Posts Tagged: Emily C. Dooley

Winter atmospheric rivers gave pathogens, diseases path to infect crops

Outbreaks similar to El Niño-influenced issues of the 1990s

The wave of atmospheric rivers that swept across the state this winter has created the right conditions for plant pathogens that haven't been seen for decades in California. University of California, Davis, plant pathologist Florent “Flo” Trouillas is getting more calls from growers and farm advisors concerned about potential crop damage.

“Generally, whenever you have rain events, you're going to have problems,” said Trouillas, a Cooperative Extension specialist who is based at the Kearney Agricultural Research and Extension Center in Parlier. “In wet years we get really busy because most pathogens need and like water.”

Trouillas is like a disease detective. He splits his time between the field and the lab, working to diagnose pathogens, diseases and other ailments that strike fruit and nut crops such as almonds, cherries, olives and pistachios.

On a recent visit to an almond orchard near Fresno, Trouillas joined Mae Culumber, a nut crops farm advisor for UC Cooperative Extension Fresno County. A few weeks earlier, the two had walked the orchard, taking note of the base of some trees that had gumming — a thick, jelly-looking substance indicating a pathogen had taken hold.

“A lot of what Florent is doing is trying to assess patterns on a landscape,” Culumber said. “Sometimes things may look like they are one thing, but it could be another problem.”

When the two returned weeks later, the amber-colored gumming had moved into the canopy, looking like gumballs stuck to branches, some of which were already dead. “It's getting out of control from before,” Trouillas says. “This branch was killed. This is widespread.”

From the field to the lab

Lab testing confirmed what Trouillas believed was the culprit: Phytophthora syringae, a pathogen that can affect almond crops but is rarely seen in California. If it is found, generally the site of infection are wounds caused by pruning, but that is not the case here, where the infection began in the canopy at twigs, or small branches.

It is a threat to a key crop, which according to the California Department of Food and Agriculture, generates $5 billion annually. The last time Phytophthora syringae hit California was in the 1990s after a series of El Niño-influenced storms. Trouillas, who has a photographic memory, remembered reading about it in an old manual.

“It's rare for California and one that we see mostly following atmospheric rivers,” he says.

“The disease will only happen following these extremely wet winters.”

Phytophthora is soilborne, mostly found in tree roots, and doesn't generally spread up into branches. But the intense storms created the right conditions for the pathogen to “swim” up trunks as winds blew spores into the air and rain dropped them back down into the canopy, Trouillas said.

Some of the trees in this orchard will die; others can be saved by pruning infected branches and applying a recommended fungicide, he said.

Identification, diagnosis, education

Trouillas is one of more than 50 Cooperative Extension specialists at UC Davis and each is charged with identifying problems and developing solutions for those issues in support of agriculture, the ecosystem and communities throughout the state.

In his role, Trouillas focuses not only on pathology and research but also on educating growers, nursery staff, pest control advisers and others in agriculture about ways to manage potential threats and how to prevent crop damage.

“His role is very crucial,” said Mohammad Yaghmour, an orchard systems advisor for UC Cooperative Extension Kern County. “He's not only on this mission to educate growers but he's also a source of education for us.”

Trouillas typically conducts one or two site visits a week, usually after a farm advisor reaches out about a problem they can't solve on their own.

“This allows us to be at the forefront of disease detections in California,” he said.

He likens these visits to house calls a doctor would make, only to fields instead. And one of those calls recently took him to a cherry orchard in Lodi.

“These guys help me quite a bit,” said Andrew Vignolo, a pest control adviser with Wilbur-Ellis who asked for a consult. “I bug them a lot.”

The visit starts like any consult in a doctor's office, only the questions come fast as they walk around the Lodi orchard where branches are dying, there is gumming and the trees appear stressed. Some look to be sunburned from exposure. Old pruning wounds show cankers, indicating that past disease treatments didn't get rid of whatever was affecting the trees.

Trouillas asks about the cultivar of the trees because some varieties are more susceptible to pests or diseases. He focuses on stress because that opens the door to disease.

Do they prune in the dormant winter months or in summer when pathogens are more prevalent? Does the soil get tested? How old are the trees? What about nutrition?

“I'm trying to figure out how they got infected so bad,” Trouillas said, walking the orchard. “Bacterial canker is a very mysterious disease.”

He thinks it might be a bacterial canker disease and shaves some bark to take to the lab for testing. He wants to come back next winter to take some samples to see where the pathogen is overwintering.

“We'll know in a few weeks if we have a fighting chance,” Vignolo said.

Be it Lodi, Fresno or elsewhere in the state, Trouillas focuses on local conditions. But what is learned in one field can be passed on to others, providing early warnings or advice for those in similar situations. “All these efforts at collaboration, from the field, to the lab, going through research projects, there's only one goal here — to help the farmers of California.”

UC Davis awarded grant to advance strawberry breeding, genetic tools

The $6.2 million grant centers on protecting crops in the future

The federal government is awarding $6.2 million to University of California, Davis, to study how to use breeding and genetic information to protect strawberry crops from future diseases and pests.

The four-year grant from the National Institute of Food and Agriculture (NIFA) centers on addressing expanding and emerging threats to strawberries, a popular fruit packed with Vitamin C and key to the diets of many Americans.

Enhanced plant breeding, gene editing and other technologies will be key to ensuring strawberry crops are sustainable in the face of climate change and possible restrictions on chemical use, said Steve Knapp, director of the Strawberry Breeding Center and a distinguished professor in the Department of Plant Sciences.

“We need to have the technology so that we can deal with the challenges strawberries face around the world,” Knapp said. “Can we use genetic knowledge to change the DNA in a specific way to get the resistance we need?”

USDA funding

The grant award was one of 25 announced Oct. 5 by NIFA – an agency of the U.S. Department of Agriculture – as part of the Specialty Crop Research Initiative program, which addresses “key challenges of national, regional and multistate importance in sustaining all components of food and agriculture…,” the agency said.

The strawberry industry has lagged behind crops like tomato and wheat when it comes to genetic and technical innovation, Knapp said, and the grant signifies that “now they want the foot on the accelerator.”

A key priority is identifying whether changing DNA molecules can improve disease resistance and what technologies would be needed. Ensuring some genes are expressed while others are suppressed would be part of the analysis.

“We're trying to build in natural resistance to pathogens through the genes that already exist but could be modified with this knowledge,” Knapp said. “If we were able to edit a gene that improves disease resistance, people would want us to use that in breeding.”

The intent is to produce disease-resistant cultivars and identify better ways to diagnose, prevent and manage disease. The research project will also include an economic forecast evaluating the consequences of production changes and communicating with farmers about the laboratory advances, according to the grant proposal.

Gitta Coaker from plant pathology and Mitchell Feldmann, Marta Bjornson and Juan Debernardi from plant sciences are participating in the research, as are scientists from California Polytechnic State University, UC Agriculture and Natural Resources, UC Berkeley, University of Florida and USDA's Agricultural Research Service.

Growing cereal crops with less fertilizer

Discovery could reduce nitrogen pollution, save farmers billions

Researchers at the University of California, Davis, have found a way to reduce the amount of nitrogen fertilizers needed to grow cereal crops. The discovery could save farmers in the United States billions of dollars annually in fertilizer costs while also benefiting the environment.

The research comes out of the lab of Eduardo Blumwald, a distinguished professor of plant sciences, who has found a new pathway for cereals to capture the nitrogen they need to grow.

The discovery could also help the environment by reducing nitrogen pollution, which can lead to contaminated water resources, increased greenhouse gas emissions and human health issues. The study was published in the journal Plant Biotechnology.

Nitrogen is key to plant growth, and agricultural operations depend on chemical fertilizers to increase productivity. But much of what is applied is lost, leaching into soils and groundwater. Blumwald's research could create a sustainable alternative.

“Nitrogen fertilizers are very, very expensive,” Blumwald said. “Anything you can do to eliminate that cost is important. The problem is money on one side, but there are also the harmful effects of nitrogen on the environment.”

A new pathway to natural fertilizer

Blumwald's research centers on increasing the conversion of nitrogen gas in the air into ammonium by soil bacteria — a process known as nitrogen fixation.

Legumes such as peanuts and soybeans have root nodules that can use nitrogen-fixing bacteria to provide ammonium to the plants. Cereal plants like rice and wheat don't have that capability and must rely on taking in inorganic nitrogen, such as ammonia and nitrate, from fertilizers in the soil.

“If a plant can produce chemicals that make soil bacteria fix atmospheric nitrogen gas, we could modify the plants to produce more of these chemicals,” Blumwald said. “These chemicals will induce soil bacterial nitrogen fixation and the plants will use the ammonium formed, reducing the amount of fertilizer used.”

Blumwald's team used chemical screening and genomics to identify compounds in rice plants that enhanced the nitrogen-fixing activity of the bacteria.

Then they identified the pathways generating the chemicals and used gene editing technology to increase the production of compounds that stimulated the formation of biofilms. Those biofilms contain bacteria that enhanced nitrogen conversion. As a result, nitrogen-fixing activity of the bacteria increased, as did the amount of ammonium in the soil for the plants.

“Plants are incredible chemical factories,” he said. “What this could do is provide a sustainable alternative agricultural practice that reduces the use of excessive nitrogen fertilizers.”

The pathway could also be used by other plants. A patent application on the technique has been filed by the University of California and is pending.

Dawei Yan, Hiromi Tajima, Howard-Yana Shapiro, Reedmond Fong and Javier Ottaviani from UC Davis contributed to the research paper, as did Lauren Cline from Bayer Crop Science. Ottaviani is also a research associate at Mars Edge.

The research was funded by the Will W. Lester Endowment. Bayer Crop Science is supporting further research on the topic.

Editor's note: Blumwald is affiliated with UC Agriculture and Natural Resources through the Agricultural Experiment Station at UC Davis.

UC Davis to lead $15 million research into climate-change resistant wheat

The project will also train plant breeders for the future

Wheat products account for roughly 20% of what people eat every day around the globe. As climate changes, wheat crops must adapt to new weather patterns to keep up with demand.

The University of California, Davis, is leading a five-year, $15 million research project to accelerate wheat breeding to meet those new climate realities, as well as to train a new generation of plant breeders.

“Everything is less stable,” said Jorge Dubcovsky, a plant sciences distinguished professor who is leading the grant research. “Everything is changing so you need to be fast. You need to be able to adapt fast.”

The grant from the U.S. Department of Agriculture's National Institute of Food and Agriculture will create a coordinated consortium of 41 wheat breeders and researchers from 22 institutions in 20 states. Researchers from Mexico and the United Kingdom are also participating.

Breeding needs to speed up

“Breeding crops for the future will require new traits, breeding platforms built for quick transfer of traits to elite cultivars, coordination of breeding efforts in public and private domains, and training for current and future plant breeders and researchers,” NIFA said in an announcement about this grant and others related to breeding.

The program involves on-the-ground research, identifying molecular markers and data analysis from multiple institutions to determine genes that will help wheat crops mitigate the effects of climate change. Plant breeding will follow to prove out those findings.

Wheat is unlike other crops in that 60% of the plant varieties — generating about $4 billion in annual production — are developed by public breeding programs rather than private corporations. In many states, wheat growers tax themselves to support basic breeding efforts at public institutions like UC Davis.

Increased coordinated research

The NIFA grant money will lead to more coordinated, sophisticated research. “This grant allows us to do breeding at a level that a good, modern company would do,” Dubcovsky said. “This grant is essential to maintain modern and effective public breeding programs in the U.S.”

The consortium will bring together data and research from across institutions, allowing for more expansive analysis while reducing redundancies. “We can take advantage of the data from everybody,” he said. “By doing that we don't need to duplicate efforts.”

A team in Texas will analyze plant images taken from drones at each institution to extract information about plant growth, water use, nitrogen levels and other data. “Using technology, we can see beyond our human capabilities,” Dubcovsky said. “You can extract a huge amount of information from every plant variety.”

The data from those images will allow researchers to document the plants throughout the life cycle and determine which plants fare better under certain conditions. Genotyping will help researchers obtain information about the plant genome. The combination of these two types of data could speed up breeding cycles, helping wheat crops adapt to a changing environment.

“If we can breed fast, we can adapt to change,” Dubcovsky said. “We are trying to make sustainable improvements in time.”

Training the next generation

The project will also train a cohort of 20 plant Ph.D. students in active breeding programs where they will participate in fieldwork, collect data from drones and DNA samples, and learn to integrate that information to accelerate wheat breeding. The students will participate in online and face-to-face workshops, as well as educational events and national scientific conferences.

Colorado State University, Cornell University, Kansas State University, Michigan State University, Montana State University, Oklahoma State University, Purdue University, South Dakota State University, Texas A&M University, University of Idaho, University of Illinois, University of Minnesota, University of Nebraska, University of Wisconsin, Utah State University, Virginia Tech, Washington State University, and U.S. Department of Agriculture Agricultural Research Service branches in North Dakota, Washington, Kansas and North Carolina are also participating in the consortium.

Researchers pinpoint drought-resistant traits in grape rootstocks

Findings could help wine industry adapt to climate change

Scientists at UC Davis have identified new root traits that help grapevines resist drought. The findings, published in the journal Annals of Botany, could speed up the development of grape rootstocks that protect vines from dry conditions, helping the grape and wine industry adapt to climate change.

The research, led by Department of Viticulture and Enology Assistant Professor Megan Bartlett, comes as 80% of California is experiencing extreme drought.

Most grapevines are not rooted directly into the ground but are instead grafted onto a rootstock, which forms the underground part of the plant and supports growth above ground.

“Rootstocks are an important tool to manage water stress,” Bartlett said. “Our goal was to identify traits that make rootstocks drought tolerant, so that grape breeders can amplify these traits in new varieties.”

Root cell traits

The study focused on traits measuring drought responses in living root cells.

The research specifically identified capacitance – which measures how much roots shrink as they dehydrate – as an important trait for drought tolerance.

“The water that enters the roots has to cross through a band of living cells to reach the xylem – the network of pipes that carries water up to the leaves,” said Bartlett. Most research has focused on xylem traits, but the living cells are often the first to be damaged during drought.

Water stress can shrink, deform, or even kill the living cells, causing the roots to shrivel away from the soil and lose access to the remaining soil water. Vines are then unable to replace water lost to evaporation and are forced to close the stomata – the small pores on the leaves that take in carbon dioxide for photosynthesis – to prevent severe dehydration. But closing the stomata stops photosynthesis and starves the vine of the sugars it needs to grow and ripen fruit.

This study is the first to test whether traits measuring root shrinkage and cell collapse can capture differences in rootstock drought tolerance.

Cell traits and drought tolerance

The researchers grafted Chardonnay onto eight commercial rootstocks. Half of the vines experienced drought conditions and half were kept well-watered in a greenhouse experiment.

The study found the eight rootstocks were surprisingly diverse and varied widely in their traits. The rootstocks also appeared to acclimate to drought by changing their traits in that the droughted vines were less susceptible to shrinkage and cell collapse than the well-watered vines.

Among the traits, capacitance was especially important for drought tolerance. The rootstocks with a lower capacitance (less root shrinkage) were better able to maintain photosynthesis during drought than other rootstocks.

“This research gives us a new trait to target for breeding more drought tolerant rootstocks,” study co-author and Ph.D. student Gabriela Sinclair said.

The research was supported by the American Vineyard Foundation, UC Davis, and by donations to the department from the Rossi family. Researchers at the University of British Columbia and the USDA-ARS Crops Pathology and Genetics Research Unit also contributed to the study.

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