- 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
- 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
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: Julie Sievert
The last two weeks of June were filled with the activity of high school students brought from Reedley College for experiential learning about math and science in agriculture. Kearney has played a part in Upward Bound for several years, hosting a portion of the student workshops for two weeks each June. The program is described on the Reedley College Upward Bound website:
The Reedley College Upward Bound Programs are highly successful, precollege programs for predominately low-income and first generation college bound high school students. …The general purpose of Upward Bound is to generate excitement and increase the rates of college enrollment among high school students.
Partnering with Upward Bound is an important part of the strong Outreach Program at Kearney. Please enjoy the following pictures of some of the 2019 summer learning and fun.
- Author: Julie Sievert
On the last Wednesday of June, the Nectarine Room was filled with friends, great food, laughter, and a few tears as Kearney bid farewell and happy retirement to four long time employees stationed here. Everyone from recent hires to Kearney alumni shared in the joy of the accomplishment: 113 years of service, and four happy retirees.
- Author: Cheryl Reynolds
Summer is here, and we're halfway through 2019 already! Why not get jump on finishing up your continuing education units by taking online courses from the UC Statewide IPM Program (UC IPM). If you are a license or certificate holder from the California Department of Pesticide Regulation (DPR), and your last name begins with the letters M through Z, you should be receiving your renewal packet in August.
We're excited to announce some changes.
- In January, we switched all of our online courses to a new learning system located at https://campus.extension.org/. This new system has extensive technical support, is easier to navigate, and is more stable than the old one. Note that the extension platform offers courses from all across the country, including several providers from California. Look for the UC IPM logo to be sure you are taking one of our courses.
- We are pleased to announce that a brand-new online course on the Fuller rose beetle was added to our citrus integrated pest management IPM series. Dr. Beth Grafton-Cardwell, a citrus IPM specialist and research entomologist, and Dr. Joseph Morse, emeritus professor of entomology, developed the course. The course describes the life cycle, natural enemies, and management of Fuller rose beetle and explains why it is important for countries that export citrus. Fuller Rose Beetle has been approved by (DPR) for 1 hour of credit in the Other category and by Certified Crop Advisor (CCA) for 0.5 hour of IPM credit.
- Many of our courses are now credited not only by DPR for continuing education hours, but also by the California Structural Pest Control Board (SPCB), Certified Crop Advisor (CCA), Western Chapter of the International Society of Arboriculture (WCISA), and also by Arizona Department of Agriculture.
DPR encourages license and certificate holders to avoid the end-of-the-year rush and submit renewal applications by November 1 to ensure license renewal by January 1, 2020. Submitting your renewal early avoids late fees and gives you time to address any issues that may arise such as not having enough hours to successfully renew.
Another incentive to get a jump on completing your needed continuing education units (CEUs) with UC IPM's online courses is that we are offering an early-bird price for four of our most wanted courses until November 1st.
- Proper Pesticide Use to Avoid Illegal Residues (2 hours Laws and Regulations; early bird price $40, full price $80)
- Proper Selection, Use, and Removal of Personal Protective Equipment (1.5 hours Laws and Regulations; early bird price $30, full price $60)
- Pesticide Resistance (2 hours Other; early bird price $20, full price $40)
- Pesticide Application Equipment and Calibration (1.5 hours Other; early bird price $15, full price $30)
You can find all of our twenty-one courses listed on the UC IPM website at http://ipm.ucanr.edu/training/.