The Science of Crop Breeding – Creating a Better Basil with Dr. Robert Pyne (FSFS220)

Dealing with plant diseases is a part of every grower’s farm experience. But have you ever thought of growing a plant that’s resistant to a disease?

Joining us is Dr. Robert Pyne of Van Drunen Farms. Dr. Pyne is part of the team that developed a variety of basil that is resistant to downy mildew (DM).


How did you come to be a molecular biologist who works on seeds? (2:30)

I was always drawn to the life sciences. After that, it was a mix of going to a university with a good plant breeding program, meeting great people, and my basic interest in plants.

What are some misconceptions around plant breeding? (4:00)

I don’t know if they’re misconceptions per se, or if the science community just isn’t doing the greatest job to explain the science behind it and keeping people up-to-date. Since it’s kind of a niche subject, it’s hard to gauge people’s awareness of what goes into it. I think there would be less misunderstanding and apprehension in genetically modified crops, and more recently, gene-edited crops, if more information is shared to the public.

What’s the difference between a GMO vs s Crop bred for certain traits? (6:30)

It all comes down to the process.

With GMO technology, you’re transferring genes from one crop to another that couldn’t mate with one another. The genes can come from two species of the same crop that couldn’t mate because of a reproductive barrier. It could even come from further than that, like taking a gene from a bacteria and inserting it into a corn plant.

Although it’s important to note that there should be greater encouragement to plant crops in less monoculture because that’s where you get issues like the boom and bust cycle where you have this one GMO that performs fantastically against a pathogen. But while the GMO is performing well, likewise, the pathogen is evolving to overcome that GMO which then causes a complete wipeout of crops. A good example of this is the late blight of potato in the Irish potato famine.

As far as health and environmental effects, they are yet to be seen especially considering the amount of studies around how the world population has been eating GMO’s for more than thirty years and yet there’s not one single health incidence reported.

In terms of plant breeding, where are things going? (12:00)

Nothing has fundamentally changed in traditional breeding, principles are the same. What changed is the speed at which it’s accomplished. There are strategies such as seed breeding where life cycles are optimized and reduced, and environmental parameters are altered to reduce grow out time. We also use DNA markers that greatly helps in screening out plants and finding out which ones have the trait we’re breeding for and which ones don’t. You can imagine how much time that saves. 

One of the most common methods to breed for a specific trait is to go out and look at a ton of varieties and find one that has that trait. And that’s what we did—we looked at the entire USDA Germplasm seed catalogue for heirloom basil seeds and eventually found a lot of plants with disease resistance.

Have we, over the years, bred out the disease resistance in favor of size, flavor, or appearance of a variety? (19:30)

Yes, I think that a lot of crops got into a genetic bottleneck which is a sharp reduction in population and genetic diversity.

What you find in seed catalogues represent a really narrow section of the genetics available for that crop which may be a result of breeding for certain traits without knowing about the need to maintain a diversity of genetics.

The only things previously bred for were shelf life, disease resistance, and yield. But recently, people have started going back to wild plants in search of flavor because it was a trait left out of the main gene pool.

When you sought to breed a DM-resistant basil, was it enough to say that it’s a hardy crop, or do you have to go deeper and add other traits (leaf size, flavor, etc.) to make it comparable to the ones out in the market and make it kind of like a booster pack? (23:30)

When we started breeding for DM resistance, we found a wild basil plant that was sexually compatible with the commercial type. In our case, the wild type was potentially native to Zanzibar, and the plant did not look like basil at all. The leaves were really undulated and deeply serrated, and it had purple stems and flowers.

If things were as simple as looking for a basil species that had disease resistance, it would have ended there. But of course, no one would want to eat that, let alone recognize it as basil.

So the question is, how far do we have to go to get this wild plant to look hopefully indistinguishable from one of the best commercial varieties? We do traditional breeding.

In our case, we did that through a pedigree breeding strategy, which simply means we were continually crossing back to our commercial basil while always maintaining the disease resistance by screening the plants.

After a while, started putting on a very strong selection pressure on things like yield and flavor (the wild parent had a very, very strong licorice flavor that isn’t acceptable in the industry). At the same time, we had to get rid of all the negative traits from the wild plant like the purple stem and the intolerance to overwatering.

“If you don’t provide the traits necessary for a farmer to get a good yield and to bring it to market, it’s really all for nothing.”

What’s the rough timeline on this actual project from conceptualization to market? (27:30)

Typically it varies from crop to crop in vegetables—anywhere between 4-10 years depending on what you want to accomplish. It all comes down to the amount of cycles you can get in a year.

For us, we did it at around 5 years, the main reason being basil’s life cycle. We could yield three generations in one year. Other crops produce just one generation per year, others longer. It’s also helpful to have a winter nursery location so you can do breeding and selection during off-season.

Are there multiple projects ongoing while you’re working on the DM-resistant basil? (29:55)

Yes. When you’re breeding for a certain variety, you optimize the life cycle as much as you can until you can come up with a set timeline for a single variety. So while we’re working on the DM-resistant basil, we have staggered projects based on the timelines we’ve come up with so that we have new varieties released sequentially.

In some cases, the new releases are improvements from our previous varieties, like right now, we’re beefing up beefing up disease resistance. We’re also working on chill intolerance and shelf life, which is an issue in greenhouse growers.

How many generations does it take to get a DM-resistant basil? (32:48)

It takes about 8 generations to get you to a stable plant, meaning each plant you get from each seed is phenotypically indistinguishable from one another because they’re genetically identical. After we get a stable plant, then we scale up the production. A hundred-foot row of plants would produce the foundation seed lot. Five to ten pounds from that foundation seed lot can, in turn, produce a commercial seed lot on a multiple acre basis.

Does DM mutate? Are the genetics different depending on geographical location? (35:00)

Yes, the genetics differ depending on location. Different pathogens have different rates of evolution, and DM would be in the higher end of that which means it might take a few more years before it mutates, which is why we’re constantly monitoring the evolution of new races.

In crops like lettuce and spinach, you see an extremely rapid evolution of DM-resistance. There’s also about 16 diff races of DM in spinach.

Could you build resistance to most vegetable resistance given enough time and funding? (39:40)

Given the necessary resources, I think it’s possible. With new factors like climate change, it seems like there are new pathogens emerging more quickly.

Although whether it’s complete immunity or not is another question entirely, and oftentimes it has to be paired with some kind of chemical treatment especially when you have situations with very high disease pressure.

Wives’ Tales: A plant growing in healthy soil may exhibit certain chemicals that help deter pests. If this is true, can you breed pest resistance? (40:55)

This is a true occurrence. Some plants carry these compounds throughout their own evolution and natural selection. A good example is a set of compounds called glucosinolates in brassica crops. Glucosinolates are natural pest deterrents, and you can breed for higher levels of it.

Plants have lots of biochemical tools that they use naturally that can be beefed up by plant breeding. Another example is reactive oxygen species that build into the plant’s immune system and respond to the infecti0n of plants. You can breed for the production of those compounds.

What’s interesting with basil is if you look at a leaf under a microscope, you’ll see these balloon-like glands called trichomes which contain aromatic compounds. So when you brush against the leaf or when you chop the leaves, you smell those compounds. There’s plenty of evidence to show that it can detract and prevent pests and predators.

Does the soil health have any effect on disease resistance in plants? Can a plant that doesn’t have the DM-resistant gene be resistant to DM? (44:00)

That can be true in certain situations. One of the major concepts in plant breeding is called gene-environment interaction. Based on a personal anecdote, DM is more successful in organic set-ups probably because the plants a little more stressed out.

I do think that the environment (daylight, soil health, precipitation, etc.) definitely interacts with the severity of the disease, oftentimes making the conditions ideal for the pathogen and while hampering the physiological ability of plants as well as its response to the pathogen.

You say that just because a plant has a gene for resistance doesn’t mean it’ll show up. It needs to be activated first. What activates that inactive gene? (47:30)

Oftentimes it’s response to the environment. Theoretically, it could be that if a plant is in poor soil conditions, it can only respond in those conditions, it could be that the gene and the immune response are compromised. There are a lot of factors that can turn a gene on or off. It could also be that there was just not enough copies of that gene being produced to combat a disease.

I’m a home gardener and I grow tomatoes in my backyard. Is it too much to think that saving the seeds from my best tomatoes gives me a more locally adapted plant or is there not enough population to get more genetic diversity? (49:20)

I don’t see a reason why you wouldn’t get a more locally adapted variety, it’s completely logical. Going back to the population size, depending on the trait, if you have just a handful of plants (5-10 are practical for a home gardener) and there’s a good amount of diversity among them, you’re likely to realize you’re nowhere near the optimum genetics required to get a really nice yield.

Could going GMO fast track the project? (51:50)

GMO technology can substantially reduce the amount of time. I wouldn’t want to give a number, but it would definitely shake years off the process.

In our case, if we had used GMO technology, we could have just gone and taken the gene that’s conferring resistance in that wild plant and transfer it into the commercial plant. The only thing different about that commercial plant is a single gene out of tens of thousands of genes. There wouldn’t be a need to breed out any negative characteristics.

Cutting off public bias against GMO’s, why would people do traditional breeding over using GMO technology when you can cut out all those generations and directly target the issues? (55:20)

There are a lot of factors at play here. One impediment is that while there are really good protocols for transformation (acquiring the desired gene from an individual and inserting it into another individual) in big crops like corn and soybean, those protocols aren’t available for other crops, so it would take some time and R&D investment just to develop protocols to begin with to be able to even create a GMO crop.

The second reason is the burdensome regulatory system. It takes tens of millions of dollars to go through the regulatory process with the USDA, FDA, and sometimes with the EPA. You need to be quite a big company to put up those resources.

The third reason is definitely public perception.

What other things do you guys have in the pipeline that people could look forward to? (58:50)

Within basil, we plan to have varieties with improved DM-resistance. We also plan to have new varieties tailored more specifically to fresh-cut field growers, and we’re putting a big R&D focus into tailoring plants for the greenhouse industry which has completely different requirements and needs. We also crowdsource from different growers to find out what their specific needs are and see if there’s anything else we could improve with our current varieties.


Got you interested to learn more about the Rutgers line of Downy Mildew-Resistant Basil? Hop on over to Van Drunen Farms! You can also follow them on Instagram!   


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