QBE Lab Department of Plant Pathology UC Davis

QBE Lab UC Davis Department of Plant Pathology

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QBE Lab Blog

APS 2015 in Pasadena


APS president Rick Benett speaking at the opening award ceremony for APS 2015.

APS 2015 was a roaring success for the QBElab!

Neil began the meeting with a Saturday afternoon workshop focusing on using multivariate statistics in R (for more information, look here). The workshop was well attended, with the room practically full to bursting. Neil and Paul Esker talked about different methods for multivariate statistics, including principle coordinates analysis, principle components analysis, and hierarchical clustering. They demonstrated how to use these analyses to explore relationships within your data that may not be obvious. The workshop was really well organized, with well commented code and a useful explanation of when to use the different sorts of analyses.

On Sunday, Kari presented her work on Grapevine Leafroll Associated Virus epidemiology in the North Coast region of California. Kari looked at aggregation of infected plants, and used her analyses of virus presence at different planting booms to support the need for clean plant propagation programs.

On Monday, Robin presented his work on the epidemiology and control of spinach downy mildew in the Salinas Valley. Robin looked at spore trap and disease data from the valley to correlate conducive weather conditions. Robin also discussed several different avenues of research into controlling the disease, as well as how disease affects supply and demand patterns in the crop.

On Tuesday, Christophe presented his research on the spatial and temporal dynamics of angular leaf spot of strawberry, caused by Xanthomonas fragariae. Christophe has worked closely with strawberry nurseries around the state to track disease progression and spread within fields. His findings suggest that the disease is highly aggregated, and likely spreads within-row.


Phytobiomes 2015


Steve Lindow (UCB) talking about colonization of leaf surfaces by airborne bacteria

This June, I was able to attend the 2015 Phytobiomes meeting in Washington D.C. I am originally from the Washington DC area, so it was really nice to go to a meeting and see my family at the same time.

The Phytobiomes Initiative is a collaboration between APS and other groups in an effort to understand how microbes influence the growth and health of plants as a whole. As plant pathologists, we obviously care about what microbes make plants sick, but this initiative wants to explore both healthy and sick plants, and look at how to direct the microbial populations to support healthier plants. To do this, they have invited speakers from many different areas, including human health, seed protection, and agriculture to speak on how they have explored these topics.

I have recently begun to research how biofungicides and downy mildew disease affect the microbial communities on the phyllosphere of spinach. This is a rich and emerging area within plant pathology that has recently had a re-emergence with the reduction in costs for next generation sequencing. Our department’s Johan Leveau is leading the charge on exploring how non-pathogens play a role in the colonization and exclusion of plant pathogenic microbes. Neil and I began this project alongside Johan and Nilesh Maharaj (Johan’s grad student) because there is very little information about how disease or biofungicides impact phyllosphere communities. This is especially relevant in spinach, a crop in which the entire above-ground portion is eaten.

One thing that struck me about the meeting was the need for applications of epidemiology to microbial ecology research. When plants emerge from their seeds, they are (relatively) sterile. Recent research has shown that there is very little overlap between soil microbes and the microbes that eventually colonize the leaf and root surfaces. Where do the colonizers come from? Tracking the dispersal and spread of colonizers is a classic problem for epidemiologists. While plant disease epidemiology is a bit easier (you can simply look for symptoms), I believe that the basic processes that we have described for epidemics will be applicable here.

Our own research will probably fall a bit short of this lofty goal though, as our objective was to describe what organisms were present under different conditions. However, the area of non-pathogen forensics is ripe for epidemiology. In the future, I would like to combine our epidemiological knowledge of colonization and weather conditions with our knowledge of microbial ecology.

Its a brave new world out there and we are only beginning to scratch the surface.

Upcoming Conferences

Conferences and annual meetings are great ways to network with other scientists, researchers, and growers. These venues allow for a meeting place where we can display and discuss our work, and also a great way to learn about current work in our research fields. A few of the QBE lab members are planning to present their work at a number of conferences this summer, namely the American Phytopathological Society (APS) annual meeting in Pasadena, CA, and the American Society for Enology and Viticulture (ASEV) annual meeting in Portland, OR. Robin Chourdhury, a Melhus award winner, will present his work on the “Epidemiology and Control of Spinach Downy Mildew in Coastal California” at the 2015 APS meeting. The research is a collaboration with Steven T. Koike, Alan Fox, Krishna Subbarao, and Steven J. Klosterman. Christophe Gigot will present his work on “Spatial pattern analysis of the incidence of strawberry angular leaf spot under outdoor growing conditions in California”at the 2015 APS. Christoph’s research involves a collaboration with William Turechek. Kari Arnold will present work on “Assessing the benefits of disease management by interpreting an ecological survey of grapevine viruses when contrasted with “planting booms” at 2015 APS and at ASEV 2015 she will discuss “Interpreting a multi-virus survey and designing and delivering virus sampling protocols for industry-wide benefits”, of these involve collaboration with Monica Cooper and Deborah Golino.

So Far, So Good, So What? An Update on Leafroll

Ok, I may have intended to quote something in the title, but I will let you figure that out….unless you already know, and if so, I will offer you a digital high five.  Either way, the current status of the leafroll project and I parallels the saying “So far, so good, so what?” quite eloquently, and here’s why…

As a part of my transition into PhD-hood, I have had to review my leafroll (GLRaV-3) story many times over in presentation form and award application/proposal form, in order to tell others what has happened so far, ensure them that it is in fact “good”, and what importance in the big picture does it represent (the “so what?” part), so the retrospect aspect on my shuttle bus ride into Davis is coming in quite handy.  Yet every time I tell the story, I am still stunned to think that we made it this far.  It takes an interesting batch of people to assess the appropriate amount of information, and relay that information back to those who need it, then back away and wait to see if the up take will lead to change within the system.  It is a careful balance, we have worked diligently, watched wondering, waiting to see if it will work…..so far, so good….so what?  Here’s my story, thus far:

Background and Rationale:
Grapevine leafroll associated virus -3 (GLRaV-3) is a grapevine virus that reduces vigor and yield in vines, and qualitative parameters in wine (Mannini et. al. 1996, Mannini et. al. 2006). A certification program is in place in response to the need for virus tested clean stock (Alley and Golino, 2000, Olmo, 1951); however the use of noncertified stock is still common in California vineyards (Golino, et. al. 2008). Four species of mealybugs commonly found in California vineyards are known to transmit GLRaV-3 and GLRaV-3 is currently spreading in Napa Valley (Golino, et. al. 2008).
Current Work:
Knowledge of the active dispersal of GLRaV-3, mixed with the regional arrangement of multiple landowners and corporate agencies farming vineyards under multiple variations of cultivation, means the control of GLRaV-3 was and still is highly dependent upon area wide management groups. Yet barriers to adoption of new practices by farmers come in many forms, including lack of familiarity, uncertainty about the potential value, or mistrust about the extent to which others will participate in collective actions (Gent, et. al. 2013, Lubell, et. al. 2012). Two studies began simultaneously, in order to promote regional neighbor related action in terms of GLRaV-3 control. The first study, a Q-method (Stephenson, 1954a) approach, was used to assess collective concerns involving GLRaV-3 management. The second study was an epidemiological characterization of GLRaV-3 with the use of multiple diagnostically verified disease maps from Napa and other parts of the world, in order to better understand parameters of disease dispersal for GLRaV-3 management. As a result of presenting preliminary data to growers, area wide management groups have formed, and new ones are forming in order to control GRaV-3 on a regional level.
The first study used Q-method in order to assess the opinions of the growers’ subjectivities on the subject of GLRaV-3 management. Three workshops were held in the Napa Valley at which invited participants were asked to write down their views in response to a set of open-ended questions about leafroll, its’ impacts and the prospects for cooperative management of the disease. Responses were sorted into thematic groups (e.g. statements about financial issues, clean plant material, interpersonal trust, etc.). A small subset of response statements which encapsulated the groups of opinions was extracted. This resulted in a set of 47 statements. Invitations were issued via email and by personal contacts to a further group of participants drawn from the Napa Valley grower and winemaker communities generating a participant group of 37 individuals, then later an additional 12 participants from central CA. These people were interviewed on a one-to-one basis and the participants ranked the statements by the degree to which each one accorded with their own views. The resulting two-way table of data, in which each row gives the numerical rank assigned to each statement by one participant, was then subjected to a principal components analysis to extract information regarding the distribution of opinions over the group of participants and to identify meaningful classifications of the responses. The analysis revealed a wide diversity of opinion distributed among some broad categories of response. This information was then quickly redistributed to growers in the form of multiple presentations at grower conferences in order to assist in team building among potential grower groups. A journal article is currently in preparation from this work.

The second study utilized field maps from previous literature as well as from diagnostically RT-PCR verified industry disease maps showing the disease status of individual vines. These census maps were analyzed by exhaustive quadrat-based mapping in order to better understand the epidemiology of GLRaV-3; particularly to support sampling strategy and disease detection. The nature of the vector and the nature of the virus acquisition and transmission lead the pattern of disease in the field to be aggregated. The early juvenile stages of mealybugs are considered the most efficient at acquisition and transmission, (Golino et. al. 2008) and these juveniles are unable to fly. Therefore, apart from being passively dispersed in wind gusts, they typically crawl along vine rows. The data for disease incidence at individual vine, quadrat and block scales were analyzed using a number of different statistical approaches appropriate for disease incidence data, including variance-variance analysis, incidence-incidence analysis and test of goodness of fit for quadrat frequency. Preliminary results of these studies suggest the potential of three stages to the epidemiology of this disease in the field.
1. Initial infections result from the random introduction of virus airborne viruliferous mealybugs.
2. Vine-to-vine transmission by crawlers leads to aggregated disease foci developing around the initial infections (first 5 to 15 years). This phase may demonstrate an exponential increase in disease incidence, although further work is needed to justify this.
3. The typical plateau where the likelihood of a viruliferous mealybug coming in contact with a healthy vine is lowered, due to the high level of GLRaV-3 infected vines already within the vineyard block.
These three stages need better characterization in order to formulate future models and management practices on an area wide disease management level. A journal article on GLRaV-3 epidemiology is currently in preparation.
Area wide management groups have formed in Napa Valley, one in particular which we are currently working with hands on. Participants in this group are currently assessing adult male mealybug trap counts and the current status of GLRaV-3 incidence in vine blocks. Grower-collected data are collated and visualized via ArcGIS and GPS. Participants also attend meetings every month, where they discuss current control strategies, current mealybug trap counts, symptom expression, rogueing (removal of infected vines) and management success stories thus far. Other groups are also forming, some in connection to this group, others in response to presentations and outreach via grower conferences and personal contacts.
Future Work
With the formation of work groups, questions related to control can be better understood, answered and associated given these new lines of communication.  In order for GLRaV-3 regional control to be maintained, the following objectives must be fulfilled:
1. Epidemiological Study: Further characterization of the 3 potential stages of GLRaV-3 in the field to formulate future models and management practices on an area wide disease management level.
a. Sampling Calculator: utilize information gained from the epidemiological study to appropriate a potential online tool for use by growers for assessment of disease incidence in field with and without symptoms.
b. Economic Study: Based on information gained from the epidemiological study, financial values can be associated with the 3 stages of the field progression of GLRaV-3, assisting growers in better management decisions based in practice and economics by associating risk with GLRAV-3.


Wow, what a mouthful right?  What isn’t stated in the above description is the fact that these growers, who started the project, who participated in the studies, who are participating in the work groups, who are listening to the information and using it; these industry folks wanted to do something about leafroll (GLRaV-3, the one spreading around in fields).  Yet they felt powerless because neighborhood cooperation is a must in this situation, and quite frankly no one wants to be that guy, knocking on doors and telling people what to do (and quite frankly, no one listens to him, because he’s “that guy”).  This story’s big picture goes all the way back to simply knowing how to be a good neighbor, but with real life, financial consequences, and the desire and need for cooperation to be voluntary, NOT regulated by the law (or “that guy” who thinks he’s the law).  The UC presence gave these guys a chance to stand on neutral ground, discuss the issues, and start solving the problem, TOGETHER.  They are no longer powerless to this virus and it’s movement into their fields, because they are united and updated with shared success stories and management strategies–FROM WITHIN THE GROUP, this is not UC telling them what to do either.  We are merely present to answer questions and discuss matters that arise with a scientific background and understanding.

I think we could all take a little something from this in terms of society as a whole……so far, so good, that’s what.

Peruse the ‘Grapevine Leafroll Disease’ page for information on collaborators and other information on the topic.  Thanks for reading!


1. Alley L, Golino D. 2000. The origins of the grape program at Foundation Plant Materials Service. Proc 50th Annu Am Soc Enol Viticulture meeting, Seattle, WA. Am J Enol Vitic 51:222–30.
2. Gent, David H., Mahaffee, Walter F., McRoberts, Neil, and Pfender, William F. 2013. “The use and role of predictive systems in disease management.” Annual review of phytopathology 51:267-289.
3. Lubell, Mark, Hillis, Vicken, Hoffman, Matthew. 2012. “The perceived benefits and costs of sustainability practices in California viticulture.” Research Brief. Center for Environmental Policy and Behavior. Univ. of Cal. Davis.
4. Golino, D.A. and Almeida, R. 2008. Studies needed of vectors spreading leafroll disease in California vineyards.(pdf) Sidebar. California Agriculture 62(4):174.
5. Mannini, F., Aramante, N., Credi, R. 1996. Improvement in the quality of grapevine ‘Nebbiolo’ clones obtained by sanitation. Acta Hort. 427: 319-324.
6. Mannini, F., Argamante, I.N., Cuozzo, D., Credi, R. 2006. Modification in field behavior and grape quality, with focus on terpenes, after GLRaV-3 eradication in a clone of white muscat (Vitis vinifera L.). Extended abstracts 15th Meeting ICVG, Stellenbosch, South Africa, 3 –7 April 2006, pg. 136 – pg. 138.
7. Olmo HP. 1951. A proposed program for the introduction, improvement, and certification of healthy grape varieties. Wines Vines 32 (7):7–9.
8. Stephenson, W. 1954a. Comments on Cronbach and Gleser’s review of: The study of behavior: Q-technique and its methodology. Psychometrika, 19, 331-333.

Spore Trap Locations


In 2013, spore traps were set up at 4 locations throughout the Salinas Valley. These locations were chosen for the density of crops grown nearby and for the even distance between the traps.

Back to downy mildew in organic leafy greens

How do these spore traps work?

Preliminary data

Bridging the Gap Between Field and Lab


Dr. Ozgur Batuman speaking on IPM with Tomato Spotted Wilt Virus in processing tomatoes

Last week the department of Plant Pathology and Entomology held a joint meeting with UCCE and UCANR. The meeting was intended to introduce farm advisors to the 9(!) new faculty between our two departments. The meeting went off without a hitch, with both groups learning a lot about each other. I got to meet several farm advisors and faculty that I had only known by name and reputation, and it was nice to be able to put a face to a name. I was only able to attend the first day because of obligations on the second day, but I learned a lot about pollinator biology and ecology during the special session. I have so frequently heard about colony collapse disorder (CCD) that I felt well informed; however the meeting proved that there are many facets to the disorder that I did not know about, like the rising demand for almonds, the unnatural nature of the close proximity of bee hives in managed fields, and the role of both behavior and innate immunity in fighting off pathogens. I also learned a lot from the vector borne diseases session, with updates from Ozgur Batuman about tomato viroids, Li-Fung Chan about curlytop virus, and Bruce Kirkpatrick about difficulties in Pierces Disease management in grapes.

While the meeting was very informative about the session topics, I also learned alot about how research topics are chosen by PIs and farm advisors. A lot of the people during the discussion section talked about a growing divide between what farm advisors do and what we in the university do. One way to address this is to do exactly what we did – put all of us together in one room and allow for plenty of talking time. The only way that we can move forward against this gap is to meet and exchange information on what is new in the field and what is new in the lab.


New Lab Website and Twitter

If you are reading this, you are part of the future! (super corny, don’t worry, keep reading)

After several iterations of lab websites, we have finally settled down to a new lab website hosted by wordpress on the department server. The other websites that we developed were nice but were lacking one thing or another. Our current website is easily modifiable, professional, and everyone in the lab can write blog posts (now to see whether they will write blog posts).

Neil wanted a new website that we could have everything in one place. We also wanted to present a good face; as an epidemiology lab we do a lot of work with computer modeling and simulation, so it kind of looks bad if our website breaks every five minutes. We also wanted a lab Twitter account so that we could have more outreach and a more prominent public face.

So cheers to the new website and Twitter, and here’s to a productive 2014!


2013 in review!

2013 was a rather quiet year for QBE lab, even though we got a LOT of stuff done! Some of this was due to being busy, but most of it was due to random headaches caused by going through various lab webpages that did not have blogging ability.

Things that happened to QBE lab in 2013:

-Greg passed his Qual!

-Robin got his master’s degree and started a new project!

-Robin passed his Qual!

-Neil visited China to present his work!

-Kari, Robin, and Neil presented work at APS 2013!

-We got our new office! (Carrie working hard)IMG_0658[1]

-We got a new post-doc, Christophe Gigot!

So a lot has happened, hopefully now that we have our new website we will have more blogposts!


Sweet Potatoes in Uganda!

posted 13 Dec 2012 14:45 by A.J. Campbell   [ updated 13 Dec 2012 14:47 ]


A farmer group in Kisiha visits a sweet potato demo plot
Working in a developing country is something I have wanted to do for quite a long time. This fall I worked on a project funded by Horticulture CRSP’s Trellis fund dealing with IPM strategies and general crop management for sweet potatoes in Uganda. Before I left I wrote the aims of the project and never got around to sharing. So, post-travel, here is a description of the project I worked on and the NGO I worked for, for 2 weeks in Hoima district, western Uganda.  

Vitamin A deficiency is a serious issue in rural Uganda. The NGO Environmental Conservation and Agricultural Enhancement Uganda (Eco-­Agric Uganda) seeks to help change this situation through their project, “Promoting Orange-­Fleshed Sweet Potato for Improved Livelihoods in Hoima District.” Their target group is subsistence farmers around Hoima district, western Uganda. The orange-­fleshed sweet potato (OFSP), both high in calories and nutrients, including vitamin A and beta-carotene, is a healthy, ideal crop for subsistence farming. The farmers included in the project, 70% of whom are women representing women-­headed households, face many challenges including obtaining clean planting material, managing pests and diseases throughout the growth, harvest, and post harvest and storage phases of sweet potato cultivation, and adding value to the crop to increase its desirability in the market. Eco-­Agric Uganda, with experience in successfully establishing and maintaining similar programs with tomato and beans farmers in other parts of Uganda, has orchestrated a project utilizing multiple approaches to improve the livelihoods of sweet potato growers, and increase the benefit of growing orange fleshed sweet potatoes.
A group of farmers in Kisiha visits a sweet potato demo plot.

The time was well spent, and had some concrete accomplishments. If you’d like to learn more about the trip, what was done, diseases seen, fun travel facts, or what those accomplishments actually were, check back- maybe someday I’ll get around to writing about that part too.

Growth, happiness and Danish Dreams

posted 18 Oct 2012 12:23 by Neil McRoberts   [ updated 18 Oct 2012 16:18 ]


Will more pie satisfy you?

Sometimes there are strange little coincidences in life when unlikely connections occur. Here’s an example. A recent item in the deluge of media coverage on the US election caught my eye:
We have to figure out how best to grow the pie so it helps everyone,” Paul Ryan, Republican VP candidate, 2012, quoted in a New York Times online article, here.
Although this statement was made by the Republican VP candidate, it might easily have been made by his Democratic Party counterpart, Joe Biden, or by almost any mainstream politician in any country. The reference to pie reminded me of this question, asked by the economist Fred Hirsch in the late 1970’s:
Why has modern society become so concerned with distribution – with the division of the pie – when it is clear that the great majority of people can raise their living standards only through production of a larger pie?“. Sir Fred Hirsch, The Social Limits to Growth. (1978).
While Hirsch seems to be in complete agreement with Ryan, and is arguing against redistribution as a useful idea, in fact his question is part of the set-up for a sustained critical evaluation of the idea that making a bigger economic pie will make more people happy.   Hirsch’s analysis reveals that economic growth inherently leads to increase in dissatisfaction once everyone’s basic needs are met. We can make a bigger pie, he argues, but this will make a larger number of people happier only as long as they’re happy to eat pastry, because the rare and tasty treats that go into the filling are scarce and can’t be made more available by making more crust. Furthermore, the people who already get more of the tasty filling, will still be in that position no matter how big a pie we bake and how many people we invite to share it. Indeed, the promise of pie only makes people feel disappointed when they realize they’re only getting a chance to smell it baking and nibble on the pastry.
In the brilliant introduction to Social Limits Hirsch summarizes the problem with focusing on growth:
Acting alone each individual seeks to make the best of his or her position. But satisfaction of these individual preferences itself alters the situation that faces others seeking to satisfy similar wants. … the sum of such acts does not correspondingly improve the position of all individuals taken together… Opportunities for economic advance, as they present themselves serially to one person after another, do not constitute equivalent economic advance by all. What each of us can achieve, all cannot.”.
Hirsch’s analysis is sobering. One of the central pillars of modern economic democracy is found to have a structural problem: economic growth leads to a growth in dissatisfaction. The solution requires a population-level change in attitudes so that we do not pursue the idea that through sufficient hard work and good fortune we can all join the ranks of the rich. We can’t. And the reason we can’t is that part of what makes the rich rich is the appropriation of goods that are either impossible to share out, or which, when shared out,  come in such small portions that ownership or consumption of them doesn’t lead to a feeling of wealth, or which lose their value as markers of wealth when they lose their exclusivity.
It is the drive to overcome these problems generated by economic growth which leads to the preoccupation with distribution that Hirsch identified. Hirsch argued that growth in a laissez faire economy will lead to increased general dissatisfaction even as it increases the material wealth of a growing proportion of the population. He was writing in the 1970s so we have the benefit of hindsight to evaluate his analysis. Since that time laissez faire economic policies have been pursued by governing parties of the left and right in both the USA and UK. We have seen increasing disparity in wealth (as those who started this recent 30 year rat race with most were best placed to exploit the chance to accumulate riches). The rate of increase in disparity has been lower when left-leaning parties have governed, but disparity in wealth has increased nonetheless.  Anyone who tried to argue that happiness had increased across the population in either country over those 30 years would have a tough row to hoe.
So what about national happiness? There are well-known problems with efforts to construct simple happiness, or well-being, indices comparable with economic indicators such as GDP. These problems notwithstanding, one of the more recent and well-received efforts generated the following set of countries as the top 10 on a national well-being index
1 – Denmark, 2 – Switzerland, 3 – Austria, 4 – Iceland, 5 – The Bahamas, 6 – Finland, 7 – Sweden,
8 – Bhutan, 9 – Brunei, 10 – Canada
One interesting feature of the list is that the European countries that appear in the top 10 have relatively flat income distributions; the rich in these countries are not astronomically many times richer than normal people (the people we now call “middle class” but who used to be called both middle class and working class – Hirsch’s ratchet can be seen working in the fact that we no longer appear to have a working class). On the same ranking, the UK is 41 and the USA 23. The fact that Denmark is ranked 1 brings me to the second coincidence that stimulated this post. In snatched moments of quiet I’ve been reading Peter Hoeg’s The History of Danish Dreams and in the last few days came across this quotation:
and with wealth we can say it is progress indeed when few have too much and still fewer are in need“. N.F.S. Grundtvig quoted in Peter Hoeg’s The History of Danish Dreams.
Grundtvig is widely acknowledged for shaping the Danish social conscience so perhaps it is not surprising it should be a happy place, given Grundtvig’s opinions on wealth and Hirsch’s analysis of the effects of growth on happiness?
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