Archive for the ‘Pest diagnostics’ Category

Growers can use a test kit to detect ToBRFV before plants even shows signs

Knowing, for sure, that your crop is infected before the plants show signs. Growers have wanted that since the Tomato brown rugose fruit virus (TOBRFV) reared its ugly head. And preferably quickly, too. This summer, the Dutch company Spark Radar launched a grower test kit for that. Growers can use it to detect, with high reliability and within three hours, whether their crop is contaminated.

According to Spark Rader’s co-founder, Rogier van der Voort, its virus test’s reliability and sensitivity can well well-compared to that of a PCR test. “However, you don’t have to send our test’s samples to a service lab. That saves considerable time – crucial when detecting and containing a possible outbreak.”

When the COVID-19 pandemic broke out, he and Bas Rutjens, who founded Spark Genetics, put their heads together. That company has been supporting breeding companies with genetics issues since 2018. “When the pandemic began, the laboratory had to partially close. We started asking ourselves how we could offer the market something that was much needed. That had to be a reliable, sensitive pathogen test that anyone could perform on-site,” says Rogier.

Testing before symptoms show
The test works pre-symptomatically, meaning you can test for the virus’ presence early. Rogier draws a parallel with COVID-19. “You can now do a self-test for that. But, that’s an antigen test you use when you’re already showing symptoms.” In the case of the coronavirus, for example, a runny nose.

One of the ToBRFV’s symptoms is spots on the fruit or signs on leaves. “Antigen tests, however, aren’t as reliable as PCR tests, and their lower sensitivity means they don’t work pre-symptomatically. You can also only test two to three plants at once,” Rogier explains.

Leaf material
Currently, growers can test 60 plants at a time using Spark Radar test kits. Testing can be done in three ways. “We started with leaf samples. A piece of leaf the size of a fingernail is enough. Growers collect the leaf sample in a bag we provide, and once collected, testing can begin.”

The test kits include the test material and hardware so that growers can run the tests themselves. “We’ve developed equipment to read the tests. We use magnetic and sensing racks for that. The magnetic rack lets us extract the virus from the sample, which helps ensure our tests’ high sensitivity,” Van der Voort continues.

A part of the test kit. The white container is lined with magnets. Detection is done using a different rack.

Surface and water tests
Growers, however, prefer to test more than just leaf material. “There’s plenty of market demand for swab tests too, which allows for testing for the presence of the virus on things like carts or blades. It’s like the cotton swab you use in your throat and nose when doing a COVID-19 self-test.”

They developed a third testing protocol for water. “Growers can test for the ToBRFV in, say, their drainage system,” Rogier elaborates. These last two testing methods are currently in their final market introduction stages. “We’re fully in the testing phase for these new applications and are using trial feedback to make the swab and water test kits are durable as possible.” The company plans to market these two testing kits in December commercially.

Spark Radar also wants to start offering the kits internationally, and this fledgling company has taken the first steps toward that. “A large North American party has been using our test for several months. They want to deploy it more widely during the next harvest period. We have a commitment from a Dutch party with overseas farms too. They want to use our tests outside the Netherlands,” states Rogier.

A virus test must be reliable. The test kits, thus, include a clear manual (you can also watch an online video). For now, it is in Dutch and English, but the company wants to include other languages as well. “We’re currently focusing on producing the tests. We’ve gained new clients after presenting the test at a recent event.”

Testing for other pathogens
ToBRFV is undoubtedly receiving global attention. That begs the question: Does Spark Radar have the clout to help growers combat this virus? Spark Radar’s co-founder thinks so. “We were recently chosen to participate in the Foodvalley and government investment fund, InvestNL’s Fast Lane program. We had to give an answer to what’s needed to become even more influential, scale up and maintain our test’s current and projected speed.”

That speed does not only apply to the ToBRFV but to other plant viruses, bacteria, and fungi. Spark Radar is also working on a test kit for cucumber fur virus and Pepino mosaic virus in tomatoes. “Those will be similar tests to the ToBRFV ones,” concludes Rogier.

For more information:
Rogier van der Voort
Spark Radar
8 Padualaan
3584 CH, Utrecht, NL
Email: rogier@sparkgenetics.com 
Email: info@sparkradar.bio 
Website: www.sparkradar.bio

Publication date: Fri 25 Nov 2022

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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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Agdia launches rapid molecular test kit for tomato mottle mosaic virus

Agdia has launched a RNA-based assay, on their AmplifyRP XRT platform, for the detection of Tomato mottle mosaic virus (ToMMV). 

Global tomato and pepper production has been significantly disrupted in recent years by emerging pathogens. One such pathogen, Tomato brown rugose fruit virus (ToBRFV, Tobamovirus), is thought to have caused billions of dollars in damage to the tomato industry alone over the past few years. While advancements in breeding for pathogen resistance traits over the past two decades have largely protected tomato and pepper crop production from viral threats, ToBRFV was able to bypass resistance with devastating consequences. The virus continues to cause disruption of the global seed supply chain along with affecting yield and marketability of tomato fruit when not properly excluded from production facilities.

Much like ToBRFV, Tomato mottle mosaic virus is also able to break through well-established viral resistance traits, and thus represents yet another significant threat to tomato and pepper production worldwide.

Initially found in tomato crops in Mexico in 2013, Tomato mottle mosaic virus has since been detected in the United States, Brazil, Europe, Africa, Asia and Iran. Several other Tobamovirus-infected samples collected prior to 2013 which were previously attributed to Tobacco mosaic virus (TMV) or Tomato mosaic virus (ToMV) have since been distinguished as ToMMV infections via high-specificity molecular methods which were not previously available.

Symptoms caused by ToMMV infection include mottling, necrosis, flower abortion and leaf distortion. Much like other Tobamoviruses, ToMMV is highly transmissible via mechanical means (pruning, harvesting, etc.) and may also be present in seed, although further studies are needed to demonstrate whether vertical transmission occurs at any significant level.

Agdia’s AmplifyRP XRT for ToMMV has been validated for use with tomato and pepper seeds and leaf in addition to other secondary matrixes such as peas (Pisum sativum) and petunia. As a rapid, field-deployable molecular method requiring far less training than traditional PCR methods, this assay provides users with greater flexibility to deploy detection capabilities where they need it, when they need it. Use cases for this assay include, but are not limited to:

  • In-field monitoring at remote production sites as a stand-alone assay.
  • Screening incoming plantlets & monitoring production crops in commercial greenhouses
  • Laboratory-based molecular diagnosis with crude or purified extracts with faster time-to-result than traditional PCR or qPCR methods. This assay can be used with Agdia’s AmpliFire isothermal fluorometer or with most real-time PCR machines.

Agdia’s AmplifyRP XRT for ToMMV is highly specific to ToMMV and has been proven through experimentation and in-silico analysis to detect isolates from around the world. No cross-reactivity was observed with high titer samples from other Tobamoviruses, including Cucumber green mottle mosaic virus (CGMMV), Kyuri green mottle mosaic virus (KGMMV), Pepper mild mottle virus (PMMoV), Tobacco mosaic virus (TMV), Tomato brown rugose fruit virus (ToBRFV), Tomato mosaic virus (ToMV), Tobacco mild green mosaic virus (TMGMV), Zucchini Green Mottle Mosaic Virus (ZGMMV) and more.

For more information:
52642 County Road 1
Elkhart, IN 46514
phone 1-574-264-2615
fax 1-574-264-2153

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Sky Islands: Isolated Mountaintops Teem With Unique Insect Communities


For a study of the communities of parasitic wasps on mountains in the Interior Highlands of Arkansas, one of the sites chosen was Mount Magazine State Park in Arkansas, which rises 709 meters (2,326 feet) above sea level. With cooler, wetter climates than lowlands nearby, such each feature their own communities of parasitic wasps—and likely other insects—that differ from the insect fauna found on other mountains and in the surrounding valleys, according to a new study published in August in Environmental Entomology. (Photo courtesy of Allison Monroe)

By Ed Ricciuti

Ed Ricciuti

It’s not quite Sir Arthur Conan-Doyle’s Lost World of dinosaurs, but the insect life found by scientists atop so-called “sky islands” in Arkansas ranks as truly unique.

“Sky island” is a term popularized in the 1960s to describe isolated mountains with environments markedly different than that of surrounding lowlands. Conan-Doyle prefigured such environments in his story about an expedition that explored a plateau rising above jungle, where prehistoric dinosaurs, reptiles and “ape men” had survived the ages.

Although not as dramatic as dinosaurs, isolated endemic populations of animals of any size excite scientists. According to a study published in August in Environmental Entomology, such distinct assemblages of insects in the order Hymenoptera (sawflies, bees, wasps, and ants) live atop uplands in Oklahoma, Arkansas, Missouri, and Illinois called the Interior Highlands.

The study, by student researchers at Hendrix College in Conway, Arkansas, focused on parasitic wasps inhabiting three mountains, but the results can be extrapolated to other sky islands in the region and their insects in general, the researchers say.

“Given that each sky island in our study showed unique community characteristics of Hymenoptera, it is reasonable to predict that other insects follow the same pattern,” the authors write. Mountains studied were Petit Jean Mountain at 253 meters (830 feet) in elevation, Mount Magazine at 709 meters (2,326 feet) and Rich Mountain at 747 meters (2,451 feet).

field site

Parasitic Hymenoptera are a multitudinous group, with 50,000 or so identified species and perhaps millions in all. Typically, they parasitize other insects by laying their eggs in host eggs, larvae, or pupae. They are of immense ecological importance because they are fine-tuned to specific hosts, including many pest species, which they can regulate, like natural pest control managers. “We chose parasitic Hymenoptera as our focal group because they are considered bioindicators of broader diversity patterns, especially those of other insects,” the authors write.

The Interior Highlands, centered in Missouri and Arkansas and including the Ouachita Mountains and Ozark Plateau, were chosen as a study site because they have been above sea level for 320 million years, likely serving as a refuge for ecological communities avoiding the impact of the Pleistocene glaciers. The region is the only major mountainous area between the Appalachians and the Rockies, covering much more area than the Black Hills of South Dakota. Typical of the Interior Highlands, Mount Magazine is 10 degrees Fahrenheit cooler than normal temperatures in the landscape down below and wet, with an annual rainfall of 54 inches. Crowned with upland hardwood and upland pine-hardwood forests, these mountains rise from grasslands, with vegetation ranging from tallgrass prairie to lowland pine-hardwood and bottomland hardwood forests.

Much of the area where the research was conducted lies in state and federal lands. Sweating in the hot summer sun, the research team trekked along hiking trails from grasslands into woodlands. They set up traps, then collected insects from them.

“Though evidence is accumulating that the Interior Highlands host unique species relative to other areas of the North American continent, there is less known about how mountaintops within the region compare in terms of biodiversity,” the researchers write. “We used parasitic Hymenoptera to explore biodiversity patterns across high elevation areas in Arkansas to determine whether these patterns are similar to those exhibited by other sky island regions.”

malaise trap
research team

Each mountaintop had its distinct community of parasitoid species, indicating that the same applies to Hymenoptera in general and even to other groups of insects. On a given mountaintop, communities differed stratigraphically, with those on the ground distinct from those in the forest canopy.

The results of the study suggest the need for additional research. “Our study suggests that these highland areas are important regions of North American biodiversity and that they should be evaluated individually for conservation efforts in order to preserve their distinctive community structure,” the authors write.

Elaborating on the study, lead author Allison Monroe, says, “This study is important for a variety of reasons. Parasitic wasps are deeply important to our environment but are often overlooked if not deeply hated.”

Monroe, now a Ph.D. candidate at the Oregon State University College of Forestry, says, “Arkansas is an incredibly biodiverse state with high rates of agricultural production, yet little research exists on insect biodiversity trends and their applied impacts on diverse land management strategies within this system. We hope that this paper brings to light the extraordinary diversity housed in Arkansas, the importance of insect biodiversity more broadly, and the significance of parasites in our pursuits of nature conservation.”

Read More

Biodiversity of Parasitic Hymenoptera Across Sky Islands of Arkansas, United States

Environmental Entomology

Ed Ricciuti is a journalist, author, and naturalist who has been writing for more than a half century. His latest book is called Bears in the Backyard: Big Animals, Sprawling Suburbs, and the New Urban Jungle (Countryman Press, June 2014). His assignments have taken him around the world. He specializes in nature, science, conservation issues, and law enforcement. A former curator at the New York Zoological Society, and now at the Wildlife Conservation Society, he may be the only man ever bitten by a coatimundi on Manhattan’s 57th Street.

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Bringing tech to crop disease identification

Bringing tech to crop disease identification

Courtesy of IntelinairSmall dot of tar spot on a corn plant

HARD TO SPOT: Catching a crop disease like tar spot early helps control it before it does too much damage. Disease Alert from Intelinair adds thermal imaging to conventional image capture from airplanes, and when combined with machine learning, the system can spot disease areas in fields (like the small dot on this corn plant) and help target spraying and weed control.

The AgMRI platform from Intelinair can help provide an early-warning system for spotting crop diseases.

Willie Vogt | Jul 06, 2022


Illinois and Indiana farmers will be on the cutting edge of a new technology from Intelinair that can help spot crop diseases early. The company’s AgMRI platform offers Disease Alert, which provides a kind of early warning of trouble in your fields.

The program, which is starting in those two states this year, will expand over time, according to Kevin Krieg, director of product marketing for Intelinair. He shares with Farm Progress about how this disease alert system works and what it brings for farmers who can use it in 2022.

“AgMRI works at the high level of taking in imagery, weather data and machine data together,” he says. The high-resolution remote imagery feeds through a computer system, and machine learning works to understand patterns.

To help detect disease, a thermal camera is used with other imagery and machine learning. “We have this relative temperature detection even when flying over the fields,” he says. “We’re looking at where there’s a good, healthy crop in the field. But if the temperature is higher than the relative temperature of other plants within the field, that’s a sign of trouble,” he says.

The thermal properties show a specific pattern if crop disease is present. “Our engineers built analytics around a lot of different factors, but those are at the high level of an increased temperature with a unique pattern as it’s impacting the plants,” Krieg says. Almost like a fever in humans, those warmer plants are a warning that disease is present, he adds.


Airplanes at work

Intelinair is using fixed-wing aircraft to fly fields and gather data. The company is primarily in Illinois and Indiana, where it can put those thermal cameras to work. Combined with other imagery, the plant temperature tips off trouble.

As for moving beyond the two-state area? “So the challenge with this is that we need thermal information from a disease perspective,” Krieg says. And while Intelinair has looked at satellite imagery, the airplane-based approach has been most successful for now.

Going forward, he notes that the company is looking at how to bring that same value to other areas and expand it in the future.

Krieg says the system isn’t identifying the disease, but rather the potential for disease presence in a field when those temperature indicators rise. “We don’t know if it’s tar spot or any specific disease,” he notes. “Our whole thing is that we identify an area of the field that has the probability for some disease. Then you scout the field to figure out what it is.”

Tar spot is the attention-grabber right now, and early detection is key to getting control. However, Krieg notes in 2021 during tests, they found soybean rust, brown spot and other diseases. The key was identifying impacted fields earlier for more targeted scouting.

There’s even the potential for more “early warning” as planes fly an area, Krieg says. “We’re not just flying the customer’s field that has signed up for the service; we’re flying the complete area,” he notes. That means if they spot disease potential in a neighboring field, that can be a scouting advantage, too.

“If they’re seeing tar spot in other places or disease setting in, then [the retailer] can start looking at fields that are susceptible to that as well,” Krieg says. “So a neighboring field might have disease — that gives the retailer a cue that it is in the area and to be on heightened alert.”

The value of imagery and machine learning to recognize patterns in imagery can advance a range of crop management practices for disease identification. The more imagery captured and matched with ground truthing through scouting, the better these models will get.

For farmers outside the two-state area, the tech will head farther out as the company works to establish image and data capture systems. You can learn more about the system and what it brings to scouting by visiting intelinair.com.


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News reporting

‘Nose Knows Scouting’ uses trained dogs to sniff out Potato Virus Y

A North Dakota potato breeder brings in a speaker from Wyoming who has trained a dog to detect potato virus diseases using their nose.

A woman takes a black Labrador dog to smell bags of potato tubers on a driveway, as researchers look on.
Andrea Parish of Dayton, Wyoming, sniffs bags of potato seed tubers for disease in the North Dakota State University potato breeding program, as NDSU potato breeder Asunta “Susie” Thompson and technician Kelly Peppel look on. Photo taken May 17, 2022, at Fargo, North Dakota.

By Mikkel Pates

May 23, 2022 05:30 AM


 We are part of The Trust Project.

FARGO, N.D. — Good news: the newest high-tech tool for diagnosing crop disease is also man’s best friend — a friendly dog….

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Lucidcentral Identification and Diagnostic Tools   Lucid May 2022 Newsletter   Introduction   Last year we released a major Lucid v4 update that allows authors to build new dichotomous keys or to import existing paper-based keys and transform them to online, interactive keys.    A recent example of such a conversion concerns a series of keys to insects and spiders that can be found in rice in West Africa.   The original book in which these keys were published – E A Heinrichs and Alberto T Barrion (2004) Rice-feeding insects and selected natural enemies in West Africa: Biology, ecology, identification, has been out of print for a number of years.    Fortunately a digital copy was published online by the University of Nebraska – Lincoln, providing the digital text and figures for the conversion of these keys to  Lucid, and are now hosted on Lucidcentral.    A similar key to rice pests found in S.E. Asia is to be published shortly. This will be one of the largest dichotomous keys we’ve come across: 852 couplets and 1740 leads, covering 862 taxa!   It’s also pleasing to see how many new and diverse keys have just been released. This includes commercial timber identification, sawflies, tropical ferns and lycophytes, Calanoid Copepods, trees of the Diamantina located in Serra do Espinhaço, Brazil, a place recognized by UNESCO as a Biosphere Reserve, and finally, a key used by police forensic units for the identification of third instar larvae of 12 species of Calliphoridae.   We hope you enjoy reading our latest newsletter.   Regards,   The Lucid Team   Spotlight on Lucid keys supporting plant taxonomy at Missouri Botanical Garden While most Lucid identification keys aim to provide public access to taxonomic and diagnostic expertise (via online and mobile apps), there are situations where Lucid keys can be used to support the taxonomic process itself. This spotlight article illustrates how Lucid is being used by Dr Tom Croat at the Missouri Botanical Garden, St Louis, USA to support the taxonomic work of his team, as well as providing an online identification aid.  Tom Croat with 100,000th collection Anthurium centimillissimum photo by Dan Levin  Tom Croat with the 100,000th collection Anthurium centimillissimum photo by Dan Levin. For many years, Tom’s taxonomic work has focussed on the philodendron or aroid family (Araceae). The genera of this family are often large and morphologically challenging, particularly the genus Anthurium, possibly the world’s largest genus with over 3,000 species. As Tom puts it – “Araceae is a family with still thousands of undescribed species: the only way one can deal with such large groups is to use Lucid. Without Lucid, I could not deal with it, since there are now 1650 species in Lucid keys for Anthurium. We also have Lucid Keys for Adelonema, Dieffenbachia, Dracontium, Philodendron and Stenospermation. Current work is on constructing a key for Spathiphyllum”.  Over the years, Tom has collected more than 109,000 herbarium collections, more than 10,000 living plants, and maintains the world’s largest and most comprehensive collection of living aroid plants in the Garden’s greenhouses. Lucid matrix keys are initially used as a means of “cataloguing” new species that are introduced to the collection. The major taxonomic features of the living plants, as well as of dried herbarium specimens, are described in detail. The characters (more than 100 in all) are recorded into the existing Lucid Matrix, and new feature/states are added as necessary, together with their respective scores.    With the recent availability of the new dichotomous (pathway) key construction option, that has recently been upgraded and incorporated in the Lucid Builder software, Tom thinks there may be new opportunities here. “Having a Lucid dichotomous key would allow us to prepare keys to separate species in many groups that remain poorly known. While the Lucid matrix key enables us to select species that have already been incorporated into the key, a dichotomous key allows one to decide where a given species needs to be placed that is not already in the key.  Moreover, published revisions are expected to have dichotomous keys that are an integral part of the revision, so a Lucid Key, workable as it might be, will not serve that purpose. Thus, it is important that the Lucid Program should provide a means whereby a dichotomous key can be constructed from the existing taxonomic data stored within it. There are a number of large genera in Araceae, where we have 250 or more species. A dichotomous key allows one to visualize where new elements should fit and then one can decide if it should be fully described and entered into the Lucid matrix key”.  Tom has been in touch with us regarding further ideas he has on how both Lucid matrix and dichotomous keys might be adapted to help in this taxonomic process, which we are looking into. For further information about Tom’s work go to a recent publication – Araceae, a Family with Great Potential February 2019 Annals of the Missouri Botanical Garden 104(1):3-9      Digital Keys to the Calanoid Copepods Latest keys SawFly GenUS Sawfly GenUS This latest release from the Identification Technology Program (ITP) within the Animal and Plant Health Inspection Service (APHIS) includes a wealth of information about sawflies, keys to sawfly genera of North America, as well as keys to Sirex species of the World. https://idtools.org/id/sawfly/BRAZILIAN COMMERCIAL TIMBERS – Interactive wood identification key Brazilian Commercial Timbers – Interactive wood identification key This is an interactive key created to identify timbers commonly traded in Brazil. The identification is based on general characters and macroscopic anatomical features of wood. https://keys.lucidcentral.org/search/madeiras-comerciais-do-brasil/ This key is available in English and Portuguese.Australian Tropical Ferns and Lycophytes Australian Tropical Ferns and Lycophytes Australian Tropical Ferns and Lycophytes is a fern and lycophyte identification and information system for species occurring in northern Australia. https://keys.lucidcentral.org/search/australian-tropical-ferns-and-lycophytes/ Also available as an Android or iOS app. — Keys to the Calanoid Copepods These keys are looking to facilitate the identification of calanoid copepods (adult specimens (males and/or females)) to the level of family in the first instance and to the level of genera for the group of copepods known as the ‘Bradfordians’ and the families Centropagidae, Calanidae and Megacalanidae. Developed by scientists in the National Institute of Water and Atmospheric Research, New Zealand and CSIRO, Australia. https://keys.lucidcentral.org/search/calanoid-copepods/Tubulifera Australiensis Tubulifera Australiensis In the insect Order Thysanoptera, the suborder Tubulifera includes only a single family of living thrips, the Phlaeothripidae, and this family includes at least 66% of the thrips species known from Australia. This illustrated Lucid identification system helps to distinguish the 150 genera of Phlaeothripidae recorded from Australia. https://keys.lucidcentral.org/search/tubulifera-australiensis/Diamantina trees Diamantina trees Interactive identification key to trees that occur in and around Diamantina. Diamantina is located in Serra do Espinhaço, Brazil, a place recognized by UNESCO as one of the Biosphere Reserves. https://keys.lucidcentral.org/search/diamantina-trees/ — A tool for identifying insects and spiders in West African Rice A tool for identifying insects and spiders in West African Rice Keys to insects found in rice in 17 West African countries provides online help to identify specimens in rice insect collections and collected from the field. These are the first comprehensive taxonomic keys to West African rice arthropods and provide illustrations for 275 species of insects and 69 species of spiders associated with rice agroecosystems https://keys.lucidcentral.org/keys/v4/west_african_rice_insects_and_spiders/nteractive identification key for third instar larvae of Calliphoridae (Insecta, Diptera) of Neotropical forensic importance Interactive identification key for third instar larvae of Calliphoridae (Insecta, Diptera) of Neotropical forensic importance This key was developed to allow the identification of third instar larvae of 12 species of Calliphoridae (Insecta, Diptera, Oestroidea) of forensic importance that can be found in Brazil and in the Neotropical region. It was developed with the aim of helping police experts, students, and various professionals with, who may have limited familiarity with taxonomy, to obtain a safe and reliable diagnosis. https://keys.lucidcentral.org/search/chave-larva-calliphoridae/ This key is available in English and Portuguese.   Software Updates Lucid v4 Lucid v4  A new update of Lucid v4 (4.0.25 20220503) has been released and is available to download via Lucidcentral.org. See the release notes for bug fixes and changes. https://apps.lucidcentral.org/lucid4/updates.html   Download (login required) via: https://www.lucidcentral.org/my-account/downloads/   Fact Sheet Fusion logoA new update of Fact Sheet Fusion will be released at the end of May.   Modify your subscription    |    View online   Lucidcentral.org
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Thursday, 14 April 2022 07:06:00

Grahame Jackson posted a new submission ‘USDA ITP: Sawfly GenUS is now complete’


USDA ITP: Sawfly GenUS is now complete


Sawfly GenUS

ITP collaborator: Washington State Department of Agriculture

Authors: Quinlyn Baine, Chris Looney, Spencer K. Monckton, David R. Smith, Nathan M. Schiff, Henri Goulet, and Amanda J. Redford

USDA Animal and Plant Health Inspection Service’s Identification Technology Program (ITP) is pleased to announce the final release of Sawfly GenUS. The first release (February 2020) included identification support for all but the most diverse families of sawflies; this release adds that family and a new searchable host plant list. The website includes fact sheets, images, and keys to support a wide variety of users. 

Please find the attached PDF announcement to see an overview of ITP’s newest identification tool for PPQ and its partners. Please also feel free to forward this email or the attachment to your colleagues.

Sawfly GenUS can be accessed at: ​https://idtools.org/id/sawfly/ 

Visit our website to learn more about ITP’s tools and mobile apps

Interested in assisting ITP with tool development by being a beta reviewer for an upcoming ITP tool? We are seeking to increase our pool of beta reviewers for a variety of pest groups. Beta reviewers can be experts or non-specialists. Please contact us at itp@usda.gov. If you did not receive this email directly from ITP, and you would like to be included in future ITP announcement emails, please send a request to itp@usda.gov

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MARCH 4, 2022

Detecting plant leaf disease using deep learning on a mobile device

by David Bradley, Inderscience

diseased leaf
Credit: Pixabay/CC0 Public Domain

The visual and tactile examination of plant leaves is a standard method for identifying disease in crops and horticultural products. However, such an approach can be highly subjective and is dependent on the skills of the examiners. Writing in the International Journal of Computational Vision and Robotics, a team from Egypt describes a new approach to plant leaf disease detection using deep learning on a mobile device. The team’s tests against a standard database of diseased leaf images showed their system to be capable of up to 98% diagnostic accuracy. The process is rapid and showcases the sophisticated computational power available in modern mobile phones for this kind of intensive task.

Shaheera A. Rashwan and Marwa K. Elteir of the Informatics Research Institute at the City of Scientific Research and Technological Applications in Alexandria, suggest that for busy farmers in remote regions with no immediate access to plant disease experts, a mobile application that can help them spot disease and so treat the crops in a timely manner could be vital to their ongoing agricultural viability.

The team’s approach exploits the recent evolution of computational systems and especially graphical processing units (GPUs) that allow machine learning operations to be carried out efficiently in ways that previous generations of devices simply could not match for speed. Such operations facilitate the running of tools such as convolutional neural networks, which mimic certain characteristics of brain function, and allow image recognition and related tasks to be carried out quickly. The team thus embedded image recognition of the characteristics of disease in leaves for the present research.

Despite the great speed and accuracy of disease diagnostics that the team has shown, there is still room for improvement. They highlight an issue with shadows on images and confusing backgrounds when a user takes a photo of a suspect leaf. They hope to be able to develop a pre-processing step that will reduce any problems and the inaccuracies that might arise if the acquired leaf image is not as perfect as it might be for image recognition. Fundamentally, automated light level adjustment in the image would preclude issues arising because of shadows, while a step that isolates the leaf from its background in the image and effectively removes said background would ease the whole process still further and hopefully nudge the accuracy upwards.

Explore further

Identifying crop diseases—there’s an app for that

More information: Shaheera A. Rashwan et al, Plant leaf disease detection using deep learning on mobile devices, International Journal of Computational Vision and Robotics (2022). DOI: 10.1504/IJCVR.2022.121151

Provided by Inderscience 

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Minimizing Further Insect Pest Invasions in Africa

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Esther Ngumbi

Jun 20, 2018

Photo: Tamzin Byrne/ICIPE

This was written by Esther Ngumbi, and appeared on Sci Dev Net

USAID recently offered prize money for the best digital tools that can be used to help combat the fall armyworm (FAW), an invasive pest that has spread across Africa. The winners will be announced in the coming months.
Identified in over 35 African countries since 2016, the FAW is expected to continue to spread, threatening food security and agricultural trade in African countries.

Map of areas affected by Fall Armyworm (as of January 2018)

Map of areas affected by Fall Armyworm (as of January 2018) Credit: FAO

But this is not the first invasive pest the African continent is dealing with. Just a few years ago, African smallholder farmers battled the invasive South American tomato moth, Tuta absoluta. According to recent research, five invasive insect pests including T. absoluta cost the African continent US$ 1.1 billion every year.
Around the world, invasive pests are causing US$ 540 billion in economic losses to agriculture each year despite the fact that many countries are doing their best to prevent insect invasions now and into the future.

Tackling invasive pests reactively

To deal with invasive insects, African countries assisted by other stakeholders, including aid agencies such as USAID, research institutions such as the International Center for Insect Physiology and Ecology, the Center for Agriculture and Bioscience International (CABI, the parent organization of SciDev.Net) and the United Nations Food and Agriculture Organization (UN FAO) have repeatedly taken a reactive rather than a proactive approach in tackling the invasive pests only after they have established a foothold and caused considerable damage.
Ghana, for example, established a National Taskforce to control and manage FAW after the worms had invaded local fields. This taskforce mandate includes sensitizing farmers and making them aware of the symptoms of armyworm attacks so they can report infestations to authorities and undertake research aimed at finding short and long term solutions to combat the spread of FAW.

“While many of these strategies are working, one cannot help but wonder what it would take for African governments to get ahead of this problem.”

Esther Ngumbi, University of Illinois

Malawi’s government prioritized the use of pesticides as an immediate and short-term strategy to fight the FAW after many of their smallholder farmers lost crops to this invasive insect. Further, the government intensified training and awareness campaigns about this pest and installed pheromone traps to help monitor the spread only after the pest had established a foothold.
The FAO, a leader in the efforts to deal with invasive pests in Africa, has spearheaded many efforts including bringing together experts from the Americas, Africa and other regions to share and update each other on FAW. The FAO has launched a mobile phone app to be used as an early warning system tool. But again, many of these efforts happened after the first detection of the FAW.
While many of these strategies are working, one cannot help but wonder what it would take for African governments to get ahead of this problem. How can aid agencies such as USAID, UN FAO and other development partners that are currently spending billions to fight the invasive FAW help Africa to take the necessary steps to ensure that it is better prepared to deal with invasive insects now and into the future?

Anticipate and prepare

Recent research predicts that threats from invasive insects will continue to increase with African countries expected to be the most vulnerable. African governments must anticipate and prepare for such invasions using already available resources.
Early this year, CABI launched invasive species Horizon Scanning Tool (beta), a tool that allows countries to identify potential invasive species. This online and open source tool supported by United States Department of Agriculture and the UK Department for International Development allows countries to generate a list of invasive species that are absent from their countries at the moment but present in “source areas,” which may be relevant because they are neighboring countries, linked by trade and transport routes, or share similar climates. Doing so could allow African countries to prepare action plans that can be quickly rolled out when potential invaders actually arrive.

Learn from other regions

Africa can learn from other regions that have comprehensive plans on dealing with invasive insects and countries that have gone through similar invasions. The United States and Australia are examples of countries that have comprehensive plans on preventing and dealing with insect invasions, while Brazil has gone through its own FAW invasion.

“African governments must learn to be proactive rather than reactive in dealing with invasive insects.”

Esther Ngumbi, University of Illinois

Through workshops and training programs that help bring experts together, African countries can learn how to prevent and deal with future insect invasions. Moreover, key actors should help organize more workshops and training programs to enable African experts to learn from their counterparts overseas. At the same time, the manuals, and all the information exchanged and learned during such workshops, could be stored in online repositories that can be accessed by all African countries.   

Strengthen African pest surveillance

A recent Feed the Future funded technical brief, which I helped to write, looked at the strength of existing African plant protection regulatory frameworks by examining eight indicators including the existence of a specified government agency mandated with the task of carrying out pest surveillance.
It reveals that many African countries have weak plant protection regulatory systems and that many governments do not carry out routine pest surveillance which involves the collection, recording, analysis, interpretation and timely dissemination of information about the presence, prevalence and distribution of pests.
The International Plant Protection Convention offers a comprehensive document that can help African countries to design pest surveillance programs. Also, the convention offers other guiding documents that can be used by African countries to strengthen their plant protection frameworks. African countries can use these available documents to strengthen national and regional pest surveillance abilities.

Set up emergency funds

Invasive insects know no borders. Thus, African countries must work together. At the same time, given the rapid spread of invasive insect outbreaks, the African continent must set up an emergency fund that can easily be tapped when insects invade. In dealing with the recent FAW invasion, it was evident that individual African countries and the continent did not have an emergency financing plan. This must change.

By anticipating potential invasive insects and learning from countries that have comprehensive national plant protection frameworks, Africa can be prepared for the next insect invasion. African governments must learn to be proactive rather than reactive in dealing with invasive insects.
Doing so will help safeguard Africa’s agriculture and protect the meaningful gains made in agricultural development. Time is ripe.
Esther Ngumbi is a distinguished postdoctoral researcher with the Department of Entomology at the US-based University of Illinois at Urbana Champaign, a World Policy Institute Senior Fellow, Aspen Institute New Voices Food Security Fellow and a Clinton Global University Initiative Agriculture Commitments Mentor and Ambassador. She can be contacted at enn0002@tigermail.auburn.edu 
This piece was produced by SciDev.Net’s Sub-Saharan Africa English desk. 


[1] USAID: Fall Armyworm Tech Prize (USAID, 2018). 
[2] Briefing note on FAO actions on fall armyworm in Africa (UN FAO, 31 January 2018) 
[3] Corin F. Pratt and others  Economic impacts of invasive alien species on African smallholder livelihoods (Global Food Security, vol 14, September 2017).
[4] Abigail Barker Plant health-state of research (Kew Royal Botanic gardens, 2017).
[5] US Embassy in Lilongwe United States assists Malawi to combat fall armyworm. (US Embassy, 13 February 2018).
[6] Joseph Opoku Gakpo Fall armyworm invasion spreads to Ghana (Cornell Alliance for Science, 19 May 2017). 
[7] Kimberly Keeton Malawi’s new reality: Fall armyworm is here to stay (IFPRI, 26 February 2018).
[8] Malawi’s farmers resort to home-made repellents to combat armyworms (Reuters, 2018). 
[9] Fall Armyworm (UN FAO, 2018). 
[10] FAO launches mobile application to support fight against Fall Armyworm in Africa (UN FAO, 14 March 2018).
[11] Dean R. Paini and others Global threat to agriculture from invasive species (Proceedings of the National Academy of Sciences of the United States of America, 5 July 2016).
[12] CABI launches invasive species Horizon Scanning Tool (CABI, 2018).
[13] United States Department of Agriculture Animal and Plant Health Inspection Service(USDA APHIS, 2018).
[14] Australia Government Department of Agriculture and Water Resources (Australia Government, 2018).
[15] Plant protection EBA data in action technical brief (USAID FEED THE FUTURE, 26 January 2018).
[16] Guidelines for surveillance (International Plant Protection Convention, 2016)FILED UNDER:AGRICULTURAL PRODUCTIVITYMARKETS AND TRADEPOLICY AND GOVERNANCERESILIENCE

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Plantwise National Data Centre established in Pakistan

The plant health information collected through Plantwise plant clinics is a valuable resource. The Department of Plant Protection has set up a new National Data Centre in Karachi to collate clinic data. Plant health partners, stakeholders and other knowledge delivery systems will be able to use this information to make evidence-based decisions that strengthen plant health systems.

Farmer in Pakistan
Farmer in Pakistan

Techniques for managing data have become essential and are now common in business and services. With this in mind, Plantwise has now established the first-ever National Data Centre in Karachi, for the assimilation of Plantwise data in Pakistan. This robust management system will collate data coming from more than 1,000 plant clinics throughout the country.

National Data Centre training

The Plantwise programme has provided data management training to plant clinic staff in order to ensure the long-term collection of data. These staff members include local implementing organisation such as agriculture extension departments in each of the Pakistan provinces. 

As well as consolidating all the data and information, the National Data Centre aims to offer central hosting and managed services for all Government institutions including the Plantwise programme’s partners.

Data-driven decision-making

The new data centre will enable reliable, efficient and secure access to plant clinics’ plant health data, meaning partner organisations will no longer be required to host their own applications. In addition, partners will receive quicker and more secure networking facilities that will allow them to better showcase their services to end customers.

The National Data Centre will demonstrate how data-driven decision-making is essential for increasing production and improving quality in agriculture.

National Data Centre, Karachi
Setting up the National Data Centre, Karachi

The aim of Planwise was to increase food security and improve rural livelihoods by reducing crop losses. This has been achieved by establishing sustainable networks of local plant clinics, run by trained plant doctors, where farmers receive practical plant health advice. Data collected from these clinics allow for better response and monitoring especially in case of new pest outbreaks, and plant health data is made available for decision making while it is still relevant.

Consolidating data – National Data Centre

It was evident that the data collected from the provincial plant clinics in Pakistan needed to be securely stored with proper access controls.  Many of the individual government organisations, such as agricultural extension departments, had set up their own servers, or rather data centres, with high human resource and operational costs.

Therefore, it was considered vital that CABI, in consultation with its LIOI’s, establish a National Data Centre to reduce the cost of data management and increase the value of the clinics’ data. The National Data Centre will also provide the opportunity for cross-validation and high data security.

Help inform plant health services

The plant clinic data coming into the National Data Centre can be used to inform plant health services in various ways. For instance, this data can help to identify new and emerging plant health problems and act as an early warning system to the regulatory bodies, such as the Department of Plant Protection, that are responsible for pest and disease surveillance and response.

Further reading


CABI’s new global programme, PlantwisePlus, will support low and lower-middle-income countries to predict, prepare themselves for and prevent plant health threats in a changing climate – reducing crop losses and empowering farmers to increase income, food security and food safety by producing more and higher quality food.

PlantwisePlus will therefore focus on (a) strengthening detection of and response to pest outbreaks; (b) providing public and private agricultural service providers with better digital advisory tools to support farmers in sustainable crop management; (c) enhancing the availability of nature-positive and low-risk plant protection products to reduce reliance on high-risk farm inputs; (d) increasing consumer demand for and supply to local markets of safer, higher quality and locally produced food.PakistanPlantwisedata managementAgriculture and International Development

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