Molecular Plant Testing

Viruses, viroids, and phytoplasma cause more than $30 billion in damage annually around the world. These diseases can lie dormant (latent) in a tree for years, escaping detection, before environmental or biological conditions cause symptoms. However, by testing rootstock and scion mother plants before investing in a new planting, the risk of planting infected material can be greatly reduced. Similarly, testing symptomatic plants can confirm the cause to be a virus (compared to abiotic stress, for example), allowing you to manage the disease.

A collaborative approach. We work together with partners like CPCNW, WSU, and WSDA to bring effective testing to the industry. And as part of Qualterra’s continuing mission to innovate, Qualterra has been awarded Small Business and Innovation grants to compare several Little Cherry Disease (LCD) detection methods and develop high throughput methods for sensitive, quick turnaround and cost-effective detection.

A full list of all the plant pathogens we screen for can be found here: Qualterra Virus Database 2023 (60kb)

RT-PCR and RT-qPCR both provide a quick and accurate diagnosis of infected crops. These tests will identify only the viruses that are tested for, giving you sensitive detection without overcomplication. These methods are ideal for rapid screening of individual plants for up to four viruses at a time.

How it works: RT-PCR and RT-qPCR are both extremely sensitive tests which target a small section of genetic material unique to each virus tested. The target sequence is amplified through a process called polymerase chain reaction, until there is enough material to be accurately detected using fluorescent dyes. These two testing types are very similar; the difference between them is that RT-PCR provides a simple yes/no answer as to whether the virus is present in the sample, while RT-qPCR can provide a quantitative measure of how much virus is present.

Fluorescent probe detection curves in RT-qPCR in Hops. Three viruses (Hop Latent Virus shown in red, American Hop Latent Virus shown in green, and Hop Mosaic Virus shown in blue) and one viroid (Hop Stunt Viroid shown in yellow) can be detected in a single reaction along with the RNA quality control marker NAD5 (shown in purple). In this case, curves that begin to amplify before cycle 36 are considered positive for the virus. Amplification curves that begin at earlier cycles indicate a higher titer of virus. No amplification curve indicates that the sample is negative for virus.

Mixups do happen … we’re all human. Our True-To-Type testing services deliver fast, reliable results to help maintain accuracy in the nursery or field. Our offerings are commonly used to check blocks for trueness to type, determine the identity of an unknown variety, or establish a fingerprint and protect a new variety.

How it works: We use Single Nucleotide Polymorphism (SNP) genotyping to verify plant variety; SNPs are single-base changes to the genome which can be detected by targeted PCR reactions. By looking at several SNPs, we can generate a “fingerprint” for each variety, and compare fingerprints to determine whether two plants are the same variety. Qualterra has an extensive database of fingerprints for Apple, Cherry, Grape, Hops, and Pear, and we source new varieties annually to update and validate our database.

(a)

(b)

We use 7-20 SNP Markers to generate a fingerprint for each variety. (a) Each SNP is detected by qPCR, and (b) the results for all SNPs are compiled to generate a fingerprint for each variety. We can determine if an unknown sample matches one of the known fingerprints in the database, or if it is unique.