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Scientists engineer crops to conserve water, resist drought

Published March 6, 2018
Kromdijk, Long, and Glowacka
Kromdijk, Long, and Glowacka

URBANA, Ill. – Agriculture already monopolizes 90 percent of global freshwater—yet production still needs to dramatically increase to feed and fuel this century’s growing population. For the first time, scientists have improved how a crop uses water by 25 percent without compromising yield by altering the expression of one gene that is found in all plants, as reported in Nature Communications.

The research is part of the international research project Realizing Increased Photosynthetic Efficiency (RIPE) that is supported by Bill & Melinda Gates Foundation, the Foundation for Food and Agriculture Research, and the U.K. Department for International Development.

“This is a major breakthrough,” said RIPE Director Stephen Long, Ikenberry Endowed Chair of Plant Biology and Crop Sciences. “Crop yields have steadily improved over the past 60 years, but the amount of water required to produce one ton of grain remains unchanged—which led most to assume that this factor could not change. Proving that our theory works in practice should open the door to much more research and development to achieve this all-important goal for the future.”

The international team increased the levels of a photosynthetic protein (PsbS) to conserve water by tricking plants into partially closing their stomata, the microscopic pores in the leaf that allow water to escape. Stomata are the gatekeepers to plants: When open, carbon dioxide enters the plant to fuel photosynthesis, but water is allowed to escape through the process of transpiration.

“These plants had more water than they needed, but that won’t always be the case,” said co-first author Katarzyna Glowacka, a postdoctoral researcher who led this research at the Carl R. Woese Institute for Genomic Biology (IGB). “When water is limited, these modified plants will grow faster and yield more—they will pay less of a penalty than their non-modified counterparts.”

The team improved the plant’s water-use-efficiency—the ratio of carbon dioxide entering the plant to water escaping—by 25 percent without significantly sacrificing photosynthesis or yield in real-world field trials. The carbon dioxide concentration in our atmosphere has increased by 25 percent in just the past 70 years, allowing the plant to amass enough carbon dioxide without fully opening its stomata.

“Evolution has not kept pace with this rapid change, so scientists have given it a helping hand,” said Long, who is also a professor of crop sciences at Lancaster University.

Four factors can trigger stomata to open and close: humidity, carbon dioxide levels in the plant, the quality of light, and the quantity of light. This study is the first report of hacking stomatal responses to the quantity of light.

PsbS is a key part of a signaling pathway in the plant that relays information about the quantity of light. By increasing PsbS, the signal says there is not enough light energy for the plant to photosynthesize, which triggers the stomata to close since carbon dioxide is not needed to fuel photosynthesis.

This research complements previous work, published in Science, which showed that increasing PsbS and two other proteins can improve photosynthesis and increase productivity by as much as 20 percent. Now the team plans to combine the gains from these two studies to improve production and water-use by balancing the expression of these three proteins.

For this study, the team tested their hypothesis using tobacco, a model crop that is easier to modify and faster to test than other crops. Now they will apply their discoveries to improve the water-use-efficiency of food crops and test their efficacy in water-limited conditions.

“Making crop plants more water-use efficient is arguably the greatest challenge for current and future plant scientists,” said co-first author Johannes Kromdijk, a postdoctoral researcher at the IGB. “Our results show that increased PsbS expression allows crop plants to be more conservative with water use, which we think will help to better distribute available water resources over the duration of the growing season and keep the crop more productive during dry spells.”

The paper, “Photosystem II subunit S Overexpression Increases the Efficiency of Water Use in a Field-Grown Crop,” is published in Nature Communications. Co-authors also include Katherine Kucera, Jiayang Xie, Amanda Cavanagh, Lauriebeth Leonelli, Andrew Leakey, Donald Ort, and Krishna Niyogi.

Realizing Increased Photosynthetic Efficiency (RIPE) is engineering crops to more efficiently turn the sun’s energy into food to sustainably increase worldwide food productivity. The project is supported by the Bill & Melinda Gates Foundation, theFoundation for Food and Agriculture Research, and the U.K. Department for International Development.

RIPE is led by the University of Illinois in partnership with the University of Essex, Lancaster University, Australian National University, Chinese Academy of Sciences, Commonwealth Scientific and Industrial Research Organisation, University of California, Berkeley, and Louisiana State University, and USDA/ARS.

Start your vegetable garden early with cool season crops

Published March 6, 2018
Kale with frost

URBANA, Ill. – After a long winter, gardeners are always eager to get outside again. “Get a head start on your vegetable garden by planting cool-season crops,” says Gemini Bhalsod, a University of Illinois Extension horticulture educator. “Cool spring weather favors vegetables like leafy greens, root vegetables, and members of the onion and cabbage family.”

Most cool-season vegetables, also known as “cold crops,” can withstand light frosts. Cool-season vegetables can be direct-seeded or transplanted outside much earlier than late summer favorites like tomatoes.

Bhalsod explains that these plants are more frost-tolerant than others because the cool weather triggers the plant to produce more sugars, which act as a natural antifreeze for plant tissues. When this happens, we also benefit by getting sweeter tasting produce.

So what plants are cold hardy? “First, we need to go over some definitions,” Bhalsod says. “’Hardy’ plants can withstand the coldest air and soil temperatures. These plants can be planted outside about four weeks before the frost-free date in your area. In some places, that is as early as April. ‘Hardy’ plants include spinach and kale.”

Frost-tolerant, or “half-hardy,” plants can tolerate cool temperatures and can be seeded outdoors in early May, or about two weeks before the predicted frost date in the spring. Frost –tolerant plants include cabbage, carrots, chard, and broccoli.

“Be aware that the frost date is location-based, so check with your local Extension office for specific dates,” Bhalsod suggests.

In general, root crops do not do well being transplanted and should be direct-seeded. Thin seedlings to three to four inches apart, but be sure to read your seed packet to learn your plants’ specific requirements. Thin seedlings when they are a few inches tall and enjoy them as microgreens, or wait until the leaves are bigger and eat the tops.

“With root vegetables, it is important to make sure your soil is loose and well-drained,” Bhalsod says. “This prevents root stunting and gives plants ample space to grow.”

Plants with a longer growing cycle should be started indoors about five weeks before planting outside. Harden plants off by gradually and progressively exposing them to outdoor conditions. This works well for crops like head lettuce, collards, kale, broccoli, cauliflower, and Brussels sprouts. Starting these plants indoors means earlier maturation and harvest.

Most cold crops have two “seasons” in a vegetable garden, one in spring and again in the fall. Avoiding the high temperatures and long days of summer is key. Long summer daylight causes salad greens, for example, to produce flowers and set seed, also called “bolting,” which results in a bitter tasting, unpleasant salad.

No matter what plants you decide to grow, do not forget to plan your garden to get the most out of your space. Stagger your planting times to increase your harvest period and consider intercropping different varieties or plants to maximize your production.

Visit the University of Illinois Extension, “Watch your Garden Grow” website at, for more information.

News Writer:

University of Illinois Extension

A positive outlook for corn

Published March 6, 2018

URBANA, Ill. - A strengthening trend in corn consumption, smaller corn acreage, and the developing production issues in South America signify a positive outlook for corn in 2018. The expectations for corn in the 2018 crop year put forth in this analysis show lower production leading to decreased ending stocks in 2018-19. 

According to University of Illinois agricultural economist Todd Hubbs, “The big ending stocks projected for this marketing-year continue to hang over corn prices and an upward price movement in corn during 2018 appears likely under a reduced production scenario.”

Corn consumption currently is showing signs of building strength in exports, ethanol production, and other domestic uses. As 2018 progresses, an expectation of continued growth in corn consumption is the baseline for this analysis.

“Expectations for the 2018-19 marketing-year for consumption exceed projected production, which leads to a lower level of ending stocks by the end of the marketing year. Corn exports will be influenced by trade policy, world corn production, and economic growth,” Hubbs explains.

While changes in trade policy may impact corn exports over the next year, the following analysis assumes a minimal impact due to trade disruptions. “Corn export projections by the USDA for the current marketing-year sit at 2.05 billion bushels. Current production issues in South America and the competitiveness of U.S. corn export prices increase the probability of exceeding the current USDA marketing-year projection,” Hubbs adds.

Current corn production projections for Brazil (3.7 billion bushels) and Argentina (1.53 billion bushels) appear likely for downward revisions in the upcoming USDA reports due to adverse weather. The potential for 400 million fewer bushels is increasingly probable in the two major South American countries.

With a revision in South American production, world production projections come in approximately 4.5 percent lower in 2018. Building on the strength expected in export markets for the remainder of this marketing-year, 2018-19 corn export projections in this analysis sits at 2.025 billion bushels.

Corn used for ethanol production during this marketing-year continues to show tremendous consumption potential. “Through February 28, an estimate of corn use for ethanol sits slightly above 2.8 billion bushels. An expectation of small increases in gasoline consumption in 2018 and 2019 combined with growth in the ethanol trade balance provide support to the continued increase in corn used for ethanol,” Hubbs says.

Corn used for ethanol expectations increase to 5.57 billion bushels in the 2018-19 marketing-year. An assumption of moderate growth in other domestic uses for corn is projected for the next marketing-year. Total food, seed, and industrial use projections come in at 7.065 billion bushels.

According to Hubbs, the pace of corn consumption for feed appears set to pull back from recent growth in the 2018-19 marketing-year. Livestock production growth over the last few years will moderate and reduce corn feed use during the upcoming marketing-year. Recent increases in soybean meal prices combined with increased distiller’s grain availability portray a mixed picture for corn use.

Increased availability of feed grains across the board may suppress some corn feed use. Residual use of corn could be reduced if the 2018 crop is smaller than the 2017 level. “Feed and residual use is projected down slightly at 5.25 billion bushels. Overall, corn consumption shows moderate growth in the 2018-19 marketing year. Total consumption is projected at 14.6 billion bushels and may outpace domestic production,” Hubbs says.

Current market consensus projects farmers to plant fewer corn acres in 2018 than the 90.2 million acres planted last year. The current profitability advantage for soybeans over corn along with stronger prices in other crops create an incentive to reduce corn acres.

The USDA Outlook Forum projected 2018 corn acres at 90.0 million acres. Various estimates from trade analysts set corn acreage in a range of 89 to 92 million acres. In this analysis, Hubbs explains that a reduction of corn acreage is expected. Planted acreage at 89.5 million acres would lead to around 82.2 million acres harvested for grain in 2018.

Yield expectations typically use trend yield analysis to generate yield projections for the next crop year. National average corn yield came in above trend for the last four growing seasons and culminated in an estimated 176.6 bushels per acre in 2017. Using a linear trend of actual U.S. corn average yields from 1960 forward, the trend estimate for 2018 is 168.6 bushels per acre.

By adjusting the trend estimation for weather influences and recent trend deviations, we generate a national corn yield expectation of 172.3 bushels per acre. “At this yield level, the 2018 crop projection is 14.2 billion bushels. By including the current projections for ending stocks of 2.36 billion bushels with 50 million bushels of imported corn, the 2018 corn supply comes in at 16.6 billion bushels. The 2018 corn supply estimate is 332 million bushels less than the current marketing year supply estimation,” Hubbs explains.

The potential for lower corn acreage in 2018 combined with an increased consumption scenario presents a positive outlook for corn prices in 2018. While the corn price will continue to struggle with ending stocks, an upward price movement in corn during 2018 appears likely.

“Current expectations for corn consumption in the 2018-19 marketing year are 14.6 billion bushels. Ending stocks would be 2.00 billion bushels, which is 350 million bushels lower than the current marketing year projection. Based on this analysis of corn production and consumption, season average market price comes in at a range of $3.50 - $3.60 for the 2018-19 marketing year,” Hubbs concludes.

Go Further With Food: March National Nutrition Month

Published March 5, 2018

URBANA, Ill. - The Academy of Nutrition and Dietetics celebrates March as National Nutrition Month® to promote healthy eating and daily physical activity to attain and maintain optimal health. Laura Barr, a nutrition and wellness educator with University of Illinois Extension explains that the 2018 theme, “Go Further with Food,” is a two-fold message focusing on choosing nutrient-dense foods for energy and planning meals and snacks to decrease food waste.

“Go Further with Food” is a reminder to eat a variety of fruits, vegetables, and proteins, as well as whole grains and low-fat dairy products or other calcium-rich foods. This diet is recommended by the United States Department of Agriculture’s Dietary Guidelines for Americans, designed to help consumers eat for health benefits in accordance with their energy needs.

“These messages are also an important part of U of I Extension’s nutrition and wellness programs, which deliver evidence-based nutrition education and safe food handling information to the public, “Barr says. “After attending nutrition and wellness programs, participants make healthier food and activity choices, decrease food waste, and may have less incidence of food-borne illness.

“Physical activity and healthy eating are the power twins for strong bodies. Adults should get at least 150 minutes of physical activity per week, while children ages 6-17 need 60 minutes per day. The key to consistency is finding activities that are enjoyable, and schedule them in your calendar,” she adds.

The Dietary Guidelines for Americans of 2015-2020 report that:

  • About three-fourths of the population has an eating pattern that is low in fruit, vegetables, dairy, and oils.
  • More than half of the population is meeting or exceeding total grain and total protein foods intake, but would benefit from increasing the variety of foods consumed within these food groups to improve their nutrient intake.
  • Most Americans exceed the recommendations for added sugars, saturated fats, and sodium.
  • Most Americans are consuming too many calories.

The Guidelines recommend that Americans follow a healthy eating pattern that accounts for all food and beverages within an appropriate calorie level. A healthy eating pattern limits saturated and trans fats, added sugars, and sodium. Instead diets should include:

  • A variety of vegetables from all of the subgroups— dark green, red and orange, legumes (beans and peas), starchy, and others.
  • Fruits, especially whole fruits.
  • Grains, at least half of which are whole grains.
  • Fat-free or low-fat dairy, including milk, yogurt, cheese, and/or fortified soy beverages.
  • A variety of protein foods, including seafood, lean meats and poultry, eggs, legumes (beans and peas), and nuts, seeds, and soy products.
  • Oils

“Go Further with Food” also addresses food waste management. The Journal of Nutrition and Dietetics published a study, based on the data of 2012 USDA statistics, which revealed that 31 to 40 percent of our food is disposed of after it’s harvested. “This practice is on the front end of the food line,” Barr says.

The federal government’s goal is to reduce food waste by 50 percent by the year 2030. “On a personal level, consumers are advised to shop with a game plan to reduce waste. This includes reviewing ‘in stock’ items on your cabinet shelves or the refrigerator, so that repurchasing isn’t necessary,” Barr explains.

“Next, consider the meals you will prepare. Purchase what you need to eat fresh or freeze for a few days, then plan on how to use leftovers later in the week. It may take extra effort in the beginning, but this practice will reap monetary rewards in the long run.

“‘Go Further with Food’ is a message to become physically healthier and be better stewards of our abundant food supply.”

News Source:

Laura Barr

Illinois Performance Tested Bull Sale results

Published March 2, 2018
bull sale

URBANA, Ill. – The Illinois Performance Tested (IPT) Bull Sale was the lead-off event of the 2018 Illinois Beef Expo held on Feb. 22 at the Illinois State Fairgrounds in Springfield. The sale averaged $3,875 on 50 lots.

"This sale continues to be one of the best sources for total performance genetics in the Midwest," said Travis Meteer, IPT sale manager. "During the past 50 years, the sale has sold 4,740 bulls, valued at over $8.7 million."

There were three breeds represented in the 2018 sale: Angus, Simmental, and Polled Hereford. Meteer said a yearling Angus bull was the top seller, selling for $9,000. The bull, MG Leupold 11E, was sold by Murphy Angus LLP, Illiopolis, to John Brunner, Springfield. Murphy Angus LLP also had the second-highest-selling bull. He was lot 9 and sold for $6,000.

The top-selling Simmental bull was consigned by Rincker Cattle Company. He sold for $5,800 to Dean Nelson, Oneida. The second-highest-selling Simmental bull, and highest-indexing Simmental bull, was consigned by Rincker Simmentals and he sold for $5,300 to Thomas Lave, Effingham.

The top selling Polled Hereford bull was consigned by Sturdy Herefords, Rochester. He sold for $4,300 to Melvin Smith, Effingham. Travis Hagen, Hamburg, took home lot 62 for $4,000. Lot 62 was the high-indexing Hereford bull consigned by Rabideau Polled Herefords.

The University of Illinois (U of I) Extension, U of I Department of Animal Sciences, and consigning breeders sponsored the sale. Also, Vita-Ferm, ABS, Boehringer-Ingelheim, Zoetis 50K, Illinois Angus Association, and Illinois Simmental Association provided industry support, Meteer said.

Producers interested in viewing a breakdown of all the prices can visit the IPT Bull Sale website at Also included on this site are the individual bull prices from the 2018 sale and the numbers and averages from the previous 49 sales.

Seed-stock breeders interested in consigning to the 2019 IPT Bull Sale should contact Travis Meteer at 217-430-7030 or to request a copy of the rules and regulations and nomination form. Nominations need to be made by Dec.15, 2018, for the 2019 sale.

News Source:

Travis Meteer, 217-236-4961

News Writer:

University of Illinois Extension

Scientists seeking rare river crayfish aren't just kicking rocks

Published March 2, 2018

CHAMPAIGN, Ill. — As far as anyone can tell, the cold-water crayfish Faxonius eupunctus makes its home in a 30-mile stretch of the Eleven Point River and nowhere else in the world. According to a new study, the animal is most abundant in the middle part its range, a rocky expanse in southern Missouri – with up to 35,000 cubic feet of chilly Ozark river water flowing by each second.

Because the crayfish is so rare, environmental authorities are considering listing F. eupunctus as an endangered species. But doing so requires a thorough accounting of its population size and distribution. To achieve this, researchers at the Illinois Natural History Survey at the University of Illinois used both old-school techniques and newer, high-tech methods.

“The traditional way to find crayfishes in this type of river is a method called kick-seining,” said graduate research assistant Christopher Rice, who conducted the study with Christopher Taylor, the INHS curator of fishes and crustaceans, and Eric Larson, a U of I. professor in the Department of Natural Resources and Environmental Sciences. The INHS is a division of the Prairie Research Institute at the U of I.

“You take a mesh seine attached to two poles and stand out in the stream, and someone else kicks rocks and flushes water and crayfishes down into the net,” Rice said. Once caught, the animals can be counted, measured and sexed – all valuable data for those hoping to conserve them. In the new study, the team kick-seined a dozen 1-square-meter plots at each of 39 sites along the river and in several smaller tributaries feeding it.

That effort found F. eupunctus at 21 of 39 sites sampled. None of the crayfish were found in any of the tributaries.

The researchers also used a technique called environmental DNA. They collected river water at each of the 39 sites, taking it back to the lab to filter and test it for F. eupunctus DNA.

“One of our goals was to compare eDNA with kick-seining, to see how these methods performed in relation to one another,” Taylor said.

Scientists are still trying to work out how to use eDNA to study animals in different habitats. Using the technique in streams and rivers can be especially tricky, Larson said.

“An animal’s DNA can degrade within hours or days in the water, depending on a lot of factors,” he said. Temperature, ultraviolet light and the acidity of the water can influence the rate at which it degrades.

“This makes eDNA a very useful detection tool,” Larson said. If the DNA stuck around for years, scientists might mistakenly believe that an animal was present when it had died out years earlier.

River water also moves, transporting the DNA away from where it was originally shed by the animal in the form of skin, other tissues or secretions. The team didn’t know whether eDNA would be able to detect crayfishes in the portions of the Eleven Point River where they were present.

The eDNA testing corroborated the kick-seining data, detecting F. eupunctus DNA at 19 of the 21 sites where the team had found it before. It also found no evidence of the critter in the smaller streams feeding the river.

This adds to the evidence that F. eupunctus is very rare and lives only in the Eleven Point River, providing useful information for conservationists and resource managers, Taylor said.

While eDNA could fairly reliably determine whether an organism was present, it was not useful as a way of measuring abundance at specific locales, the researchers found.

“The ability of eDNA to work in this type of ecosystem is very exciting,” Taylor said. “But our study also shows the value of doing traditional sampling. We did find the species at two locations where the eDNA did not. We also were able to directly measure abundance with the kick-seining method.”

The article, “Environmental DNA detects a rare large river crayfish but with little relation to local abundance,” is published in the journal Freshwater Biology. The United States Department of Agriculture National Institute of Food and Agriculture Hatch Project and the Missouri Department of Conservation supported this research.

Scientists monitor crop photosynthesis, performance using invisible light

Published February 27, 2018
field sensor
Field sensor

URBANA, Ill. – Twelve-foot metal poles with long outstretched arms dot a Midwestern soybean field to monitor an invisible array of light emitted by crops. This light can reveal the plants’ photosynthetic performance throughout the growing season, according to newly published research by the University of Illinois. 

“Photosynthetic performance is a key trait to monitor as it directly translates to yield potential,” said Kaiyu Guan, an assistant professor in the Department of Natural Resources and Environmental Sciences at U of I and the principal investigator of this research. “This method enables us to rapidly and nondestructively monitor how well plants perform in various conditions like never before.”

The Illinois team led by Guofang Miao, a postdoctoral researcher in NRES and the lead author of the paper, reports on the first continuous field season to use sun-induced fluorescence (SIF) data to determine how soybeans respond to fluctuating light levels and environmental stresses.

“Since the recent discovery of using satellite SIF signals to measure photosynthesis, scientists have been exploring the potential to apply SIF technology to better agricultural ecosystems,” said study collaborator Carl Bernacchi, an associate professor of plant science at the Carl R. Woese Institute for Genomic Biology (IGB). “This research advances our understanding of crop physiology and SIF at a local scale, which will pave the way for satellite observations to monitor plant health and yields over vast areas of cropland.”

Photosynthesis is the process in which plants convert light energy into sugars and other carbohydrates that eventually become our food or biofuel. However, one to two percent of the plant’s absorbed light energy is emitted as fluorescent light. And that emitted fluorescent light is proportional to the rate of photosynthesis.

Researchers capture this process using hyperspectral sensors to detect fluctuations in photosynthesis over the growing season. They designed this continuous study to better understand the relationship between absorbed light, emitted fluorescent light, and the rate of photosynthesis. “We want to find out whether this proportional relationship is consistent across various ecosystems, especially between crops and wild ecosystems such as forests and savannas,” said Miao.

“We are also testing the applicability of this technology for crop phenotyping to link key traits with their underlying genes,” said co-author Katherine Meacham, a postdoctoral researcher at the IGB.

“SIF technology can help us transform phenotyping from a manual endeavor requiring large teams of researchers and expensive equipment to an efficient, automated process,” said co-author Caitlin Moore, also a postdoctoral researcher at the IGB. 

A network of SIF sensors has been deployed across the U.S. to evaluate croplands and other natural ecosystems. Guan’s lab has launched two other long-term SIF systems in Nebraska to compare rainfed and irrigated fields in corn-soybean rotations. “By applying this technology to different regions, we can ensure the efficacy of this tool in countless growing conditions for a myriad of plants,” said Xi Yang, an assistant professor at the University of Virginia, who designed this study’s SIF monitoring system.

“Our ability to link SIF data at the leaf, canopy, and regional scales will facilitate the improvement of models that forecast crop yields,” Guan said. “Our ultimate goal is to monitor the photosynthetic efficiency of any field across the world to evaluate crop conditions and forecast crop yields on a global scale in real time.”

The paper, “Sun-induced chlorophyll fluorescence, photosynthesis, and light use efficiency of a soybean field from seasonally continuous measurements,” is published in the Journal of Geophysical Research – Biogeosciences, available online (DOI: 10.1002/2017JG004180) or by request. Co-authors also include Joseph A. Berry, Evan H. DeLucia, Jin Wu, Yaping Cai, Bin Peng, Hyungsuk Kimm, and Michael D. Masters.

This work was supported by the NASA New Investigator Award, the Institute for Sustainability, Energy, and Environment (iSEE), a NASA Interdisciplinary Science Award and the TERRA-MEPP (Mobile Energy-Crop Phenotyping Platform) research project that is funded by the Advanced Research Projects Agency-Energy (ARPA-E).

TERRA-MEPP (Mobile Energy-Crop Phenotyping Platform) is a research project that is developing a low-cost phenotyping robot to identify top-performing crops. TERRA-MEPP is led by the University of Illinois in partnership with Cornell University and SignetronInc. and is supported by the Advanced Research Projects Agency-Energy (ARPA-E).

New, detailed understanding of the elephant genome from both ancient and modern DNA may aid conservation efforts

Published February 27, 2018

URBANA, Ill.—Elephants—the largest living terrestrial mammal—began walking the earth 5 to 10 million years ago in Africa. Today there are fewer than 500,000 elephants alive, making this group of iconic animals a highly protected species, especially in Africa where the perils of ivory-trade continue to threaten them. The shrinking population of elephants makes them an “isolated branch” in evolution, with only three currently recognized species: the Asian elephant, the African savannah elephant, and the African forest elephant.

A consortium of scientists, including researchers at the Broad Institute of MIT and Harvard, Harvard Medical School, Uppsala University, the University of Potsdam, McMaster University, and the University of Illinois, used advanced sequencing technology to recover complete genomes from both living and extinct elephant species.

In a paper published in Proceedings of the National Academy of Sciences today, the authors provide a comprehensive genomic portrait of not just the living elephants, but also members of extinct mammoths and straight-tusked elephants, as well as the American mastodon, an extinct distant relative of the elephant family. The paper reveals that gene flow between elephant species was a common feature of their history, contrary to previous studies which represented their relationships as simple trees.

“This paper, the product of a grand initiative we started more than a decade ago, is far more than just the formal report of the elephant genome. It will be a reference point for understanding how diverse elephants are related to each other and it will be a model for conducting similar studies in other species groups,” said co-senior author Kerstin Lindblad-Toh, a senior director of vertebrate genomics at the Broad Institute and professor in comparative genomics at Uppsala University in Sweden.

“There’s been a simmering debate in the conservation communities about whether African savannah and forest elephants are two different species,” said David Reich, another co-senior author at the Broad Institute who is also a professor at the Department of Genetics at Harvard Medical School (HMS) and a Howard Hughes Medical Institute Investigator. “Our data show that these two species have been isolated for long periods of time, making each worthy of independent conservation status.”

The paper confirms that the African savannah and forest elephants are two distinct species, findings that should help to make the case to protect both.

Alfred Roca, faculty in the Department of Animal Sciences at the University of Illinois and co-author of the study, added, "Analyses of full genomes revealed that there is a dearth of gene flow between African forest and savanna elephants, and that their genetic isolation goes back half a million years or even longer. Currently, the forest elephant has a smaller population size and is declining faster than the savanna elephant, and measures to protect this species are urgently needed."

The Broad Institute generated the genomes for all the present-day elephants as well as a high-quality genome from an extinct 120,000-year-old straight-tusked elephant obtained from a sample prepared at the University of Potsdam in Germany. “This is one of the oldest high-quality genomes that currently exists for any species,” said Michael Hofreiter at the University of Potsdam, a co-senior author who led the work on the straight-tusked elephant.

Eleftheria Palkopoulou, a post-doctoral scientist in Reich’s lab at HMS, led the analysis for the study.

The extinct straight-tusked elephants were traditionally grouped with present-day Asian elephants because of morphological similarities in their skulls and teeth. However, a paper published last year by Hofreiter, Palkopoulou, David Reich, and others, revealed that straight-tusked elephants were on average most closely related to African forest elephants, and not to Asian elephants.

“We were puzzled by the discrepancy between morphological and genetic results, but our analyses show that the ancestry of straight-tusked elephants was highly composite including three ancestral components,” said Palkopoulou. The paper reveals that the extinct giant descends from a mixture of lineages related to an ancient African elephant, the woolly mammoth, and the present-day forest elephant.

Co-senior author Hendrik Poinar of McMaster University in Canada added said, “The combined analysis of genome-wide data from all these ancient elephants and mastodons has raised the curtain on elephant population history, revealing complexity that we were simply not aware of before.”

Future studies will need to explore the diversity of both living and ancient elephants and investigate population structure changes over distance and time.

“Obtaining a technicolor picture of elephant population structure may also be of immediate value for conservation efforts,” said Reich, pointing to work by colleagues showing that with sufficient genetic data, black-market tusks can be localized to the regions in Africa from which they were obtained.

Approximately 50,000 elephants are killed each year from poaching, putting many populations in danger. The mastodons and mammoths, who were their close relatives, are gone. Understanding the genetic heritage of elephants has the potential to play a valuable role in future conservation efforts and in preventing these creatures from going extinct.

The article, “A comprehensive genomic history of extinct and living elephants,” is published in PNAS. The research was funded by NHGRI grant U54 HG003067-08, the USFWS African Elephant Conservation Fund. B.L.A., Wellcome Trust grants WT098051 and WT108749/Z/15/Z, NSF (HOMINID) grant BCS-1032255 and NIH (NIGMS) grant GM100233.

News Source:

David Cameron, 617-714-7184

News Writer:

ACES Research

DOE grants $10.6 million to Illinois to produce more biodiesel, biojet fuel

Published February 27, 2018
Energy crops
Energy crops. Credit: L. Brian Stauffer

URBANA, Ill. – The U.S. Department of Energy (DOE) on Sunday awarded the University of Illinois a $10.6 million, five-year grant to transform two of the most productive crops in America into sustainable sources of biodiesel and biojet fuel. The new research project, Renewable Oil Generated with Ultra-productive Energycane—or ROGUE—kicked off on Feb. 25 with a team meeting held in conjunction with the 2018 Genomic Sciences Program Annual Principal Investigator Meeting in Tysons, Virginia.

“The U.S. continues to enjoy cheap, abundant energy but more than 80 percent of it is derived from natural gas, coal, and petroleum,” said ROGUE Director Stephen Long, an Ikenberry Endowed Chair at Illinois. “Heavy, diesel-powered semitrailers and the aviation industry desire other options, but electric batteries are not feasible, and current biofuel crops cannot meet demands for biodiesel and biojet fuel.”


ROGUE will engineer energycane, a bioenergy crop derived from sugarcane, and Miscanthus to produce the oil that is used to create biodiesel and biojet fuel. The work is guided by computer models, which project that these crops can achieve 20 percent oil content in the plant—a dramatic increase from natural levels of less than a tenth of one percent.

“If fully successful, these crops could produce as much as 15 times more biodiesel per unit of land compared to soybeans, a food crop that currently produces half of our nation’s biodiesel,” said Long, who leads the project’s efforts at the Carl R. Woese Institute for Genomic Biology.

Previous work, funded by the DOE Advanced Research Projects Agency-Energy (ARPA-E), achieved 8 percent oil accumulation, and now ROGUE will further increase oil production and target oil accumulation in the stem where it can be accessed more easily with ROGUE’s patented extraction technologies.

“Redirecting these plants to produce oil rather than sugar will enable us to make full use of these productive crops for biodiesel and biojet fuel production,” Li-Qing Chen, an assistant professor of plant biology at Illinois.


ROGUE will also improve the efficiency with which these crops can turn the sun’s energy into plant energy to fuel their biological oil production. Improving these crops’ photosynthetic efficiency will ensure that the production of energy-dense oil will not lower yields or suppress plant defenses. Improving photosynthetic efficiency will also help the plant conserve limited resources such as water and nitrogen, particularly under stress.

“Photosynthesis is the process ultimately underlying the production of all our food and much of our fiber and increasing amounts of our fuels,” said Don Ort, Robert Emerson Professor in Plant Biology and Crop Sciences, who will co-lead the project’s photosynthetic work with Long. “By improving this process, we can fortify these crops to create a more efficient, productive, and sustainable source of bioenergy.”


ROGUE will translate its bioenergy and sustainability discoveries into energycane and Miscanthus using synthetic biology, which applies engineering principles to optimize and speed up the design of biological systems. The project will also develop energycane to be more cold-tolerant to expand its growing region and extend its growing season.                

“Our crop technologies could thrive on 235 million acres, turning untold underutilized, marginal acreage into sustainable sources of bio-oil,” Long said. “What’s more, we have the existing infrastructure in place to immediately grow, harvest, and process their bio-oil using existing sugarcane mills. These oils can be processed into biofuels with existing technologies and sold through existing marketplaces.”


ROGUE will ensure the efficacy of its crop technologies through techno-economic analyses and replicated field trials. Energycane will be evaluated at Florida and Mississippi, and Miscanthus will be tested at Illinois. In tandem, the project will continue to perfect and evaluate its patented method to separate oil from biomass and its processing technologies.

“According to our models, ROGUE crops will be much more productive and profitable per acre than corn or soybeans,” said Vijay Singh, director of the Integrated Bioprocessing Research Laboratory, who will lead the project’s techno-economic analyses and processing technologies.

ROGUE is a collaboration amongst researchers from Illinois as well as Brookhaven National Lab, University of Florida, and Mississippi State University, with support from the DOE Office of Science (Office of Biological and Environmental Research).

Hog prices increase, but so do feed costs

Published February 27, 2018

URBANA, Ill. - The pork market has been favored by strong demand and that remains supportive for hog prices this year. Prospects remain positive for higher producer prices again in 2018, even in the face of a 3 to 4 percent increase in supply. However, according to Purdue University agricultural economist Chris Hurt, a new threat to profit margins is being driven by dry weather in Argentina, therefore pushing up feed costs.

On the demand front, all signals continue to be positive. So far in 2018, pork supplies have been up by 2.5 percent, yet hog prices have also been higher by nearly 4 percent. There are several signs of positive demand growth. “First, January retail pork prices were 18 cents per retail pound higher this year compared to January of 2017. This indicates that consumers are willing to pay more for pork even though there is more pork available.

“Second, packer margins have narrowed since last August as new capacity came online and continues to increase production. More competition among packers for hogs is helping strengthen bids for hogs and increasing the farmers’ share,” Hurt says.

Finally, exports remain strong with 22 percent of our production being exported in 2017. USDA is expecting exports to be 4 percent higher again this year.

“The market has caught on to a strong demand with live prices so far this year averaging about $1.80 per hundredweight higher than the same period last year. In addition, the lean hog futures market has been strong as well,” Hurt adds.

Using those futures prices and historic basis, expected live hog prices for 2018 would average about $53.50 compared to $50.48 last year. “The prospect of hog prices this year being $3 per live hundredweight higher is a reflection that the futures market recognizes the strong demand outlook for this year. Time will tell if the current optimism can turn into reality.

“Those expected prices are about $51 per live hundredweight for the first quarter, around $57 for the second and third quarters, and then near $48 for the final quarter,” Hurt explains.

He adds, “Higher hog prices are a joyful sound to hog producers, but there are two catches. The first uncertainty is whether hog prices can actually be as strong as current markets expect and the second uncertainty is feed cost.”

The pork industry, like all animal agriculture, has believed that feed supplies are abundant and that corn and soybean meal will remain cheap. Why? For the four crop years from 2014 to 2017, farm-level corn prices received have averaged $3.49 per bushel and in the past three calendar years from 2015 to 2017, high-pro soybean meal at Decatur has averaged $328 per ton.

Since the beginning of this year, hog price prospects have increased, but so have anticipated feed costs. For hog producers, the increase in soybean meal prices has had a bigger impact on feed costs than increases in corn prices.

March 2018 soybean meal futures have increased from about $320 per ton at the start of the year to $380 currently. Hurt estimates that a $60 per ton increase in meal price increases the costs per live hundredweight by $1.85 per hundredweight. March 2018 corn futures have risen by about 16 cents per bushel raising costs by $.70 per hundredweight.

Combining the estimated $1.85 costs per hundredweight increase from higher meal prices and the $.70 from corn means about $2.50 higher potential costs.

So far this year, hog price prospects are higher but so are anticipated costs. The net effect is to reduce profit prospects modestly. Profits above all costs in 2017 were estimated at about $5 per head. “In January of this year, our outlook suggested profit prospects for 2018 were for profits of $5 to $10 per head. With these recent developments, the outlook is lowered modestly to expected profits from $0 to $10 per head. Since the start of the year, costs prospects have risen somewhat more than hog price prospects,” Hurt says.

Hurt concludes that pork demand should remain positive through the year with strong U.S. and world economic growth. Longer-term however, higher wage rates, higher inflation, and higher interest rates may begin to constrain economic growth.

“Global demand for feed ingredients continues to grow, but favorable weather has resulted in near record global yields for the last four years. A shift to less favorable global weather has obvious consequences for animal industries.

“As a reminder, the pork industry should strive to keep breeding herd expansion to around 1 percent per year. Keeping breeding herd growth to about one percent per year will increase production by about 2.5 percent per year which seems to be a sustainable growth rate,” Hurt says.