Crop Sciences

Drones are what’s next for plant breeders

Published February 20, 2017
Drone in flight
Drone in flight
  • Crop breeders grow thousands of potential varieties at a time; until now, observations of key traits were made by hand.
  • In a new study, unmanned aerial vehicles, or drones, were used successfully to remotely evaluate and predict soybean maturity timing in tests of potential varieties.
  • The use of drones for this purpose could substantially reduce the man-hours needed to evaluate new crops. 

URBANA, Ill. – When plant breeders develop new crop varieties, they grow up a lot of plants and they all need to be checked. Repeatedly. 

“Farmers might have a 100-acre field planted with one soybean variety, whereas breeders may have 10,000 potential varieties planted on one 10-acre field. The farmer can fairly quickly determine whether the single variety in a field is ready to be harvested. However, breeders have to walk through research fields several times in the fall to determine the date when each potential variety matures,” explains University of Illinois soybean breeder Brian Diers.

“We have to check every three days,” masters student Nathan Schmitz adds. “It takes a good amount of time during a busy part of the year. Sometimes it’s really hot, sometimes really muddy.”

To make things easier, an interdisciplinary team including breeders, computer scientists, engineers, and geographic information specialists turned to unmanned aerial vehicles – commonly known as UAVs or drones.

“When drones became available, we asked ourselves how we could apply this new technology to breeding. For this first attempt, we tried to do a couple simple things,” Diers says.

One goal was to predict the timing of pod maturity using images from a camera attached to the drone, along with sophisticated data and image analysis techniques. “We used multi-spectral images,” Schmitz explains. “We set up an equation in the program to pick up changes in the light frequency reflected off the plant. That color change is how we differentiate a mature plant from an immature one.”

The researchers developed an algorithm to compare images from the drone with pod maturity data measured the old-fashioned way, by walking the fields. “Our maturity predictions with the drone were very close to what we recorded while walking through the fields,” Diers notes.

Predictions made by the model achieved 93 percent accuracy, but Diers says they might have done even better without some of the inherent limitations of flying drones. For example, they could only fly it and obtain good images on sunny days with little wind.

Drones are increasingly recognized for their potential to improve efficiency and precision in agriculture—especially after new FAA rules went into effect in August 2016—but this is one of the first studies to use drones to optimize breeding practices. Diers notes that the application could be particularly useful to large breeding companies, which test hundreds of thousands of potential varieties annually. If breeders can save time and effort using this technology, new varieties could potentially be developed and made available to farmers on a faster timeline—a welcome improvement.

The article, “Development of methods to improve soybean yield estimation and predict plant maturity with an unmanned aerial vehicle based platform,” is published in Remote Sensing of Environment. In addition to Diers and Schmitz, Neil Yu, Liujun Li, Lei Tian, and Jonathan Greenberg, all from the University of Illinois, are co-authors.

Snap beans hard to grow in cover crop residue

Published February 16, 2017
Snap beans growing through residue
Snap beans growing through residue
  • Vegetable farmers have been slow to adopt no-till practices with cover crops in part because of the difficulty of managing surface residues.
  • A new study evaluated cover crop mortality and snap bean yield when planted in rye and vetch cover crops, controlled mechanically both with and without herbicides.
  • Roller-crimping was not completely effective at terminating cover crops and snap bean yields often were lower when planted in cover crops than in bare-soil plots.

URBANA, Ill. – More no-till farmers are using cover crops to conserve soil and suppress weeds, but many vegetable producers are reluctant to get on board. That’s because many small-seeded vegetable crops struggle to emerge through thick cover crop residues. However, the potential benefits of no-till cover crop systems compelled researchers to give it a try with snap bean.

“There’s interest in both cover crops and no-till vegetable production, but adoption has been slow,” says University of Illinois and USDA-ARS ecologist Marty Williams. “We designed a study to look at a scenario that had a better chance of success. We used snap bean, which is relatively large-seeded, and planted later to allow sufficient time to grow and then kill a cover crop.”

In both Illinois and Washington, Williams and USDA-ARS agronomist Rick Boydston grew vetch, rye, and a combination of the two cover crops before killing them with a roller-crimper—a machine that evenly flattens and crimps standing plant biomass—or with a combination of the roller-crimper and a burndown herbicide.

“The roller-crimper weighs about 2 tons. As it bends the stalks over, metal fins crimp the stalks in multiple places so that, in theory, the cover crop lays flat and dies,” Williams explains. For organic growers, the roller-crimper offers a way to kill the cover crop without herbicides or tillage.

The researchers tracked cover crop mortality, weed biomass, and snap bean yields during the experiment. Unfortunately, the roller-crimper did not effectively kill the vetch, even with an application of herbicide. Instead, vetch became weedy and caused yield losses in snap bean. Rye was easier to kill, but heavy plant residues complicated planting.

“Timing of roller-crimping is very important,” Williams notes. “In general, grass cover crops like rye need to be fully flowering when roller-crimped, or else the cover crop may not die. Vetch needs to be rolled a bit later, after pod development. A problem encountered with the cover crop mixture in this study was that rye reached the correct growth stage for roller-crimping before vetch.

“Another issue was adequate seed-to-soil contact, which can become a challenge with excessive plant residues on the soil surface. Closing the seed furrow becomes difficult with increasing soil moisture, which isn’t uncommon in central Illinois soils, especially during typical spring rainfall events, or with moderate to high levels of surface residues,” Williams says.

Ultimately, none of the cover crops or control methods offered any consistent yield advantages for snap bean. In fact, some of the greatest yields occurred in bare-soil treatments. When asked if he would tell farmers to avoid this method, Williams laughs and admits the results of this particular study do not look particularly promising in central Illinois. He points out that other researchers were successful with soybean in a similar system, but thinks different cover crops or management techniques may be more suitable for snap bean.

Williams emphasizes the importance of balancing key elements to maximize the chances of success.

“One needs sufficient cover crop biomass to aid weed suppression, yet it’s important to avoid excessive surface residue, which can be detrimental to the crop. Using the roller-crimper certainly adds an additional challenge because the cover crop needs to be at an advanced growth stage to be successfully terminated,” Williams says.

The article, “No-till snap bean performance and weed response following rye and vetch cover crops,” is published in Renewable Agriculture and Food Systems.

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  • Roller crimper flattening cover crop
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Modeling the future for soybeans in the Midwest

Published February 2, 2017
soybean field

URBANA, Ill. – How will the rising temperatures expected to occur with global climate change affect soybean growth in the Midwest? Rather than wait and see, researchers at the University of Illinois will use real crop data and computer modeling to better predict future impacts of higher temperatures on agricultural production and identify promising targets for adaptation.

The project is being funded with a $420,000 USDA National Institute for Food and Agriculture grant. U of I environmental scientist Kaiyu Guan is the project director. Carl Bernacchi and Elizabeth Ainsworth are co-project directors. Both are plant physiologists in the U of I Department of Plant Biology and Department of Crop Sciences.

The project will look at how temperature affects major plant processes such as photosynthesis and respiration.

“Higher temperatures in the future may result in accelerated crop growth rate and shorter growing seasons,” says Guan. “There will likely be direct heat stress effects on the various stages in plant reproduction, including number of flowers and pods produced and aborted and the higher temps may increase the plants’ demand for water. All of these factors will play a role in soybean crop yield.”

Guan says the team will combine the temperature free-air controlled enhancement (T-FACE) experiment and a newly developed crop modeling framework (CLM-APSIM).  Infrared heating arrays will be used to heat three soybean varieties, representing the major groups planted across the Midwest for two growing seasons, and multiple physiological and biochemical measurements will be taken simultaneously.

“We will then use the experiment results to improve and calibrate the model at the site level,” Guan says. “Using the calibrated model, we will attribute the historical yield loss due to increase temperature to different physiological mechanisms. Ultimately, we will project crop yield for the whole Corn Belt under the various climate scenarios, and quantify the contribution of each mechanism.”

In addition to being an assistant professor in ecohydrology and geoinformatics in the Department of Natural Resources and Environmental Sciences in the College of Agricultural, Consumer and Environmental Sciences at U of I, Guan has a joint appointment as a Blue Waters professor affiliated with the National Center for Supercomputing Applications (NCSA).



News Source:

Kaiyu Guan
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University of Illinois Plant Clinic publishes 2016 herbicide resistance report

Published January 26, 2017
Palmer amaranth
Palmer amaranth

URBANA, Ill. – The University of Illinois Plant Clinic has been diagnosing plant problems since 1976, but the array of services provided has grown and become increasingly sophisticated in recent years. Two years ago, the Plant Clinic began using molecular protocols to test for herbicide resistance to glyphosate and PPO inhibitors in waterhemp. Last year, they expanded the service to Palmer amaranth and recently added a method for distinguishing waterhemp and Palmer using molecular methods. In a U of I Bulletin post, the Plant Clinic published a report of their findings for the 2016 season.

“Almost twice as many whole fields were tested in 2016 compared to 2015: 593 vs. 338,” says U of I Extension assistant dean for agriculture and natural resources and Plant Clinic director Suzanne Bissonnette.

The clinic received samples from 10 states across the Midwest in 2016, with the majority of samples coming from Illinois. In the 378 samples from Illinois, 48 percent were resistant to both glyphosate and PPO inhibitors. Resistance to both herbicides was detected in 82 percent of samples from Missouri, but only 11 samples were tested from that state.

“Fields with plants that are positive for both glyphosate and PPO inhibitor resistance are of particular concern, due to the limited possibilities for control of these weeds,” says plant diagnostic outreach Extension specialist Diane Plewa.

Palmer amaranth in Illinois was not known to be resistant to PPO inhibitors, but that is no longer the case according to the Plant Clinic results. “Several samples from southwestern Illinois were confirmed to be PPO inhibitor-resistant (three from Madison, and one from St. Clair counties) in our testing,” Plewa reports.

The tests detect the most common mechanism of resistance to the two chemicals: target-site mutations. However, waterhemp and Palmer amaranth are known to use metabolic pathways to detoxify herbicides in other classes. Therefore, even though more than half of the fields sampled in Illinois did not show resistance to glyphosate and PPO inhibitors, farmers should not assume these weeds can be killed by alternative herbicides.

For more information and to see all 2016 testing results, please visit the Bulletin and the Plant Clinic website.



Herbicide resistance goes viral

Published January 24, 2017
Hager and Tranel
Aaron Hager (left) and Patrick Tranel discuss herbicide resistance

URBANA, Ill. – “Think differently. Behave differently. Diversify however you can. Not every practice fits on every acre.” That was the message from University of Illinois weed scientists Aaron Hager and Patrick Tranel when they discussed overcoming herbicide resistance during a Twitter chat last week.

#AskACES Twitter chats have been putting researchers from the College of Agricultural, Consumer and Environmental Sciences in the hot seat for a little more than a year now, challenging them to formulate pithy answers to questions asked live by the public during the hour-long chat.

It was an eye-opening experience for Tranel and Hager. “This morning, I told my son to check out ‘pound-sign AskACES’ during the lunch hour. He said, ‘Dad, that’s a hashtag,’” Tranel said. The concept may have been new to the pair, but they clearly enjoyed the 140-character challenge. Hager jokingly answered many questions with “yup” or “nope,” before being coaxed to provide more detail.

But the pair got a chance to expand on their answers during a podcast recorded immediately following the Twitter chat. Hager and Tranel, who represent U of I Extension and academic research staff, respectively, provided both the scientific context and some practical guidance for the problem of herbicide resistance during the 15-minute interview. 

The discussion ranged from economics to the evolution of herbicide resistance to strategies for farmers to combat the problem in the field.

Bottom line?

“We really have to rethink the idea of simply controlling weeds and give more consideration to how we better manage these populations,” Hager said. “There’s a lot of things that we can do, but one size fits all across the entire state or Midwest? Certainly not. Using a lot of little hammers in the long run is going to be much more sustainable than any one big hammer.” 

That’s 354 characters, in case you’re counting.

Find the podcast and more in the #AskACES series at the ACES website and on Twitter.

Potential biological control agents found for fungal diseases of soybean

Published January 24, 2017
Soybean fungus infected with mycovirus has little effect on leaves.
  • Fungal diseases cause yield losses in soybeans and many other crops.
  • A new study identifies viruses that affect important fungal pathogens, including some that are virulent and stable in the environment.
  • Fungal viruses could be used to create biological control agents to kill pathogenic fungi and improve crop yield.
  • Although the research focuses on fungal viruses affecting soybean, the results have implications for human health, as well.

URBANA, Ill. – Viruses are everywhere. They affect all forms of life, from complex mammals down to the mere fungus. We may not give much thought to fungal viruses, or mycoviruses, but new research from the University of Illinois suggests they deserve a closer look.

“There’s been a lot of work done with human and animal and plant viruses. There isn’t as much known about fungal viruses or insect viruses, because if they get infected with a virus, no one cares,” explains U of I and USDA ARS virologist Leslie Domier.

It turns out there are good reasons to care about mycoviruses. Fungal diseases account for approximately 10 percent yield losses annually in corn and soybean. When certain mycoviruses infect those fungi, they can become less virulent – good news for crop yields. These forms were the targets of a recent investigation by Domier and his colleagues.

“In addition to viruses that make fungi less virulent, we were also looking for those that might be transmitted outside of the fungus the way a cold virus is transmitted, where you can pick it up off a surface without having direct contact with another person. Therefore, we were particularly interested in viruses that were encapsidated, or that formed virus particles,” Domier explains.

The team extracted genetic material, DNA and RNA, from five major types of plant-pathogenic fungi and used computers to search for genetic sequences that resembled those of known viruses.       

“We found a lot of sequences that were very similar to previously described fungal viruses, but we also found some encapsidated forms that were similar to plant viruses. Those were the ones we were most interested in, because they reduce fungal virulence and can be transmitted outside the fungus,” he says.  

This key combination may make it possible for these viruses to be used as biological control agents. “Some mycoviruses have been shown in laboratory or greenhouse studies to be very effective biocontrol agents,” Domier says. One day, the encapsidated forms they discovered may be sprinkled on a field to kill pathogenic fungi and improve soybean yield.

Interestingly, the research could also improve medical treatment options for human fungal diseases.

“The biochemical pathways in fungi are relatively close to humans, so it’s often difficult to find something that will kill a fungus and not damage the person. Ultimately, we are hoping to explore whether we can use mycoviruses to reduce the severity of human disease to the point where normal immune response could clear the disease from the body,” Domier says.

The article, “Identification of diverse mycoviruses through metatranscriptomics characterization of the viromes of five major fungal plant pathogens,” is published in the Journal of Virology. The research was funded by the National Sclerotinia Initiative and the United States Department of Agriculture’s Agricultural Research Service.

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Boxwood blight confirmed in Illinois

Published January 23, 2017
boxwood branch

URBANA, Ill. - Boxwood blight, a serious fungal disease, has been confirmed in Illinois. According to a University Diagnostic Outreach Extension Specialist, two boxwood samples were submitted to the University of Illinois Plant Clinic in late 2016. The samples came from Lake and Cook Counties in northeastern Illinois. Both were from recent landscape additions.

“Although the characteristic leaf spots were not apparent on the samples, defoliation and stem cankers were noted,” says Diane Plewa. 

The samples were quarantined and, after sufficient incubation, fungal spores consistent with the Calonectria spp. fungi were recovered. The Illinois Department of Agriculture was notified, and samples were sent to the United States Department of Agriculture Animal Plant Health Inspection Service Laboratory in Maryland, where the genus identification was confirmed. Species identification is ongoing. 

“To our knowledge, the infected plants where not from Illinois production facilities,” Plewa adds.

Symptoms of boxwood blight include leaf spots, stem cankers, and defoliation. Leaf spots usually appear as light or dark brown circular lesions, often surrounded by a large yellow halo. If the infection occurs near the margin of the leaf, the lesion may be semi-circular or V-shaped. Stem cankers are easiest to see on new, green stem tissue. The cankers are dark brown or black, and are often linear or diamond-shaped.

“Defoliation occurs as the final symptom,” says Suzanne Bissonnette, director of the U of I Plant Clinic.

“Because these symptoms can be similar to other, common fungal and environmental problems on boxwood, we strongly suggest submitting samples to the U of I Plant Clinic for confirmation. We recommend scouting boxwood and pachysandra plants, especially those that were installed in the last few years or plants that are near host plants that were planted recently.”

Boxwood blight is a potentially devastating disease affecting members of the Buxaceae family. The disease has been found on boxwood, pachysandra, and sarcococca. The disease is caused by the fungi Calonectria pseudonaviculata (syn. Cylindrocladium pseudonaviculatum and C. buxicola) and Calonectria henricotiae. To date, C. henricotiae has not been found in the United States.

Bissonnette adds that boxwood blight was formerly federally regulated, but is now regulated at the state level. “Although it can cause widespread death of hosts in the environment, the spores of the pathogen do not appear to travel extensively, reducing its overall impact. However, in production facilities where equipment can be contaminated and expose hundreds or thousands of plants, the pathogen is a much larger concern.”

The pathogen was identified for the first time in the United States in 2011, and has since been found in 18 states. Most are located in the eastern part of the country, though confirmations have been made in Missouri and Ohio.



Calling Illinois soybean growers

Published January 19, 2017

URBANA, Ill. – Last spring, a new multi-state research project funded by the North Central Soybean Research Program was initiated to investigate the effects of weather, soils, and management on soybean yields. The project’s University of Illinois leader put out a call to soybean farmers to help gather data for the project.

“We were looking to gather basic information on at least 500 Illinois soybean fields for each of the crop years 2014 and 2015; the project runs through 2017,” says U of I crop sciences professor Emerson Nafziger. “We appreciate that some farmers provided information, but we ended up with less than a quarter of the fields we needed for the first two seasons.”

The team is asking for help to fill in the holes. Producers are asked to provide information for up to four soybean fields on a form (one per crop year, 2014 to 2016). The form is located at

The form requests about 20 pieces of information for each field, including field location, planting date, variety, and seeding rate. Most farmers will be able to record information for a field in 10 or 15 minutes.

“This project can be described as a search to find what we should work on next with regard to soybean research. The goal is to have thousands of fields in a large database, then to see how soil, weather, and management interact to produce yield,” Nafziger explains.

Nafziger encourages FFA and college students to participate, giving them experience with scientific studies and a reward for their efforts.

To provide an incentive, anyone who fills out information forms and returns a gift card request form along with the information sheets will receive a $50 gift card.

“The more fields we’re able to get information on, the more useful this effort will be,” Nafziger explains. “As the largest and best state for soybean production, we are hoping to produce the largest and best set of information of all states involved in this effort.”

Farmers who want to participate can fill out the form posted at the link given above, or can contact Nafziger at or to have forms sent by email. The project is also described on the Bulletin.