Archive for the ‘Diagnostics’ Category

New app identifies rice disease at early stages

by David Bradley, Inderscience

rice plant
Credit: Unsplash/CC0 Public Domain

Rice is one of the most important food crops for billions of people but the plants are susceptible to a wide variety of diseases that are not always easy to identify in the field. New work in the International Journal of Engineering Systems Modelling and Simulation has investigated whether an application based on a convolution neural network algorithm could be used to quickly and effectively determine what is afflicting a crop, especially in the early stages when signs and symptoms may well be ambiguous.

Manoj Agrawal and Shweta Agrawal of Sage University in Indore, Madhya Pradesh, suggest that an automated method for rice disease identification is much needed. They have now trained various machine learning tools with more than 4,000 images of healthy and diseased rice and tested them against disease data from different sources. They demonstrated that the ResNet50 architecture offers the greatest accuracy at 97.5%.

The system can determine from a photograph of a sample of the crop whether or not it is diseased and if so, can then identify which of the following common diseases that affect rice the plant has: Leaf Blast, Brown Spot, Sheath Blight, Leaf Scald, Bacterial Leaf Blight, Rice Blast, Neck Blast, False Smut, Tungro, Stem Borer, Hispa, and Sheath Rot.

Overall, the team’s approach is 98.2% accurate on independent test images. Such accuracy is sufficient to guide farmers to make an appropriate response to a given infection in their crop and thus save both their crop and their resources rather than wasting produce or money on ineffective treatments.

The team emphasizes that the system works well irrespective of the lighting conditions when the photograph is taken or the background in the photograph. They add that accuracy might still be improved by adding more images to the training dataset to help the application make predictions from photos taken in disparate conditions.

More information: Shweta Agrawal et al, Rice plant diseases detection using convolutional neural networks, International Journal of Engineering Systems Modelling and Simulation (2022). DOI: 10.1504/IJESMS.2022.10044308

Provided by Inderscience 

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The correct identification of insect pests and their natural enemies is critical for developing sound and sustainable pest management strategies: this is particularly so for rice. In the 1960’s, a comprehensive rice insect pest and natural enemy collection was established at the International Rice Research Institute (IRRI) in the Philippines, with the aim of helping those in national rice research programs to identify rice arthropods. 

A similar project was begun in West Africa in 1990, establishing a rice insect and natural enemy collection at WARDA (West African Rice Development Association), which subsequently became AfricaRice.

Associated with both of these collections, dichotomous keys were developed and published in the following books on rice arthropods:
Biology and Management of Rice Insects,
edited by E. A. Heinrichs (1994) and published by IRRI, and 
Rice Feeding Insects and Selected Natural Enemies in West Africa, authored by E. A. Heinrichs and Alberto Barrion (2002).

While the printed versions of both books have been out-of-print for several years, a recent upgrade of the Lucid software program, which makes it possible to convert paper-based, dichotomous keys to interactive pathway keys, means that both keys are now freely available to use on the Internet, courtesy of IAPPS (International Association for the Plant Protection Scientists) at: http://www.plantprotection.org

 Adding arthropod images: Note that the IRRI key now includes a large number of color images of important insect pests and natural enemies. E.A. Heinrichs (eheinrichs2@unl.edu) would appreciate any good resolution images that colleagues would be willing to submit for adding to the key – with due acknowledgement

IRRI arthropod key

West African arthropod key

© Copyright International Association for the Plant Protection Sciences. All rights reserved 2022.

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Genome studies uncover a new branch in fungal evolution

New research helps to resolve evolutionary origins of the ‘platypus of fungi’

Date:November 23, 2022Source:University of AlbertaSummary:About 600 seemingly disparate fungi that had resisted categorization have been shown to have a common ancestor, according to a a research team that used genome sequencing to give these peculiar creatures a new classification home.Share:


About 600 seemingly disparate fungi that never quite found a fit along the fungal family tree have been shown to have a common ancestor, according to a University of Alberta-led research team that used genome sequencing to give these peculiar creatures their own classification home.

“They don’t have any particular feature that you can see with the naked eye where you can say they belong to the same group. But when you go to the genome, suddenly this emerges,” says Toby Spribille, principal investigator on the project and associate professor in the Department of Biological Sciences.

“I like to think of these as the platypus and echidna of the fungal world.”

Spribille, Canada Research Chair in Symbiosis, is referring to Australia’s famed Linnaean classification system-defying monotremes — which produce milk and have nipples, but lay eggs — that were the source of debate as to whether they were even real.

“Though nobody thought our fungi were fake, it’s similar because they all look totally different.”

Using DNA-based dating techniques, the team found that this new class of fungi, called Lichinomycetes, descended from a single origin 300 million years ago, or 240 million years before the extinction of dinosaurs.

David Díaz-Escandón, who performed the research as part of his PhD thesis, explains that these “oddball” fungi were previously sprinkled across seven different classes — a high-level grouping that in animals would be equivalent to the groups called mammals or reptiles.

Working with a team of researchers from seven countries to get material from the fungi, he sequenced 30 genomes and found that all classes but one descended from a single origin.

“They were classified, but they were classified into such different parts of the fungal side of the tree of life that people never suspected they were related to each other,” says Díaz-Escandón.

These fungi include forms as varied as earth tongues — eerie tongue-shaped fungi that shoot up vertically out of the ground — beetle gut microbes, and a fungus found in tree sap in northern Alberta. They also include some unusual lichens that survive in extreme habitats such as South America’s Atacama Desert, the driest non-polar desert in the world.

“What is really fascinating is that despite these fungi looking so different, they have a lot in common at the level of their genomes,” says Spribille. “Nobody saw this coming.”

Based on their genomes, which are small compared with those of other fungi, the team predicts that this group of fungi depend on other organisms for life.

“Their small genomes mean this class of fungi have lost much of their ability to integrate some complex carbohydrates,” said Spribille. “When we go back to look at each of these fungi, suddenly we see all of them are in a kind of symbiosis.”

He notes the new research will be important to the broader study of fungal evolution, specifically how fungi inherit important biotechnological features such as enzymes that break down plant matter.

The new group also could be a source of new information about past fungal extinctions.

“We think it’s likely that the diversity we see today is just the tip of the iceberg that survived. And we don’t have that many examples of this kind of thing in fungi.”

The research appears online in the journal Current Biology.

Story Source:

Materials provided by University of Alberta. Original written by Michael Brown. Note: Content may be edited for style and length.

Journal Reference:

  1. David Díaz-Escandón, Gulnara Tagirdzhanova, Dan Vanderpool, Carmen C.G. Allen, André Aptroot, Oluna Češka, David L. Hawksworth, Alejandro Huereca, Kerry Knudsen, Jana Kocourková, Robert Lücking, Philipp Resl, Toby Spribille. Genome-level analyses resolve an ancient lineage of symbiotic ascomycetesCurrent Biology, 2022; DOI: 10.1016/j.cub.2022.11.014

Cite This Page:

University of Alberta. “Genome studies uncover a new branch in fungal evolution: New research helps to resolve evolutionary origins of the ‘platypus of fungi’.” ScienceDaily. ScienceDaily, 23 November 2022. <www.sciencedaily.com/releases/2022/11/221123125118.htm>.

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Insect DNA barcoding results delight UniSC entomologist

  • Education
  • 14 Nov 2022 2:18 pm AEST

University of the Sunshine Coast

Insect DNA barcoding results to be released publicly today show exciting progress in the tri-state Insect Investigators project, coordinated across regional Queensland by a UniSC entomologist.

“I’m absolutely blown away by the results to date, and by the enthusiasm of school students and teachers to engage in insect research,” said insect ecology researcher Dr Andy Howe of the University of the Sunshine Coast’s Forest Research Institute.

Seventeen Queensland schools (listed below) are among 50 schools involved in the ongoing citizen science project, led by the South Australian Museum.

Only about 30 percent of the estimated 225,000 insect species in Australia are formally named and described.

Thousands of new insects have now been successfully recorded in the project, which connects regional and remote school students with researchers to learn about Australia’s rich biodiversity.

Beerwah State High School was among those that set a Malaise trap on their grounds in March to collect and monitor local insects over a four-week period. It was one of many that Dr Howe has visited across the state to provide updates on insect species through the taxonomic process.

“It makes so much sense to engage our schools in research on insect taxonomy; schools are located throughout many environment types, which means they can collect a huge diversity of insects, simultaneously,” Dr Howe said.

“We can then use the data to not only name undescribed species, but importantly contribute to distribution maps of thousands of insects and spiders, which contributes to managing the environment sustainably.”

Overarching project leader Dr Erinn Fagan-Jeffries said more than 14,000 insect specimens were selected to be DNA barcoded by the Centre for Biodiversity Genomics at The University of Guelph in Canada, and today the DNA barcoding results will be released.

Dr Fagan-Jeffries said DNA barcoding involved sequencing a small section of the genome and using the variation among these barcodes to discriminate species.

“While the gold standard is always going to be identifying and describing insects using DNA data in combination with their physical characteristics, the DNA barcodes provide a fast and cost-effective way of shining a light on the remarkable diversity of insects in Australia that we know so little about,” she said.

Through Insect Investigators, participating schools have added more than 12,500 new DNA barcodes to the international online repository, the Barcode of Life Database.

The variation among these barcodes suggests that there are more than 5,000 different species present among the specimens, and just over 3,000 of those are brand new records on the database.

Each of these DNA barcodes relates back to an individual insect specimen that will be deposited in the entomology collections at the South Australian Museum, Queensland Museum and the Western Australian Museum.

Taxonomists from around Australia will then be able to examine and determine if they represent undescribed species.

“It is highly likely that all contributing schools have found species new to Western science which is really exciting, but how many of these species we are actually able to describe is dependent on the resources and support available for taxonomy,” said Dr Fagan-Jeffries.

“Despite there currently being many more insect groups than taxonomists, we are hopeful that the taxonomists will be able to spot some new species that can be described, and in those cases, the students will then be invited to name the unique species that they have discovered.”

Participating Queensland schools:

  • ​Back Plains State School
  • ​Beerwah State High School
  • ​Belgian Gardens State School
  • ​Blackall State School
  • ​Cameron Downs State School
  • ​Columba Catholic College
  • ​Gin Gin State High School
  • ​Glenden State School
  • ​Kogan State School
  • ​Mornington Island State School
  • ​Mount Molloy State School
  • ​Prospect Creek State School
  • ​Springsure State School
  • ​St Patrick’s Catholic School, Winton
  • ​Tamborine Mountain State School
  • ​Yeppoon State High School
  • ​Yeronga State School

Dr Howe, whose PhD in 2016 examined an exotic ladybird in Denmark, said students enjoyed the information in his talks, designed to be entertaining as well as inspiring.

He said increasing Australia’s knowledge of its insect species could have benefits ranging from better management of the environment and effects of climate change and natural disasters to controlling pests and developing new medicines.

The DNA barcoding results will be released on the website https://insectinvestigators.com.au.

Insect Investigators received grant funding from the Australian Government, is led by the South Australian Museum, and involves 17 partner organisations.

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Number I                                                                                                                     January, 2023


The correct identification of insect pests and their natural enemies is critical for developing sound and sustainable pest management strategies. As agriculture intensified and insect pests became more problematic, identification of major insect pests and their natural enemies became increasingly relevant when designing appropriate pest management strategies, especially for rice. 

Appointed as the first entomologist at the International Rice Research Institute (IRRI) based in the Philippines, Dr. Mano D. Pathak, established a comprehensive rice insect pest and natural enemy collection in the early 1960s. The aim was to support national rice research programs identify specimens in their own rice arthropod collections. Subsequently, to support this objective, a dichotomous key to over 862 species was published in the chapter Taxonomy of Rice Insect Pests and their Arthropod Parasites and Predators, authored by insect and spider taxonomist, Alberto T. Barrion, with James A. Litsinger, in the book, Biology and Management of Rice Insects,edited by E. A. Heinrichs and published by IRRI in 1994.

In the 1990s, a similar collection program was begun to establish a rice insect and natural enemy collection at WARDA (West African Rice Development Association), now AfricaRice. Specimens of major insect pests and natural enemies found in West African rice were identified by Dr Barrion, who then created an illustrated, dichotomous identification key which was published in the book, Rice Feeding Insects and Selected Natural Enemies in West Africa, authored by E. A. Heinrichs and Alberto Barrion (2002).

Since the printed versions of both books have been out-of-print for several years, a recent upgrade of the Lucid software program https://www.lucidcentral.org provided the possibility of creating interactive, digital versions of both keys. Initially developed for creating matrix identification keys, the Lucid builder now enables paper-based dichotomous keys to be converted and “published” as online, interactive pathway keys. Courtesy of IAPPS, the IRRI and West African keys are now freely available online. You can access them here. Please note that we will soon add 450 photos of rice insect pests and their natural enemies to the Taxonomy of Rice Insect Pests and their Arthropod Parasites and Predators key. For further information, please email support@plantprotection.org

Prof. Geoff Norton

IAPPS President

E-mail: geoffn86@gmail.com

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“The conk (above) is the only distinguishing symptom of the disease and indicates a palm tree is not recoverable,” says Braham Dhillon. (Credit: Lourdes Mederos/U. Florida)


You are free to share this article under the Attribution 4.0 International license.




A DNA-based diagnostic method confirms a wood-decaying fungus in palms months before the symptoms of Ganoderma butt rot appear.

More than 65 species of palm trees in the United States are vulnerable to a wood-decaying fungus that can damage or destroy palms.

A fungus, Ganoderma zonatum, causes the lethal disease known as Ganoderma butt rot of palms. Its mysterious nature has stunted research for decades, making early detection of the silent killer impossible until now.

As reported in the journal Plant Disease, previously compiled sequence data from genetically validated North American Ganoderma species were used to develop the tool. The result is a diagnostic protocol that can detect the genetic make-up of the lethal Ganoderma zonatum pathogen.

“We were able to find the unique genetic markers exclusive to Ganoderma zonatum,” says Braham Dhillon, a molecular plant pathologist at the University of Florida Institute of Food and Agricultural Sciences (UF/IFAS) Fort Lauderdale Research and Education Center.

“This has great implications for developing management methods for the disease from this point forward. It saves time and money and opens the doors for additional research on understanding how this pathogen survives and spreads in the landscape.”

A tree specialist can collect samples as wood shavings from the trunk and submit them to a lab for diagnosis with the new procedure. Results are available in a week.

The detection method can be readily adopted into protocols of plant diagnostic facilities since the technology and equipment are routinely available without the need for additional instrumentation or chemicals.

“Early detection of the fungus, or any disease, is a crucial step towards building and implementing better disease management strategies and mitigating potential risks from palm deaths and destruction of property due to palm tree decay,” says Dhillon.

Palm trees of all varieties grace the lands of homeowners, public parks, business complexes, and roadways. The fungus, common in homeowner and public spaces, is a slow-growing pathogen, occupies the trunk, and degrades the vascular water-conducting tissue. This produces initial symptoms of wilting and dying palm fronds in the lower part of the canopy. These symptoms are also associated with other diseases like Fusarium wilt and lethal bronzing, which makes it difficult to properly diagnose.

In the later stages of the disease, a fruiting body called a conk, or basiodiomata, appears at the lower surface of the trunk and confirms the presence of Ganoderma butt rot.

“The conk is the only distinguishing symptom of the disease and indicates a palm tree is not recoverable,” says Dhillon. “The conk produces millions of spores that can travel by wind contributing to disease spread.”

As the fungus moves up the trunk, it compromises the structural integrity of the palm, says Dhillon. “In later stages of the disease, the decayed palm trunk is susceptible to breaking and becomes a hazard to properties, pedestrians, and vehicular traffic. Depending on the girth of the trunk, the decay process can take up several months to a year.”

Until now, the appearance of the conk, or an invasive dissection of the infected trunk and culturing of the fungus, are the only ways to confirm the diagnosis of the lethal disease, explains Dhillon.

For the study, scientists sequenced a variety of samples, including 24 cultures from 15 Ganoderma species collected from a previous study and archived at the Center for Forest Mycology Research Culture Collection and Herbarium, US Department of Agriculture Forest Service.

They also collected healthy and naturally infected sawdust palm samples from eight palm species. Infected palms in the study were categorized for one of two symptoms: wilted palm fronds or presence of a conk. Other samples included conks, infected tissues, soil, and DNA from palm-infected lethal yellowing and lethal bronzing specimens. Researchers validated the method on DNA isolated from 60 samples.

Source: University of Florida

Original Study DOI: 10.1094/PDIS-12-21-2837-RE

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June 17, 2022 

Ditya Lamichhaney 

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Plantwise: helping female farmers in Nepal access advisory services 

In almost all regions of Nepal, women have a greater involvement than men in farming activities. The World Bank estimates that 74% of Nepalese women work in agriculture, yet they struggle to have equal access to agricultural resources. 

Female tomato farmer in Nepal. Image CABI

A new study highlights gender integration in the Plantwise programme and identifies the strengths and limitations in Nepal. It focuses on three districts that have implemented activities to improve women’s participation in agricultural advisory services.

Lesson on improving access to plant clinics

In Nepal, farming tasks are often divided by gender, with men mostly involved in the hard manual work such as ploughing and operating heavy agricultural machinery. However, due to male migration, this division of labour is changing. Male migration has led to some women undertaking all farming activities, from planting to harvesting and marketing. As a result, women’s workloads are increasing. More of the farming activities, coupled with unpaid care and domestic work, leave little time for female farmers to participate in agricultural advisory services. 

The Plantwise programme has adopted several strategies to help female farmers to access extension services. One such approach was to consult with women farmers on the timings of plant clinic. As a result, Plantwise clinic sessions were held late morning or early afternoon when female farmers were more likely to attend. 

Plant clinic in Nepal. Image CABI

Socio-cultural barriers in Nepal

In places where socio-cultural norms discouraged women from consulting male plant doctors, the programme has worked hard to make sure women plant doctors are available either at a clinic or through a phone call or individual visit to farmers. 

Nepalese Plantwise programme staff observed women farmers were more likely to consult female plant doctors than males. Possible reasons include women feeling more comfortable with or trusting female plant doctors as a result of socio-cultural norms or due to curiosity about female plant doctors.

Lessons on the remote provision of plant health advisory services 

Covid-19 curtailed plant clinic operations. However, Nepalese farmers still needed information and advice. During the pandemic plant doctors used online platforms, such as Zoom and WhatsApp, to conduct almost all activities. 

The study found that while virtual advisory activities were generally a positive experience, there were also challenges. These included limited access to devices and an internet connection and a lack of knowledge and experience using social media. Planning and organizing activities remotely were also difficult and time-consuming. 

Women farmers especially have poor internet facilities and limited knowledge or use of social media. The experience showed the need for improving digital literacy among the farming community, especially women farmers.

Plant clinic in Nepal. Image CABI

Lessons on uptake of plant doctor advice in Nepal

Plant clinics provide farmers with advice such as crop pest diagnosis and identification and diseases and management recommendations. 

Although farmer feedback on plant clinics was generally positive, there were challenges to implementing some of the plant doctor’s advice. For example, input dealers are not always local to farmers, making it hard to purchase the recommended pest management products on time.

Access to inputs in Nepal

Female farmers, in particular, face challenges accessing inputs. Socio-cultural restrictions may mean they cannot visit input dealers to buy recommended products, while financial limitations prevent them from purchasing and using them. Furthermore, female farmers have limited decision-making powers and say in household finances allocation, including what inputs and technologies to buy.

In response to these challenges, Plantwise has aimed to develop crop pest and disease management recommendations based on integrated pest management practices, with chemical recommendations as a final option. The data showed that most recommendations made to farmers were for locally available solutions and cultural practices, which the farmer can implement on-farm. 

Recommendations for the gender-sensitive advisory services

The study recommends the following actions to sustain gender-sensitive plant health advisory services in Nepal. 

• Training increasing numbers of female plant doctors and facilitators, equipping them with the IPM solutions at hand. 

• Providing female plant doctors with some mobilization funds to empower them with digital tools. 

• Collaborating with local government to conduct gender-inclusive awareness programmes. 

• Educating farmers’ groups at various project locations on gender equality and social inclusion. 

• Involvement of an equal number of women in agriculture decision-making platforms.

Further reading

Find out more about CABI’s new global PlantwisePlus Programme

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

NepalPlantwisefemale farmersgender

Agriculture and International Development

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