DNA Innovations Could Solve Potato Scab

Published online: Sep 30, 2013 Richard Allison, Farmers Weekley UK
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New high-tech DNA techniques are proving valuable in the fight against foreign diseases at borders, as well helping scientists gain a better understanding of costly problems like potato scab.

Speaking at the AHDB Crop Research Conference in London, Rick Mumford of the Food and Environment Research Agency (FERA) highlighted the difficulty in identifying pathogens in imported plants and seed.

"Detection in the field is not easy," he said. "There is the sheer volume of imports, inspections are not carried out in the ideal environment for DNA testing and symptoms may not be visible."

However, one advance that is helping inspectors is a new portable DNA analyzer, allowing testing to move out of the lab and into the field.

He explained that the device is based on loop-mediated isothermal amplification (LAMP), which offers many other benefits over the existing PCR-based (polymerase chain reaction) methods, including rapid results in just 10 to 15 minutes (rather than days) and better reliability.

The device has been successfully trialed by inspectors and the system has been deployed at Heathrow and Zurich airports. "Forestry Commission inspectors have also used it in the field to identify ash dieback."

But what about the unknown pathogens? He highlighted that on average, there are 1.3 new viruses a year discovered by Food and Environment Research Agency (FERA). "There is a lot of stuff out there."

The second area being developed by FERA is the use of genomics for the rapid identification of new or unusual pathogens. Recent developments mean they can compare whole genomes of organisms rather than a handful of genes or study whole populations, such as soil microbes.

One example is the Horticulture Development Company-funded project tackling internal browning of carrots. This has been a long-standing issue with no known cause.

Affected carrots exhibit brown necrotic patches, leading to whole crop rejection on processing lines where more than 5 percent of carrots are affected.

Conventional techniques failed to identify the cause. So researchers used the new technique and found DNA from many viruses, including some unexpected and novel. It revealed that carrot yellow leaf virus was the cause.

Another project is looking at potato scab. "We know that irrigation helps reduce scab, but how does this exactly work?"

Researchers are hoping to find what groups of soil microbes are causing the problem. Greenhouse experiments show that in the absence of soil microbes, irrigation has no effect on scab level.

"The aim is to help farmers better target irrigation for scab control."

Harnessing Nature

Like animals, plants also have a defense system against disease and one researcher believes it could be harnessed to protect crops from future attacks.

It has been known for some time that plants can have their defenses switched on or off, says Jurriaan Ton, lecturer and research fellow at the University of Sheffield.

"But we now know that there is a 'primed' state in between. These plants then subsequently have a faster and stronger immune response to future infection."

There are a number of ways of priming plants, including pathogen attack, beneficial soil microbes, chemical signals released by other plants under attack and some chemicals.

Priming gave broad-spectrum protection, but what was the cost? he asked.

"There is a minor reduction in growth, but in high disease pressure situations, there is an overall benefit in growth and seed production," said Ton.

He is now looking at possible strategies such as inherited priming from parent plants exposed to disease. Up to the third generation, he saw a reduction in grapevine downy mildew in arabidopsis (mouse-ear cress) plants when exposed to the pathogen.

Looking ahead, he believes priming could have a role, but added that as it was not 100 percent effective, it wouldn't be used alone by the farmer. "It could be integrated with other approaches, as part of integrated pest management."