College of ACES
College News

Two new mechanisms for herbicide resistance found in Palmer amaranth

Published April 4, 2017
palmer amaranth infestation
Palmer amaranth infestation
  • Last year, scientists discovered a gene mutation responsible for Palmer amaranth’s resistance to PPO-inhibiting herbicides.
  • Because not all PPO-resistant Palmer amaranth plants had the mutation, University of Illinois researchers went looking for another explanation.
  • The team discovered two additional mutations that confer resistance to PPO-inhibitors, and developed a diagnostic test can be used in other labs.

URBANA, Ill. – Palmer amaranth is a nightmare of a weed, causing yield losses up to 80 percent in severely infested soybean fields. It scoffs at farmers’ attempts at control, having evolved resistance to six classes of herbicides since its discovery in the United States 100 years ago. And now, scientists have discovered it has two new tricks up its sleeve.

About a year ago, a group of researchers discovered Palmer is resistant to the herbicide class known as PPO-inhibitors, due to a mutation—known as the glycine 210 deletion—on the PPX2 gene.

“We were using a quick test that we originally developed for waterhemp to determine PPO-resistance based on that mutation. A lot of times, the test worked. But people were bringing in samples that they were fairly confident were resistant, and the mutation wasn’t showing up. We started to suspect there was another mechanism out there,” says University of Illinois molecular weed scientist Patrick Tranel.

Tranel and his colleagues decided to sequence the PPX2 gene in plants from Tennessee and Arkansas to see if they could find additional mutations. Sure enough, they found not one, but two, located on the R98 region of the gene.

“Almost all of the PPO-resistant plants we tested had either the glycine 210 deletion or one of the two new R98 mutations. None of the mutations were found in the sensitive plants we tested,” Tranel says.

Furthermore, some of the resistant plants had both the glycine 210 deletion and one of the new R98 mutations. Tranel says it is too early to say what that could mean for those plants. In fact, there is a lot left to learn about this resistance mechanism.

“We don’t know what level of resistance the new mutations confer relative to glycine 210,” Tranel says. “There are a lot of different PPO-inhibiting herbicides. Glycine 210 causes resistance to all of them, but we don’t know yet if the R98 mutations do.”

The team is now growing plants to use in follow-up experiments. Tranel hopes they will be able to determine how common the three mutations are in any given population. “That way,” he says, “when a farmer sends us a resistant plant and it doesn’t come back with the glycine 210 deletion, we will be able to tell him how likely it is that he’s dealing with another one of these mutations.”

In the meantime, other research groups or plant testing facilities could use the new genetic assay to detect the mutations in Palmer samples. Tranel hopes they will. “The more labs testing for this, the more we learn about how widespread the mutation is,” he says.  

The article, “Two new PPX2 mutations associated with resistance to PPO-inhibiting herbicides in Amaranthus palmeri,” is published in Pest Management Science. The work was supported by a grant from the USDA’s National Institute of Food and Agriculture.

UI study determines areas vulnerable to riparian erosion

Published April 3, 2017
Fort Cobb watershed in Oklahoma
  • Riparian erosion is one of the major causes of sediment and contaminant load to streams.
  • Soil type and land use are two of the most important variables in riparian erosion.
  • Identifying the most vulnerable areas for riparian erosion allows conservation and management practices to focus on areas needing the most attention and resources.

Urbana, Ill. - Researchers at the University of Illinois collaborated with colleagues in Oklahoma to identify areas along a riparian zone, that is, alongside rivers that are susceptible to erosion.

Maria Chu, an assistant professor in agricultural and biological engineering (ABE), and Alejandra Botero-Acosta, a Ph.D. student in ABE, developed a modeling framework which they used to identify those areas in the Fort Cobb Reservoir Experimental Watershed (FCREW) in southcentral Oklahoma. The FCREW has three sub-watersheds: Cobb, Lake, and Willow. Chu, Botero-Acosta, and their colleagues used readily available USDA environmental data from the area.

“A healthy riparian buffer intercepts suspended solids, nitrogen, and phosphorous,” says Botero-Acosta, “reducing sediment load and nutrient pollution in the rivers. We found in our literature review that 50 percent of the sediments in the river were coming from the riparian zone. We wanted to identify those locations so conservation and management practices can be focused on those points.”

Predicting riparian erosion at the watershed scale is challenging because of the complex interactions between the different variables that govern soil erosion and the inherent uncertainties in measuring those processes. In this study, Botero-Acosta says they found that soil type and land use were the two most important variables.

“The most vulnerable areas for erosion were found to be located at the upper riparian zone of the Cobb and Lake sub-watersheds. The soil there is sand and silt, which is very prone to erosion,” she says. “Land use was also important. Livestock grazing and row crops thinned the vegetation, so that increased erosion.”

Hydrological variables that are dynamic, such as rainfall, lateral and overland inflow, and discharge, were not as significant in predicting the location of erosion. However, Botero-Acosta says “In order to convert flow into velocity, we needed a cross section of the river, and we didn’t have that data. For future work, implementing that kind of data will give us better results regarding hydrological variables, because we do think that discharge can affect riparian erosion.”

Botero-Acosta says mitigating riparian erosion is ultimately beneficial to the population at large. “A watershed provides ecosystems services to the community, which people sometimes take for granted. Fresh water to drink, water to irrigate crops, oxygen-rich water to support fish populations, those are all connected to a healthy watershed.”

Chu will be conducting a similar study in the Upper Sangamon Watershed, near Decatur. The Sangamon watershed is almost twice the size of the Fort Cobb watershed, and the area is approximately 90 percent agricultural, as opposed to 60 percent agricultural in Oklahoma. Chu received funding from the USDA’s National Institute of Food and Agriculture to do a hydrologic assessment of the watershed. The study will use a suite of hydrologic and environmental models to simulate different land management practices and their effects on ecosystems services such as water clarity, nutrient reduction, and fish species richness.

The Fort Cobb study, “Riparian erosion vulnerability model based on environmental features,” is written by Chu and Botero-Acosta, along with colleagues Jorge Guzman, research hydrologist at the Center for Spatial Analysis, University of Oklahoma; Daniel Moriasi, research hydrologist at USDA-ARS Grazinglands Research Laboratory, El Reno, Oklahoma; and Patrick Starks, soil scientist at USDA-ARS Grazinglands Research Laboratory, El Reno, Oklahoma. It appears in the Journal of Environmental Management, and a pdf of the full paper is available online.



Implications of the Prospective Plantings and Grain Stocks reports for corn and soybeans

Published April 3, 2017

URBANA, Ill. – On March 31, the USDA released the Prospective Plantings and Grain Stocks reports. The Grain Stocks report gives an opportunity to assess the pace of consumption for corn and soybeans during the current marketing year.  The Prospective Plantings report provides the first indication of the potential size of corn and soybean crops during 2017.

The following analysis from University of Illinois agricultural economist Todd Hubbs recaps the information in corn and soybean markets provided in the reports and the price implications associated with them.  

March 1 corn stocks were estimated at 8.62 billion bushels. The stocks estimate allows for a calculation of feed and residual use of corn during the second quarter of the 2016-17 marketing year. Total disappearance during the quarter was 3.77 billion bushels. Estimates of corn exports during the quarter are at 552 million bushels. Corn used for ethanol and co-product production during the quarter totaled 1.386 billion bushels. Corn processed domestically for other food and industrial products was likely near 360 million bushels.

The remaining disappearance, estimated at 1.482 billion bushels, consists of the feed and residual category. Feed and residual use during the first half of the marketing year are estimated at 3.776 billion bushels. Feed and residual use during the first half of last year accounted for 68 percent of the marketing-year total of 5.550 billion bushels. Based on current stocks estimates, it appears feed and residual use this year may not reach the projection of 5.550 billion bushels and could be adjusted by USDA in the next World Agricultural Supply and Demand Estimates report.

March 1 soybean stocks estimates indicated 1.73 billion bushels, which came in above trade expectations. The stocks estimate allows for a calculation of seed and residual use of soybeans during the second quarter of the 2016-17 marketing year. Total disappearance during the first half of the marketing year was 2.78 billion bushels. Exports during the first half of the marketing year are estimated at 1.65 billion bushels. Soybean crush during the first half totaled 976 million bushels. Seed and residual use calculations proceed from the remaining disappearance adjusted for soybean imports. Seed and residual use for the first half of the marketing year are estimated at 158.1 million bushels. 

Corn producers reported intentions to plant 90 million acres of corn this year, 4 million less than planted last year. Soybean planting intentions indicated farmers plan to plant 89.5 million acres of soybeans. The soybean acreage intentions came in at the high end of market expectations.  This switch is particularly prominent in the western Corn Belt. North Dakota, South Dakota, Nebraska, Minnesota, and Kansas each produced record-high soybean acreage planting intentions. The current harvest futures price ratio between corn and soybeans sits at 2.44. The current price ratio is significantly lower than the 2.57 level on March 1 before the survey on planting intentions commenced. Depending on field conditions during the planting season, the changing price relationship suggests that some producers could plant more corn acreage than reported in March but it requires a significant shift in the current price ratio relationship.  The June Acreage report will provide more clarification.

In addition to the allocation of acreage to particular crops, the magnitude of total principal crop acreage shows a 2.3 million acre decrease from 2016. The USDA estimates that acreage planted to principal crops in 2017 will total 316.9 million acres. The planned reduction in total planted acreage from a year ago is particularly acute in feed grain crops.

  • Sorghum acreage is projected to be 933,000 acres lower than a year ago at 5.76 million acres.
  • Winter wheat acreage decreased 3.4 million acres to 32.74 million acres. 
  • Barley and oats decreased by 504,000 and 119,000 acres respectively.

The lower levels of prospective planting for feed grains in 2017 highlights the importance of yields in 2017 as a key factor in feed grain prices.

The high March 1 stock numbers provide some bearish sentiment for old-crop corn and soybean prices in 2017. The larger-than-expected soybean stock number may have some implications for the size of the 2016 soybean crop, but the final estimate will not be known until September. The large corn stocks number impact the consumption of corn in the feed and residual category directly during the current marketing year and an expectation of reduced feed and residual use is prudent moving forward.

Planting intentions confirmed the belief that farmers would switch to soybean production in 2017. The large Brazilian soybean crop this year combined with stable demand over the next marketing year gives an indication of lower prices for soybeans next marketing year. The lower corn planting intentions provide some support for corn prices despite the large March 1 stock estimate.  If consumption maintains its current pace, the 2017-18 marketing year should see stable-to-higher corn prices.


New lecture series named for renowned aquatic biologist

Published March 29, 2017
James R. Karr
James R. Karr

URBANA, Ill. – What makes a stream or river healthy? In the years following the growth of the environmental movement in the United States and passage of the Clean Water Act, researchers and managers struggled with this question of just how to measure the condition of our waters.

One prominent answer came from the University of Illinois, where alumnus and faculty member James R. Karr proposed the idea of an “index of biotic integrity” (or IBI) in 1981. Karr’s central solution to the question of measuring river health was to use the organisms that live in freshwaters to tell us about their condition – a concept that has subsequently been widely adopted in the United States to evaluate and enforce Clean Water Act compliance, as well as similar management goals internationally.

Karr’s first IBI used fish communities of the Midwest to determine the condition of rivers on a gradient from the highly impaired or even fishless, like parts of the Chicago River at the time, to more healthy rivers with intact native fish communities, such as the Embarras River south of Champaign-Urbana. Yet over time, the IBI method has evolved to include a suite of additional freshwater organisms, from algae to insects, that can help us understand if rivers and streams are receiving too many nutrients, too much sediment, or are experiencing modifications to their flow or temperature regimes beyond the range that their organisms can tolerate. The IBI concept even jumped to marine and terrestrial ecosystems, where managers and scientists have sought to use vegetation or bird communities to tell us about the condition of land and water. Karr’s publications proposing and developing the IBI remain among the most influential papers ever published in the fields of fisheries and freshwater biology, continuing to be cited by researchers and influence policy and management every year.

In recognition of his contributions to aquatic biology and environmental management, a new James R. Karr Lecture in Aquatic Biology will kick off on Friday, April 14 with an inaugural address from its namesake. Co-sponsored by the University of Illinois Department of Natural Resources and Environmental Sciences in the College of Agricultural, Consumer and Environmental Sciences and the Illinois Natural History Survey within the Prairie Research Institute, this lecture series will seek to bring a prominent scientist to campus every year to interact with faculty, staff, and students, and give a public lecture in the spirit of Karr’s efforts to conduct integrative science in the service of environmental issues and aquatic biology.

The lecture will begin at 3 p.m. on Friday, April 14 in the Monsanto Room of the College of ACES library at 1101 South Goodwin Avenue, Urbana.

“Clean water is not enough to ensure healthy rivers” is the title of Karr’s April 14 lecture.

About his talk, Karr says “For most of the twentieth century, water managers remained largely unaware of the collapse of aquatic ecosystems. They saw water narrowly, as a fluid to be consumed or used as a raw material in agriculture or industry. The 1972 Clean Water Act call to ‘restore and maintain the chemical, physical, and biological integrity of the Nation’s waters’ did not halt the declines. Efforts to protect water resources emphasized control of chemical contaminants; preserving aquatic life was not the intent.”

According to Karr, development of the index of biotic integrity provided a more integrative approach to measuring the biological status of streams. In addition, framing the ways people alter aquatic communities in terms of water quality, flow regime, physical habitat structure, energy source, and biotic interactions opened the door to a better understanding of the causes of water resource declines.

“IBI and what I call the five-factor model explicitly recognize the many connections between aquatic and terrestrial ecosystems and show that protecting chemical water quality alone is not enough to conserve or rehabilitate life in streams. Direct biological monitoring and assessment furnish a mechanism to directly assess the condition of water bodies, diagnose the causes of degradation, define actions to attain conservation and restoration goals, and evaluate the effectiveness of management decisions. These tools are now used by water managers throughout the world in diverse aquatic and terrestrial ecosystems. But society is still short on agency and political leadership needed to protect and restore living systems.”

Karr’s cosmopolitan career included far more than just developing the IBI concept. Following his Ph.D. in ecology from the University of Illinois, he worked as a professor at Purdue University, Virginia Tech, the University of Washington, and his alma mater from 1975 to 1984. He also served as deputy director of the Smithsonian Tropical Research Institute in Panama during the 1980s. His broad interests outside of freshwater biology include ornithology, tropical forest ecology, and environmental policy. He published highly influential papers on the community ecology of birds and their forests in both the tropics and Illinois, and trained a generation of successful scientists. He is a fellow in the American Association for the Advancement of Science, and received major career achievement awards from the American Fisheries Society and Society for Freshwater Science.

Kurt Faush, a professor in fisheries at Colorado State University who worked with Karr at the University of Illinois as a post-doctoral researcher, says “Jim Karr is a unique scientist, whose interests range from testing theories in community ecology to applying ecological principles to solve watershed management problems. He was a supportive and inspiring mentor to those of us privileged to work with him. He encouraged us to think big, and by his own example showed us how a scientist could work beyond the boundaries of science and outside their comfort zone to make a real difference.”

One of Karr’s former U of I doctoral students, Paul Angermeier, who is currently the assistant leader of the United States Geological Survey Cooperative Fish and Wildlife Research Unit at Virginia Tech says, “Jim has for several decades been a tireless advocate for applying sound science to environmental issues. His approach to these issues is consistently integrative, innovative, and synthetic. Remarkably, he is equally capable of seeing the biological world through the eyes of birds, fishes, insects, and corals. His thinking and analysis goes well beyond ecology to explore how knowledge from disciplines such as anthropology, economics, law, medicine, and political science figure into solving today’s wickedly complex environmental problems. Jim was doing ‘sustainability science’ decades before it was labeled as such.”

The James R. Karr Lecture in Aquatic Biology is free and open to the public.

Revisiting corn and soybean planting date

Published March 28, 2017

URBANA, Ill. – Unusually warm, dry weather in the past month has led some central Illinois growers to get a jump on fieldwork. While there is nothing wrong with getting fields in shape early, University of Illinois crop sciences professor Emerson Nafziger says that planting well ahead of normal is unlikely to result in higher yields.

“We know that some corn and possibly some soybeans were planted as early as February this year,” Nafziger says. “While there were reports in 2016 of higher yields from early- compared to late-planted crops, ‘the earlier the better’ typically doesn’t work well when it comes to planting corn or soybeans. Yields are usually no higher for crops planted in March or early April compared to those planted in late April or early May, so there’s little reward for taking the risk of very early planting.”

The primary cause of stand loss in both crops is heavy rainfall soon after planting; Nafziger says stand problems due to wet soils are as common with May planting as with April planting. The danger of frost damage, which was once a major reason to delay planting, is not as significant for either crop these days, but it is higher with very early planting.

Planting very early also affects insurability and, if the crop needs to be replanted, can increase production costs. For corn, the earliest insurable dates for planting are April 10, April 5, and April 1 for northern, central, and southern Illinois, and for soybean they are April 24, April 20, and April 15.

Nafziger’s recent research shows that, on a percentage basis, yield penalties from delayed planting are almost identical for corn and soybean. That is a departure from earlier findings that showed corn yield declined faster than soybean yields as a result of planting delays through May.

“Our long-held idea of planting corn first and then starting to plant soybean requires rethinking and possible adjustment,” Nafziger says. “One approach is that those with more than one planter might start planting both crops at the same time rather than finishing corn first. If planting is delayed past mid-May, though, then planting corn becomes a higher priority because corn yield declines more quickly than soybean yield when planting is very late. Of course, we hope that we can get both crops planted by early May so they can get off to a good start.”

Visit the Bulletin for more details and help in making planting decisions.

How to get adults to eat their vegetables? Study explores potential of spices and herbs use

Published March 28, 2017
Cassandra Nikolaus (left) and Brenna Ellison.

URBANA, Ill. - Parents may have their tricks to get kids to eat their vegetables, but what about getting adults to eat theirs?

According to recent reports, most Americans, of all ages and genders, do not meet the recommended vegetable intake of 2 to 3.5 cups per day, consuming an average of only 1.5 cups per day. Although tactics such as providing vegetables as a juice or hidden as a puree in entrees have been suggested, many people still say no thanks to vegetables, citing adverse taste perception.

Researchers at the University of Illinois interested in developing interventions to encourage adults to make better food choices are investigating whether using more spices and herbs, like ginger, curry, rosemary, or garlic, for example, can help adults consume more vegetables as part of their diet.

Cassandra Nikolaus, a nutrition doctoral student at U of I, says that for registered dietitians, recommending the use of spices and herbs to promote healthy food choices is already encouraged. “If you use spices and herbs to flavor up your dishes, then you’re not adding sodium or fat, which we are trying to reduce in the diet, generally,” she says.  

But Nikolaus and Brenna Ellison, an assistant professor of agricultural and consumer economics at U of I conducted a study to first establish which consumers already use spices and herbs, and to determine how they use them. The results are published in the American Journal of Health Behavior.

“We want to see if spices and herbs can be a facilitator to increase vegetable intake, but what’s not in the literature so far is how people use them, or which ones they use,” Ellison says. “We really don’t know much about that. So this was the first attempt, to help inform future studies, to see which spices and herbs are well liked and frequently used. And, who is using them? This information can help us identify target populations for study interventions and provide insight on the best spices and herbs to promote to these groups.”

In their study, the researchers collected information on what spices and herbs consumers like, how frequently they use them, whether they are used when cooking vegetables, and whether the participants feel proficient in cooking with spices and herbs. Participants were given a list of 20 spices and herbs to choose from.

Nikolaus says the results were surprising.

Younger respondents in the survey (18-29 years) and those who identified as Asian/Pacific Islander or other used 19 of the 20 spices and herbs more frequently than their older and white/Caucasian, African-American, or Hispanic counterparts. Women were more likely to use spices and herbs when cooking at home. Women and individuals ages 18-49 felt more confident in their ability to cook with spices and herbs, while those who identified as white/Caucasian or those with an annual income below $50,000 exhibited less confidence.

“The high level of variability across groups was the biggest takeaway,” Nikolaus says.   

But does identifying these socio-demographics really matter when trying to get adults to eat more vegetables?

Ellison says it does.

For one thing, Ellison explains that the data show that age and cultural differences were linked to which ones, out of the 20 spices, people were more inclined to like or use. For example, she says that older participants were less inclined to like and use bolder spices and herbs like cayenne pepper or cilantro and tended to stick to milder flavors such as paprika or garlic.

Knowing information like that can help dietitians or other health educators when developing intervention strategies. Nikolaus explains, “There are so many community education efforts that are already underway. If they have one more piece of evidence to determine recipes for certain groups of people, they can select something more well-liked by that population.”

As part of the study, Nikolaus created a chart categorizing which spices were most well-liked, less well-liked, and least well-liked, based on the demographic subpopulations that participated in the study. Ellison says this is a resource that nutrition or health educators can use as they make recommendations for healthier food choices.

Another piece of information the researchers learned from the study is that some people simply don’t feel confident in cooking vegetables, or cooking with spices and herbs.

“What can we do to educate these groups of people on how to use spices and herbs in hopes of improving their vegetable consumption? One issue may be limited knowledge on how to cook vegetables in the first place,” Ellison says. “We actually had questions on the survey about which cooking methods people used. Boiling and steaming were the most common cooking methods, so spices and herbs might be useful there to enhance flavor.”

Nikolaus adds that along with low knowledge of culinary techniques, the availability of specific cooking equipment—think zucchini spiralizer—might also determine if (and how) consumers will prepare vegetables for themselves.

The researchers, as part of a larger team, are currently collecting data in an actual dining setting, observing diners’ consumption of vegetables when spices or herbs have been added. They want to see if diners choose the vegetables that have been cooked with spices and herbs, and if less of those vegetables go to waste.

“Taste is king. That is one of the most powerful reasons behind why we make our food choices,” Nikolaus says. “If we can make things more appealing based on spices and herbs and flavors that people are more prone to appreciate, they may choose to eat more vegetables because they enjoy what they are consuming.”

“Spice and herb use with vegetables: Liking, frequency, and self-efficacy among U.S. adults” is published in the American Journal of Health Behavior. Co-authors include Cassandra J. Nikolaus, Brenna Ellison, Pamela A. Heinrichs, Sharon M. Nickols-Richardson, and Karen M. Chapman-Novakofski, all of the University of Illinois.

This research was supported by a grant from the McCormick Science Institute.