Archive for the ‘Pest diagnostics’ Category


[COTONOU, BENIN] Researchers have launched a free interactive tool that can be used to identify nearly 200 weeds that harm rice production in Africa.

The tool, which has been launched by agricultural research institutions AfricaRice and the Centre for International Cooperation in Agronomic Research for Development (CIRAD), can be accessed online and offline on laptops and CD-ROMs or as an application on smartphones and tablet computers.

People such as researchers, students and farmers can use the tool to identify weed species that affect the rice farming lowlands in East and West Africa.

“The tool works through a schematic image of a [weed] plant where, for different plant parts, you can select shape, colour and other characteristics,” according to AfricaRice weed scientist Jonne Rodenburg. “By selecting characteristics for different [weed] plant parts, the number of likely species gradually decreases.”

After identifying the specific weed, he said, users can use a database to select appropriate interventions. “The tool will guide the user to information on its biology, ecology and management,” he said. “The database contains species-specific weed management advice. In most cases, the advice is categorised according to weed categories. For instance, broad-leaved weeds, grasses, sedges, parasitic weeds, aquatic weeds, perennial weeds and annual weeds.”

People with specific questions, Rodenburg told SciDev.Net when journalists attending the First West Africa Science Journalists Conference last month (26-28 November) visited AfricaRice’s headquarters, can also access online weed science network Weedsbook  for more documents and the possibility to interact with weeds scientists across the continent or even around the world.

The researchers, who worked in close collaboration on the project with the African Weeds of Rice project financed by the European Union and the Africa Caribbean Pacific Science and Technology Programme, took three years to produce the tool.

In Sub-Saharan Africa, weeds cause estimated annual rice production losses of at least 2.2 million tonnes and US$1.45 billion, equivalent to 10 million hectares of rice annually, said Rodenburg.

But Antoine Adidéhou, permanent secretary of the Council of Rice Farmers in Benin said that many rice that farmers lacked the computer skills or Internet access and so would find it hard to make use of this valuable resource.

“They will have some difficulties in trying to make good use of this tool,” he said.

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Speed read

  • Pests are going undetected in developing nations and severely harming harvests
  • For example, Myanmar may be detecting only about half of estimated 720 pests
  • Investment in research capacity in needed to tackle the problem

[SANTIAGO] The number of different pests plaguing crops in the developing world may be vastly underestimated, contributing to severely reduced harvests in some of the world’s most important food-producing nations, say researchers.

About 200 pests and pathogens per country fly under the radar of researchers and policymakers in the developing world due to a lack of technical capacity to detect them, according to a study.

“Highly-productive countries such as Brazil, China, India, Indonesia and the Philippines are likely to be harbouring hundreds more crop pests than currently known,” says the study published in New Phytologist last month (11 February).

It adds that crop pests and pathogens pose a significant threat to globalfood security, with around one sixth of the world’s agriculturalproduction lost to them each year.

The team used a statistical model to relate the known distribution of about 2,000 crop destroying-organisms in 195 countries to physical and socio-economic factors, such as agricultural production, climate, and research and development (R&D) expenditure.

The researchers used the model to estimate how many pests would be found if all countries had the same GDP (gross domestic product) and R&D spending as the United States. The difference between this and the known pest numbers indicated how many pests may be going undetected: around 205 per country on average.

For example, Myanmar, which produces large amounts of rice but spends little on R&D, has reported 359 pests. The model found it may have as many as 723 pests, which may mean that only about half of the total pest burden is being detected.

“To tackle pests and pathogens we need to know they are there. Our paper suggests that more investment is needed in developing countries to help identify pests,” lead author Daniel Bebber, from Exeter University, United Kingdom, tells SciDev.Net.

This is especially true for microorganisms, which require greater technological capacity to identify them than larger pests such as insects, say the researchers.

Jan Breithaupt, an agricultural officer for the UN Food and Agricultural Organization’s division of Pest and Pesticide Management, says the study underlines the importance of facilities and expert knowledge “to prevent crop damage and manage pests proactively, particularly in developing countries”.

He says local farmers’ knowledge of their own environment — rarely taken into account in pest detection studies — should be used too.

He also warns that climate change will likely compound the problem as it will increase the number of pests affecting crops.

Francisco Morales, based at the International Center for Tropical Agriculture in Colombia, agrees that in Latin America more investment in research would increase capacity to detect and identify pests.

But he points out the need for tougher quarantine measures for imported agricultural products, too.

Link to full paper in New Phytologist   


New Phytologist doi: 10.1111/nph.12722 (2014)

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by Clint Thompson, news editor with the UGA College of Agricultural and Environmental Sciences

Is there an unwanted invasive insect or plant on your farm or in your garden that you don’t recognize? The University of Georgia College of Agricultural and Environmental Sciences has an app for that.

Identify invasive pests with UGA apps

Mobile applications are a way to identify unwanted invasive pests. Image credit: Submitted photo.

Invasive species trackers at the UGA Center for Invasive Species and Ecosystem Health have developed a suite of apps to help farmers, forestry personnel and home gardeners identify strange unwanted invasive pests. They can now identify their problem invasive pests in the field, rather than breaking away to sit down at a computer and look it up.

Apps developed by the center’s technology director Chuck Bargeron and his co-workers provide direct links to different databases specializing in informing and educating the public about invasive species, those not native to an area that has been introduced and causing damage to agriculture and forestry. Such species include the kudzu bug that munches on soybeans and the spotted wing drosophila which affects blueberry crops.

“For the IOS platform, we’ve had more than 25,000 downloads of apps. The most successful one was the first one we did which was for Florida, which was focused primarily on pythons in south Florida. It’s probably been the most successful because it had the most press coverage when it first came out,” Bargeron said.

The app is one of 17 the center has developed. It provides different apps for different parts of the country because, for example, farmers in the Western United States aren’t concerned with the same species that growers in the Southeast are concerned with. Working a regional perspective allows users to focus on species in their geographic area.

Bargeron and members of the Center for Invasive Species and Ecosystem Health have had great success with database web-based resources of information, especially after the pictures image archive were added to the website in 2001. When Keith Douce and David Moorhead, — co-directors of the center formally known as Bugwood Network, — launched the website in 2001 they added pictures from 35mm slides. Approximately 3,500 pictures were available. As more and more people began using the website and recognizing its value, they started sharing their own pictures. The database of pictures increased greatly in the 12 years since the website was started. Now, more than 200,000 pictures from more than 2,000 photographers are in the systems database.

These resources have also changed the way forestry and agriculture classes are taught. An entomology professor at Texas A&M told Douce the resources caused him to completely restructure how he teaches his classes.

According to Douce, the center website generated 9.3 million users last year and 260 million hits.

For more information, visit the website at bugwood.org or go to http://apps.bugwood.org/apps.html.

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App developers:    The University of Queensland QAAFI Biological Information Technology (QBIT) and USDA-APHIS Identification Technology Program (ITP)

App partners:         California Department of Food & Agriculture, Colorado State University, Delaware State University, Florida Department of Agriculture & Consumer Services, North Carolina State University, Southern Plant Diagnostic Network, University of Florida, and University of California

PH Quads initiative: the Lucid Mobile project is a 2013 “Plant Health Quadrilaterals Initiative”.

The Identification Technology Program (ITP) team, in cooperation with The University of Queensland’s QAAFI Biological Information Technology (QBIT), is pleased to announce the release of 10 Lucid Mobile apps for Android phones and tablets. These apps are available at no cost by searching on the text “USDA APHIS ITP” through Google Play (Google Play USDA APHIS ITP).

Ø  The Lucid Mobile apps were created from existing Lucid keys contained within ITP’s identification tools (http://idtools.org/).

Ø  The 10 Lucid Mobile apps will be available early next year for your iPhone and iPad.

 Further details about Lucid Mobile and ITP’s Lucid Mobile apps are given in the attached document. A direct link for downloading an app onto your Android phone is provided on the second page of the document.

 If you did not receive this email directly from Terrence Walters and you would like to be included in future ITP product announcement emails, please send a request to itp@aphis.usda.gov.

 Terrence Walters, USDA•APHIS•PPQ•S&T•FCL•ITP


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From: Robin Blackstone, ENN  http://www.enn.com/
Published October 2, 2013 01:13 PM

Photo by GEF Small Grants Programme.

Bugging Iran

Up until now, on a scale of 1 to 10, practical pest control management ranks about a “1″ with regard to the availability of information on scale insects in Iran! Yet even the most basic tool for pest control management in Iran has been unavailable jeopardizing crop yields. Dr. Masumeh Moghaddam of the Iranian Research Institute of Plant Protection, Tehran has changed that by publishing the first ever detailed annotated checklist of the scale insects of Iran.

This publication features 275 insect species from 13 families of the Coccoidea superfamily of the order Homoptera. Most of these parasitic insects are known to impart serious economic damage to crops making the identification and control of them very important to agricultural interests.

The Coccoidea family is made up of 49 families of roughly 8,000 species. Scale insects permanently attach to plant parts, pierce them, envelope themselves in a waxy coating for defense and suck the sap and moisture right out of the plant. This ultimately degrades or even destroys the plant. The waxy coating makes it difficult for many insecticides to penetrate their shell. They will reproduce and stack one on the other to resemble the scales of a fish or reptile.  Most varieties of these parasites emerge from their eggs free moving. They totter around for an attractive spot onto which they latch. Once secure, they lose their legs and hunker down.

The new Iran specific study individually lists the locally identified scale insect species, their regional data and host plants. It is anticipated that this information will help Iranian growers gain stronger area knowledge of the Coccoidea family’s plant intrusion for resulting improvements in crop health. The new study is published in Zookeys.

Read more at: PensoftThe Bug Guide

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Plant Clinics Taking Root in East Africa

FILE - A worker is seen at a tea plantation near Kasese town, some 500 km west of Uganda's capital, Kampala.FILE – A worker is seen at a tea plantation near Kasese town, some 500 km west of Uganda’s capital, Kampala.
Nick Long
CABI is trying to change that with a crop protection program called Plantwise.  In the past three years, the program has trained nearly a thousand so-called plant doctors in 24 countries, including one near Kampala, Uganda.It’s market day in Mukono, a village about 15 kilometers from Kampala.  Plant doctor Daniel Lyazi has arrived by motorbike to set up his clinic next to a stall where a traditional healer is trying to sell herbal remedies to shoppers.

There is no remedy for the diseased plant samples that people bring to Lyazi’s clinic, which is basically just a table under a small tent.

The slime-covered cabbage that a farmer plunks on the table is not going to get any better, nor will the rest of his cabbages.  But Lyazi’s recommendations may save the next season’s crop.

“So he’s telling me there’s a small caterpillar which eats [the cabbages] starting from the youngest leaf.  He’s told me that the whole garden has been attacked and affected by this caterpillar.  So according to me, I know that it’s a diamondback moth and I’m going to give him recommendations,” says Lyazi.

The farmer has been using an insecticide but Lyazi says it’s the wrong one.

FILE - Farmers attend one of the plant clinics in East Africa (Courtesy - CABI).FILE – Farmers attend one of the plant clinics in East Africa (Courtesy – CABI).

What Lyazi means is the farmer should interplant onions between the rows of cabbages as an additional protection measure.

The clinic lasts about three hours and in that time Lyazi advises about 20 farmers. The head of a local farmers’ group, Erifazi Mayanja, says they are really benefiting from this twice-a-month clinic, which started last year.

“That’s why they have come in great number today, because of the good advice they are getting from our master here,” says Mayanja.

Program popular and growing

Plantwise says there are now about 90 of these clinics in Uganda, and this year donors spent around $290,000 training plant doctors and expanding the system in the country.

Coordinating the Plantwise program in Uganda and Zambia is Joseph Mulema.  He argues that plant clinics are a far more effective model for getting advice to farmers than the traditional one where agricultural extension workers, in theory, visit farms.

“Plant clinics can help so many farmers in a very short time.  In fact, more farmers are seen in a plant clinic session, if good mobilization is done, than actually an extension officer can look at in an entire month,” says Mulema.

Government crop protection officer Robert Karyeija says training plant doctors has been vital, because even though there were thousands of agricultural extension workers, they just didn’t know enough.

“They were there.  But the problem [was] they would be general agriculturalists who knew agronomy but didn’t know much about pests and diseases,” says Karyeija.

Since 2010, CABI has set up Plantwise clinics in 12 African countries – nine in East Africa and  three in West Africa.

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From the Hindu Business Line by L. N. Revathy

Tamil Nadu Agricultural University’s e-Velanmai adopts technology to speed up crop-salvaging operations

High yield is not just about timely sowing. Much also depends on receiving appropriate plant protection measures to limit crop loss, say farmers.

And these farmers had enrolled as members in the “e-Velanmai” (e-Agriculture) scheme offered by the Tamil Nadu Agricultural University. They were offered advisory services by agricultural scientists. According

Narrating his experience, V. Dhanasekaran of Thuravi Village in Villupuram district said: “I spotted the leaf spot disease in the groundnut crop I had cultivated on about 2 acres in my farm one morning. I immediately called the field coordinator who visited the farm, captured the image of the affected plants, and sent it to the scientist concerned for advice. Within two hours, the field coordinator returned with the prescription. I was able to save the crop and limit the yield loss.”

Another woman farmer, Sivakami, of Senjerimalai village, said she noticed aphids and pod borer pests in her avarai crop, which she had cultivated on about one acre. “I was advised to spray 250 gm of Acephate an acre. I later realised that I achieved 450 kg additional yield. But for the timely intervention, I would have lost completely.”

Many farmers said that they were pleased to receive the recommendation at their doorstep.

Farmers concede that prior to the introduction of eVelanmai project they depended on input dealers for crop protection guidance. “Now, there is social recognition and we are able to share the information with confidence,” said Latha of Valem village.

There were some who felt that they were unable to reap the benefit of the recommendation, possibly due to the unexpected rainfall after the spray, while a few others said that they were not sure if the pesticide prescribed by the expert was the same as the one issued by the input dealer.


But the number of farmers enrolling themselves in this scheme is on the rise. From 1,181 in the pilot phase in 2007 -11, it has risen to over 12,000 now, says C. Karthikeyan, Project Coordinator of the eVelanmai scheme.

“It is an ICT (Information and Communication Technology) based, demand-driven participatory extension approach, seeking to provide timely advisory services (by scientists) to farmers using ICT tools,” said Karthikeyan, explaining the concept.

This World Bank-aided TN-IAMWARM project of the Government of Tamil Nadu has since been extended to 26 sub-basins (irrigation project command areas) in the State.

World Bank team is slated to review the project on May 20.

Karthikeyan meanwhile said that it has been proposed to recommend the project for adoption to the State Department of Agriculture.

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New research conducted in the major potato growing regions of the United States, has found that the Tomato-potato psyllid (TPP) – a highly destructive pest affecting potato crops – can survive even the harshest of winter conditions.  

“Despite it being an extremely cold winter in some of the key potato regions of the United States earlier this year, researchers there identified living psyllids in these areas, proving just how resilient this highly destructive pest can be,” said AUSVEG Spokesperson, Luke Raggatt. 

“These findings from the US reaffirm how critical the research and development (R&D) work that is being conducted on the TPP within the Australian potato industry continues to be for growers and processors alike,” said Mr Raggatt.  

Amongst Australian research on the TPP is a project currently being conducted by the Tasmanian Institute of Agriculture (TIA), which is monitoring the distribution and prevalence of native psyllid populations in key potato growing areas across Eastern Australia using sticky traps. The use of the traps aims to provide the industry with an effective early warning system for incursions of the TPP, which is not currently found in Australia. 

“It is critical that the Australian potato industry remains vigilant to ensure that it can swiftly and effectively identify a potential outbreak of the Tomato-potato psyllid,” said Mr Raggatt.  

“While Australia is currently free from the psyllid, there is a real possibility of the pest entering our shores through a number of different means, including the transit of plant materials arriving from affected countries such as the US or New Zealand,” said Mr Raggatt.  

R&D activities in Australia conducted in this area have included an investigation into the role of psyllids as vectors of disease; raising the awareness of Zebra Chip disease within the industry; developing rapid diagnostic tools for the detection of pathogens associated with Zebra Chip; and Integrated Pest Management (IPM) strategies that would help to control the psyllid.   

“In the last few years, the Australian potato industry has invested heavily in a range of R&D projects in an attempt to ensure that potato growers and processors are in a position to deal with this devastating pest and its associated disease, should it arrive here in the future,” said Mr Raggatt.  

“Research findings from the United States, Australia, New Zealand and elsewhere, have all re-enforced how much there is still to learn about the behaviour of the TPP and the spread of the destructive disease that it harbours,” said Mr Raggatt.   

The US research was conducted by the Idaho, Washington State and Oregon Potato Commissions.

For more information:
Luke Raggatt
Tel: +61 (03) 9822 0388
Mob: +61 0403 827 822

Publication date: 4/26/2013

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by MONI on MARCH 1, 2013

Josie Lynn Catindig
International Rice Research Institute, Los Baños, Philippines

Bar coding sequential steps

Bar coding sequential steps

Expertise in arthropod taxonomy is now very scarce.  There are very few taxonomic experts in the world who can identify specimens to species levels and describe new species discovered in nature. In the national systems, many scientists working on pest management are unable to identify pests and natural enemies to species levels. The shortage of specialists in pest and natural enemy diagnosis is acute and there is a need to find new diagnostic tools. One way to overcome the shortage is through the use of remote microscopy and the internet to link national scientists and taxonomic specialists. Such a system will still require communication between scientists in the field and taxonomic expertise.

The usual way of identifying insects is the use of identification keys based on their morphological features. This is highly dependent of specialized taxonomic expertise and is also time consuming.  DNA bar coding can be a useful tool for identification in taxonomy. It is a process where a short but specific gene tags or barcodes are utilized to distinguish one species from another (Hebert & Gregory 2005).  The technique was first proposed by Hebert et al in 2003 as a universal species diagnostic in their paper entitled “Biological identification through DNA barcodes”.  The mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. Working in collaboration with Dr David Gopurenko, a scientist in molecular systematics in New South Wales, Department of Primary Industries, IRRI is beginning to barcode and establish a barcode reference for identified hymenopteran parasitoids from IRRI’s arthropod collection to be available for use in species matching and identification.

Species identification using DNA barcodes starts with a specimen either fresh or dried. In the laboratory short pieces of DNA that are diagnostic for a species is collected. For example, a tiny piece of the specimen’s tissue such as a leg is used to extract its DNA.


Screen capture of the BOLDSYSTEM (picture credit - D. Gopurenko)

Screen capture of the BOLDSYSTEM (picture credit – D. Gopurenko)

The BOLDSYSTEMS, established in 2005, is like a library with a searchable repository for barcode records. It is an online workbench that aids collection, management, analysis, and use of DNA barcodes. It has three main components: first, it is a repository for the specimen and sequence records that form the basic data unit of all barcode studies; second, it is a workbench that aids the management, quality assurance and analysis of barcode; and third, it provides a vehicle for collaboration across geographically dispersed research communities by coupling flexible security and data entry features with web-based delivery.

To guide the users, the BOLDSYSTEMS has the following menu: Databases link to access resources such as a public data portal, barcode index number, publication and primers used in the generation of barcodes; Taxonomy link provides a page that displays the kingdom of life being bar coded, their images, distribution map and other details for each taxon; Identification link provides access to identification engines of animal, plant and fungi; Workbench link provides access to BOLD data analysis, records of specimen data submitted,  and management workbench; and Resources link provide access to site documentation, training materials and workflow documents.

DNA bar coding as a taxonomic tool along with the barcode library such as in the BOLDSYSTEMS will help scientists rapidly sort, compare and identify specimens. It will also emphasize taxa or reveal cryptic species, which may represent new biological species.

The DNA sequence of a specimen can be placed into BOLDSYSTEM and compared with the barcode database.  In this case the DNA was from Drosophila yakuba and it matched several other barcodes in the database 100%.

The DNA sequence of a specimen can be placed into BOLDSYSTEM and compared with the barcode database. In this case the DNA was from Drosophila yakuba and it matched several other barcodes in the database 100%.


BOLDSYSTEMS in http://www.barcodinglife.com

Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. 270:313-321.


Hebert PDN, Gregory RT. 2005. The promise of DNA barcoding for Taxonomy. Systematic Biology 54(5): 852-859.




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From:  pestnet@yahoogroups.com

By Dennis O’Brien

April 30, 2012

Barcodes may bring to mind the sales tags and scanners found in supermarkets and other stores. But U.S. Department of Agriculture (USDA) scientists are using “DNA barcodes” to monitor insects that damage crops as diverse as wheat, barley and potatoes, and to make pest management decisions.

In DNA barcoding, scientists sequence a designated part of an organism’s genome and produce a barcode from it for a systematic comparison with the sequenced DNA of other closely related species. DNA barcodes are being developed on a wide range of plants and animals as part of a global effort to catalogue the diversity of life on Earth.

Matthew Greenstone, an Agricultural Research Service (ARS) entomologist at the agency’s Invasive Insect Biocontrol and Behavior Laboratory in Beltsville, Md., is using DNA barcodes in an unconventional way: to identify insect predators best equipped to control the Colorado potato beetle, which is the single most damaging insect pest of potatoes in the Eastern United States.

ARS is USDA’s chief intramural scientific research agency, and this research supports the USDA goal of promoting agricultural sustainability.

Numerous studies have analyzed the gut contents of predatory insects to evaluate their ability to control pests in a field. But predators digest prey at different rates, so simple gut analysis is insufficient for accurately comparing the effectiveness of different predators. Greenstone has fine-tuned the approach, using barcodes to come up with a way to factor in how quickly different insects digest prey.

He and his colleagues collected four potato beetle predators, fed them lab-raised potato beetles and determined how long the pest’s barcoded DNA could be detected in the predators’ guts. The results, published in the journal Entomologia Experimentalis et Applicata, show the importance of taking digestive rates into account when evaluating insect predators as biocontrol agents. They also may provide guidance to growers on the most effective control strategies for combating a voracious pest.

Read more about this research in the April 2012 issue of Agricultural Research magazine.

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