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New method developed for testing herbicide resistance in weeds

Published April 7, 2016
waterhemp
waterhemp growing in the greenhouse
  • Herbicide-resistant weeds are becoming increasingly common in agricultural landscapes.
  • Existing methods for confirming herbicide resistance require knowledge of the genes responsible for target-site resistance, but this information is not always known.
  • A new method, developed by University of Illinois researchers for waterhemp, can test for herbicide resistance without prior knowledge of the genes involved.

URBANA, Ill. – Ask any farmer, and you’ll hear that weeds are a major headache. Even worse are weeds that have developed resistance to the herbicides designed to kill them. This is the case for waterhemp, a broadleaf weed commonly found in corn and soybean fields. Many populations of waterhemp and its aggressive cousin, Palmer amaranth, have become resistant to atrazine, mesotrione, and a number of other commonly used herbicides, sometimes leading to significant yield losses in corn and soy crops.

“If you continue to spray the same herbicide on plants, there is a chance that a very small number of them will survive and reproduce. Some of their offspring will be resistant to the herbicide. By using the same herbicide over generations, we are selecting for weeds that are resistant to that chemical,” says University of Illinois postdoctoral researcher Rong Ma.

Plants use a variety of mechanisms to avoid the toxic effects of herbicides. The most common mechanism, known as target-site resistance, comes from a gene mutation that keeps the herbicide from attaching to the proteins it is designed to destroy. The presence of these mutations in waterhemp populations can be quickly tested genetically, if the site of the mutation is known in advance. 

Another mechanism is known as metabolic resistance. In this case, the plant uses common enzymes to detoxify the herbicide before it even reaches the protein it is meant to destroy.

“Humans also have these broad, detoxifying enzymes. They can help detoxify drugs or chemicals we consume,” Ma explains.

The enzymes responsible for metabolic resistance aren’t always known, although they generally fall into one or two broad classes, P450s or GSTs.

“The problem is that plants have hundreds of these P450s or GSTs and we haven’t yet identified which are responsible for resistance to the particular herbicide,” says U of I weed scientist Dean Riechers.

Since the genes for those enzymes are usually unknown, it is not possible to test for them using the traditional genetic methods. Ma, along with a team of researchers at U of I led by Riechers, have developed a new technique that can accurately test for metabolic resistance without relying on knowledge of the specific gene(s) involved.

The new method involves exposing a single small leaf blade to a radioactively labeled herbicide and then determining how much of the herbicide is left after the leaf has a chance to metabolize it. The less herbicide remaining over time, the more resistant the plant is.

The study tested three populations of waterhemp and two herbicides, mesotrione (Callisto®, an HPPD inhibitor) and primisulfuron-methyl (Beacon®, an ALS inhibitor). Although different populations appeared to detoxify the two chemicals using different biochemical mechanisms, the new method worked for both.

“The method should work for additional herbicides and even different weeds or crops,” Riechers says. “We tested a third herbicide using the method with excised soybean leaves, and it worked. And as long as the leaf or petiole can fit in the tube, it should work for almost any plant.”

Although the new method does not pinpoint the exact genes responsible for enhanced herbicide metabolism in resistant populations, it does indicate the general class of genes and the mechanism involved. The next step for the research team is to identify specific genes and eventually develop markers for rapid testing using conventional genetic methods.

Riechers says that other universities and companies are already using the new technique.

The article, “Measuring rates of herbicide metabolism in dicot weeds with an excised leaf assay,” is published in the Journal of Visualized Experiments. Joshua Skelton, also from U of I, was a co-author on the article with Ma and Riechers. Funding was provided by Syngenta Crop Protection.

A 10-minute video offering a step-by-step description of the new method accompanies the article; both are available at http://www.jove.com/video/53236?access=6gkjgqfs.

High resolution images are available for this story at http://www.jove.com/video/53236?access=6gkjgqfs

Can urban gardeners benefit ecosystems while keeping food traditions alive?

Published April 5, 2016
urban garden
  • Urban gardeners have the potential to contribute to ecosystem services by growing a diverse array of plants that could benefit wildlife.
  • In Chicago, African American, Chinese-origin, and Mexican-origin gardeners grew a wide variety of plants, but their use of synthetic fertilizer and avoidance of shade trees may limit benefits to the ecosystem.
  • Each cultural group grows unique crops that contribute to food security and a sense of community.

URBANA, Ill. – When conjuring up an image of a healthy ecosystem, few of us would think of a modern city. But scientists are increasingly recognizing that the majority of ecosystems are now influenced by humans, and even home gardens in urban landscapes can contribute important ecosystem services.

“Ecosystem services are the benefits that ecosystems provide to humans. In a natural ecosystem, these are things like natural medicinal products or carbon that’s sequestered by forest trees. In an urban context, it would be similar types of things. For example, shade from trees provides microclimate control to keep us more comfortable,” explains University of Illinois landscape agroecologist Sarah Taylor Lovell.  

Lovell and her colleagues investigated the ecosystem services and disservices provided by home food gardens in Chicago, adding a cultural dimension by looking at gardening practices in specific ethnic communities. In an earlier study, they found a high density of food gardens in Chicago were in African American, Chinese-origin, and Mexican-origin communities.

The team visited and interviewed nearly 60 households across the city, noting the types and relative abundance of the edible plants, ornamental plants, and trees in each garden.

“The number of species grown across all of the gardens was comparable to the number of species found in a remnant native prairie near Chicago,” Lovell reports. “But the vast majority of garden species were not native to the region.”

The number of plant species in an area can have a direct impact on insects, birds, and other wildlife, but non-native crops may not benefit wildlife in an urban context to the degree that native plants might. The researchers identified additional consequences to urban food gardens in terms of ecosystem services.

“Most of the gardeners were using synthetic fertilizers to really optimize production,” Lovell explains. “In doing so, they were increasing some nutrients to a level that could lead to runoff and contamination of surrounding environments. We also identified a tradeoff between needing sunlight for your vegetable garden and preferring a treed habitat for microclimate control. Gardeners would sometimes remove trees or reduce the level of shade and shrubs.”

Despite these issues, the researchers noted that urban gardens play an important role in the cultural lives of gardeners and may lead to greater food security where fresh produce is not easily available.

“Each cultural group was specifically selecting ethnic crops and propagating plants that were familiar to them,” Lovell says. “I think, in some ways, especially for first generation immigrants to Chicago, it’s a way to bring a feeling of home.”

Several food crops, such as squash and herbs in the mint family, were common in many of the gardens, but each cultural group grew plants that were unique to that group. For example, collards and okra were only found in the gardens of African Americans. Only Mexican-origin gardeners grew Papalo and tomatillo, and only Chinese-origin gardeners grew bitter melon, yardlong bean, winter melon, fuzzy gourd, and bok choy.

Chinese-origin gardens had the most unique assemblage of plants overall, whereas there was more overlap between crops grown by African American and Mexican-origin gardeners. Chinese-origin gardeners also were more likely than other groups to utilize all available space for food crop production, often creating tiered trellis structures to maximize space for vines and other twining plants.

The work was innovative in terms of bringing a cultural dimension into the study of urban ecosystem services, but, for the researchers, the bottom line came down to people.

Lovell notes, “It was mainly about the interesting and unique connection between cultures and their foodways. The study demonstrated a special connection between what you can grow, how you grow it, and what your background is. Gardens may have the potential to connect you to a historic past or your own community. If there’s a certain ethnic group in a community, gardening becomes a way to communicate with their neighbors, as a unique social network option.” 

The article, “Ecosystem services and tradeoffs in the home food gardens of African American, Chinese-origin and Mexican-origin households in Chicago, IL,” appears in Renewable Agriculture and Food Systems. Lead author, John R. Taylor, is an assistant professor at Chatham University. Lovell and additional co-authors, Sam Wortman and Michelle Chan, are at U of I. The research was supported by the USDA National Institute of Food and Agriculture Hatch program.

The full text of the article is available at: http://bit.ly/1pNX8XZ.

Corn consumption and acreage

Published April 4, 2016

URBANA, Ill. – The USDA’s March 1 Grain Stocks  report released on March 31 provides an opportunity to assess the progress of corn consumption during the current marketing year and to re-evaluate prospects for the magnitude of year-ending stocks. In addition, the Prospective Plantings report, also released on March 31, provides an opportunity to evaluate the potential size of the 2016 corn crop.

According to University of Illinois agricultural economist Darrel Good, March 1 corn stocks were estimated at 7.808 billion bushels. The stocks estimate allows for a calculation of feed and residual use of corn during the second quarter of the 2015-16 marketing year. Total disappearance during the quarter was 3.45 billion bushels. Exports during the quarter are estimated at 334 million bushels, although the Census export estimate for February 2016 to be released on April 5 will allow for a more accurate estimate for the quarter. Corn used for ethanol and co-product production during the quarter totaled 1.313 billion bushels. Corn processed domestically for other food and industrial products was likely near 335 million bushels. 

“The remaining disappearance, estimated at 1.468 billion bushels, is allocated to the feed and residual category,” Good says. “Feed and residual use during the first half of the marketing year is estimated at 3.641 billion bushels. Use during the first half of the 2015-16 marketing year represents 68.7 percent of the current USDA projection of 5.3 billion bushels to be used during the entire year. Use during the first half of last year accounted for 68.9 percent of the marketing year total. It appears feed and residual use this year is on target to reach the projection of 5.3 billion bushels.”

The USDA currently projects 2015-16 marketing-year corn exports at 1.65 billion bushels. Good says the pace of shipments was very slow during the first half of the marketing year, averaging only 25 million bushels per week.  “With 22 weeks left in the year, corn exports need to average about 38.6 million bushels per week to reach the projected level for the year,” he says. “Weekly inspections averaged 40.1 million bushels per week for the three weeks that ended March 31. With the accelerated pace of shipments and current unshipped sales of 504 million bushels, exports should reach the projected level.”

The USDA projects 2015-16 marketing-year use of corn for ethanol and co-products at 5.225 billion bushels, 0.5 percent more than used last year. Estimates provided by the USDA’s Grain Crushings and Co-Products Production report indicate that 2.614 billion bushels were used for that purpose during the first half of the marketing year, 1.7 percent more than during the same period last year. In addition, sorghum used for ethanol production during the first half of the year exceeded that of a year ago by about 50 million bushels. Ethanol production in March 2016 exceeded that of a year ago by nearly 4.5 percent.

“With domestic gasoline consumption continuing well above the level of a year ago and with ethanol exports remaining strong, it appears that ethanol production and corn use could exceed the current USDA projection,” Good says. “Even with increased use of sorghum, it appears that corn used for ethanol and co-product production could reach or exceed 5.25 billion bushels. Year-ending stocks of corn might be 25 million bushels less than the current USDA projection of 1.837 billion bushels.”

Corn producers reported intentions to plant 93.6 million acres of corn this year, 5.6 million more than planted last year. Increased corn (and cotton) acreage is planned at the expense of wheat and oilseeds. “The surprising acreage intentions resulted in continued adjustment in corn, soybean, and spring wheat prices following the release of the report,” Good says.   

From Feb. 22, when the USDA initiated the month long acreage survey process, through April 1, December 2016 corn futures declined by 21 cents, November 2016 soybean futures increased by 41 cents, and July 2016 spring wheat futures increased by 32 cents. “The changing price relationships suggest that some producers may plant less corn acreage and more acreage of other crops than reported in March,” Good says. “After all, one of the main objectives of the acreage survey is to provide producers with   information to re-evaluate their plans.

“In addition to the allocation of acreage to individual crops, the magnitude of total planted acreage in 2016 is still in question,” Good says.

The USDA estimates that acreage planted to principal crops in 2016 will total 317.3 million acres, 1.2 million less than planted last year and 9.1 million less than planted in 2014. (Intentions for proso millet, rye, tobacco, and summer and fall potatoes for 2016 are not surveyed in March and are assumed to be at last year’s level of 3.97 million acres).

“The planned reduction in total planted acreage from that of a year ago is somewhat of a surprise because 6.7 million acres were reported as ‘prevent plant’ in 2015,” Good says. “It would not be a complete surprise if total planted acreage exceeded March intentions.

“With the continued uncertainty about the magnitude of total planted acreage and the mix of crops, expectations for corn acreage and production will remain in a wide range,” Good says. “For example, planted acreage of 93.6 million acres, harvested acreage of 86 million acres, and an average yield near the USDA’s calculated trend of 168 bushels would result in a crop of 14.448 billion bushels and 2016-17 marketing year-ending stocks near 2.4 billion bushels. Alternatively, planted acreage of 92 million, harvested acreage of 84.4 million, and a yield of 162 bushels resulting from stressful summer weather as the current El Niño episode fades would result in a crop of only 13.689 billion bushels and 2016-17 marketing year-ending stocks near 1.7 billion bushels.” 

 

Biofuel producers with poor soil should consider prairie cordgrass

Published March 31, 2016
Switchgrass and cordgrass
Switchgrass (left) and cordgrass (right) on saline-sodic soil
  • Salt-affected land is not useful for producing food crops, but biomass producers could take advantage of salt-tolerant perennial grasses to make use of that land.
  • In a greenhouse study, germination of prairie cordgrass was greater than switchgrass in high-salt conditions.
  • Three prairie cordgrass accessions and one switchgrass cultivar showed tolerance to high salt conditions in terms of dry biomass production.

URBANA, Ill. – Most prime agricultural land is used to produce food crops, leaving biofuel producers to establish crops on marginal land. The soil on marginal land is often salty, making crop production difficult. But University of Illinois researchers have found several varieties of perennial grasses that can withstand high salt concentrations.

“We evaluated germination and plant growth for prairie cordgrass accessions and switchgrass cultivars in a greenhouse study,” says crop scientist D.K. Lee.

In crop production, too much salt in the soil can interfere with the plant’s ability to absorb water. Water moves into plant roots by osmosis, and when solutes inside root cells are more concentrated than in soil, water moves into the root. In salt-affected soil, the difference in solute concentration inside and outside of the root is not as great, meaning that water may not move in. So, even where soil is moist, plants experience drought-like conditions when too much salt is present.

Certain mineral salts are also toxic to plants. When they are taken up along with soil water, plant tissue damage can occur.

“Saline soils are characterized by high concentrations of soluble salts, such as sodium, chloride, calcium chloride, or magnesium sulfate, whereas sodic soils are solely characterized by their high sodium concentrations,” Lee explains. “Many soils are both saline and sodic.”

The researchers subjected six prairie cordgrass accessions and three switchgrass cultivars to different levels of sodicity and salinity over two years of growth. The team conducted a similar experiment in an earlier study, but only looked at one cordgrass (‘Red River’) and one switchgrass (‘Cave-In-Rock’) cultivar, over only one growing season. 

“In that study, we found that ‘Cave-In-Rock’ switchgrass was not good at all in terms of salt tolerance. ‘Red River’ cordgrass was far superior,” Lee recalls.

The expanded study showed that prairie cordgrass had, on average, much higher germination rates than switchgrass in saline and sodic conditions. Dry biomass production was not as clearly split between the two species in salty conditions, however.

Three prairie cordgrasses, pc17-102, pc17-109, and ‘Red River’, and one switchgrass, EG-1102, produced equivalent amounts of dry biomass when subjected to high-salt conditions. However, they produced approximately 70 to 80 percent less biomass in salty conditions than they did with no added salt. In contrast, the salt-susceptible switchgrass cultivar, EG-2012, produced approximately 99.5 percent less biomass in high-salt treatments than it did without added salt.

The next step for the researchers is to bring this work out of the greenhouse, where climate is controlled and water is unlimited, to real-world scenarios. Preliminary field research has shown that prairie cordgrass is very successful in salt-affected areas in Illinois and South Dakota.

“Even in highly saline soils, prairie cordgrass can do very well. Unlike switchgrass, it can take up salt dissolved in water without getting sick because it can excrete it out through specialized salt glands. Then, once the plants grow deep roots, they can access less salty water,” Lee explains.

More research and agronomic improvements are needed before prairie cordgrass can be recommended widely as a biomass crop, but Lee sees a lot of potential in this species.

“Prairie cordgrass is an interesting species,” he says. “As a warm season grass, I think it is unique in being able to handle low temperatures, and it is also well adapted to poorly drained soils and lands with frequent flooding. And even in high-salt conditions in the field, we’re getting pretty good yields: up to 8 or 9 tons per acre.”

The article, “Determining effects of sodicity and salinity on switchgrass and prairie cordgrass germination and plant growth,” is published in Industrial Crops and Products. Lee’s co-authors, Eric Anderson, Tom Voigt, and Sumin Kim are also from the U of I. The project was funded by the Energy Biosciences Institute.

The article can be accessed at http://www.sciencedirect.com/science/article/pii/S0926669014007031.

One crop breeding cycle from starvation

Published March 29, 2016
seedlings
Seedlings with enhanced photosynthetic capacity
  • Global population growth, urbanization, and a changing climate mean staple food crops will need to achieve much higher yields in the near future.
  • New research proposes genetic engineering solutions to improve photosynthetic efficiency of food crops, boosting yield under higher temperatures and carbon dioxide levels.
  • Because it can take 20 to 30 years of breeding and product development efforts before new crops are available to farmers, those efforts must start now.

URBANA, Ill. – In the race against world hunger, we’re running out of time. By 2050, the global population will have grown and urbanized so much that we will need to produce 87 percent more of the four primary food crops – rice, wheat, soy, and maize – than we do today.

At the same time, the climate is projected to change over the next 30 years, with warmer temperatures and more carbon dioxide (CO2) in the atmosphere. Crop plants can adapt to change through evolution, but at a much slower rate than the changes we are causing in the atmosphere. Furthermore, the land available for growing crop plants is unlikely to expand to accommodate the predicted rise in demand. In fact, land suited to food crop production is being lost on a global scale.

“We have to start increasing production now, faster than we ever have. Any innovation we make today won’t be ready to go into farmers’ fields for at least 20 years, because we’ll need time for testing, product development, and approval by government agencies. On that basis, 2050 is not so far off. That’s why we say we’re one crop breeding cycle away from starvation,” says University of Illinois crop scientist Stephen P. Long.

Researchers at U of I, along with their large, multi-institution team, say a solution lies in genetically engineering photosynthetic mechanisms to take advantage of the projected rise in global temperatures and CO2, and to achieve much higher yields on the same amount of land. 

“The rate of photosynthesis in crops like soy and rice is determined by two factors,” Long explains. “One is the enzyme which traps the CO2: we call that rubisco. Under lower atmospheric CO2 levels and at high temperatures, rubisco can make a mistake and use oxygen instead of CO2. When it uses oxygen, it actually ends up releasing CO2 back into the atmosphere.”

Under higher levels of CO2, such as those projected for future climates, rubisco becomes much more efficient and photosynthesis rates naturally increase as it makes fewer mistakes. The carbon fixed by rubisco is eventually turned into carbohydrates that the plant can use as an energy source for producing grains, fruits, and vegetative structures.

However, rising temperatures are projected to accompany increased CO2. Unfortunately, rubisco’s increased efficiency under high CO2 begins to break down in hot climates. That’s why project partners are looking to improve rubisco so that it will operate efficiently in both high temperature and high CO2 conditions. 

“Our partners are looking at a wide range of rubiscos from different organisms to see whether they can find one that will make fewer of these mistakes in hot climates,” Long says.

But the team is not stopping at improving rubisco.

Long adds, “The second factor that can limit photosynthesis is the rate at which everything else in the leaf regenerates the CO2-acceptor molecule, known as RuBP. As we go to higher CO2 levels, instead of being limited by rubisco, we’re limited by this regeneration step. We’re looking at ways to manipulate the speed of that regeneration.”

The researchers developed mathematical models that showed how, by altering the way nitrogen is divided between parts of the photosynthetic apparatus, more carbohydrate could be made under conditions of higher temperature and CO2 without the crop requiring more nitrogen fertilizer.

The models were then taken for a test-run in the field. Using genetic engineering methods, the team tried to speed up the regeneration of RuBP in tobacco plants while subjecting them to high-CO2 environments. The proof of concept worked: photosynthesis rates and yield increased.

The group’s next step will include tests on staple food crops in controlled environments and in field trials. Long stresses that this potential solution won’t be ready for commercial roll-out for many years, but they won’t give up.

“In the face of the extraordinary challenges ahead, we simply do not have the luxury to rule out the use of any technology that may hold promise to improve crop performance,” he notes.

The article, “One crop breeding cycle from starvation? How engineering crop photosynthesis for rising CO2 and temperature could be one important route to alleviation,” is published in Proceedings of the Royal Society B. Lead author Johannes Kromdijk is also at U of I. The project, Realizing Increased Photosynthetic Efficiency (RIPE), is supported by the Bill and Melinda Gates Foundation.

The full text of the article can be found at: http://rspb.royalsocietypublishing.org/content/283/1826/20152578

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