Discovery increases likelihood of growing food despite drought

Dr. Mauricio Reynoso and Dr. Germain Pauluzzi, molecular geneticists in the Bailey-Serres group at UCR.


University of California scientists have discovered genetic data that will help food crops like tomatoes and rice survive longer, more intense periods of drought on our warming planet.

field-grown rice roots
Field-grown rice roots sampled for research. (Germain Pauluzzi/UCR)

Over the course of the last decade, the research team sought to create a molecular atlas of crop roots, where plants first detect the effects of drought and other environmental threats. In so doing, they uncovered genes that scientists can use to protect the plants from these stresses.

Their work, published today in the journal Cell, achieved a high degree of understanding of the root functions because it combined genetic data from different cells of tomato roots grown both indoors and outside.

“Frequently, researchers do lab and greenhouse experiments, but farmers grow things in the field, and this data looks at field samples too,” said Neelima Sinha, a UC Davis professor of plant biology and the paper’s co-author.

The data yielded information about genes that tell the plant to make three key things.

Xylem are hollow, pipe-like vessels that transport water and nutrients from the roots all the way up to the shoots. Without transport in xylem, the plant cannot create its own food via photosynthesis.

“Xylem are very important to shore up plants against drought as well as salt and other stresses,” said lead study author Siobhan Brady, a professor of plant biology at UC Davis.

In turn, without plant mineral transport in xylem, humans and other animals would have fewer vitamins and nutrients essential for our survival. In addition to some typical players needed to form the xylem, new and surprising genes were found.

The second key set of genes are those that direct an outer layer of the root to produce lignin and suberin. Suberin is the key substance in cork and it surrounds plant cells in a thick layer, holding in water during drought.


tomatoes growing in a field
Tomatoes grown in Davis, CA and sampled to obtain genetic material for this research. (Siobhan Brady/UC Davis)

Crops like tomatoes and rice have suberin in the roots. Apple fruits have suberin surrounding their outer cells. Anywhere it occurs, it prevents the plant from losing water. Lignin also waterproofs cells and provides mechanical support.

“Suberin and lignin are natural forms of drought protection, and now that the genes that encode for them in this very specific layer of cells have been identified, these compounds can be enhanced,” said study co-author Julia Bailey-Serres, a UC Riverside professor of genetics.

“I’m excited we’ve learned so much about the genes regulating this moisture barrier layer. It is so important for being able to improve drought tolerance for crops,” she said.

Genes that encode for a plant’s root meristem also turned out to be remarkably similar between tomato, rice, and Arabidopsis, a weed-like model plant. The meristem is the growing tip of each root, and it’s the source of all the cells that make up the root.

“It’s the region that’s going to make the rest of the root, and serves as its stem cell niche,” said Bailey-Serres. “It dictates the properties of the roots themselves, such as how big they get. Having knowledge of it can help us develop better root systems.”

Brady explained that when farmers are interested in a particular crop, they select plants that have features they can see, such as bigger, more attractive fruits. Much more difficult is for breeders to select plants with properties below ground they can’t see.

“The ‘hidden half’ of a plant, below ground, is critical for breeders to consider if they want to grow a plant successfully,” Brady said. “Being able to modify the meristem of a plant’s roots will help us engineer crops with more desirable properties.”

Though this study analyzed only three plants, the team believes the findings can be applied more broadly.

“Tomato and rice are separated by more than 125 million years of evolution, yet we still see similarities between the genes that control key characteristics,” said Bailey-Serres. “It’s likely these similarities hold true for other crops too.”

Researchers find peptide that treats, prevents killer citrus disease

New research affirms a unique peptide found in an Australian plant can destroy the No. 1 killer of citrus trees worldwide and help prevent infection.

Huanglongbing, HLB, or citrus greening has multiple names, but one ultimate result: bitter and worthless citrus fruits. It has wiped out citrus orchards across the globe, causing billions in annual production losses.

treated versus untreated plants
​Untreated citrus plants on the left, as compared to treated ones on the right. (Hailing Jin/UCR)

All commercially important citrus varieties are susceptible to it, and there is no effective tool to treat HLB-positive trees, or to prevent new infections.

However, new UC Riverside research shows that a naturally occurring peptide found in HLB-tolerant citrus relatives, such as Australian finger lime, can not only kill the bacteria that causes the disease, it can also activate the plant’s own immune system to inhibit new HLB infection. Few treatments can do both.

Research demonstrating the effectiveness of the peptide in greenhouse experiments has just been published in the Proceedings of the National Academy of Sciences.

The disease is caused by a bacterium called CLas that is transmitted to trees by a flying insect. One of the most effective ways to treat it may be through the use of this antimicrobial peptide found in Australian finger lime, a fruit that is a close relative of citrus plants.

cytosol leakage after peptide treatment
Arrows point to areas of fluid leakage from the bacterial cell after treatment with the antimicrobial peptide. (Hailing Jin/UCR)

“The peptide’s corkscrew-like helix structure can quickly puncture the bacterium, causing it to leak fluid and die within half an hour, much faster than antibiotics,” explained Hailing Jin, the UCR geneticist who led the research.

When the research team injected the peptide into plants already sick with HLB, the plants survived and grew healthy new shoots. Infected plants that went untreated became sicker and some eventually died.

“The treated trees had very low bacteria counts, and one had no detectable bacteria anymore,” Jin said. “This shows the peptide can rescue infected plants, which is important as so many trees are already positive.”

The team also tested applying the peptide by spraying it. For this experiment, researchers took healthy sweet orange trees and infected them with HLB-positive citrus psyllids — the insect that transmits CLas.

After spraying at regular intervals, only three of 10 treated trees tested positive for the disease, and none of them died. By comparison, nine of 10 untreated trees became positive, and four of them died.

In addition to its efficacy against the bacterium, the stable anti-microbial peptide, or SAMP, offers a number of benefits over current control methods. For one, as the name implies, it remains stable and active even when used in 130-degree heat, unlike most antibiotic sprays that are heat sensitive — an important attribute for citrus orchards in hot climates like Florida and parts of California.

In addition, the peptide is much safer for the environment than other synthetic treatments. “Because it’s in the finger lime fruit, people have eaten this peptide for hundreds of years,” Jin said.

Researchers also identified that one half of the peptide’s helix structure is responsible for most of its antimicrobial activity. Since it is only necessary to synthesize half the peptide, this is likely to reduce the cost of large-scale manufacturing.

The SAMP technology has already been licensed by Invaio Sciences, whose proprietary injection technology will further enhance the treatment.

Following the successful greenhouse experiments, the researchers have started field tests of the peptides in Florida. They are also studying whether the peptide can inhibit diseases caused by the same family of bacteria that affect other crops, such as potato and tomato.

“The potential for this discovery to solve such devastating problems with our food supply is extremely exciting,” Jin said.

This UCR News article was written by Jules Bernstein and can be viewed here, while the PNAS paper can be viewed here.

Delicious and disease-free: scientists attempting new citrus varieties

UC Riverside scientists are betting an ancient solution will solve citrus growers’ biggest problem by breeding new fruits with natural resistance to a deadly tree disease.

The hybrid fruits will ideally share the best of their parents’ attributes: the tastiness of the best citrus, and the resistance to Huanglongbing, or HLB, displayed by some Australian relatives of citrus.

Breeding project team members from UC Riverside’s Department of Botany and Plant Sciences. (Chandrika Ramadugu/UCR)

There is no truly effective commercial treatment for HLB, also called citrus greening disease, which has destroyed orchards worldwide. The disease has already been detected in California, where 80 percent of the country’s fresh citrus is grown. However, it has not yet been detected in a commercial grove.

To prevent that from happening, the National Institute of Food and Agriculture has awarded a UC Riverside-led research team $4.67 million.  Chandrika Ramadugu, a UCR botanist leading the project, helped identify microcitrus varieties with natural resistance to HLB about eight years ago.

“HLB is caused by bacteria, so many people are trying to control it with antimicrobial sprays,” Ramadugu said. “We want to incorporate resistance into the citrus trees themselves through breeding, to provide a more sustainable solution.”

Part of the challenge with this approach to solving the HLB problem is that it’s possible to breed hybrids that are resistant to the disease but don’t taste good, Ramadugu said. “Hence the need to generate a lot of hybrids and screen them for the ones that will be most ideal for the citrus industry.”

Microcitrus, such as the Australian finger lime, tends to have a sharper, more bitter taste than its relative citrus fruits, like oranges. The perfect cross will have just the right mix of genes to give it sweetness and HLB resistance.

Ramadugu’s team includes collaborators from Texas A&M University, the University of Florida, Washington State University and the U.S. Department of Agriculture, as well as scientists from UC Riverside’s Department of Botany and Plant Sciences.

Currently, the team is studying differences in the genetic makeup of the hybrids they’ve already bred. Analyzing the new plants’ DNA will help the team see whether enough disease resistance has been bred into the fruit, but not so much that the flavor is compromised.

Cross section of a hybrid fruit bred for this project. (Chandrika Ramadugu/UCR)

Another challenge with breeding is the time it takes for new citrus varieties to flower naturally, which can be several years. With the help of Sean Cutler, UCR professor of plant cell biology, the team is hoping to accelerate the time it takes for the hybrid plants to bear fruit in a greenhouse.

This way the hybrids can be analyzed for taste much sooner. Clones of the best hybrid plants will then be grown in Florida and Texas field trials.

UC Riverside scientists are using a variety of approaches to fight HLB. While some hope that altering soil and root bacteria will improve plants’ immunity to the disease, others are trying to improve HLB resistance by tweaking citrus metabolism, or by using an antibacterial peptide to clear HLB from an infected plant.

The fruit produced through Ramadugu’s method will appeal to many consumers because it will not have genes introduced into them by scientists. Breeding has been done for thousands of years to improve crops and is considered a more natural practice.

Additionally, Ramadugu says she’s excited about her approach because it will ultimately produce a product useful for growers and consumers.

This UCR News article was written by Jules Bernstein and can be viewed here.

Grant enables first nationwide effort to save native bees

UC Riverside entomologist Hollis Woodard and bee researchers at 11 other institutions are leading the charge to gather the kind of data that will help governments and land managers justify new protective regulations for native bees.

Wild bee in Yosemite

In a new Biological Conservation paper, Woodard and her colleagues lay out the need for this alliance of researchers, environmental organizations and federal entities including the U.S. Geological Survey, the U.S. Forest Service, and the Bureau of Land Management.

These reasons include the fact that wild bees contribute significantly to the success of the world’s most nutritious and economically valuable crops, their critical role in pollinating threatened plant species, and their declining health.

Supported by a $380,000 grant from the US Department of Agriculture, anyone with the time and inclination can join this first-of-its-kind monitoring network. Training opportunities will be available to help people learn how to go outside and look for bees in a standardized way.

One of the challenges facing the new research alliance is tracking the bees in a systematic way across the wide variety of ecosystems found across the country, including deserts, rainforests, dry forests, tundras, and plains. Woodard, however, feels the alliance is primed to face the challenge by a shared drive to understand and assist the bees.

“It’s exciting that we’ll be capitalizing on a lot of momentum that’s been building to monitor native bees,” Woodard said. “It’s a new direction for my lab, for me, and for the country, thinking about working together and cooperating in this way.”

Visit the network’s website for more information on the project or to learn how to get involved.

This UCR News article was written by Jules Bernstein and can be viewed here.


Olfaction may affect mammals’ motivation in exercising

A research team led by a scientist at the University of California, Riverside, has found olfaction — or smell — may play an important role in motivating mammals to engage in voluntary exercise.

Performed in lab mice, the study may open up new areas of research and have relevance for humans. Study results appear in PLOS ONE.

“Exercise, which is essential for both physical and mental health, can help prevent obesity and other inactivity-related diseases and disorders in humans,” said Sachiko Haga-Yamanaka, an assistant professor of molecular, cell and systems biology at UC Riverside and the study’s lead author. “Some people like to exercise more than others do, but why this is so is not well understood.”

To determine genetic contributions to voluntary exercise-related traits, Haga-Yamanaka and her team subjected mice to voluntary wheel running, or VWR, a widely studied behavior in which rodents run spontaneously when given access to running wheels.

Her collaborator and co-author Theodore Garland Jr., a distinguished professor of evolution, ecology, and organismal biology at UCR, established independent, artificially evolved mouse lines by selectively breeding mice showing high VWR activity. Regular mice — those not genetically engineered in any way — constituted the controls. To their surprise, the researchers found high-runner mice developed genetic differences in their olfactory system that made them perceive smells differently from the controls.

Next, the researchers plan to conduct experiments to isolate particular chemicals produced by mice, perhaps from their urine, and determine if and how these chemicals increase motivation for exercising.

Haga-Yamanaka and Garland were joined in the research by Quynh Anh Thi Nguyen, David Hillis, Timothy Harris, and Crystal Pontrello of UCR; and Sayako Katada of Kyushu University in Japan.

The study was partly funded by the National Science Foundation.

The research paper is titled “Coadaptation of the chemosensory system with voluntary exercise behavior in mice.”

This UCR News article was written by Iqbal Pittalwala and can be viewed here.


Jason Stajich & Hailing Jin Elected to the American Academy of Microbiology

Jason Stajich and Hailing Jin joined a class of 73 total fellows elected to the American Academy of Microbiology. The academy is a leadership group of scientists from around the globe within the American Society of Microbiology elected annually through a selective, peer-reviewed process.

Additionally, Stajich was elected as a fellow of the Mycological Society of America this summer, a distinction awarded for a record of solid research, successful teaching, and significant service to society. He also joined the 2020 class of fellows of the American Association for the Advancement of Science (AAAS) for his research into the evolution of fungi and other microorganisms.

This Inside UCR article was written by Jules Bernstein and can be viewed here

Jason Stajich
Hailing Jin

10 UCR researchers make 2020 ‘Highly Cited’ list

Ten researchers at the University of California, Riverside, have been included in the 2020 Highly Cited Researchers list compiled by Clarivate Analytics, which was previously part of Thomson Reuters.

The list includes the 6,167 most frequently cited researchers in the physical and social sciences, recognized as “researchers who demonstrated significant influence in their chosen field.” This influence was demonstrated through the publication of multiple highly cited papers during the last decade.

This year, researchers were celebrated for their performance in 21 fields of science, and some have also been identified for performance that crossed into more than one field.

While the Highly Cited list includes researchers from more than 60 countries and regions, the United States has the highest number with 2,650 authors.

UCR researchers who made the list include:

  • Julia Bailey-Serres, University of California MacArthur Foundation Chair and distinguished professor of genetics (plant and animal science category)
  • Alexander Balandin, University of California Presidential Chair Professor and distinguished professor of electrical and computer engineering (cross-field category)
  • Sean Cutler, professor of plant cell biology (plant and animal science category)
  • Pingyun Feng, professor of chemistry (cross-field category)
  • Timothy Lyons, distinguished professor of biogeochemistry (geosciences category)
  • Bahram Mobasher, professor of physics and astronomy (space science category)
  • Sang-Youl Park, associate specialist in botany and plant sciences (plant and animal science category)
  • Wei Ren, professor of electrical and computer engineering (engineering category)
  • Prue Talbot, professor of cell biology (social sciences category)
  • Yadong Yin, professor of chemistry (chemistry category)

This Inside UCR article was written by Jules Bernstein and can be read in full here.

Pictured from left to right: Julia Bailey-Serres, Sean Cutler, & Sang-Youl Park

Thomas Eulgem & Karine Le Roch collaborate on Arabidopsis thaliana PHD-finger protein EDM2: A prime example of across organisms and borderless scientific activities in IIGB

Thomas Eulgem
Karine Le Roch

A prime example of across organisms and borderless scientific activities in IIGB was achieved by Thomas Eulgem and Karine Le Roch, with a well-executed collaboration bringing together researchers working in very different areas of genome biology. The project was initiated in Thomas Eulgem’s lab as the PI on the critical roles of the chromatin-associated Arabidopsis thaliana protein EDM2 in coordinating plant immune responses. Karine Le Roch’s group contributed expertise and experience on epigenome profiling to the study.

The PLOS Genetics paper, “The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression”, can be viewed here.


Xuemei Chen, Robert Jinkerson, and Meng Chen received an NSF EAGER grant

Xuemei Chen, Robert Jinkerson, and Meng Chen received an NSF grant to establish a transformative RNA sequencing technology for studying plastids.

Plastids in plant cells (Image found here)

The plant cell stores its DNA in not only the nucleus but also the plant-specific organelles, the plastids. Plastid DNA can be transcriptionally programmed to instruct the differentiation of plastids into diverse types, such as the well-known photosynthetically active chloroplasts. In fact, plastids function far beyond photosynthesis in a variety of essential roles in development, metabolism, signaling, and immunity in plants. However, because each plant cell harbors tens to hundreds of plastids, current RNA sequencing approaches – even those using single cells – average plastid transcriptomic profiles, and thereby, potentially obscure biologically relevant transcriptomic variations that distinguish unique plastid types. As a result, our understanding of plastid types and their functions remains rudimentary.

A UCR team consisting of IIGB faculty Xuemei Chen, Robert Jinkerson, and Meng Chen have been awarded an NSF EAGER grant to tackle the long-standing problem in plant biology. The NSF EAGER (Early-concept Grants for Exploratory Research) mechanism supports radically different and potentially transformative research ideas or approaches. The two-year grant of $300,000, entitled “spRNA-seq: high-throughput transcriptome analysis of single plastids”, is aimed at establishing a cutting-edge technology to sequence RNA molecules from single plastids, namely single-plastid RNA sequencing (spRNA-seq). spRNA-seq allows the determination of molecular signatures of thousands of individual plastids in one experiment, making it possible to create a complete plastid-type atlas and elucidate their functions. This enabling technology is expected to revolutionize research on plastids and will generate novel insights into how plastids affect plant biology, ecology, and evolution.