Posts Tagged: Sorghum
Director of the UC Kearney Research and Extension Center retires
As a Peace Corps volunteer in Niger in the early 1980s, Dahlberg was intrigued by sorghum, a staple food being cultivated by the country's vast population of subsistence farmers.
“I was impressed with the fact that sorghum was so drought tolerant,” Dahlberg said. “Nigerien farmers relied solely on rain for their sorghum and millet crops.”
Upon returning to the U.S., he earned a master's degree at the University of Arizona and a Ph.D. at Texas A&M, where his research focused on sorghum. He worked with the USDA Agricultural Research Service in Puerto Rico for 7 years and then spent the next 10 years as research director with the National Sorghum Producers in Lubbock, Texas.
When Dahlberg took the helm of the 330-acre UC agricultural research center in 2010, he and colleagues at the UC West Side Research and Extension Center and at UC Davis began conducting sorghum forage variety trials. Sorghum wasn't new to California. In the past, it had mainly been used for animal feed. But Dahlberg believed the crop's adaptability – excellent for forage, biofuels and gluten-free human food – offered the grain a rosy future in the Golden State.
"With our research, we have provided California farmers who are thinking about growing sorghum access to locally generated, research-based information to help them make the decision," Dahlberg said.
In 2015, Dahlberg and UC Berkeley specialist Peggy Lemaux launched a sweeping drought research project at KARE. The five-year study, funded with a $12.3 million grant from the Department of Energy, researched the genetics of drought tolerance in sorghum and how soil microbial communities interacted with sorghum roots to battle drought stress.
A journal article published in Proceedings of the National Academy of Sciences in 2018 presented the first detailed look at the role of drought in restructuring the root microbiome. The plant switches some genes on and some genes off when it detects water scarcity and access to water.
“That has implications for feeding the world, particularly considering the changing climate and weather patterns,” Dahlberg said.
In recent years, Dahlberg helped reestablish tea research at Kearney, initiated nearly 60 years ago in a study funded by Thomas J. Lipton, Inc. At the time, Lipton was seeking to grow tea for the instant tea market. When the Kearney tea research program was scrapped in 1981, a researcher had a handful of the best tea clones planted in the landscape around buildings at Kearney.
Those shrubs became the basis for a new tea research trial planted at Kearney in 2017 with UC Davis professor Jackie Gervay Hague to determine whether drought stress impacts the production of phenolics and tannins in the tea.
“We know we can grow good tea here and we can grow high tonnage,” Dahlberg said. “We want to determine if we can do that on a consistent basis and whether we can improve tea quality through irrigation management.”
In retirement, Dahlberg plans to relocate to Lake Ann, Mich., to be close to family. UC Cooperative Extension irrigation specialist Khaled Bali will serve as interim director of the UC Kearney Agricultural Research and Extension Center.
Kearney Alfalfa and Forage Virtual Field Day: September 23, 2020
SIGN UP TODAY! Date: September 23, 2020 Time: 8:30 AM - 12:00 PM Location: Zoom...
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
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.
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 JointGenome Institute is supported by the Office of Science of the DOE contractDE-AC02-05CH11231.
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
UC research could help farmers face droughts worldwide
Sorghum is not only a potential drought-tolerant crop for the San Joaquin Valley, it also presents the opportunity for scientists to understand the mechanism behind drought tolerance at the genetic level, said UCCE sorghum specialist Jeff Dahlberg in a segment on ABC 30 Action News.
Reporter Cristina Davies spent an hour and a half at the UC Kearney Agricultural Research and Extension Center in Parlier during the sorghum harvest to learn about the potential of sorghum research.
"If we can elucidate the genetics behind (drought tolerance), what we believe is we can use those genetics to see if the genetics are available in corn, or in rice, or in wheat," Dahlberg said. "I think the genes may be there. We just don't have the tools yet to search for the genes in those crops."
Conducting drought-tolerance research in California is ideal because the summer is typically devoid of rain. Researchers can control exactly how much water is applied to each sorghum plot. The research has revealed more than 100 genetic markers that may confer drought tolerance.
"We've been really thrilled with the data that's been coming out of this. Like most research, we are learning so many things we don't understand," Dahlberg said.
The research is being conducted in collaboration with the USDA's Agricultural Research Service research center, which is across the street from Kearney. USDA research scientist Devin Coleman-Derr was present for the sorghum harvest.
"Like humans take probiotics, there may be a use for microbes in sort of promoting better and better yields in the field," Coleman-Derr said.
The 330-acre UC Kearney Agricultural Research and Extension Center is the University of California's largest off-campus agricultural research facility.
UCCE specialist Jeff Dahlberg studies sorghum at the UC Kearney Agricultural Research and Extension Center in Parlier.