Grant to help screen crops for viruses – The Daily Evergreen
Cherry growers are losing parts of their trees to disease
Researchers from NuPhY and Texas A&M University have received a grant from the United States Department of Agriculture (USDA) to research and develop ribonucleic acid (RNA) sequencing technology for virus detection in horticultural crops.
NuPhY is a spin-off from a WSU graduate program. The program is led by Amit Dhingra, professor and department head of horticultural sciences at Texas A&M University and adjunct professor of genomics and biotechnology.
Seanna Hewitt, a scientist at NuPhY and a graduate student at Dhingra, initiated and currently leads the research and development of RNA sequencing technology, a form of virus screening that will extract and sequence plant and viral RNA.
Dhingra’s lab will assist with data analysis for sequencing. The WSU Genomics Ward in Spokane will provide the sequencing services, he said.
RNA sequencing will be used to screen for viruses in horticultural crops, with a focus on fruit trees. One of them is the “little cherry virus,” a fruit tree virus in Washington that is currently decimating the cherry industry. This causes the cherries to become smaller and produce an awful taste, Hewitt said.
“The disease is so endemic; cherry growers have lost a significant portion of their trees,” Dhingra said.
Most viruses have double-stranded RNA instead of DNA. RNA sequencing will sequence double-stranded viral RNA along with single-stranded plant RNA, Dhingra said.
“If we isolated all the RNA molecules from a plant cell, the double-stranded RNA would belong to the virus and the single-stranded RNA would belong to the plant,” he said.
Examination of RNA samples will allow a more accurate conclusion of viruses present in plants, Hewitt said. It can also examine several viruses, regardless of their activity or mutation.
“Being able to detect any pathogen present at any given time is useful because previously growers had to screen one test or one pathogen at a time,” she said. “Often there are several things [growers] are interested.
All plant viruses are transmitted by insects which naturally harbor them. Contaminated tools can also transmit viruses, Dhingra said.
Breeding or developing virus-resistant crops will prevent disease in plants, but the process would take five to 10 years, he said. Currently, prevention is the best cure.
Viruses cause damage to an entire field if left untreated. It is expensive to replant orchards and cultivated fields. Disease-carrying crops also impact the economy, Hewitt said.
“When you plant disease-carrying plants, it has a big economic consequence,” Dhingra said. “These plants lose their leaves, they die, and it’s very expensive to plant these orchards.”
The current method of testing for the virus is the polymerase chain reaction (PCR) test. PCR testing is a reactive approach used to determine if plants contain a virus. The test is used once a plant shows symptoms of disease, he said.
“PCR is a molecular method that allows the detection of specific genetic material – in this case, viral genetic material – even when present at very low concentrations,” Hewitt said.
The test has many disadvantages compared to RNA sequencing. PCR can only detect one virus at a time if enough virus is present in a plant and cannot detect inactive or mutated viruses, Dhingra said.
“When we do PCR, we can completely miss [the virus] if there is a change in the genetic code because of mutations,” he said. “It takes a lot of effort to standardize detection.”
PCR tests have also become expensive in the long run because a test can only be performed on one plant at a time, Hewitt said.
“With PCR, you would have to run [multiple] tests as many viruses as you want,” Hewitt said. “There are several that are problematic for most cultures and [hundreds] for some crops.
Phase I of the project began earlier this year and will be completed in the spring. Cutting-edge diagnostics based on RNA sequencing will also be offered, Dhingra said.