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Not Just Another Bandage for Pecan Scab

A discovery about pecan scab reproduction could give producers a new way to fight the fungus and potentially save them thousands of dollars in the process.

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In a bad year, Buck Paulk has lost 40 percent of his crop to pecan scab, costing him upwards of $5 million.

“Pecan scab is our No. 1 concern,” says Paulk, owner of Shiloh Farms in Georgia. “That’s our major battle. It’s not a minor issue, it is the issue.”

Thanks to aggressive treatment with fungicides, Paulk predicts he will only lose 10 percent of his crop this year. However, the cost to protect crops from pecan scab can be nearly as expensive as the loss itself. With a 3,400-acre orchard, Paulk spends more than $1 million a year on fungicide, equipment and fuel for spraying.

“You might say, ‘Wow, that’s a high input on fungicide,’ but look at what you stand to lose,” he says. “It’s not something you do to get a 5 percent bump. On certain pecan varieties, you’re either in business or out of business.”

Georgia is particularly susceptible to pecan scab because of its high heat and humidity, conditions in which the fungus flourishes. But growers in the Southern Great Plains aren’t immune. In North Texas, Cecil Crabtree, owner of Crabtree Pecans, says he sprays several times a season to protect his 300-acre farm, costing him tens of thousands of dollars.

“You can put $1,000 in a sprayer and put it in the air, and there goes your $1,000,” Crabtree says. “But it’s cheaper to prevent scab than it is to stop it. I do everything I can to prevent it before it starts.”

With consultation from Charles Rohla, Ph.D., Noble Research Institute pecan and specialty agriculture systems manager, Crabtree sprayed earlier this season, starting in March before his trees started to bud. He has also tried a new prevention tactic: burning his orchard. While the practice sounds extreme, recent research out of Noble suggests that burning the ground vegetation and leaf debris around trees in the winter could be one way to prevent pecan scab from taking hold.

Using these strategies, Crabtree says he’s been able to cut his spraying in half this year. So how are these new prevention methods so effective? Like a teacher chaperoning a high school dance, they’re stopping the fungus from having sex.

examplePecan scab can cause significant yield and quality losses at harvest time in pecan orchards across the U.S.Planting scab-resistant cultivars, removing orchard floor debris, and thinning and pruning trees can help control the disease. Currently, however, the best way to manage scab in an established orchard of susceptible trees is with multiple applications of fungicide.

What Is Pecan Scab?

Since its discovery in the 1800s, pecan scab has always been thought to spread by asexual reproduction — cloning itself and traveling to new leaves and trees through the wind and rain.

The fungus starts as a small black spot on the young leaves, shucks and twigs of the pecan tree. Under a microscope, the black lesions can appear fuzzy, like mold growing on a piece of bread. This fuzziness indicates the fungus has sporulated, meaning it has cloned itself and started to release tiny bits of baby fungus. These spores are then carried to the leaves or shucks of neighboring trees, where they create a new lesion. Pecan scab can generate spores in as little as a week, meaning the fungus has the potential to reproduce and spread dozens of times during the growing season, eventually infecting an entire orchard.

Scab impacts both the harvestable nuts and the tree as a whole. If most of the shuck is covered in scab, the nut inside will be smaller and the edible meat will be lower quality. Loss in size is a big deal in pecan economics because growers sell by the pound, so a smaller nut means more pecans will have to be harvested to make up a pound. If more than 75 percent of the shuck is covered in scab, the pecan may not be sellable. On the leaf, scab can decrease the photosynthetic capacity of the tree, which will impact the following year’s crop.

Like Paulk and Crabtree, pecan growers manage scab with fungicides, but the fungus can develop resistance to the treatments. Other farmers grow pecan varieties that are resistant to the fungus, either naturally or because the varieties were bred that way. However, over time if the pathogen adapts, the trees could lose their immunity. This adaptation — both to the fungicides and to resistant varieties — is key because it means the pathogen is evolving, and that means it’s reproducing sexually.

“The literature says scab is an asexual fungus, which means that it clones itself to reproduce, and yet there is a lot of diversity within the population,” says Carolyn Young, Ph.D., Noble Research Institute molecular mycologist. “And those two things are counter-intuitive.”

exampleThe fungus starts as a small black spot on the young leaves, shucks and twigs of the pecan tree. Under a microscope, the black lesions can appear fuzzy, like mold growing on a piece of bread. This fuzziness indicates the fungus has sporulated, meaning it has cloned itself and started to release tiny bits of baby fungus.

A Major Breakthrough

In 2015, Young and senior research associate Nikki Charlton, Ph.D., set out to determine, once and for all, whether the fungus reproduces asexually or if it also uses sexual reproduction. Working with Clive Bock, Ph.D., a scientist at the U.S. Department of Agriculture’s Agricultural Research Service in Georgia, Young and Charlton searched for genes in the pecan scab genome that would indicate sexual reproduction. Thanks to the pecan scab’s close cousin, known as apple scab, which is known to reproduce sexually, the researchers had a good idea of what this so-called mating-type gene should look like. With one quick scan across the pecan scab genome, the scientists were able to identify a mating type gene that closely matched the apple scab gene.

But that was only the first step. In order to mate sexually, two different mating type genes — a male and a female version — must be present in the population of the fungus. Young and Charlton tested 14 samples of pecan scab taken from farms across the Southeast and Southern Great Plains, again looking for the mating-type gene. They identified the original mating-type gene in half of the samples and discovered a second mating-type gene in the other seven.

“Just within that small subset of randomly selected samples, we had a 50-50 mix of both mating types, which is evidence of sexual reproduction,” Charlton says. “So we screened another 1,200 samples and still found a 1-to-1 ratio between the two mating-type genes. That was the first concrete sign that pecan scab was a sexually active fungus.”

Young and Charlton have subsequently recreated the sexual stage in the lab by pairing two fungi with the male and female genes together in a petri dish. After “wintering” together in the refrigerator for four months, the fungi mated and produced unique offspring spores.

Just because the fungus reproduces sexually, though, doesn’t mean it can’t spread asexually as well. A lot of fungi undergo both modes of reproduction, and there are advantages and disadvantages to each method.

“Typically, asexual reproduction is energy efficient so it is really quick — seven to nine days for pecan scab to reproduce asexually. But the disadvantage of that is you have a clonal population, so all of those spores are genetically the same,” Young explains. “Under sexual reproduction, you have to have both mating partners present and they have to be able to find one another and interact, which is very energetically costly and takes a lot longer. But that does introduce genetic diversity into the population, which allows it to better adapt to a changing environment.”

exampleTwo isolates of Venturia effusa, the fungus that causes pecan scab, grow in a petri dish as part of a test to understand their mating behaviors. The black is a wild type, or the most common form of the fungus, while the white, or albino, is a natural variant isolated from the wild type.

The Search Is On

The researchers’ next step is to identify the sexual stage in the field. Similar to the apple scab, Young, Charlton and Rohla think that sexual reproduction of the pecan scab occurs early in the season and is the cause of the initial infection. The rest of the season, the fungus goes through an asexual cycle, repeatedly cloning itself and spreading via the wind and rain.

“If we can identify when that mating occurs, then we’ll have a heads-up on management,” Rohla says. “Just a single earlier spray may be able to stop the sexual cycle from causing that initial infection, which would hopefully limit the amount of scab present in the orchard for the rest of the season and reduce the number of sprays necessary.”

exampleCarolyn Young, Ph.D., (left) and Nikki Charlton, Ph.D., have found that the pecan scab pathogen (Venturia effusa) has a sexual cycle that may initiate the disease at the beginning of the growing season. By better understanding the pathogen, they and others can work toward providing growers with new ways to manage pecan scab.

To Georgia grower Buck Paulk, that would be a huge benefit. “My most expensive input from year to year is my disease control. If there was some way I could back off my input, if there was another avenue we could use to control scab, that would be a godsend for us,” he says.

The other question is where pecan scab sexual reproduction occurs. Apple scab’s sexual cycle occurs on the leaf litter, so the researchers have been looking on the discarded leaves, shucks and twigs around the tree bases. Getting rid of that dead material may help remove some of the fungus that lies dormant there and potentially prevent the scab from sexually reproducing.

Crabtree says that after burning the ground vegetation in his orchard last winter, he’s noticed a reduction in pecan scab. “I’ve learned more in the last two years than I’ve learned in the last 10,” Crabtree says about working with Rohla and the Noble Research Institute. “We in the pecan industry often think we’ve learned all there is to know, but I’ve been in the industry 50 years and I’m still at first base.”

Charlie Graham, Ph.D.