Carrot Country

UC Research Promises Help for Identifying Fields at Risk for Developing Cavity Spot

Fall 2006
Carrot Country

University of California researchers hope to have a method of genetic finger printing in place later this fall that will enable carrot growers to quantify Pythium levels in prospective fi elds before planting. If the science materializes, growers should be able to avoid the thousands of dollars lost each year due to cavity spot, a major disease problem in carrots. The disease causes small cavities and lesions on the tap roots that render the carrots unmarketable. Cullage can be high, and a few fi elds each year are literally abandoned.

“While many of these cavities and lesions are often superfi cial, some are deep enough that the carrots cannot be used even for cut and peel,” says Mike Davis, the UC-Davis researcher heading the project.
Davis is a Cooperative Extension specialist and professor in the Department of Plant Pathology.

Pythium Present in Most Soils Cavity spot is caused primarily by the fungi Pythium violae and Pythium sulcatum. Pythium species of one type or another are found in most soils but at different levels, Davis explains. Some are threatening to carrot crops; others are not or, if the populations are low, can be controlled with crop protectants such as Ridomil.

“In doing this research, one of the problems we had was there was no method of quantifying Pythium in the soil,” Davis points out. “Thus, we have been unable to provide growers with reliable information on how to predict the risk of cavity spot in particular fields.”

One of the reasons is both Pythium violae and Pythium sulcatum are slow growing species, he says. Hence, when researchers attempt to grow them out on a Petri dish, the faster growing Pythium species, also in the soil, overrun them and make it impossible to quantify their levels in the soil.

In his search for answers, Davis came up with a system of genetic fingerprinting that shows great promise.

“It is a DNA method of quantifying the individual Pythium species,” he explains. “The first thing we did was collect lots of isolates of Pythium species associated with cavity spot. We then developed some specific primers (short pieces of DNA) for use in a preliminary chain reaction (PCR) test.”

What that means is Davis can now extract the DNA of various Pythium species present in the soil and identify which is which.

“Getting the methodology to work from soil has been the challenge,” he admits, adding, however, that signifi cant strides in the right direction have been made.

“Based on our current technology, we can extract DNA from the soil and detect individual species of Pythium,” he informs, “but that’s not enough because we need to quantify it so we can develop some kind of risk model for growers to use. They need to know whether a particular fi eld is low or high risk so they can manage the disease appropriately.”

Reduces the Risk
If a particular field is high risk for cavity spot, a grower could opt out of planting it in favor of a less threatening alternative. On the other hand, if the risk were low, he could feel safer in planting his crop.

“We’re using a real-time PCR method,” Davis explains, “and real time allows you to quantify how much DNA was in your sample at the start. The PCR machine multiplies the DNA that is there. It multiples the minutest amount of DNA in the soil and allows you to work backwards and determine how much you started with and quantify how much DNA of a particular organism was in the soil sample. In turn, that tells you how much inoculum was there for that organism.”

The methodology for identifying Pythium species in the soil “has come a long ways,” Davis acknowledges, “but we still need to optimize our assay for quantifying these different species, and that is what we are working on right now. I believe we are making real progress.” By the end of the year, the researcher hopes to be able to begin applying what has been developed in the laboratory to fi eld assays. The next step will be to collect samples from various fields and quantify the DNA to determine if there is a correlation between the DNA amounts of these organisms and the level of cavity spot in carrots.

“We hope to be able to help growers avoid losing fi elds as well as reduce some of the extra, unnecessary spray applications being made,” Davis says. “We’re seeing growing resistance to Ridomil in some of the Pythium populations. In several of the fields recently abandoned because of high levels of cavity spot, for example, we were able to identify about two dozen isolates that are resistant to Ridomil.”

Once the final refinements to the methodology are made, Davis hopes to begin collecting soil samples from questionable fields. Determining what would represent an accurate portrayal of the actual Pythium numbers in the field will be important. The sampling must be representative of the whole fi eld, he cautions.

“Pythium populations in the fi eld are not equally distributed,” the researcher points out. “They tend to be in clumps, so we’re working on coming up with an appropriate sampling scheme. Once that is accomplished, we will sample the fi elds, bring the samples back to the lab and run a real-time PCR to quantify the number of Pythium propagules in the soil. We will then be able to alert the grower that the cavity spot risk is low, moderate or high.”

Assisting Davis in this work are Jianjun Hao, a post-doctoral researcher at the UC Davis, and Joe Nunez, a vegetable/plant pathology advisor at the UC Cooperative Extension. Nunez is doing the source collections in the Bakersfi eld area and sending them to Davis and Hao for the laboratory research study.

Editor’s note: Mike Davis can be contacted by e-mail at rmdavis@ ucdavis.edu.