UK: Plant breeders to benefit from online research tools


United Kingdom – Plant breeders to benefit from online research toolsSelect
April 3, 2024
 An exciting new project will look to put cutting-edge research tools in the hands of plant breeders, providing access to genomic resources to accelerate the development of more resilient and climate-resistant crops.The collaboration brings together the collective expertise of the Earlham Institute, IBM Research, the Science and Technology Facilities Council (STFC) Hartree Centre, and RAGT Seeds UK with the aim of simplifying and speeding up the transition of cutting-edge genome research tools, workflows, and software into industrial applications.The one-year Excelerate project is part of the Hartree National Centre for Digital Innovation (HNCDI) programme from STFC designed to close the gap between academic and industrial applications of digital technologies – such as artificial intelligence (AI) and quantum computing.The UK is home to some of the most exciting and innovative life science research. Institutions are pioneering the use of new technologies to overcome issues of scale and complexity in data-intensive bioscience, such as developing approaches that could be used to accelerate crop breeding in line with EU safety and ethical regulations.At the Earlham Institute, this includes crop pangenomes and the tools required to analyse them, developed through its Decoding Biodiversity strategic programme – funded by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UKRI.But the transition of this knowledge into usable technology – and its uptake by industry – remains a significant challenge.“Modern plant breeding practices are based on understanding and then using genetic resources – made possible by digital innovations – that breeders can incorporate into their programmes,” Professor Anthony Hall, project lead and Head of Plant Genomics at the Earlham Institute explained.“Bioinformatics and machine learning techniques are playing an increasingly important role in deciphering genetic diversity. But they bring significant overheads in terms of the bioinformatics skills and computing power required to develop and implement new workflows.”The plant breeding industry has a crucial role to play in addressing the global challenges of food security, water conservation, and net zero. To realise the enormous potential of UK science and innovation, initiatives are needed to bridge the gap between research and industry.This new project brings together leaders from academia and industry to provide cloud-based tools that can be easily adopted by the plant breeding companies to support the development of next-generation crops with greater climate resilience and improved nutritional properties.The Earlham Institute is working with IBM Research and STFC to develop new cloud-based tools – including those optimised for exploring plant pangenomes – which RAGT Seeds UK will be road testing.“The Earlham Institute is home to some amazing research infrastructure, innovation, and expertise,” says Professor Hall. “This helps us to develop the technology needed to answer the big questions that will be critical in addressing urgent global challenges, such as how we find new sources of diversity for breeding more resilient crops.”
 The project team photographed with the London skyline behind them.
The project team from left to right: Robin Kennedy Reid, STFC, Rachel Rusholme-Pilcher, Earlham Institute, Laura Jayne-Gardiner, IBM Research, Will Davies, STFC, Anthony Hall, Earlham Institute, Chris Burt, Heidi Town, and John Baison, RAGT Seeds UK.
 Dr Rachel Rusholme-Pilcher is a Senior Postdoctoral Researcher at the Earlham Institute, and has played a central role in developing the workflows that will be used in this partnership.“The tools we’re developing and optimising will allow plant breeders to interact with their complex datasets in a way they simply couldn’t before,” explained Dr Rusholme-Pilcher. “It should provide new information they can rapidly incorporate into their existing breeding programmes.“We’ll also be using this project to look at how we can embed the adoption of FAIR approaches – the movement to make all research data Findable, Accessible, Interoperable, and Reusable. Making this kind of research FAIR can be a challenge but these collaborations will hopefully change that – transforming the impact of emerging technologies.”Excelerate is one strand of a number of projects from HNCDI embedding AI solutions across UK industry. To both accelerate and simplify the adoption of compute intensive bioinformatics workflows in the plant breeding industry, this project will use an on-demand, scalable, Hybrid Cloud delivery model.Dr Laura-Jayne Gardiner, Senior Research Scientist at IBM Research, said: “Our HNCDI Excelerate projects are enabling businesses to adopt new technologies – including artificial intelligence and hybrid cloud – to overcome industrial challenges, such as allowing complex biological data analytics at increased scale and speed.”Robin Kennedy-Reid, Senior Research Software Engineer at the STFC Hartree Centre, said: “At the Hartree Centre, we use applied research and innovation to turn good ideas into industry-ready solutions for long-term societal and economic impact. This is made possible by working with a network of partners, both industry and academic leaders, as well as drawing on the work of open source communities like nf-core.“In this project, this will deliver new bioinformatics and machine learning capability to the plant breeding industry; with a view to assisting the search for more sustainable wheat varieties.”Dr John Baison, Cereals Research and Genomics Manager at RAGT Seeds UK, said: “Genome-based breeding holds promise for expediting wheat breeding, aiming to ensure sustainable wheat production by creating high-yielding, climate-resilient cultivars with superior nutritional quality.“The plant-breeding sector is positioning to confront these targets by leveraging the dynamic UK research community. However, bridging the gap between research and industry is crucial for optimising the potential of UK science and innovation.“As RAGT delves deeper into genomics activities, it has become increasingly evident that we must harness advanced computing tools to navigate the vast amounts of data generated from genetics and genomics projects. RAGT is excited to be at the forefront of this collaborative effort, which could revolutionise the application of genomics to plant breeding.” 

More news from:
    . Earlham Institute
    . RAGT Seeds Limited
Websitehttp://www.earlham.ac.ukPublished: April 3, 2024

new way to identify pesticide resistance


new way to identify pesticide resistance

Tina Deines

Sun, April 7, 2024 at 12:00 PM CDT·2 min read

Researchers are exploring an exciting new approach that uses genomics to help monitor and identify pesticide resistance in the insects that munch on our crops.

Pest management is important for farmers, but insects often become immune to pesticides, making them less effective. In the new research, published in the Proceedings of the National Academy of Science, a team of scientists from the University of Maryland (UMD) presents a new strategy that analyzes genomic changes in pests to monitor and identify emerging resistance to specific toxins early on.

They zoned in on one pest in particular: the corn earworm, a crop-destroying caterpillar that has developed widespread resistance to a number of natural toxins bred into corn. They were able to identify resistance to toxins among these caterpillars after just a single generation of exposure. They also identified how common strategies for avoiding resistance could actually be doing the opposite.

“As it currently stands, the evolution of resistance across many pests of agricultural and public health importance is outpacing the rate at which we can discover new technologies to manage them,” said senior author Megan Fritz, an associate professor of entomology at UMD, per Phys.org. “I’m really excited about this study, because we’re developing the framework for use of genomic approaches to monitor and manage resistance in any system.”

The new research is one of many that is helping farmers to produce more successful harvests.

For instance, a team of American and Chinese researchers found a way to genetically engineer plants that can survive heat waves. University of Minnesota scientists are on their way to developing a “Super Grape” that could stave off powdery mildew and reduce the need for fungicide.

Watch now: What’s the true environmental impact of renewable energy?

These developments in agriculture come at a critically important time — as our planet continues to warm, there are frequent heat waves and droughts, which threaten our food security. Plus, climate change scientists predict that a warming world will drive a surge in certain insect pests that attack our crops, further threatening food security and causing economic losses for those in the agricultural sector.

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Kansas, USA: Robots developed to take on a labor-intensive process — cutting weeds down


Harvest Public Media | By Celia Hack

Published April 8, 2024 at 4:00 AM CDT

LISTEN • 3:20

GreenField robots at sunset.

Greenfield Robotics, a Kansas-based company, is hoping to move agriculture away from herbicides. They’ve developed robots to take on a labor-intensive process — cutting weeds down.

Three yellow, bug-like creatures crawl in perfectly straight lines across the dead grass of a flat, brown February field in Cheney, Kansas.

These are the namesake of GreenField Robotics. Two lights peer out from each side of the boxy machines, almost appearing like eyes. Blades whir at their base, about a half an inch from the ground – the perfect height to chop weeds, though there’s nothing to cut down on a frigid winter day.

They stick out in an otherwise rural landscape – and GreenField CEO Clint Brauer said he frequently hears from curious passersby.

“All the time,” Brauer said. “I’m always surprised, though, how little people notice.”

Brauer founded the company in 2018. The start-up has now grown large enough to attract investment from Chipotle’s $100 million venture capital fund and to secure partnerships with dog food and baking mix brands.

Brauer grew up on a family farm in Haven, Kansas, but moved to California after high school to work in the tech industry. In 2010, he returned home after his dad was diagnosed with Parkinson’s disease. He attributes the use of herbicides to his dad’s diagnosis.

“The more I learned about farm chemicals and stuff … the more I thought there’s a decent chance that this came from that,” Brauer said.

GreenField Robotics CEO and Founder Clint Brauer with two robots in Cheney, Kansas.
GreenField Robotics CEO and Founder Clint Brauer with two robots in Cheney, Kansas.

The move sucked Brauer back into the world of agriculture, where he started seeking ways to eliminate herbicides. He tried farming organically, but it was too expensive to be accessible to many buyers.

Another option was no till farming, where farmers avoid turning over the dirt to reduce erosion and improve soil health. But it’s a method that leans on herbicides.

And in 2015, Brauer was starting to notice the weeds in his fields were becoming resistant to chemicals anyway.

“There was no good way to get rid of those weeds, even though we had sprayed many times,” Brauer said.

“So, what do we do? And so that was the beginning of this idea of – what if we just cut those weeds?”

Cutting weeds by hand wasn’t exactly a 21st-century answer. So Brauer thought: What about robots? He reached out to software and machine-vision experts and started prototyping robots.

By 2021, the company had manufactured a two-and-a-half foot-tall working robot. And it pulled together different technologies, like drones, to create extremely precise maps of crop fields. The robots follow the maps, so that they’re unlikely to accidentally chop down a crop instead of a weed.

“They plant the crop, we count about 10 days, normally, the crops emerge, and we fly over it with a drone,” Brauer said. “ … That’s where AI – we have machine vision that automatically recognizes everything that’s going on in that field.”

Thirty to 40 days later, Brauer sends out the robots.

GreenFields' robots working a field.
GreenFields’ robots working a field.

In 2022, the company partnered with MKC, a major agricultural cooperative, to reach farmers who might use the product. In 2023, GreenField Robotics worked with 25 to 30 Kansas farmers, Brauer said. The company currently has a fleet of 20 robots and 15 employees

This summer, Brauer said the company is planning to work the weed-cutting robots on over 20,000 acres.

John Niemann is a farmer in Reno County. He tested GreenField Robotics for the first time last spring on 80 acres of a sorghum field, leaving 10 acres untouched to compare results. He had treated the entire crop with herbicides earlier in the season.

“We saw higher yields where we used the robots, versus the 10 acres that we did not,” Niemann said.

That’s because the weeds that didn’t get chopped down in the 10 acres competed with the crop for moisture, hampering the yield.

“The robots are part of a toolbox, is how I would look at them,” Niemann said. “There is no magic bullet in farming practices. You need to have a lot of tools in your toolbox.”

Niemann says the robots are a useful tool to reduce reliance on chemicals. Plus, he said the cost was comparable to herbicides.

Brauer said the economics is always his first pitch to farmers, and the robots are compelling because they damage less of the crop than chemicals do.

The company is also adapting the robots for other uses, like planting cover crops and soil testing.

“We are on a mission,” Brauer said. “This is not about enrichment. This is – we’re building something that can’t be undone. And so we’re going to eliminate these chemicals.”

This story was first aired and produced by KMUW. It’s being distributed by Harvest Public Media, a collaboration of public media newsrooms in the Midwest. It reports on food systems, agriculture and rural issues.

Tags

News farmingregenerative farmingrobotsagriculture

Jamaica: Lethal yellowing of coconut palm


Saturday, 09 March 2024 10:37:00

Grahame Jackson posted a new submission ‘LETHAL YELLOWING, COCONUT PALM – JAMAICA’

Submission

LETHAL YELLOWING, COCONUT PALM – JAMAICA

ProMED
http://www.promedmail.org

Source: Jamaica Observer [summ. Mod.DHA, edited]
https://www.jamaicaobserver.com/2024/03/05/spread-lethal-yellowing-disease-reduced-70/

Through the work of the Coconut Industry Board (CIB), Jamaica has been able to reduce the spread of the lethal yellowing disease in the coconut industry by 70%. CIB have contributed significantly through research which has allowed the development of varieties and hybrids with optimum resistance/tolerance to lethal yellowing. In addition, increased yields are obtained from these locally developed varieties that are adapting better to the climatic conditions.

Within the region, the disease was first discovered in the Cayman Islands in 1834 and was found in Jamaica in 1884. It became a real threat to Jamaica after 1961 and became even more significant in the 1970s when some 10 million trees of the ‘Jamaican Tall’ variety were destroyed. Lethal yellowing has caused severe economic losses in Jamaica.

Communicated by:
ProMED

[Lethal yellowing (LY) diseases of coconut and other palms are caused by phytoplasmas of the palm lethal yellowing (16SrIV; _Candidatus_ Phytoplasma palmae strains) group. A number of LY strains have been described from the Caribbean, Latin America, Africa and southern Asia. LY has seriously jeopardised coconut industries in the respective areas. LY-type diseases like Cape St Paul wilt (CSPW) in Ghana, the “maladie de Kaincope” in Togo and Awka disease (lethal decline, LD) in Nigeria, previously included in the 16SrIV group, have been reclassified as the new group 16SrXXII (Nigerian coconut lethal decline group, _Ca._ P. palmicola strains; see link below).

Symptoms include premature nut drop, blackening of inflorescences, yellowing of fronds; death of the palm usually occurs within 4 to 6 months. The planthopper _Myndus crudus_ is suspected to be the vector in the Americas, but different vectors may be involved in the spread of LY strains elsewhere. Seed transmission of the pathogens cannot be excluded; some weed species may serve as pathogen reservoirs. Jumps of LY across apparently unaffected coconut populations have been observed, possibly due to aerial spread of infectious vector insects or human activities. Even with strict controls, including certification of nuts and their parent trees, excluding infectious vector insects requires large quarantine efforts.

While LY affects many palm species, at least for coconut palm susceptibility may vary between cultivars or even within cultivars, depending on the region where they grow. Symptoms can be suppressed by tetracycline treatments, usually applied as trunk injections. The antibiotic inhibits multiplication of the pathogens but does not eliminate them. Therefore, treatments need to be repeated regularly. Commercial control of the diseases mostly relies on phytosanitation followed by replanting with resistant varieties.

An unexplained resistance breakdown of some widely used hybrids occurred earlier in Jamaica (ProMED post 20070522.1643) and caused great concern.

Pictures
LY symptoms on coconut and other palms:
https://www.growables.org/information/TropicalFruit/images/LethalYellowingFoliarSymptoms.jpg,
https://bugwoodcloud.org/images/768×512/1504008.jpg,
https://guyanachronicle.com/wp-content/uploads/2017/04/Lethal-Yellowing.jpg (leaf) and
http://www.cphdforum.org/wp-content/uploads/2015/06/LethalYellowingCoconutSymptom.jpg (fruit)
_Myndus crudus_:
https://bugwoodcloud.org/images/768×512/0725079.jpg

Links
Story also at:
https://jis.gov.jm/spread-of-lethal-yellowing-disease-reduced-by-70/ and
https://jamaica-gleaner.com/article/news/20240304/spread-lethal-yellowing-disease-coconut-industry-reduced-70
Lethal yellowing information:
https://doi.org/10.1079/cabicompendium.38647,
https://doi.org/10.3389/fpls.2016.01521,
https://doi.org/10.1111/j.1744-7348.2011.00480.x,
https://www.cphdforum.org/index.php/2015/06/03/about-lethal-yellowing-of-coconut/,
http://edis.ifas.ufl.edu/pp146 and
https://www.apsnet.org/edcenter/disandpath/prokaryote/pdlessons/Pages/LethalYellowing.aspx
16SrIV LY phytoplasma group taxonomy and species list:
https://www.uniprot.org/taxonomy/85624
16SrXXII classification of some LY-type diseases:
https://doi.org/10.1099/ijs.0.65000-0
16SrXXII LDN phytoplasma group taxonomy:
https://www.uniprot.org/taxonomy/590462
Phytoplasma resource centre:
https://plantpathology.ba.ars.usda.gov/phytoplasma.html
Information on LY vectors via:
https://bugguide.net/node/view/63
– Mod.DHA


EU: Food security top priority for 2024-2029


By Sofia Sanchez Manzanaro | Euractiv

 Est. 3min

 Apr 9, 2024 (updated:  Apr 10, 2024)

Content-Type: News

The Strategic Agenda, which defines the EU’s priorities for the 2024-2029 mandate and provides guidance for the Brussels-based institutions, will be adopted by the 27 heads of state and government during the European Council meeting of 27-28 June. [EPA/OLIVIER HOSLET]

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EU leaders are expected to put food security at the heart of the bloc’s agricultural policy for the next five years, according to a leaked draft of the EU’s Strategic Agenda seen by Euractiv.

The programme defines Europe’s priorities for the 2024-2029 mandate, providing guidance to the EU institutions, and will be adopted by the 27 heads of state and government during the European Council meeting on 27-28 June.

The internal document, created on 27 March, predates the most recent exchanges between the EU leaders, and points to food security as a key priority for a “prosperous and competitive Europe,” despite the issue hardly being discussed at EU summits in recent years.

“Ensure our food security through a vibrant agriculture sector,” reads one of the bullet points of the draft outline.

The two-page text does not explicitly reference the sustainability of the agricultural sector or the protection of the environment, even though it prioritises “preparing for the new realities stemming from climate change.”

From sustainability to security

This initial draft marks a departure from the 2019 priorities, which included “promoting sustainable agriculture” and “calling on all EU countries to move forward and step up their climate action”.

In response to widespread farmer protests across the EU, the European Commission has already shelved or backtracked some of its plans to improve the sustainability of the farming sector in recent months.

Faustine Bas-Defossez, director for health, nature, and environment at the European Environmental Bureau (EEB), described the absence of sustainable agriculture in the leaked 2024 agenda as “deeply troubling”.

“By prioritising’ food security’ over sustainability in agriculture, EU leaders are ignoring the reality that climate change and natural disasters pose the greatest threats to our food security,” she warned.

A study commissioned by the European Parliament’s Agricultural Committee found that while food availability in the EU “is not generally considered to be at risk,” the bloc relies too heavily on imports from a reduced group of suppliers for animal feed and fertilisers.

According to the report, those dependencies, exacerbated by an uncertain geopolitical situation and climate change, could threaten the long-term resilience of the EU food system.

The study however also found that sustainable farming practices, such as organic agriculture and the promotion of lower consumption of animal products, could decrease the bloc’s need for imports.

EU is too dependent on animal feed and fertiliser imports, warns Parliament study

The EU remains heavily reliant on animal feed and fertilisers imports from outside the bloc, as highlighted in a recent study commissioned by the European Parliament’s Agriculture Committee (AGRI).

[Edited by Angelo Di Mambro and Rajnish Singh]



The genetic composition of fungi and its role in plant health


by University of Ottawa

Population analyses of R. irregularis. Credit: Nature Microbiology (2023). DOI: 10.1038/s41564-023-01495-8

The complex and very diverse world of fungi is often referred to as the fifth kingdom of organisms. It includes various yeasts, molds, and mushrooms. A team of scientists from the University of Ottawa (uOttawa) has uncovered the genetic secrets of a mysterious fungus, revealing the presence of two distinct nuclear populations within them, each playing distinct roles in how they interact with plants.

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Arbuscular mycorrhizal fungi (AMF) are tiny fungi that live in harmony with plants, sharing their genetic diversity and creating a vibrant atmosphere in plant roots and with below-ground microbes. Scientists have been studying AMF for years but are still puzzled by it. Its bodies are like bags packed with thousands of nuclei cells, and how these fungi cooperate with plants has long been unclear.

“There were numerous unresolved questions regarding AMF, mainly because these fungi are always multinucleated and do not exhibit observable sexual characteristics,” says Professor Nicolas Corradi, who holds the Chair in Microbial Genomics at the Department of Biology, University of Ottawa. “It has been proposed that AMF possess unique genetics and have undergone an unconventional evolution.”

Professor Corradi and colleagues investigated the asexual reproduction of AMF, specifically Rhizophagus irregularis. In 2016, they discovered strains that showed signs of sexual reproduction, with two populations of nuclei co-existing in large cells. “We found that strains having two populations (AMF heterokaryons) are more resilient and could access plant roots more easily, an indication they could be better bio-stimulants.”

However, without their complete genome, the researchers could not know why these strains are more successful plant symbionts.

Exploring the genetic composition of fungi and its role in plant health
Phylogenetic tree constructed with 65 R. irregularis strains. Haplotypes from AMF heterokaryons are shown in yellow squares. Based on relative branch lengths, the phylogeny resolves at least nine clades, which are highlighted in color. The tree was made using IQTREE algorithm, in GTR-FO mode with 1,000 bootstrap replicates. Scale bar represents 0.05 substitutions per site. When available, the MAT type of the strain is shown in parentheses. Note: the G1 strain located in clade VI noted with an asterisk is homokaryotic and does not represent the heterokaryotic isolate G1 (DAOM-970895) from clade IV. Credit: Nature Microbiology (2023). DOI: 10.1038/s41564-023-01495-8

To address this, Professor Corradi and his team employed advanced sequencing techniques, including RNA sequencing and third-generation DNA sequencing, to analyze differences in structure, content, and expression between the co-existing genomes.

“AMF heterokaryons have two haplotypes that physically separate among a large number, possibly millions, of co-existing nuclei. This phenomenon is unprecedented in any other organism,” explains Professor Corradi.

Their analyses also demonstrated that the two populations act very differently depending on their surrounding environment and their plant host. “Not only did we find that the two populations differ dramatically in the genes they harbor, but also that these are differently expressed and change in abundance depending on which plant they interact with,” adds Professor Corradi.

The symbiotic interactions between AMF and host plants are crucial for nutrient exchange, pathogen protection, and ecosystem sustainability. Studying these interactions will help improve agricultural practices by producing tailored biostimulants, enhancing plant growth, and promoting ecosystem health.

The study, titled “Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions,” was published in Nature Microbiology.

More information: Jana Sperschneider et al, Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host–plant interactions, Nature Microbiology (2023). DOI: 10.1038/s41564-023-01495-8

Journal information: Nature Microbiology 

Provided by University of Ottawa 


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In symbiosis: Plants control the genetics of microbes

Horizontal gene transfer: How fungi improve their ability to infect insects


by Eva Sittig, Kiel University

The research team investigated genetic changes of Metarhizium fungi during infection of the invasive Argentine ant, shown here are its workers, on the right with brood. Credit: Sina Metzler & Roland Ferrigato, ISTA

Researchers at the Kiel Evolution Center have investigated for the first time in detail how a fungus important for biological plant protection can pass on an advantageous chromosome horizontally, using a previously little-studied way of exchanging genetic information.

https://9ac9fe61267363bec791a45a3bf0ef66.safeframe.googlesyndication.com/safeframe/1-0-40/html/container.html

Sustainable plant protection measures that are not based on chemical pesticides rely on various organisms and biological agents to protect crops from pests. Such organisms used for biological plant protection are, for example, microscopic fungi of the genus Metarhizium, which can attack and kill a variety of plant-pathogenic insects and are used, for example, in South American sugar cane cultivation.

The molecular mechanisms of fungal infection and the immune response of insects are in an ongoing process of mutual evolutionary adaptation. In a joint project with colleagues from the Institute of Science and Technology Austria (ISTA), a research team from Kiel University investigated the genetic changes in the fungus during infection of the invasive Argentine ant (Linepithema humile).

The researchers examined the genomes of different strains of the fungi Metarhizium robertsii and Metarhizium brunneum from an earlier co-infection experiment in which ants had been infected with the fungus mix.

In the study, the outgrowing spores were used to infect new ants over 10 consecutive infection cycles. When analyzing the fungal genomes from these infection series, the fungal geneticist and first author of the study, Dr. Michael Habig from Kiel University, made an exciting observation: his analyses showed that a single chromosome was very frequently exchanged horizontally between two different strains.

This chromosome contains certain genes that the scientists suspect may give the fungus an advantage in infecting its hosts. The horizontal transfer of entire chromosomes has rarely been described scientifically and has now been studied in detail for the first time. The researchers from the Kiel Evolution Center (KEC) and ISTA published their results in the journal Proceedings of the National Academy of Sciences.

Horizontal chromosome transfer detected in insect-damaging fungus

Scientists use the term horizontal gene transfer to describe how living organisms can transfer genetic material between different individuals, including those of other species. In this way, bacteria exchange extensive genetic information, often in the form of plasmids, in order to quickly adapt to changing environmental conditions or to adapt to the host. The rapid evolution of various pathogens is based on such mechanisms, among other things.

“In fungi and many other so-called eukaryotic organisms, however, horizontal gene transfer in the form of entire chromosomes is very rare and has hardly been researched to date,” says Dr. Michael Habig, research associate at Kiel University.

“The analysis of the genetic information of the fungal strains shows that M. robertsii independently transferred a single chromosome a total of five times during the co-infection experiments, but no other genetic information from one strain to another via horizontal transfer,” continued Habig.

Further analyses also indicated that the same chromosome can also be found in the distantly related, also insect-damaging fungus species Metarhizium guizhouense, whose common evolutionary origin with M. robertsii dates back around 15 million years.

“The chromosome in M. guizhouense is significantly less altered than would be assumed for the long period of separate evolution of the two fungal species. The chromosome therefore also appears to have been passed on naturally between these different fungal species—and probably horizontally,” says Habig.

Analysis of the chromosome indicates possible survival advantages for the fungus

The chromosome examined is a so-called accessory chromosome. This means that it does not occur in all individuals of a species and contains non-essential genetic information.

“The experiments showed that, under certain conditions, the fungus that had received the accessory chromosome had competitive advantages over fungi of the same strain that had not received the chromosome and were able to prevail against them. We want to investigate the details of these advantages in more detail in the future,” says Habig.

The Kiel research team has already been able to derive initial indications from the analysis of the genes on the chromosome. “The chromosome contains hundreds of genes whose potential functions we will only be able to decipher in the future. However, we have already been able to identify 13 candidate genes that could presumably be responsible for so-called effector proteins, which can interact with the insects’ immune system, for example,” Habig continues.

The transfer of the chromosome may therefore have advantages for the fungus, the functional basis of which is still unclear. However, one plausible possibility is the transfer of certain genes that produce chitin-cleaving enzymes and can thus improve the ability to infect the insects.

“It is remarkable that we have found the genes of three such enzymes, among others, which presumably play a role in the degradation of the chitin-containing cuticle of the host insect. This could influence a crucial step in the infection process, as the fungal spores are dependent on penetrating the protective exoskeleton of the host in order to infect it,” says Professor Sylvia Cremer, last author of the study, from the Institute of Science and Technology Austria (ISTA).

Overall, the research work offers interesting new aspects on a way of exchanging genetic information that has been little studied in fungi to date.

“Our new work shows that horizontal chromosome transfer occurs regularly in fungi and that this mechanism can confer advantages to the recipient strain, at least in experiments under certain conditions,” says Habig.

The Kiel research team and its collaboration partners from ISTA thus describe in detail for the first time a new aspect in the genome evolution of fungi, which may be able to use bacteria-like mechanisms of rapid evolutionary adaptation, for example to increase their virulence or harmfulness to their host organism and to transfer genetic information across species boundaries.

In the future, the researchers want to use the example of M. robertsii to investigate the relationships between horizontal chromosome transfer, possible fitness advantages and the mutual adaptation of fungi and insects in detail and thus gain further insights into this organism, which is important for plant protection.

More information: Michael Habig et al, Frequent horizontal chromosome transfer between asexual fungal insect pathogens, Proceedings of the National Academy of Sciences (2024). DOI: 10.1073/pnas.2316284121

Journal information: Proceedings of the National Academy of Sciences 

Provided by Kiel University 


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Examining the promotion of Arabidopsis immune responses by a rhizosphere fungus

Zambia: FAW control with Metarhizium rileyi


Successful on-farm trials using Metarhizium rileyi in Zambia

The fall armyworm (Spodoptera frugiperda) has wreaked havoc on Zambia’s agriculture, devastating smallholder farmers with staggering losses. But amidst the struggle, a promising solution emerges.

Through activities on the PlantwisePlus programme and the Village-based biocontrol of fall armyworm in Zambia project, funded by ACIAR, CABI has delved into combating this agricultural menace with various biological control options.

Project Leads from CABI, ZARI and UNZA

Fungus to fight fall armyworm in Zambia

Metarhizium rileyi, a highly specific fungus that kills fall armyworm, stands out among these. What’s even more remarkable? Scientists from Zambia Agricultural Research Institute (ZARI), University of Zambia (UNZA), and CABI in Zambia have identified the presence of this fungus naturally occurring in certain areas when fall armyworm started devasting maize, offering a beacon of hope in the fight against this invasive pest. In 2023, the CABI-led project, funded by ACIAR, embarked on a journey alongside key partners ZARI and UNZA. Their mission? To tackle the fall armyworm crisis head-on through village-based biocontrol initiatives. The project’s official launch marked the beginning of comprehensive field trials across various sites in Zambia.

How effective is Metarhizium rileyi?

The heart of these trials lies in the application of M. rileyi.  The process involves using a mixture of a calculated amount of M. rileyi spores and local sand treatment and applying it in four maize sites infested with fall armyworm. Scientists applied the mixture every two weeks. To compare the efficacy of the fungus, the team also used other treatments: sand only, chemical, and no application. This innovative approach, coupled with meticulous monitoring, aimed to evaluate the feasibility and effectiveness of M. rileyi as a biological control agent.

Showing farmers the efficacy of M. rileyi in the field

Despite facing challenges like drought in some trial sites, the results have been promising. Visual assessments revealed stark differences between treated and untreated plots, showcasing the efficacy of M. rileyi.

Notably, the fungal and chemical-treated plots exhibited substantial control over fall armyworm populations, with numerous dead specimens discovered in the fungal treatments.  In the fungal-treated plots, there were also thriving populations of beneficial insects, which contributed to further pest suppression over time.

A sustainable approach

A dead fall armyworm showing the green fungus Metarhizium rileyi

As we reflect on these encouraging findings, it’s evident that nature holds powerful solutions to our agricultural challenges. The local presence of naturally occurring M.rileyi offers a sustainable and environmentally friendly approach to combatting fall armyworms in Zambia and beyond. Looking ahead, continued research and collaboration are paramount. By amplifying our efforts and leveraging the potential of biocontrol, we can mitigate the impact of invasive pests, safeguarding livelihoods and fostering resilience in agricultural communities.

Find out more

PlantwisePlus in Zambia

CABI Projects: Village-based biological control of fall armyworm in Zambia

Fall armyworm portal (CABI Digital Library)

How can Metarhizium be used to address pests and diseases?

Study examines potential for collective action to fight fall armyworm with biological controls in rural Zambia

Project advocates village-based biological control of fall armyworm in Zambia


Images: courtesy of the authors

PlantwisePlus gratefully acknowledges the financial support of the Directorate-General for International Cooperation (DGIS), Netherlands; European Commission Directorate General for International Partnerships (INTPA, EU); the Foreign, Commonwealth & Development Office (FCDO), United Kingdom; and the Swiss Agency for Development and Cooperation (SDC). 

Fall armywormSpodoptera frugiperdabiocontrolfungusmetarhiziumpesticide risk reductionsustainable agriculturezambia

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Related News & 

Early detection and tracking of ToBRFV virus entry point


“It is important to be prepared and to understand the virus infection in order to effectively mitigate its spread or prevent a potential epidemic,” explains Harmen Hummelen, production quality manager at Bayer.

The tomato brown rough fruit virus (ToBRFV) is becoming increasingly widespread. In the event of infection, it is important to be prepared, understand the viral infection, and manage its spread.

A ToBRFV infection that is not properly managed can have a significant impact on plant quality and yield. Detecting the virus early after infection is essential, and this article presents some tips and suggestions for early detection.

Recognition in the greenhouse
Recognizing an early infection is not easy, partly because most people have never seen the disease before. There are some general guidelines to help with early detection and recognition of the ToBRFV virus, and an experienced person who can “read” plants is one of the most valuable helpers.

Such a person is more likely to detect any “anomaly” for a particular variety or time of year (for example, plants with a slightly different color or shape). These symptoms may not be directly linked to the ToBRFV virus, as they can often resemble fertilizer deficiency or other stress factors.

For example, one of the symptoms may be that the plant is a little shorter for no clear reason. These plants, or their neighbors, may have fruits that do not ripen normally. Some fruits, particularly at the top of a cluster, ripen later, or ripening is more uneven, perhaps with a few more spots. The top of the plant could also turn a little paler green. These are all symptoms that can be caused by many factors, but they can also indicate the presence of ToBRFV.

The problem is that, in some cases, the virus causes no symptoms on the plant and only manifests itself on the fruit. This seems to occur especially in older crops, where virtually no symptoms are observed, but the virus is present. This increases the risk of a missed infection spreading to the next crop cycle.

It is therefore very important to carry out another, more thorough check. The final step in determining whether ToBRFV is present is to carry out a test.

 Tomato brown rugose fruit virus | Cornell Vegetables: Tomato brown rugose fruit virus | Cornell Vegetables

“A simple and effective method of testing for the presence of ToBRFV is to take a sample from the calyx of the fruit,” explains Leonie Hogendonk, De Ruiter development manager.

Test
A laboratory or rapid test may indicate the presence of infection. In both cases, care should be taken to collect several parts of the plant, such as the calyx and actively growing shoots, in a single sample, as the virus may not be present in all parts of the plant. If the first sample does not confirm the visual diagnosis, feel free to produce another sample from a second plant or combine several plants into a single sample.

Diagnosis of drainage water is also a good way of detecting infection at an early stage. Belgian growers have analyzed this water in the laboratory, and, in some cases, a viral infection can be detected up to 10 weeks before the appearance of visual symptoms.

Caution is key when testing early in the season after a previous infection, as it is possible that RNA from the previous season’s dead virus may be detected. However, if the amount of virus increases, it is clear that it is a live virus developing in the plants.

Virus detection should be limited to a certain block or section of the greenhouse, and such early detection allows further action to be taken, thus reducing the spread of the virus within the greenhouse or nursery.

 Figure 1. The virus is not uniformly distributed throughout the plant. A virus penetrates somewhere in the plant and then moves with the phloem towards the roots. Almost at the same time, it also moves to the upper, young, and growing part of the plant, and it can take some time for the rest of the plant to become infected.

Entry point of the virus in the greenhouse
When the first plants are detected, the next question is why the infection has occurred there. In practice, it is not always possible to answer this question. The virus is invisible, and even with good prevention and hygiene measures, low levels of the virus can be introduced at any given time. The location of the virus is not necessarily the entry point.

The virus can enter via people, equipment, or animals. It is not yet known how long it takes for the virus to infect the crop from the vector (what carries the virus), and this can range from 10 minutes to a day or more. This means that the virus can appear for the first time in the middle of the greenhouse, even if it has been introduced elsewhere. The virus also needs a plant that is sufficiently sensitive to allow infection.

All these unknown factors make it difficult to trace the initial point of entry. It is therefore important to maintain high levels of hygiene in greenhouses and crops from the outset and throughout the growing season.

Set-back from infection date
In some experiments, virus symptoms appear in young plants after only 10 days. However, in older plants, no clear symptoms may be observed for months, sometimes even until the end of cultivation. Finding that first plant is a major challenge. It is very likely that the first infected plant is one of the neighboring plants and, by the time the symptoms are discovered, the infection may involve 10 to 20 plants in total.

Good screening to find the virus as early as possible and good hygiene to reduce the spread of the virus is essential to keep as many plants healthy as possible until the end of the growing cycle.

For more information: vegetables.bayer.com/frPublication date: Tue 9 Apr 20

Ghana: World Bank loan to rehabilitate plantations destroyed by the cocoa swollen shoot virus


Ghana to expand cocoa rehabilitation with $200m World Bank loan

 20th Feb 2024    |     Source: Graphic Online

Ghana Cocoa

Ghana’s COCOBOD will use part of a $200 million World Bank loan to rehabilitate plantations destroyed by the cocoa swollen shoot virus, which causes drops in yields and kills trees, the regulator’s deputy Chief Executive in charge of operations said on Thursday, February 15, 2024.

 The disease has wiped off about 500,000 hectares of farmlands and reduced cocoa output from the West African nation, the world’s second biggest cocoa producer after neighbour Ivory Coast.

Ghana’s output declined to 600,000 metric tons last year after peaking at 1.048 million tons in the 2020/21 season, as the cocoa swollen shoot virus, aging plantations, illegal mining and smuggling took a toll on the sector.

A total of $132.8 million of the loan secured by the government last year and the counterpart funding will finance Cocobod’s rehabilitation of farms and help to enhance knowledge on the virus strains, a project information document showed.

“The rehabilitation will take a minimum of five years to start getting economic production,” Cocobod’s Emmanuel Opoku told Reuters, adding that efforts had been hampered by the country’s economic crisis and the board’s limited funds.

The board will take over disease-infested farms, cut and replace sick cocoa trees, aiding growth to a fruiting stage before handing them back to farmers.

In 2018, Cocobod used part of a $600 million Africa Development Bank (AfDB) loan to rehabilitate aging plantations and those affected by the disease.

But the programme, originally meant to cover 156,000 hectares of plantations, was caught up in Ghana’s worst economic crisis in a generation during which inflation spiralled and the cedi currency depreciated sharply, Opoku said.

He said the AfDB facility benefited more than 88,000 hectares of farmlands, of which 40,000 hectares were ready to be given back to farmers in “the coming days”.

Alhassan Bukari, president of the country’s Cocoa, Coffee and Sheanut Farmers’ Association, told Reuters that rehabilitation efforts needed to be aggressive as many farmers were affected.

Ghana’s graded and sealed cocoa arrivals fell by 35% between the start of this season on Sept. 1 and Jan. 31 this year due to the intensity of the seasonal dry Harmattan wind and what Cocobod described as production.