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.

Yanran Li receives NIH New Innovator Award

Yanran Li, an assistant professor of chemical and environmental engineering, has received a New Innovator Award from the National Institutes of Health’s High-Risk, High-Reward Research Program for a project to discover plant natural products of potential medicinal value and their biosynthesis through reprograming the plant innate immunity.

Li’s research seeks to engineer and redirect plant immune signaling to activate secondary metabolic pathways that are silent under normal conditions, in order to more efficiently discover novel plant natural products.

“I was first introduced to plant immune receptors during a lunch discussion with Wenbo Ma from plant pathology back in 2016 when I first joined UCR. We came up with the idea to reconstruct and engineer plant immune complexes in yeast,” Li said. “A generous collaborative seed grant from UCR’s Office of Research and Economic Development in 2018 helped me to extend the idea toward discovery of plant natural products in this successful proposal.”

Li’s project is one of the 50 High-Risk, High-Reward awards given by NIH in 2020 to exceptionally creative early career scientists proposing innovative, high-impact projects.

The research will be supported under NIH grant number DP2 AT011445-01. Read more about these awards and the recipients on the NIH website.

This UCR News article was written by Holly Ober and can be read in full here.

Hailing Jin is awarded a $1.89M NIH grant and $900k NSF/USDA grant

Hailing Jin

Hailing Jin received a prestigious 5-year Maximizing Investigators Research Award (MIRA R35) from the NIH on “Cross-kingdom RNA communications between plant and fungal pathogens”, for a total of $1.89M. MIRA is designed to increase the efficiency of NIH funding by providing investigators with greater stability and flexibility, thereby enhancing scientific productivity and the chances for important breakthroughs. The program will also help distribute funding more widely among the nation’s highly talented and promising investigators. MIRA grants are generally for 5 years and are for both established investigators and early stage investigators. Jin’s grant is for established investigators.

Jin also received a $900k grant from the NSF/USDA titled “Development of innovative RNA-based anti-fungals to control plant fungal disease.”

Plant pathologists Caroline Roper and Shou-Wei Ding honored by international society

Caroline Roper
Shou-Wei Ding

Caroline Roper, an associate professor of plant pathology; and Shou-Wei Ding, a professor of plant pathology; are among the 2020 award winners from an international professional organization of plant pathologists.

The American Phytopathological Society, or APS, regularly honors individuals who have made significant contributions to the science of plant pathology. Roper and Ding were presented with their awards at the APS annual meeting held online Aug. 4, 2020.

Roper received the Lee M. Hutchins Award due to her series of seven papers published in APS journals in the last 10 years, including Molecular Plant-Microbe Interactions and Phytobiomes. The award is presented to authors of published research on basic or applied aspects of diseases of perennial fruit plants.

Ding received the Noel T. Keen Award for his research on the molecular basis of plant antiviral defense and virus counterdefense. The award recognizes research excellence in molecular plant pathology.

This Inside UCR article was written by Steven Valenzuela and can be read in full here.