- Author: Kara Manke, UC Berkeley science writer
- Contact: Jeannette E. Warnert
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.
- Dealing with Drought: Uncovering Sorghum's Secrets
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- Drought treatment restructures plants' microbiomes
- Microbes associated with plant roots could be a key to helping plants survive drought
Jeff Dahlberg, UC Cooperative Extension specialist at the UC Kearney Agricultural Research and Extension Center, email@example.com
Peggy Lemaux, cooperative extension specialist at UC Berkeley's Department of Plant and Microbial Biology, firstname.lastname@example.org
John Vogel, staff scientist, DOE Joint Genome Institute, email@example.com
- Author: Julie Sievert
The Pacific Division of the American Phytopathological Society recently awarded Dr. Themis Michailides their Lifetime Achievement Award.
Here are some excerpts from the presentation of the award:
Michailides is a leading authority in fungal fruit tree pathology and is nationally and internationally recognized for his innovative ecological, epidemiological, and disease management studies of devastating diseases of fruit and nut crops.
After intensive and multifaceted research on the panicle and shoot blight of pistachio caused by Botryosphaeria dothidea, a major disease that became an epidemic in 1995 to 1998 and frightened the pistachio industry, he developed tools for successfully controlling the disease. For this outstanding research, the California pistachio industry awarded him an engraved plaque entitled “Honoring 20 years of research excellence.”
Michailides has been doing pioneering research in understanding and managing aflatoxin contamination of pistachio and almond.
Michailides has published more than 235 refereed articles.
He has been very active in The American Phytopathological Society (APS), serving as a member and/or chair of various APS committees. He has also served as associate editor (1991—1993) and senior editor (1995—1997) of Plant Disease and senior editor (2006—2008) of Phytopathology. He has established cooperation with international scientists in more than 10 countries.
2011 APS Fellow
APS Pacific Division President 2012—2013
Themis has worked from Kearney for 31years now. He and his co-workers expanded the research from what they learned from the Bot of pistachio over the years to Bot (or band) canker of almond and the Botryosphaeria/Phomopsis canker dieback and blight of walnut. Themis and co-workers care about the success of the growers he serves and he is always eager in finding solutions to their disease problems.
- Author: Jeffery A. Dahlberg
Two of Kearney's researchers, Jeff Dahlberg and Khaled Bali joined Dan Putnam of UC Davis in a trip to Pakistan to talk with Pakistani researchers, academics, and farmers about forage production. Pakistan has reached out to their expertise to help understand improved forage practices that will help Pakistan meet its dairy and meat needs in the future. The three UC researchers gave presentations in Faisalabad and Multan at the Agricultural Universities. Dr. Putnam gave presentations on alfalfa, Dr. Dahlberg on sorghum as a forage, and Dr. Bali on irrigation and evapotranspiration. Their Pakistani hosts were very gracious and appreciative of their efforts. While there, they also participated in a fabulous tradition at the Ag Universities, planting of a tree in each of their names. The Kearney and Davis researchers look forward to strengthening these new relationships between Pakistani scientists and those of UC and ANR.
- Author: Jeannette E. Warnert
UC Riverside nematologist Andreas Westphal hosted lunch for staff and academics at the UC Kearney Agricultural Research and Extension Center May 11 in appreciation for their support. In April, he was awarded tenure. Congratulations Andreas!