Agriculture Commons^™

Automated Conserved Non-Coding Sequence (Cns) Discovery Reveals Differences In Gene Content And Promoter Evolution Among Grasses, Gina Marie Turco, James C. Schnable, Brent S. Pedersen, Michael Freeling

Department of Agronomy and Horticulture: Faculty Publications

Conserved non-coding sequences (CNS) are islands of non-coding sequence that, like protein coding exons, show less divergence in sequence between related species than functionless DNA. Several CNSs have been demonstrated experimentally to function as cis-regulatory regions. However, the specific functions of most CNSs remain unknown. Previous searches for CNS in plants have either anchored on exons and only identified nearby sequences or required years of painstaking manual annotation. Here we present an open source tool that can accurately identify CNSs between any two related species with sequenced genomes, including both those immediately adjacent to exons and distal sequences separated by …

U.S. Drought Monitor, July 2, 2013, Matthew Rosencrans

United States Agricultural Commodities in Drought Archive

Drought map of U.S. for July 2, 2013 (7/2/13) plus: U.S. crop areas experiencing drought (map), Approximate percentage of crop located in drought, by state (bar graph), Percent of crop area located in drought, past 52 weeks (line graph) for: Corn, Soybeans, Hay, Cattle, Winter wheat.

Storage Technique Preserves Citrus, Kills Pathogens, Gayle Volk, Jan Suszkiw

Agricultural Research Magazine

Americans consume about 84 pounds of fresh and processed citrus per person each year, with oranges topping the list at 61 pounds annually. The availability of these favored fruits in grocery stores, fresh markets, and other consumer outlets is a testament to growers’ success in managing the ever-present threat of pests and diseases to the nation’s $3.4 billion citrus crop (2011-12), most of which is produced in Florida and California.

A major threat is citrus greening disease, also known as “Huanglongbing.” First detected in Florida in August 2005, citrus greening today is the target of a multifaceted effort by federal, …

Detecting Deadly Colonies Of E. Coli, Rosalie Marion Bliss

Agricultural Research Magazine

Shiga-toxin-producing Escherichia coli (STEC) serogroup O157:H7 has long been associated with severe forms of foodborne illnesses. But these bacterial bad guys have many cousins, and six other STEC groups have also been linked to serious illnesses and outbreaks of disease.

In 2011, the U.S. Department of Agriculture’s Food Safety and Inspection Service (FSIS) announced a regulation that, as of June 2012, certain beef products that test positive for any of these six groups, nicknamed the “Big Six,” would be banned from being sold for public consumption. As USDA’s regulatory arm, FSIS employs inspectors who collect meat samples on the front …

Current Challenges Can Help Fuel Future Opportunities, Jeffrey J. Steiner

Agricultural Research Magazine

Native juniper trees and invasive plants pose an expanding threat to the survival of the sagebrush ecosystem in arid western rangelands. As the trees mature, they compete with other native plants that are valuable food sources for wildlife and cattle. After these plants die back, the bare patches of soil that remain are vulnerable to erosion and encroachment from other species like cheatgrass, an invasive nonnative annual that fuels wildfires.

Wildfires threaten livestock ranches, are suppressed in large part by efforts funded with taxpayer dollars, and increase the probability that invasive plants will spread and thrive in the postfire landscape. …

Better French Fries: Technique Helps Lower Fat, Zhongli Pan, Marcia Wood

Agricultural Research Magazine

No doubt about it. Americans love French fries.

But fries soak up a lot of oil while they’re turning a perfect golden brown in the deep-fat fryer.

Agricultural Research Service scientist Zhongli Pan and colleagues have tackled the challenge of lowering some of the fat from this favorite side order without skimping on the fries’ delicious taste and texture or their pleasing appearance and aroma. Their idea? After potatoes are peeled and sliced into strips, and just before the raw strips are dunked in the fryer, prep them with 3 minutes of infrared (IR) heat—just like that created in home …

Fungi Can Be Friends Or Foes, Amy Rossman, Jo Anne Crouch, Shannon Dominick, Sharon Durham

Agricultural Research Magazine

Fungi are a large and diverse group of organisms. Some fungi, like mushrooms, are edible and considered crops. Others, however, can cause serious diseases of crop and forest plants, and those diseases can have negative effects on local and international economies as well as on the supply of food and other materials that agriculture provides.

The Agricultural Research Service maintains a unique resource—the U.S. National Fungus Collections—for helpful and detailed information about fungi. Accurate knowledge of fungi is critical for controlling the diseases they cause.

North America’s Largest Fungarium

In 1869, the Smithsonian Institution transferred its fungal collection to the …

Measuring The Feeding Behavior Of Livestock, T. M. Brown-Brandl, Roger A. Eigenberg, Sandra Avant

Agricultural Research Magazine

Determining how much time animals spend eating could help animal caretakers identify sick livestock, improve management, and establish genetic differences within a herd. But first, a system is needed to monitor animal feeding behavior.

Scientists at the Agricultural Research Service’s Roman L. Hruska U.S. Meat Animal Research Center in Clay Center, Nebraska, have developed a new system to monitor feeding behavior of feedlot cattle and grow-finish swine in a livestock industry setting.

The system, created by agricultural engineers Tami Brown-Brandl and Roger Eigenberg in the center’s Environmental Management Research Unit, uses standard radio-frequency identification technology designed around a commercial reader. …

Agricultural Research Magazine, July 2013

Agricultural Research Magazine

Table of Contents

4 Turning Trees Into Fighter Fuels

8 Tools for Tracking Troublesome Trees

10 Better Maps Mean Better Rangeland Management

12 New, Improved Codling Moth Lures Available

13 New Strawberry Species Found in Oregon

14 Measuring the Feeding Behavior of Livestock

15 Savvy Seed Sorter Gains New Fans

16 Fungi Can Be Friends or Foes

18 Detecting Deadly Colonies of E. coli

20 Storage Technique Preserves Citrus, Kills Pathogens

22 Better French Fries: Technique Helps Lower Fat

23 Locations Featured in This Magazine Issue

July 2013- Locations Featured In This Magazine Issue

Agricultural Research Magazine

The Agricultural Research Service has about 100 labs all over the country.

Locations Featured in This Magazine Issue

Albany, California 9 research units ■ 241 employees

Corvallis, Oregon 3 research units ■ 127 employees

Great Basin Rangelands Research Unit, Reno, Nevada 1 research unit ■ 19 employees

U.S. Salinity Laboratory, Riverside, California 2 research units ■ 39 employees

Yakima Agricultural Research Laboratory, Wapato, Washington 1 research unit ■ 57 employees

Eastern Oregon Agricultural Research Center, Burns, Oregon 1 research unit ■ 27 employees

Northwest Watershed Research Center, Boise, Idaho 1 research unit ■ 18 employees

Tucson, Arizona 2 research units …

New, Improved Codling Moth Lures Available, David Nicholson, Jan Suszkiw

Agricultural Research Magazine

New lures that entice codling moths with the scent of food and a possible mate are available for use in monitoring this orchard pest and controlling it with carefully timed applications of insecticide. The research related to the development and use of the lures involved scientists Alan Knight and Peter Landolt at the Agricultural Research Service’s Yakima Agricultural Research Laboratory in Wapato, Washington, and Douglas Light at the ARS Western Regional Research Center in Albany, California.

As larvae, codling moths are major pests of apples, pears, and walnuts. Historically, growers have sprayed their orchards with insecticide to prevent the pinkish-white, …

Better Maps Mean Better Rangeland Management, Brandon Bestelmeyer, Ann Perry

Agricultural Research Magazine

Land managers are always hoping for the next best thing to help them figure out where they should spend their time and money restoring and maintaining healthy rangelands. Now Agricultural Research Service rangeland ecologist Brandon Bestelmeyer has one of the answers—an ecological-state map that identifies where rangeland is holding its own, where it could respond to restoration efforts, or where it’s already past the point of no return.

“We wanted to find a way to turn existing field-level rangeland assessments into broader tools for comprehensively managing larger landscapes,” says Bestelmeyer, who works at the ARS Jornada Experimental Range in Las …

New Strawberry Species Found In Oregon, Kim E. Hummer, Sharon Durham

Agricultural Research Magazine

A recently discovered wild strawberry species provides new genetic material for plant research and, in the future, might also provide a new class of commercial strawberries.

Agricultural Research Service scientist Kim Hummer, with the USDA-ARS National Clonal Germplasm Repository at Corvallis, Oregon, found the new species during several plant collection expeditions in the high peaks of Oregon’s Cascade Mountains. She named it Fragaria cascadensis.

The find was reported in the Journal of the Botanical Research Institute of Texas.

The new strawberry is endemic to the Oregon Cascades, hence its specific name, F. cascadensis. It is perennial, with …

Turning Trees Into Fighter Fuels, Ann Perry

Agricultural Research Magazine

In western U.S. rangelands, native juniper and pinyon pine trees are spreading beyond their historical ecological niches and disrupting the environmental balance of their expanded range. Meanwhile, Agricultural Research Service scientists are teaming with university and industry colleagues to turn this problem into a source of fuel for U.S. Navy fighter jets.

“Juniper competes with grass and forbs for water and nutrients, and this leaves bare soil that is vulnerable to erosion,” says ARS scientist Mark Weltz, who works at the Great Basin Rangelands Research Unit in Reno, Nevada. “We have also lost habitat for sage grouse and mule deer, …

Tools For Tracking Troublesome Trees, Kirk Davies, Matt Madsen, Ann Perry

Agricultural Research Magazine

In Oregon, western juniper trees are expanding their range, pushing out other plant species, reducing sagebrush habitat and livestock forage, and at times fueling catastrophic wildfires. During some of these conflagrations, fires burn even hotter because more wood is available to feed the flames—a cause-and-effect that in turn lengthens the time that temperatures remain elevated at fire-stricken sites.

To help streamline efforts to manage invasive trees, Agricultural Research Service rangeland scientists Kirk Davies and Matt Madsen are investigating ways of combining aerial photography and computer programs to quickly identify and measure affected areas. These tools could save time and money …

Beyond The Vines 02: Pathways To The Valley, Julian Adoff, Lydia Heins

Beyond the Vines: Latinos in the Oregon Wine Industry

This panel describes the journeys of Latinos to Oregon and how they became part of the wine industry.

Beyond The Vines 03: Work In The Vineyards, Julian Adoff, Lydia Heins

Beyond the Vines: Latinos in the Oregon Wine Industry

This panel describes the work in which Latino employees partake in the vineyard.

Photo Credits

1. Ofelia Galaviz Working the Harvest at Sokol Blosser Winery. Courtesy of Ofelia Galaviz.
2. Latino Employees Working the Harvest on the Vineyard. ¡Salud! Collection, Oregon Wine History Archive.
3. Latino Employee Working Harvest on the Vineyard. WillaKenzie Estates Collection, Oregon Wine History Archive.

Beyond The Vines 01: Latinos In The Oregon Wine Industry, Julian Adoff, Lydia Heins

Beyond the Vines: Latinos in the Oregon Wine Industry

This panel serves as the introduction for the exhibit, identifying the themes that the future panels will discuss.

Photo Credits

1. Leda Garside and Vineyard worker in the field. ¡Salud! Collection, Oregon Wine History Archive.
2. Seferino Flores in the vineyard, representing ¡Salud!. ¡Salud! Collection, Oregon Wine History Archive.

Beyond The Vines 06: Moving Beyond The Vines, Julian Adoff, Lydia Heins

Beyond the Vines: Latinos in the Oregon Wine Industry

This panel concludes the Beyond the Vines exhibit by tying the themes together to tell the story of Latinos in the Oregon wine industry.

Beyond The Vines 04: In The Industry, Julian Adoff, Lydia Heins

Beyond the Vines: Latinos in the Oregon Wine Industry

This panel describes the stories of two Latino workers who have expanded their roles to other areas in the wine industry.

Photo Credits

1. Employees Sorting Grapes during Harvest. Willakenzie Estate Collection, Oregon Wine History Archive.