Tracking grape pathogens from air to vine – a conversation with Lexi Heger

On the Absolute Gene-ius podcast, Lexi Heger, PhD candidate in Plant Pathology and Molecular Plant Sciences at Michigan State University, explores the molecular detection of grapevine pathogens and how qPCR and digital PCR (dPCR) are transforming plant disease research. Her research centers on downy mildew of grape (Plasmopara viticola) and the challenge of differentiating cryptic species that vary in distribution, aggressiveness, and potential fungicide response.

Through multiplex assay development, mitochondrial locus targeting, and rare allele detection, Lexi demonstrates how combining qPCR and dPCR strengthens both basic research and applied vineyard management.

Listen to the full episode on the Absolute Gene-ius webpage or on YouTube.

---

Differentiating Cryptic Species of Grapevine Downy Mildew

Question: What pathogen is at the center of your research, and why is it significant?

Answer:

“So really it starts out focused on downy mildew of grape, which is the obligate, oomycete pathogen I was just talking about. It is a very destructive disease of grapevine.”

She explains the biological complexity of working with this organism:

“I also work with oomycete, so that’s a fungal like pathogen. So people often forget that one. I’ll call it fungal-like just to keep it, you know, chill for people. But it’s also an obligate, so right, it requires a living host to survive, right, and to reproduce, and so that actually adds a whole other level when you’re working with it in the lab. I have to keep plants alive.”

Because Plasmopara viticola is obligate, laboratory research requires maintaining viable host plants, increasing experimental complexity.

---

Question: What was the goal of your qPCR assay development?

Answer:

“I first designed a tool using qPCR to differentiate these three cryptic species of Plasmopara viticola, this pathogen. And so we want to differentiate them using these molecular tools so that we could identify them in the field and do further research.”

These cryptic species—or clades—are genetically distinct yet morphologically similar. Their distribution varies geographically:

“In the United States, we have all three of these economically important clades. But in other countries, we do not.” Understanding which clade is present in a vineyard enables more targeted research and potentially improved disease management strategies.

---

Question: Why did you choose a mitochondrial locus for assay design?

Answer:

“So we used a mitochondrial loci in this study. Mitochondria usually helps us be more specific, whereas ITS or ribosomal, which is the other loci, it can be a little less. We might have increased sensitivity, but we might lose some specificity there.”

The assay was designed as a multiplex:

“And trying to eliminate maybe having multiple primers, maybe just having one primer set and then three probes. So we wanted it to be simple, it never is, but we wanted it to be simple and to be able to clearly differentiate these.”

Although optimization presented challenges, the assay successfully revealed unexpected seasonal dynamics:

“In my vineyard site, we didn’t realize we had two of the clades. We thought, because every time I sampled, we only got clade aestivalis, but we actually had clade aestivalis and riparia, because riparia isn’t as aggressive, right. And so it wasn’t colonizing the same way. So it was really cool to use this very specific tool and be like, ‘Oh, wait, we can actually detect and see the fluctuations throughout the season.'”

---

Integrating qPCR and dPCR in Plant Pathology

Question: How does qPCR support fungicide decision-making in vineyards?

Answer:

“Being able to capture these and then detect them is really important for fungicide programs.”

She explains how molecular tools can detect fungicide resistance markers:

“We can detect for FRAC 11, which is a fungicide group, we can detect for that fungicide resistance. And then you can tell the growers say, ‘Hey, you should steer clear of these, because you’re going to encourage development of resistance, which means losing control of the disease. And that’s just bad.'”

Speed is critical in agricultural applications:

“We can run X amount of sample in a 96-well plate and qPCR really quickly, relative to sequencing.”

---

Question: Where does digital PCR (dPCR) provide additional value?

Answer:

“And then we wanted to enter the world of dPCR. I was the first one, so I got thrown into the fire, but it was a cool fire.”

She highlights its strength in rare allele and SNP detection:

“You can really see the utility of it with I was looking at, again, kind of the rare alleles a little bit, or just very like specific SNPs, and so I was able to see those changes.”

Performance translated across platforms:

“I think between two of the assays that were the best in qPCR, you saw that translated to dPCR.”

Rather than replacing qPCR, she emphasizes complementary use:

“I think in the general sense, qPCR is our starting point. Because, you know, if we’re just tracking general, quick testing for pathogens, but I think when we get into fungicide resistances, single allele changes, I think that’s where dPCR is really going to come in handy with plant pathology.”

She summarizes the strategic approach:

“We suggested, you know, you should maybe use qPCR first for what this is when you’re doing general detection of the pathogen, not necessarily a clade, just pathogen detection. If you want really sensitive, you could also integrate that to dPCR, but for what we need, qPCR is enough for that. When you get down to this kind of thing where you’re differentiating between low concentrations of mixed samples of different species or clades, that’s where you kind of want to start bringing in the big guns with dPCR.”

---

Future Directions in Grapevine Pathogen Research

Question: What are the next steps for this research?

Answer:

“We haven’t done a large population genetic study looking at where the clades are– very like well sampled either. So I think it’d be interesting to kind of go further into that and look into why are they different? How are they different? Even within the same clade or cryptic species.”

She also notes the broader biological challenges:

“There’s so much more to go in there. Just people often have resisted it because of the obligate nature. It’s a pain, right. It’s a pain, so people avoid it.”

By combining multiplex qPCR, mitochondrial targeting, dPCR-based rare allele detection, and population-level analysis, this research advances both scientific understanding and applied vineyard disease management.

---

To hear the full conversation with Lexi Heger, PhD candidate in Plant Pathology and Molecular Plant Sciences at Michigan State University, visit hgthe Absolute Gene-ius Podcast webpage. Explore this episode and discover additional conversations highlighting how qPCR, dPCR, and complementary technologies are accelerating research across disciplines.

Want to learn more about the difference between qPCR and dPCR? Continue learning on the “What Is Digital PCR” blog post here.

Interested in exploring more about the technologies mentioned in this article? Learn more about Thermo Fisher Scientific’s qPCR technologies and dPCR technologies.

The Applied Biosystems QuantStudio Absolute Q dPCR system and QuantStudio qPCR systems mentioned in this article and podcast episode are for Research Use Only. Not for use in diagnostic procedures.