Feeding the Future


A Shifting Environment

Glaciers are melting, sea levels are rising, wildfires are blazing and droughts are intensifying. Our earth is in an alarming state of flux. For food producers, these climatic shifts could prove devastating.

“Modern crop varieties are usually bred to a particular latitude and longitude as well as a particular climate pattern,” says Siobhan Brady, associate professor of plant biology. “When these patterns change, it can negatively affect plant growth. Too little water, too much water, high temperatures, increased levels of carbon dioxide—these can all alter plant yield.”

California is the nation’s leader in agricultural production and exports, with food producers generating $45 billion in output in 2016. According to the Department of Food and Agriculture, the Golden State provides one-third of the country’s vegetables and two-thirds of its fruits and nuts.

“Over a few thousand years human beings have selected varieties with traits that have allowed agriculture to flourish and human civilizations to grow and evolve,” says Neelima Sinha, professor of plant biology.

Through domestication and selective propagation, agricultural producers have bred crops for efficiency, selecting lines that produce higher yields and better tastes. This interference by human hands has weakened some crops, causing some to lose adaptive traits that once helped them flourish in environments rife with stressors, like droughts and parasites. California’s intensified natural disasters and droughts undoubtedly spell trouble for the state’s crops.

UC Davis plant biologists are looking to wild relatives for hints to strengthen crops, with the hope that the key to resilience lies in their genetics.

Mining the Best Plant Traits

The arid Andean Region of South America is home to one tough wild tomato species. Drought-, salt- and pathogen-tolerant, Solanum pennellii is an ideal study in extreme plant adaptations. Strong roots and waxy-skinned fruits and leaves help S. pennellii cope with desert challenges. UC Davis researchers are immersed in understanding S. pennellii’s durability.

“The root structure is an understudied area of the plant,” says Brady. “It’s below ground, but it’s responsible for bringing up all the water and nutrients to the above-ground part of the plant, which in turn is necessary for our nutrition.”

Brady studies S. pennellii and its domesticated relative Solanum lycopersium, the garden tomato. Unlike garden varieties, the desert tomato’s roots continuously accumulate the compound suberin in its outer root layer, which enables water retention. The compound is only expressed in garden tomatoes during times of intense drought.

With cutting-edge genomics tools, Brady and her team seek the key to suberin production in the desert tomato. This data could help identify the mechanisms to introduce resilient root traits in other crops.

“If it can be expanded to other crops by breeding for a particular factor that might increase its presence, then it could provide the garden tomato’s roots with more waterproofing and a better ability to withstand drought,” Brady says.

Illustration inspired by the field notebook of the late UC Davis researcher Sharon Gray.

Tricky Parasites

A shifting climate isn’t the only threat to producing bountiful harvests. More than 4,000 different species of parasitic plants leech nutrients from host plants, leaving destruction in their wake.

“Parasitic plants are hugely significant in the world, especially in the lesser developed parts of the world,” says Sinha. “We have things like Striga, or witchweed, which causes incredible devastation.”

The parasitic plant genus Striga has been known to cause up to 90 percent loss in crop yields. According to the International Maize and Wheat Improvement Center, the weed affects more than 49 million acres of cropland in sub-Saharan Africa. It attaches to cereals like maize and sorghum, costing an estimated $1 billion in losses annually.

Witchweed actively hunts its prey. When sorghum roots are low in phosphorous, they secrete a molecule called strigolactone, which tells the roots to uptake more of the nutrient. But strigolactone acts like a smoke signal for witchweed.

Strigolactone can be hijacked by this parasitic plant,” says Brady. “When the Striga sense the strigolactone, it will grow towards the sorghum root, penetrate it and hijack all its resources.”

Since witchweed evolved in tandem with sorghum, some sorghum crops have developed resistance to the parasite. Around 70 percent show some degree of tolerance or resistance.

Brady and her colleagues investigate the genetic mechanisms of resistant sorghum strains. She recently started a project to genetically define how sorghum roots interact with the soil microbiome to either facilitate or suppress witchweed growth.

“There is one sorghum line which has been shown to be defective in strigolactone biosynthesis,” says Brady. “Without this hormone, the Striga roots can’t emerge from their seeds, invade the host plant and take it over.”

Meanwhile, Sinha studies Cuscuta, also known as dodder. Common in California, the parasitic plant grows like cobwebs of orange spaghetti as it envelops its host. Sinha studies the genetic interactions between dodder and host plants.

“This plant has no roots, and it doesn’t photosynthesize. It doesn’t have any leaves, so everything it needs to grow it gets from the tomato,” says Sinha. “It’s a significant problem for California agriculture.”

Like Brady, Sinha is trying to understand at the genetic level what makes certain crops resistant or susceptible to dodder. By investigating plant genomes, Brady and Sinha hope to find the genetic triggers that enable plant defenses. With this knowledge, researchers could introduce these traits into our crops, ensuring their survival in a shifting climate.

Understanding the Language of Plants

Plants produce an array of chemical compounds to cope with environmental challenges. From defending against predators to attracting pollinators, these chemicals, called metabolites, number in the hundreds of thousands and vary from species to species. Each plant is unique in its chemical repertoire, making them the envy of organic chemists.

“To me, the chemistry in plants is much like a language,” says Philipp Zerbe, assistant professor of plant biology. “They use chemicals to communicate, where we use words.”

Zerbe works to decode the diversity of plants by mapping the genes, enzymes and pathways that form their complex metabolic machinery. He’s particularly interested in terpenoids, the largest and most diverse class of metabolites.

Terpenoids perform many functions, from regulating growth and development to protecting plants from environmental stresses like drought and salinity.

“If we can find the genes that are involved in this chemical defense, we can target these genes very precisely,” says Zerbe. “If we listen carefully and understand plants’ language, we may translate this knowledge into new avenues to improve crop resistance and ultimately provide for our burgeoning population.”

To Zerbe and other biologists, the advent of targeted genome editing with technologies like CRISPR/Cas9 has been a game-changer. It’s now possible for plant biologists to pinpoint the genes and pathways involved in specific metabolite production, which could then be introduced into crop varieties.

“Our efforts at the moment are focused on trying to fundamentally understand the enzymatic circuitry that plants use to form the remarkable diversity of metabolites and how these contribute to plant health,” says Zerbe. “Some of these metabolites have been known for decades, but now we have the means to decode their production.”

As the earth’s climate shifts, humanity must be proactive. To maintain food security, we must develop more resilient crops. Studying the strategies of wild and parasitic plants could prove essential in preparing our crops for a changing future.

At UC Davis, plant biologists are making the foundational, multidisciplinary discoveries that will help adapt food production to thrive in a new world.


Posted in Highlights, News

Upcoming Talks and Events

Events on May 16, 2019
WCMC: Best practice in operating mass spectrometers in Metabolomics
Starts: 12:00 am
Ends: May 20, 2019 - 12:00 am
Location: Genome and Biomedical Sciences Facility, 451 Health Science Dr, Davis, CA 95616, USA
Description: Registration: https://goo.gl/forms/TGeuALrTMfTpGh0O2

This course will enhance your standing and expertise to prepare and successfully run samples in a metabolomic laboratory. It is designed to provide hands-on practical exercises using gas and liquid chromatography coupled to mass spectrometry (GC-MS & LC-MS). The course will focus on untargeted data acquisition in metabolomics with both nominal mass and accurate mass instruments. You will learn how to operate the instruments, how to collect metabolite profiles on complex samples and how to prepare and derivatize samples, troubleshoot instruments, acquire data and perform data quality control routines (QA/QC). Overall, you will receive comprehensive understanding of the current best practices in the metabolomics laboratory.

The course will include:

1. Fundamentals of mass spectrometry, chromatography, and metabolomics.
2. hands-on exercises on sample preparation, including extraction and derivatization
of complex samples for untargeted metabolomics profiling
3. Hands-on exercises to learn how to operate both gas and liquid chromatography
coupled to mass spectrometry (GC-MS & LC-MS).
4. quality control routines (QA/QC) in order to ensure comparable data, reproducibility, and instrument performance.
Events on August 19, 2019
International Summer Sessions in Metabolomics
Starts: 12:00 am
Ends: August 31, 2019 - 12:00 am
Location: UC Davis Alumni Center
Description: Registration: https://docs.google.com/forms/d/e/1FAIpQLSeVnMXxhkMtlET-RGDgW99jA3lr1wS4hypU0kI6O1yGV0GqBg/viewform?usp=sf_link

Contact: Jeannette Martins jmartins@ucdavis.edu

Please, contact us now if you need letters of support to obtain funding from your home institutions.

The West Coast Metabolomics Center organizes an instructional course for researchers for researcher which need a deeper and broader understanding in the field of Metabolomics. This course will span 12 days from August 19-30, 2019.

In order to serve the group interests best and have interesting open discussions we have a small class of 22 participants. The participants come always from all over the world and have a very diverse research background.

The course will include:

study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
sample preparation and quality control
in-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
exercises on flux analysis in cancer cells by isotope tracer analysis
untargeted data processing and exercises on MS-DIAL software (in comparison to XCMS)
exercises on identification of unknowns by cheminformatics software workflows (incl MS-FINDER, CFM-ID, and various databases and small software routines)
data normalization and transformation with and without internal standards and quality controls
multivariate and univariate statistics (incl MetDA in comparison to MetaboAnalyst)
pathway mapping (incl MetaBox consisting of MetDA, ChemRICH and MetaMapp in comparison to MetaboAnalyst)
Past course participation:
2018 course: 25 researchers from USA, Brazil, China, Japan, Korea, Taiwan, Russia, Norway, Germany, Poland, Canada
2017 course: 24 researchers from USA, Saudi-Arabia, China, , Korea, Italy, Denmark, Iran, United Kingdom
2016 course: 23 researchers from USA, Saudi-Arabia, China, Thailand, Japan, Italy, Brazil, Chile, Korea, and Canada.
2015 course: 21 researchers from USA, China, Germany, Brazil, Switzerland, Denmark, Canada, Korea, Malaysia, and Netherlands.
2014 course: 20 researchers from USA, New Zealand, Italy, Denmark, China, Canada, Turkey and Switzerland
2013 course: 20 researchers from USA, New Zealand, Costa Rica, Denmark, Luxembourg, Brazil, Columbia, Japan, Korea and Taiwan.
For questions, please contact our program representative Jeannette Martins (jmartins@ucdavis.edu).

Visiting Scientists
Participation in this course is mandatory for visiting international researchers who want to engage in collaborative research projects.
The minimum time span for such collaborative visits is 3 months, preferred is 12 months.
An additional payment of $500 for the visa has to be paid prior to arrival at UC Davis.

Each year, up to five international researchers have started such research visits, funded by agencies in their home countries.
Please contact us at least 6 months in advance to help you with letters of support, booking your course, and obtaining a visa for you.
Cancellation policy
Requests for refunds will be honored when received 2 month prior to the program. Refund requests can be only accepted in a written form. However, another person may be substituted at any time for this program, unless it requires issuing a new travel visa for international scholars.

A $150 administrative fee and the credit card fee will be deducted for cancellations.
In the unlikely event that this program is cancelled or postponed due to insufficient enrollments or unforeseen circumstances, the WCMC will fully refund registration fees but cannot be held responsible for any other expenses, including cancellation or change charges assessed by airlines, hotels, travel agencies, or other organizations.