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New technology to identify plant pathogen strains

Scientists at Virginia Tech used genetic sequencing technologies to identify diseases in crops.

Scientists at Virginia Tech have applied genetic sequencing technologies to identify diseases in crops. They combined the power of DNA sequencing with the power of new computer algorithms to interpret the DNA sequences to precisely and quickly identify pathogens.

In a study, the scientists wanted to determine if an Oxford Nanopore Sequencing MinION device and a combination of different bioinformatic programs and sequence databases would be successful in identifying bacterial pathogens down to the exact outbreak strain.

Xanthomonas perforans

When tested on tomato plants grown on the Eastern Shore of Virginia, the MinION device recognised Xanthomonas perforans, a proteobacteria responsible for bacterial leaf spot in tomato plants, as the pathogen in question.

Strain identification

The team was even able to make their identifications down to the strain level. Strain identification poses a serious challenge to scientists because strains can be difficult to distinguish from one another. Without the proper technology and databases, new strains could be misidentified and the diseases they cause go untreated.

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Marcela Aguilera Flores (left) and Parul Sharma (middle), students in the genetics, bioinformatics, and computational biology graduate program, look at the computer as Marco Enrique Mechan-Llontop, a recent doctoral graduate in the School of Plant and Environmental Sciences (right), inserts plant DNA into an Oxford Nanopore Sequencing MinIONTM device. - Photo Courtesy of Alex Crookshanks for Virginia Tech.
Marcela Aguilera Flores (left) and Parul Sharma (middle), students in the genetics, bioinformatics, and computational biology graduate program, look at the computer as Marco Enrique Mechan-Llontop, a recent doctoral graduate in the School of Plant and Environmental Sciences (right), inserts plant DNA into an Oxford Nanopore Sequencing MinIONTM device. - Photo Courtesy of Alex Crookshanks for Virginia Tech.

Deployed in the field

According to Virginia Tech, the technology could eventually be deployed in the field, along with automated sampling devices from the SmartFarm Innovation Network, an initiative of Virginia Tech’s College of Agriculture and Life Sciences, to develop and deploy innovative technologies in food, agricultural, and natural resources production systems in Virginia.

Save growers a lot of money

The researchers say that the Oxford Nanopore Sequencing MinION device is one of those technologies that will really have an impact and will save growers a lot of money. By being fast and more precise in identifying diseases, growers can intervene early and manage diseases effectively, thus reducing losses in crop yield and quality.

Read the full story on the Virginia Tech website.

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