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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 research team set up mobile labs in the field at the UC Kearney Agricultural Research and Extension Center to rapidly freeze harvested sorghum plants for later gene sequencing. (Photo: Peggy Lemaux)

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.

Frozen samples were processed and sequenced by researchers at the Energy Department’s Joint Genome Institute (JGI). (Photo: Peggy Lemaux)
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.

Understanding how sorghum survives harsh conditions could help researchers identify cereal crop cultivars that are more resilient to climate change. (Photo: Peggy Lemaux)

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.

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Posted on Monday, December 2, 2019 at 1:30 PM
  • Author: Kara Menke, kjmanke@berkeley.edu
Tags: climate change (88), drought (163), Jeff Dahlberg (17), Peggy Lemaux (8), sorghum (11)
Focus Area Tags: Agriculture

Scientists brew up a new way to reach the public

A group of UC graduate students, led by UC Cooperative Extension biotechnology specialist Peggy Lemaux, is making science more accessible to the public by hosting nighttime lectures at Bay Area beer pubs, reported Nicholas Iovino of Courthouse News Service. The monthly talks have tackled topics ranging from microbial bacteria to the search for extraterrestrial life.

The PubScience lecture series grew out of an initiative at UC Berkeley called the Communication, Literacy and Education for Agricultural Research (CLEAR) project. Lemaux launched the project three years ago with a $103,000 grant from the UC Global Food Initiative. CLEAR reaches out to students, members of the community and policymakers.

“If we're not telling people about what we're doing and why they should care, then it's going to be really easy to cut funding for science,” Lemaux said.

Peggy Lemaux started CLEAR by offering a free pint to pub patrons who asked a question about science.

The CLEAR group has grown exponentially since its inception. Lemaux believes the election of President Donald Trump and the policies that stem from his administration's denial of climate change helped spark a renewed interest in communicating science to the public. 

“The group was much smaller before Trump was elected,” Lemaux said. “Seeing the rise of political extremism driven by misunderstanding of science was a huge factor.”

 

Posted on Monday, October 1, 2018 at 2:22 PM
Tags: Peggy Lemaux (8)
Focus Area Tags: Innovation

Microbes associated with plant roots could be a key to helping plants survive drought

As sorghum plants cope with drought conditions, the plants' roots and adjoining microbial communities are communicating in a chemical language that appears to improve the plants' chances under water stress.

“It's amazing,” said Peggy Lemaux, UC Cooperative Extension specialist. “We know there are lots of microbes in the soil and, for the most part, ones in the surrounding soil stayed the same under drought conditions. We only saw changes in those microbes closely associated with the roots.”

The role of drought in restructuring the root microbiome was the first published discovery to come out of a sweeping drought research project underway since 2015 in the fields at UC Kearney Research and Extension Center in Parlier. The five-year study, funded with a $12.3 million grant from the Department of Energy, aims to tease out the genetics of drought tolerance in sorghum and its associated microbes. Using sorghum as a model, scientists hope the research will help them understand and improve drought tolerance in other crops as well. 

Sorghum growing in research plots at the UC Kearney Agricultural Research and Extension Center. (Photo: Peggy Lemaux)

The new research results from the lab of USDA's Devin Coleman-Derr at UC Berkeley, published April 16, 2018, in the Proceedings of the National Academy of Sciences, document the fate of microbes associated with sorghum roots under three distinct irrigation regimens. Because the San Joaquin Valley generally sees no rain during the growing season, it is the ideal place to mimic drought conditions by withholding irrigation water.

All plots received a pre-plant irrigation to initiate growth. In the control plots, sorghum was irrigated normally, with weekly watering through the season. In the plot simulating pre-flowering drought stress, the plants received no additional water until flowering, about halfway through the season. The third treatment was watered normally until it flowered, and then water was cut off for the rest of the season.

Beginning when the plants emerged, the scientists collected samples from each plot on the same day and time each week for 17 weeks. In a mini, in-field laboratory, roots, rhizosphere (zone surrounding the root), leaves and soil samples from 10 plants in each plot were immediately frozen and transported to Berkeley, where they were disseminated to collaborators, who investigated the plant and microbial responses at the molecular level.

“When a sorghum plant is subjected to drought, it starts sloughing off metabolites, nutrients and amino acids from the roots. The compounds appear to communicate to the neighboring microbial community that the plant is under stress,” Lemaux said. “That selects out a certain population of microbes. Certain types of microbes increase, others go away. When you add water back, the microbial community returns to its pre-drought population in just a few days.”

The researchers cultured two specific microbes that were enriched in the rootzone under drought conditions. They coated sorghum seeds with the microbes and planted them under drought conditions in a growth chamber. This treatment encouraged the plant to grow more roots.

“The microbes appear to improve plant growth during drought,” Lemaux said. “Those microbes appear to be helping plants survive drought. We didn't know that was happening before we got these results.”

Lemaux said the research might lead to future field use of the research breakthrough.

“A lot of companies are interested in the microbiome,” she said. “Some are already selling microbes to coat seeds.”

Posted on Wednesday, April 25, 2018 at 8:44 AM
Tags: drought (163), Kearney (4), Peggy Lemaux (8), sorghum (11)
Focus Area Tags: Agriculture

UC puts high science online in easy-to-read citrus research updates

California citrus farmers have their ears perked for all news related to Asian citrus psyllid (ACP) and huanglongbing (HLB) disease, but the very latest advances have been available only in highly technical research journals, often by subscription only.

UC Cooperative Extension scientists are now translating the high science into readable summaries and posting them on a new website called Science for Citrus Health to inform farmers, the media and interested members of the public.

“The future of the California citrus depends on scientists finding a solution to this pest and disease before they destroy the industry,” said Beth Grafton-Cardwell, UC Cooperative Extension citrus entomology specialist. “Our farmers want to stay on top of all the efforts to stop this threat.”

The new 'Science for Citrus Health' website can be found at http://ucanr.edu/sites/scienceforcitrushealth/

Grafton-Cardwell and UC Cooperative Extension biotechnology specialist Peggy Lemaux are the two scientists behind the new website. When scientists make progress toward their goals, Grafton-Cardwell and Lemaux craft one-page summaries with graphics and pictures to provide readers with the basics.

For example, the website outlines scientific endeavors aimed at stopping the spread of huanglongbing disease by eliminating the psyllid's ability to transfer the bacterial infection. This section is titled NuPsyllid, and contains summaries of three research papers including one by UC Davis plant pathologist Bryce Falk.

Falk is collecting viruses found in Asian citrus psyllid; so far he has identified five. He is looking into the potential to utilize one of the viruses as is or modify one of the viruses to block the psyllid's ability to transmit the bacterium.  For example, the virus might out compete the bacterium in the psyllid's body.   

Another focus of the website is HLB early detection techniques (EDTs). If HLB-infected trees are found and destroyed before they show symptoms, ACP is less likely to spread the disease to other trees. EDT research described on the website includes efforts to detect subtle changes in the tree that take place soon after infection, such as alterations in the scents that waft from the tree (studied by UC Davis engineer Cristina Davis), changes in the proteins in the tree (studied by UC Davis food scientist Carolyn Slupsky) and starch accumulation in the leaves (studied by UC farm advisor Ali Pourreza).

Other research areas on the Science for Citrus Health website are solutions for established orchards and replants.

As more research is published, more one-page descriptions will be added to the website. The website contains a feedback form to comment on the science and the summaries.

UC Cooperative Extension specialist Beth Grafton-Cardwell is one of two UC ANR scientists who have developed the Science for Citrus Health website.
Posted on Tuesday, July 18, 2017 at 8:54 AM

Science and public opinion square off in GMO debate

UC scientists are studying sorghum genetics to understand plant drought tolerance. (Photo: Wikimedia Commons)
The biggest disconnect between science and public opinion is the differing view on genetically modified foods, according to Alison Van Eenennaam, a UC Agriculture and Natural Resources specialist in animal genetics. Van Eenennaam was quoted in a story reported by Dave Marquis of ABC 10 News in Sacramento.

Van Eenenaam examined 20 years of records on the health and production of livestock populations eating GMO feed and has not found any measurable trends or changes.

"And those field observations agree with the many hundreds of carefully controlled studies that have been done by researchers globally," she said.

The story also raised consumer concerns about genetically modified foods. A Sacrament shopper interviewed for the story said she believes farmers are spraying more pesticides on GMO crops. Van Eenennaam confirmed that crops modified to resist herbicides have encouraged greater use of herbicides and some weeds have become resistant to herbicides as a result. 

"But I would argue that the trade-offs haven't been that significant and, unfortunately, this public concern around it is forestalling the development of what I would argue is much more sustainable plant and animal species," she said.

In her Twitter feed, Van Eenenaam provided links to additional information about the impact of current GMO crops.

One possible benefit of GMOs is helping crops adapt to a warmer world resulting from global climate change, reported Matt Weiser on Vox.

For the article, Weiser spoke to Peggy Lemaux, UC ANR Cooperative Extension biotechnology specialist based at UC Berkeley. Lemaux is the lead researcher on a project aimed at engineering drought resistance into crops — in this case, sorghum. Her goal is to discover how epigenetics, the process by which environmental change triggers new genetic functions, could be used to improve drought tolerance.

If she and her colleagues can figure this out for sorghum, it could be applied to other species such as tomatoes and rice, also part of Lemaux's research, through genetic engineering or by inducing mutations using radiation or chemicals.

Posted on Tuesday, January 26, 2016 at 11:13 AM
Tags: Alison Van Eenennaam (25), GMOs (12), GMOs (12), Peggy Lemaux (8)

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