addressing issues as varied as farmer seed choice, seed certification processes, and international intellectual property regimes. It will require engaging with and developing further interdisciplinary and participatory research efforts to map infrastructural obstacles and to indicate actions that different stakeholders can take to facilitate genetic diversification.

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Following a fungus from genes to tree disease: a journey in science

Published: June 30, 2022 9.36am EDT


  1. Brenda WingfieldPrevious Vice President of the Academy of Science of South Africa and DSI-NRF SARChI chair in Fungal Genomics, Professor in Genetics, University of Pretoria, University of Pretoria

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Brenda Wingfield receives funding from the South African Department of Science and Innovation via the National Research Foundation (NRF). She is a fellow of the Academy of Science of South Africa, African Academy of Science and the Third World Academy of Science She is the Secretary General of the International Society of Plant Pathology and a fellow of the American Phytopathological Society She is the current chair of the NRF Executive Evaluation Committee


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Anyone who reads even a little about science and technology will be familiar by now with the idea of genome sequencing. This process involves breaking an organism’s DNA into fragments to study their compositions or sequences. Then the fragments are aligned and merged to reconstruct the original sequence.

But why sequence an organism’s genome? What’s the value for ordinary people and the world more broadly? The answers are immediately obvious when it comes to the medical field. Understanding what makes a disease “tick” offers scientists a way to treat or prevent it. Sequencing the genome of a crop or animal can improve agricultural yields or make species hardier in shifting climates.

It’s a little tougher to explain the value of sequencing the genome of plant pathogens, the organisms that cause diseases in plants. But this has become a critical part of the work of microbiologists and plant pathologists. And it is important, far beyond the laboratory: by carefully studying plant pathogens’ genomes, researchers have been able to design specific double stranded RNA fungicides to short circuit some pathogens’ abilities to harm plants.

These fungicides have not yet been deployed commercially but have huge potential – only targeted species will be affected and so the process is likely to be more environmentally friendly than any involving chemical fungicides. This research has the potential to protect crops, benefiting agriculture and contributing to food security.

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For the past 13 years I’ve focused on sequencing one plant pathogen’s genome. Here’s where that scientific journey has led.

Pine trees at risk

sequenced the genome of a fungus called Fusarium circinatum in 2009; it was the first fungal genome sequence to be conducted on the African continent.

I started studying this pathogen more than 20 years ago because it was killing seedlings in South African pine nurseries. Fusarium circinatum causes pitch canker on pine trees, which makes trees exude pitch or resin. In severe cases the fungus causes tree death. This fungus is considered to be the most important pathogen threat to the global plantation pine industry. It is also potentially devastating in some areas of the southern US, Central America, Europe and Asia, where pines are found naturally.

Trees are extremely important in carbon sequestration. They also produce oxygen – it is estimated that, daily, one tree can produce enough oxygen for four people. Trees have huge economic value, too, providing timber for our homes and paper and packaging for many uses in our daily lives. It is difficult to estimate the total value of pine plantations globally but the South African industry is estimated to contribute more than US$2 billion to the country’s Gross Domestic Product annually.

Sequencing the genome was just the beginning. Follow-up studies published in 2021 involved knocking genes out of the genome and studying what happened. This process is a bit like first identifying and lining up all the parts, then removing these parts one at a time to see what difference they make to the functioning of the fungus. Sometimes we need to understand how gene products (proteins) interact with each other and then more than one gene might be removed from a genome.

In this way, my colleagues and I can learn which genes are important to the processes that Fusarium circinatum uses to cause pitch canker and which are not. Now we’re working to target the important genes in studies to manage the pathogen.

It’s time-consuming work: this fungus has around 14,000 genes. This is more than the yeast that is used to ferment beer, which has 6000 genes, but less than the estimated 25,000 genes in the human genome. Luckily technologies are evolving rapidly to enable routine gene knock-outs. This involves a protein which acts a bit like DNA-specific scissors allowing deletion of a specific sequence of DNA. The position where the protein cuts is guided by using small pieces of RNA sequence that are identical to the target DNA sequence.

Read more: What is CRISPR, the gene editing technology that won the Chemistry Nobel prize?

Another of our key findings is that Fusarium circinatum has acquired, through horizontal gene transfer from other organisms, a group of five genes that apparently enhance its growth.

This discovery has been very useful in developing a specific diagnostic tool using LAMP PCR (Loop-mediated isothermal amplification) to identify this pathogen. This is a special kind of highly sensitive test that was developed to allow for in-field detection of pathogens. It also doesn’t require specialised training. This is useful because trees only recently infected with Fusarium circinatum can be asymptomatic. It’s crucial to determine the presence of the pathogen as early as possible so its spread can be better managed.

New skills, new possibilities

The rise in studies that sequence plant pathogens’ genomes has also opened up opportunities for scientists to develop new skills. The data generated by genome sequencing sometimes outstrips the number of researchers available to analyse it. During pandemic lockdowns in South Africa, some students in my research programme learned how to code and developed skills in bioinformatics, using computers to capture and analyse biological data rather than working in a laboratory.

With these new skills, as well as fast-improving technology, we may well crack Fusarium circinatum’s code once and for all. And that will help to guard pine trees against a dangerous, costly pathogen.

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What role can genetics play in ‘designing’ more sustainable crops, livestock and trees?

Rodolphe Barrangou | National Academy of Engineering | July 1, 2022

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Plants, animals and microbes can be improved with gene editing. Credit: Carys-ink
Plants, animals and microbes can be improved with gene editing. Credit: Carys-ink

The ability to engineer genomes and tinker with DNA sequences with unprecedented ease, speed, and scale is inspiring breeders of all biological entities. Genome engineers have deployed CRISPR tools in species from viruses and bacteria to plants and trees (whose genome can be 10 times larger than the human genome), including species used in food and agriculture (Zhu et al. 2020).

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Starting small, bacteria used in food fermentations have had their genomes enhanced to optimize their functional attributes linked to the flavor and texture of fermented dairy products such as yogurt and cheese. The fact that CRISPR-Cas systems provide adaptive immunity against viruses in dairy bacteria led to the commercial launch, more than a decade ago, of bacterial starter cultures with enhanced phage immunity in industrial settings. Most fermented dairy products are now manufactured using CRISPR-enhanced starter cultures. Since then, a variety of bacteria, yeast, and fungi (figure 2) involved in the manufacturing of bioproducts has also been CRISPR enhanced to yield commercial products such as enzymes, detergents, and dietary supplements.

Moving along the farm-to-fork spectrum, most commercial crops—from corn, soy, wheat, and rice to fruits and vegetables—have had their genomes altered (figure 2). Genome engineering is used to increase yield (e.g., meristem size, grain weight) and improve quality (e.g., starch and gluten content), pest resistance (e.g., to bacteria, fungi, viruses), and environmental resilience (e.g., to drought, heat, frost). For instance, nonbrowning mushrooms with extended shelf life can be generated, and tomatoes with increased amounts of gamma aminobutyric acid (GABA) to enhance brain health have been commercialized. In addition, efforts are underway to enhance nutritional value.

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Credit: NAE

Livestock breeders have joined the fray, with genome engineering of main farm species such as swine (leaner bacon), poultry (CRISPR chicken), and cattle (for both meat and dairy). Swine have also been edited with a viral receptor knockout to prevent porcine reproductive and respiratory syndrome; the approach is being evaluated for regulatory approval (Burkard et al. 2017). Breeding applications include hornless cows (for more humane treatment), resistance to infectious disease (tuberculosis in cattle), and removal of viral sequences in the genome of elite commercial livestock,[1] notably swine. The CRISPR zoo also encompasses genetically diverse species—fish (tiger-puffer and red sea bream), cats (efforts are underway to develop hypoallergenic variants), and even butterflies (wing pattern)—illustrating the ability to deploy this technology broadly.

This is an excerpt. Read the original post here

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Kenyan gene hacker moves to defeat witchweed

Prof Steven Runo has edited the DNA of sorghum to give it resistance to the notorious, parasitic weed

In Summary

•Traditionally, farmers would attempt to control Striga by simple, physical means. These included physically uprooting the plants, which wasn’t particularly effective, considering that the weed knots itself within the host’s roots.

•Prof Runo is an associate professor of molecular biology at Kenyatta University.

Among the towering names in genome editing in Kenya is Professor Steven Runo

The world is making tremendous strides in the novel science of genome editing, which has wide-ranging applications in medicine and agriculture, among other fields.

Kenyan scientists have also joined the effort, with several pioneering research projects underway right within the country.

Among the towering names in genome editing in Kenya is Prof Steven Runo, an associate professor of molecular biology at Kenyatta University. Part of his research work targets Striga, also known as witchweed, a notorious weed that threatens maize, sorghum, rice and several other cereal crops.

Known in parts of western Kenya, where it is particularly rife, as Uyongo or Kayongo, Striga is a predatory plant that attaches itself to the roots of the host plant, from where it saps vital nutrients from the host. This invariably leads to stunted growth and vastly diminished production.

“Genome editing is a new technology for not only plant breeding but also animal breeding,” Prof Runo said.

“It’s a very simple strategy. Think about the DNA, which is what determines the traits of organisms. How tall or short we are, and how much yield you get from a crop, is determined by the genetic code”.

With this in mind, scientists like Prof Runo are able to introduce changes to an organism’s DNA, with an aim to alter specific traits in the organism.

“Genome editing involves going into the genome and introducing beneficial changes, and very precisely at that,” he said. “So, you can go into a specific trait and alter one or two bases – or DNA sequences – to achieve the trait that you are looking for. One of the ways that genome editing can be done is using CRISPR Cas9 technology, a very simple alteration of DNA sequence for beneficial traits”.

Traditionally, farmers would attempt to control Striga by simple, physical means. These included physically uprooting the plants, which wasn’t particularly effective, considering that the weed knots itself within the host’s roots.

And upon maturity, the weed deposits its seeds in the soil, which makes it difficult for farmers to control it.

Farmers would also practice crop rotation or intercropping with legumes, which helps control Striga’s germination. They would also apply inorganic fertiliser to enrich the soils, as Striga thrives in poor soils within low-rainfall regions.

The use of pesticides would also be recommended as a control measure against Striga, but chemical controls are normally not within reach of many small-scale farmers.

“While a few control measures have been moderately successful, the problem still persists, especially in western Kenya, eastern Uganda and lake zone of Tanzania, where farmers have frequently voiced their frustrations at the ubiquity of this invasive weed,” states The International Maize and Wheat Improvement Center (CIMMYT).

That’s where biotechnology chips in, with novel technologies that aim at controlling the proliferation of pathogenic plants, and minimizing the labour and costs in pesticides that farmers would ordinarily incur.

Prof Runo’s project, titled “Evaluation of Striga resistance in Low Germination Stimulant 1 (LGS1) mutant sorghum”, seeks to confer resistance to this parasitic weed in sorghum, an important cereal crop in Kenya and many parts of Africa.

A proof of concept has already been done for the project, and the program awaits other stages in product development, which will ultimately culminate in trials.

“This weed is present in most parts of Sub-Saharan Africa, and Kenya is one of those countries that is heavily infested by the parasite,” Professor Runo told Tuko recently.

“Depending on the level of infestation, Striga can cause between 30-100 percent in yield losses. We estimate this to cost about US$ 7 billion globally every year. This is a substantial amount of money, considering that this weed affects cereal crops, mostly grown by small-scale farmers”.

Many counties in Western Kenya have Striga infection, he adds – from Busia to Siaya, Kisumu and Homabay.

“Almost all countries within western Kenya have Striga infection”.

He is honored to be at the forefront of such groundbreaking research, and appreciates the opportunity to deploy his expertise in this highly complex science towards finding solutions for common problems that have dogged local farmers.

“You’d be happy to know that Kenya has very good human resource in terms of very well trained scientists. What we want to showcase is that these scientists can do research that is comparable to research that is done in other countries. Again, we have a long-standing history of using advances in plant sciences to develop and grow better crops”.

There are plenty of good reasons to support local scientific expertise, he adds, citing the case of Asia.

“The success that we are seeing in Asia, in terms of agricultural advancement, was because scientists were supported. They’d say, we have a critical number of scientists that have innovations, and they’d use science-based and evidence-based facts to support and make decisions and policy in agriculture. Such an approach goes a long way towards growth improvement, and ultimately improves food security”.

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