The speed at which PathoTracer is able to identify the strains of bacterial blight can be used for recommending resistant rice varieties in the next cropping season.
Photo: © IRRI

A tool that tracks and stops bacterial blight outbreaks in rice

A new, faster, and more accurate way of identifying infectious organisms—down to their genetic fingerprint—could finally put farmers a step ahead of bacterial blight.

A revolutionary tool called the PathoTracer has been developed at the International Rice Research Institute (IRRI) in Los Banos/Philippines, and it can identify the exact strain of the bacterium that causes bacterial blight present in a field in a matter of days instead of several months of laboratory work.

“It is like a paternity test that uses DNA profiling,” said Ricardo Oliva, a plant pathologist at IRRI. “It will not only tell you that you have bacterial blight in your plant. It will tell you the particular strain of the pathogen so that we can recommend varieties resistant to it.”

For more than four years, Oliva and his team worked on deciphering the genetic code of Xanthomonas oryzae pv. oryzae, the pathogen that causes bacterial blight, to develop the test. Bacterial blight is one of the most serious diseases of rice. The earlier the disease occurs, the higher the yield loss — which could be as much as 70 per cent in vulnerable varieties.

“Bacterial blight is a persistent disease in rice fields,” said Oliva. “The epidemic builds up every season when susceptible varieties are planted. The problem is that the bacterial strains vary from one place to another and farmers don’t know which ones are the resistant varieties for that region.”

Identifying the strains of bacterial blight present in the field requires a lot of labour and time. In addition, isolating the pathogens in the lab is a tedious task, and it typically takes several months or even a year to determine the prevalent strains in a region.

The PathoTracer can identify the local bacteria in the field using small leaf discs as samples. The samples will be sent to a certified laboratory to perform the genetic test, and the results will be analysed by IRRI which only takes a few days. Oliva explained, adding that with the PathoTracer, a year’s work could probably be brought down to two weeks.

“Recognising the specific local bacteria present in the current season can help us plan for the next,” Oliva said. “We can come up with a list of recommended rice varieties that are resistant to the prevalent pathogen strains in the locality. By planting the recommended varieties, farmers can reduce the risk of an epidemic in the next season and increase their profits.”

Pilot tests in the Philippines in 2017

The PathoTracer was pilot-tested in Mindanao, in the southern part of the Philippines in April 2017. The rains came early in the region, just after the peak of the dry season, and that triggered an outbreak of bacterial blight.

The IRRI scientists took samples from different fields. By the end of April, they had the results and were able to come up with a list of resistant varieties that could stop the pathogen. The farmers in the region obtained recommendation of a choice of varieties to reduce the risk. “If the farmers had planted the same rice varieties in the succeeding rainy seasons, I am sure the results would have been very bad,” Oliva said.

The PathoTracer – an efficient tool, also for extension workers

The PathoTracer is able to run thousands of samples and can, therefore, easily cover large areas, making it an essential tool for extension workers, or it can be incorporated into monitoring platforms such as the Philippine Rice Information System (PRiSM) or Pest and Disease Risk Identification and Management (PRIME) to support national or regional crop health decision-making.

IRRI is interested in expanding the genetic testing tool to include rice blast and, further down the road, all bacteria, viruses, and fungi that infect rice.

The PathoTracer has been tested in other Asian countries, and IRRI expects to roll it out during 2018. When it becomes available, the expected potential impact of the PathoTracer on a devastating disease that affects rice fields world-wide will be huge, Oliva believes.

“Imagine if this tool prevented bacterial blight outbreaks every season across Asia,” said Oliva. “It’s super cool!”


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