Provided by American Phytopathological Society

While humanity is facing the COVID-19 pandemic, the citrus industry is trying to manage its own devastating disease, Huanglongbing (HLB), also known as citrus greening disease. HLB is the most destructive citrus disease in the world. In the past decade, the disease has annihilated the Florida citrus industry, reducing orange production for juice and other products by 72%. Candidatus Liberibacter asiaticus (CLas) is the microbe associated with the disease. It resides in the phloem of the tree and, like many plant pathogens, is transmitted by insects during feeding events. Disease progression can be slow but catastrophic. Symptoms begin with blotchy leaves, yellow shoots, and stunting, and progress into yield decline, poor quality fruit, and eventually death.

Currently, the only thing citrus growers can do to protect their crops from HLB is control the insect vector. Dozens of researchers are trying to find ways to manage the disease, using strategies ranging from pesticides to antibiotics to CLas-sniffing dogs. Understanding the plant microbiome, an exciting new frontier in plant disease management, is another strategy.

Dr. Caroline Roper and first author Dr. Nichole Ginnan at the University of California, Riverside led a large research collaboration that sought to explore the microbiome's role in HLB disease progression. Their recent article in Phytobiomes Journal, "Disease-Induced Microbial Shifts in Citrus Indicate Microbiome-Derived Responses to Huanglongbing," moves beyond the single-snapshot view of the microbial landscape typical of microbiome research. Their holistic approach to studying plant-microbe interactions captured several snapshots across three years and three distinct tissue types (roots, stems, and leaves). What is so interesting about this research is the use of amplicon (16S and ITS) sequencing to capture the highly intricate and dynamic role of the microbiome (both bacterial and fungal) as it changes over the course of HLB disease progression.

Ginnan et al. surmised that HLB created a diseased-induced shift of the tree's microbiome. Specifically, the researchers showed that as the disease progresses, the microbial diversity increases. They further investigated this trend to find that the increase in diversity was associated with an increase in putative pathogenic (disease-causing) and saprophytic (dead tissue-feeding) microbes. They observed a significant drop in beneficial microbes in the early phases of the disease. Arbuscular mycorrhizal fungi (AMF) were one such beneficial group that the authors highlighted as showing a drastic decline in relative abundance.

The depletion of key microbial species during disease might be opening the door for other microbes to invade. Certain resources may become more or less available, allowing different microbes to prosper. Dr. Roper and Dr. Ginnan hypothesize that when HLB begins, this depletion event triggers a surge of beneficial microbes to come to the aid of the citrus tree. They suspect that the microbes are initiating an immune response to protect the host.

As the disease proliferates, the citrus tree and its microbiome continue to change. Dr. Ginnan, the lead author on this study, found that there was an enrichment of parasitic and saprophytic microorganisms in severely diseased roots. The enrichment of these microbes may contribute to disease progression and root decline, one side effect of HLB.

Survivor trees, or trees that did not progress into severe disease, had a unique microbial profile as well. These trees were enriched with putative symbiotic microbes like Lactobacillus sp. and Aureobasidium sp. This discovery led the researchers to identify certain microbes that were associated with slower disease progression.

Dr. Ginnan says their "aha" moment during the research was in the data analysis. "Originally we were looking for taxa that increased and decreased in relative abundance as disease rating increased," she said. "Our differential abundance analysis ended up revealing clear enrichment patterns replicated in multiple taxa." This is the moment they began to develop the individual patterns they were seeing into a broader disease model.

This research is the foundation for future projects and collaborations that the authors are excited to continue to develop. They are motivated by the potential function of the microbiome to manage crop diseases. In the near future, they hope that these discoveries and an understanding of beneficial microbes can help establish a microbiome-mediated treatment plan to protect crops from diseases like HLB. In addition, the model they've developed can be applied to understanding diseases of other tree crop systems.

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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. 

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. 

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. 

Authors: Kate Evans, Washington State University, and Michael Coe, Cedar Lakes Research Group, LLC

This blog is based on researched published in Crop Science Journal (https://acsess.onlinelibrary.wiley.com/doi/10.1002/csc2.20227)

What is the status of public plant breeding programs in the United States?

Most plant-based foods we eat today are a product of innovative plant breeding programs. Careful choice of plant parents is followed by a multitude of intentional, hand-pollinated blooms. These result in thousands of unique seeds. This is just the start of a long process to create better crops.

In a paper we published recently in Crop Science, we outline a very critical issue: U.S. public investment in plant breeding programs has fallen. The current funding model of short-term grants (1-, 2- or sometimes 5-year awards) is particularly challenging for breeding programs which require typically a 7- to 12-year process, or far longer.

Crop breeders are not just looking for characteristics like drought tolerance or disease resistance in their breeding programs. They also must create new crops with these characteristics that taste good!

1. Breeders select plant parents based on desirable characteristics. These could be taste, size, cooking ability, yield, disease resistance and more.
2. They then cross-pollinate, growing seeds that are hybrids of the parents. They are the “children.”
3. These “child” seeds are germinated, nurtured, and then meticulously evaluated. Many inferior seedlings are ultimately discarded, with only a few of them advancing to a new round of parenting.

Crops go through many such cycles of newly-created diversity and intentional selection. Eventually, the plant breeder may become satisfied that an elite seedling has what it takes to become a successful new variety.  This practice is a long-term endeavor. Some crops can be brought to market in a few years, but crops like apples can take well over a decade.

The benefits of public plant breeding programs

As a result of plant breeding, yields and quality have increased, resulting in remarkable improvements in agricultural production systems. Related species have been used as parents to give important crop plants tolerance to biological and physical stressors. New varieties are adapted to withstand harsh growing conditions or potentially devastating invasive pests or diseases. As climate conditions and ecosystems change, plant breeding is an essential tool to address our long-term food security.

Both private and public institutions have crop breeders working to improve our food supply. Public plant breeding programs often focus on crops that are important to society but may be less profitable than crops that drive the bottom line for large businesses. These crops may have long generation times or otherwise be challenging to breed. They may be the focus of regional cultural specialties or beloved niche markets. Private breeding programs usually must focus on large multinational commodity markets with a potential to generate large, near-term financial returns on private investment. Given these pressures, private companies may find it difficult or impossible to address smaller national or regional markets or longer-term needs.  

Public plant breeding programs frequently target such longer-term goals, many of which address food security issues. For example, “pre-breeding” enriches our agricultural base with diverse plant characteristics from crop wild relatives or other related plants. This requires a lot of research, and significant risk that some efforts won't pan out. But these trials can create new, superior seedlings which make it possible for public breeding programs and private breeding companies to produce important new crop varieties.

Public plant breeding programs also play a key role in educating the next generation of plant breeders and plant scientists for both public and private programs.

Funding issues cause problems

Several studies over the past 30 years have looked at the status of breeding programs. Each showed that U.S. plant breeding capacity is at risk. Budgets and personnel availability continue to decline, despite the development of new plant breeding technologies.

Our most recent survey cited above, in 2018, updated this information. The data indicates a significant reduction in public breeding program personnel over the last 5 years, and aging program leaders. Many programs report that budget shortfalls and uncertainty endanger or constrain their ability to support key personnel, maintain core infrastructure and operations, and make use of current technology.

Many surveyed said that when funding is reduced or sporadic, they focus on sustaining the most basic core operations of the program. These are items like fixing the greenhouse roof and watering the fields. Applying new scientific advances or continuing graduate student and postgraduate training opportunities are typically the first losses. This impacts not only the public program's advanced goals but also development of a long-term social resource: the next generation of plant breeders.

The bottom line is that the struggle to maintain adequate funding hampers public breeding programs. The timeline to bring new crops to market exceeds the time period of most funding sources by years. This requires program leaders to devote much of their time to the constant search for more funding, rather than focusing on their actual work. One solution is to create longer-term grant programs. Otherwise, advances in important crops that are not global commodities could start to decline.  

Our study shows public plant breeding programs are at risk of disappearing. They need reinvigorated, stable, long-term access to funding, technology, knowledge, and expertise.

U.S. plant breeding capacity as a whole (both public and private) and, more broadly, U.S. food security, natural resource resilience, and public health will erode if the trajectory of declining budgets and reduced staffing and expertise in public plant breeding programs is allowed to continue.

Public plant breeding programs are easy to overlook, but their loss would be a devastating blow to our food system.

Organic farming continues to expand in California and now includes more than 360 commodities, according to a new University of California report. The number of organic growers, acreage and farm gate sales revenue is reported by commodity, county, region and statewide in the new “Statistical Review of California Organic Agriculture, 2013-2016.” The data are collected from farms that register as organic with the California Department of Food and Agriculture.

“This report highlights the incredible diversity and abundance of organic crops being grown across so many different geographic regions in the state, which reflects California's leading role in this production sector,” said Houston Wilson, director of the new UC Organic Agriculture Institute. 

“Dairies continue to lead by value of organic production,” said Rachael Goodhue, UC Davis professor of agricultural and resource economics and coauthor of the report.

The number of organic growers in California jumped from 2,089 in 2013 to 3,108 in 2016. The top 10 organic commodities for sales value in 2016 were cow milk, strawberries, carrots, wine grapes, table grapes, sweet potatoes, almonds, raspberries, salad mix, and chicken eggs.

“This review is critical to understand the changes in the fast-growing organic agriculture sector in the state where more than 50% of the nation's organic vegetables and fruits are produced,” said Joji Muramoto, UC Cooperative Extension organic production specialist at UC Santa Cruz and coauthor of the report. “It provides statistics of all organic commodities produced across the state as well as at county level. This is the primary reference to learn about the size, diversity, and trends of organic agriculture in the state.” 

Organic strawberries ranked second in California organic commodities with $202 million in sales value in 2016. Photo by Joji Muramoto

Organic strawberries ranked second in California organic commodities with $202 million in sales value in 2016. Photo by Joji Muramoto

In 2016, California organic sales were $3.1 billion with an average of $1 million in sales per farm, but revenue varied widely among farms. For example, San Diego County had the most organic growers (313) in 2016, but Kern County's 47 organic farmers earned the most in total organic sales: $381 million on 49,727 acres, excluding pasture and rangeland, according to Muramoto.

“The average gross income of organic farms increased 14-fold from 1994 to 2016, reaching $1 million in 2016,” Muramoto said. “However, 77% of growers received less than $500,000 per year and 22% of growers who made $500,000 or more per year received 94% of the total gross sales, showing the income concentration among organic growers in the state.”

The statistical review of California's organic agriculture had been published since 1998 by the late Karen Klonsky, UC Cooperative Extension specialist, and her team after statistics for organic agriculture became available in 1992 as a result of the California Organic Food Act.

The last report published by Klonsky, who passed away in 2018, covered 2009-2012. All previous organic agriculture statistics reports can be accessed at https://aic.ucdavis.edu/research1/organic.html.

“This report of organic data continues the series of studies initiated by Karen Klonsky many years ago. It contains vital summary information for industry and policymakers as well as researchers,” said Goodhue.

Since the data collection began in 1994, the number of organic growers in California has increased 2.8-fold to 3,109 and the farm-level sales 40-fold to $3.1 billion in 2016.

Organic carrots ranked third in sales value in California at $161 million in 2016.

Organic carrots ranked third in sales value in California at $161 million in 2016.

“Accurate annual data on California organic crop production, acreage and value is critical to understanding the scale and scope of this growing agricultural sector,” said Wilson. “As the UC Organic Agriculture Institute begins to develop research and extension programs, it is important that we have a reliable way to assess the extent and geography of organic production as well as track changes over time.”

Muramoto, who became the UC Cooperative Extension organic production specialist in 2019, collaborated with Goodhue, Daniel Sumner, director of the UC Agricultural Issues Center and UC Davis professor of agricultural and resource economics; and UC Davis graduate student Hanlin Wei to produce the latest statistical review of California's organic agriculture.

More recent years are not included because the data collected by CDFA changed in 2017 and again in 2019 so they are not comparable to the data in this report. The full report can be downloaded from the UC Agricultural Issues Center website at https://aic.ucdavis.edu/2020/10/06/statistical-review-of-californias-organic-agriculture-by-wei-goodhue-muramoto-and-sumner.