Posts Tagged: grain
Genomic gymnastics help sorghum plant survive drought.
Scorching temperatures and parched earth are no match for the sorghum plant — this cereal crop, native to Africa, will remain green and productive, even under conditions that would render other plants brown, brittle and barren.
A new study published this week in the journal Proceedings of the National Academy of Sciences provides the first detailed look at how the plant exercises exquisite control over its genome — switching some genes on and some genes off at the first sign of water scarcity, and again when water returns — to survive when its surroundings turn harsh and arid.
"With this research, we are laying the groundwork for understanding drought tolerance in cereal crops," said Jeff Dahlberg, UC Cooperative Extension sorghum specialist. Dahlberg, co-author of the study, is also director the UC Kearney Agricultural Research and Extension Center in Parlier, one of nine research and extension centers in California that are part of UC Agriculture and Natural Resources.
Dahlberg said researchers can use the knowledge gained from this project to search for drought genes in other cereal crops.
"That has implications for feeding the world, particularly considering changing climate and weather patterns," he said.
The massive dataset, collected from 400 samples of sorghum plants grown during 17 weeks at Kearney, reveals that the plant modulates the expression of a total of 10,727 genes, or more than 40% of its genome, in response to drought stress. Many of these changes occur within a week of the plant missing a weekly watering or after it is first watered after weeks of no precipitation or irrigation.
Kearney is a 330-acre agriculture research facility in the heart of California's Central Valley, where field-scale, real-world research can be conducted on drought impact on plants and soil microbial communities. The climate is naturally dry throughout the summer, making it ideal to mimic drought conditions by withholding irrigation water.
"People have really shied away from doing these types of experiments in the field and instead conduct them under controlled conditions in the laboratory or greenhouse. But I believe that the investment of time and resources that we put into it is going to pay off, in terms of the quality of the answers that we get, in terms of understanding real-world drought situations," said Peggy Lemaux, UC Cooperative Extension specialist in UC Berkeley's Department of Plant and Microbial Biology and co-author of the paper.
The data was collected as part of the Epigenetic Control of Drought Response in Sorghum, or EPICON, project, a five-year, $12.3 million study into how the sorghum plant is able to survive the stress of drought. The EPICON study is run as a partnership between UC Berkeley researchers and scientists at UC Agriculture and Natural Resources (UC ANR), the Energy Department's Joint Genome Institute (JGI) and that agency's Pacific Northwest National Laboratory (PNNL).
To conduct the research, the team cultivated sorghum plants under three different irrigation conditions — pre-flowering drought, post-flowering drought and controlled applications of water — over three consecutive years at Kearney.
Each week during the growing season, members of the research team carefully harvested samples from the leaves and roots of selected plants and set up a mobile lab in the field where they could rapidly freeze the samples until they were processed for analysis. Then, researchers at JGI sequenced the RNA in each sample to create the transcriptome data, which reveals which of the plant's tens of thousands of genes are being transcribed and used to make proteins at particular times.
Finally, statisticians led by UC Berkeley statistics professor Elizabeth Purdom parsed the massive transcriptome data set to pinpoint how gene expression changed as the plants grew and were subjected to drought or relief from drought conditions.
"We very carefully controlled the watering conditions, and we sampled over the entire developmental timeframe of sorghum, so [researchers] could actually use this data not only to study drought stress, but also to study plant development," Lemaux said.
The researchers noticed a few interesting patterns in the transcriptome data. First, they found that a set of genes known to help the plant foster symbiotic relationships with a type of fungus that lives around its roots was switched off in drought conditions. This set of genes exhibited the most dramatic changes in gene activity that they observed.
"That was interesting, because it hinted that the plants were turning off these associations [with fungi] when they were dry," said John Vogel, a staff scientist at JGI and co-author of the paper. "That meshed well with findings that showed that the abundance of these fungi around the roots was decreasing at the same time."
Second, they noticed that certain genes known to be involved with photosynthesis were also turned off in response to drought and turned up during drought recovery. While the team doesn't yet know why these changes might help the plant, they provide interesting clues for follow-up.
The data in the current paper show the plant's transcriptome under both normal conditions and drought conditions over the course of a single growing season. In the future, the team also plans to publish data from the other two years of the experiment, as well as proteomic and metabolomic data.
Nelle Varoquaux and Cheng Gao of UC Berkeley and Benjamin Cole of JGI are co-first-authors of the study. Other co-authors include Grady Pierroz, Christopher R. Baker, Dhruv Patel, Mary Madera, Tim Jeffers, Judith A. Owiti, Stephanie DeGraaf, Ling Xu, Krishna K. Niyogi, Devin Coleman-Derr and John W. Taylor of UC Berkeley; Joy Hollingsworth, Julie Sievert and Jeffery Dahlberg of UC ANR KARE; Yuko Yoshinaga, Vasanth R. Singan, Matthew J. Blow, Axel Visel and Ronan O'Malley of JGI; Maria J. Harrison of the Boyce Thompson Institute; Christer Jansson of PNNL and Robert Hutmacher of UC ANR.
This research was funded in part by the Department of Energy (DOE) grant DE-SC001408; the Gordon and Betty Moore Foundation grant GBMF3834; the Alfred P. Sloan Foundation grant
2013-10-27; L'Ecole NormaleSupérieure-Capital Fund Management data science chair and the DOE's Office of Biological and Environmental Research grant DE-SC0012460. Work conducted by the DOE Joint Genome Institute is supported by the Office of Science of the DOE contract DE-AC02-05CH11231.
UC Agriculture and Natural Resources brings the power of UC research in agriculture, natural resources, nutrition and youth development to local communities to improve the lives of all Californians. Learn more at ucanr.edu.
RELATED INFORMATION
- Dealing with Drought: Uncovering Sorghum's Secrets
- Berkeley to lead $12.3M study of crop drought tolerance
- Drought treatment restructures plants' microbiomes
- Microbes associated with plant roots could be a key to helping plants survive drought
CONTACTS
Jeff Dahlberg, UC Cooperative Extension specialist at the UC Kearney Agricultural Research and Extension Center, jadahlberg@ucanr.edu
Peggy Lemaux, cooperative extension specialist at UC Berkeley's Department of Plant and Microbial Biology, lemauxpg@berkeley.edu
John Vogel, staff scientist, DOE Joint Genome Institute, jpvogel@lbl.gov
Upcoming Extension Meetings: September 2018
2018 Alfalfa and Forage Field DayWednesday, September 19, 2018Kearney Agricultural Research and...
2018 Alfalfa Day - Kearney Agenda
What's that in your cornmeal?
You're thinking about making Grandma's Southern Cornbread.
You head for your pantry. You remember that six months ago you purchased a bag of cornmeal from a local supermarket and that you immediately emptied the contents into a glass jar with a tight-fitting lid.
You open the airtight jar and notice something strange. It's moving. Moving? Moving? Yes! It's crawling with a transparent carpet of dozens of nearly microscopic critters.
What? First, what are they? If you're like me, you grab your camera--in this case, a Canon EOS 7D with an MPE-65mm lens that can magnify an insect five times its life size--and click the shutter.
You post the photo on BugGuide.Net and request an identification.
The entomologists all agree: They're booklice, Liposcelis bostrychophila.
- Class Insecta (Insects)
- Order Psocodea (Barklice, Booklice, and Parasitic Lice)
- Suborder Troctomorpha
- Family Liposcelididae (Booklice)
- Genus Liposcelis
- Species bostrychophila (Booklouse)
These Liposcelis bostrychophila, or "psocids" (pronounced "so kids"), are common pests in stored grains. They're usually unseen because they're about a millimeter long--about the size of a speck of dust--and are transparent to light brown in color. They're also wingless, but can they ever crawl!
Fact is, their name, "lice," is misleading. These tiny insects are not lice; they are not parasitic. And they're everywhere. They feed on flour, cereals, grits, molds, fungi, papers, books, pollen, dead insects and the like. In fact, you've probably unknowingly eaten them--or parts of them--in your pancakes, your oatmeal or maybe even your chocolate birthday cake.
Entomologist Jeff Smith, who curates the butterfly-moth collection at the Bohart Museum of Entomology at UC Davis, took one look at the photo and commented: "They're pretty thick in there!"
"Booklice can be scavengers and often feed on the bits of mold or fungi that grow on damp materials," Smith explained. "Very old, neglected food stuffs are also subject to them, and the key to prevention is to use food materials reasonably quickly and not store them for years, store them in a nice dry location and in airtight containers."
"They very well could have been in the food already when you bought it, but they're so common that you probably have some roaming around in the house all the time, just looking for something good to eat. They'll feed on dead bugs in window sills, stale pet foods, etc."
If you're worried about what's in your cornmeal, flour, oats, biscuit mix, cake mix and other stored foods, you can pop the contents in your oven at about 120° for a half hour, and then transfer them to an airtight container, Smith says. "Your food should be okay--albeit perhaps containing a few dead booklice. We had them in an old bag (paper) of rice one time, and in several packages of cornmeal mix that were forgotten in the back of our cupboard."
A UC Davis colleague said he's seen them crawling in his flour, but his wife made pancakes from them anyway. No issues. No problem. "Just protein!" he chortled.
And from another colleague: "I once had an entire case of instant grits. The grits were completely factory-sealed in unopened plastic bags. I opened the bags and the grits were poured into hot water, but they would not sink and mix with the water. Instead the grit floated on the top of the water. I opened a second bag and looked at the grits under my stereo microscope. Each and every grain of grit had two or three little six-legged creatures standing on each grit. These creatures were 100 percent transparent, the only color was in their bodies which was the same color as the grits they were eating. I opened every 100 percent factory-sealed bag, and every bag was contaminated in this matter."
"There is nothing new about insect contamination of grain products," she added. "Another personal experience was a biscuit mix. For no particular reason, I sifted the biscuit mix while making the batch of biscuits. After sifting several cups of biscuit mix, in the sifter screen there were 4 worm-like creatures about the diameter of a standard pencil and about an inch long. These worms were 100 percent transparent, each filled with the white biscuit mix. "Consider we all eat insects, spiders, and urine and feces of all sorts of animals."
We live in world where we all eat bugs, whether we know it or not. Sometimes we may not want to know!
Statistics indicate that the average American unknowingly eats one to two pounds of insects a year. But the U.S. Food and Drug Administration "has very specific tolerances for the amount of residue in food stuffs," said Lynn Kimsey, director of the Bohart Museum of Entomology and professor of entomology at UC Davis.
Want to know what the action level is? Check out this FDA document.
And the next time, you're yearning to make Grandma's Southern Cornbread, you might want to check for bugs first. Or maybe not. You might not want to know!
This image, taken with a Canon MPE-65mm lens, shows booklice, nearly microcopic insects, in cornmeal. The insects are about 1 millimeter long, or about the size of a speck of dust. (Photo by Kathy Keatley Garvey)
With the naked eye, booklice or Liposcelis bostrychophila, are nearly invisible. (Photo by Kathy Keatley Garvey)
Find the booklouse! It's on this penny, magnified with the powerful Canon MPE-65mm lens. (Photo by Kathy Keatley Garvey)
Odds are that the flour, cornmeal and other stored products you buy in a grocery store contain insects parts or nearly microscopic insects. It's estimated that the average American unknowingly eats one to two pounds of insects or insect parts a year. (Photo by Kathy Keatley Garvey)
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