Diagnosing trunk diseases with deep DNA sequencing

grapevine-fruit

Grapevine trunk diseases have caused major economic losses to vineyards worldwide. Trunk diseases are painful because they reduce plant vigor and cause yield loss and even death of the plants. According to the SCRI project, every vineyard in California is vulnerable to one type of trunk disease or another. Trunk diseases can negatively affect water use patterns of the plant, as can be seen below.

Trunk disease vines (grey) reduced water use from mid August onward, affecting berry sugar accumulation negatively (Source: Fruition Sciences)

Typical trunk diseases found in California include Esca, Eutypa dieback and Botryosphaeria dieback. Trunk disease symptoms range from cankers to dead arms and leaf cupping. It’s important to note that each type of disease can be caused by a vast number of fungal species. This makes the diagnosis of trunk diseases particularly complicated.    

Diagnosis of trunk diseases

In the traditional method of diagnosis, researchers would take samples from the canker of a plant suffering from trunk disease. The samples are then allowed to grow inside a petri dish so that researchers can study the morphology of fungal colonies formed and identify the pathogens causing the disease.  Another technology currently in use involves isolating the fungus, extracting the DNA, and comparing to a database to identify the species causing the disease.

Unfortunately, both technologies suffer from biases caused by culturing, according to Dario Cantu (UC Davis), who spoke at last year’s Napa Vintage Report. Some species grow fast in the plant environment but slowly on a petri dish and vice versa. Another disadvantage of these technologies is that they only analyze one species at a time and thus can be time-consuming.

Dr. Cantu proposed the use of deep sequencing technology. This involves taking DNA from the canker and processing it in a way that allows us to have markers for each of the species present in the plant. A key advantage of this technology is it allows us to analyze multiple fungal species at the same time and understand their relative abundance. We will also avoid the bias due to culturing because this step is not needed for this method. Fortunately, this technology can soon be available to vineyards due to the increasing affordability of DNA deep sequencing technology.

Furthermore, knowing all the organisms present allow us to have a better understanding of the disease and come up with appropriate preventative measures. Pruning plays a critical role in preventing trunk diseases, considering pruning wounds are highly vulnerable to fungal infections. Some best practices in pruning for young vines can be found in another Vintage Report talk by Alessandro Zanutta.

Fruition Sciences offers a full suite of products addressing a variety of vineyard needs to enhance fruit and wine quality. Physiocap helps vineyard managers identify where dry biomass accumulates in order to optimize pruning and reduce variability.

Posted by Vintage Report

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1 Comment

  1. If there were a chemical input that would remove Eutypa lata (and bot canker, Phaeoacremonium and Cylindrocarpon) from winegrape vineyards, one would think the industry would embrace it, but that has not been the case. CAWG and Lodi-Woodbridge Winegrape Commission both rejected cures, even though it was their #1 Research Priority. This begs the question: Why?

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