University of Kentucky plant pathologist Chris Schardl spends his days opening doors that lead to other doors that lead to other doors. Some people might find that frustrating, but for Schardl, who is mapping the genome of an endophyte, the work is challenging and fascinating. It also promises to benefit farmers, particularly those who depend on livestock for their livelihoods.

Endophyte, a fungus, thrives within the structure of certain common grasses, including tall fescue, a popular pasture grass in Kentucky. “It’s an extremely unusual kind of system,” said Schardl, director of the UK Advanced Genetic Technologies Center. "These things have the capability of transmitting in the seeds. This is an unusual capability. If the mother plant is infected, every seed that it produces is going to have this fungus in it.”

In a mutualistic symbiotic relationship, the endophyte both benefits the grass and derives benefits from the plant. The fungus provides the grass with increased resistance to drought, insects and nematodes, and an improved ability to acquire and utilize the essential elements, such as phosphorous and nitrogen. The grass also benefits from better root growth and seed production.

If all this sounds too good to be true, it is. There is also a downside to the relationship. Endophytes, or more accurately, the ergot alkaloids they produce, can be toxic to grazing livestock and wildlife, particularly during stressful times. In the summer months, when the temperature climbs, grazing animals can suffer from a syndrome called summer slump. Beef cattle don’t gain weight as well. In dairy cattle, milk production can be much poorer or can shut down. And with both horses and cattle, fertility problems can occur.

The question naturally arose, could the beneficial relationship between grass and endophyte be maintained while eliminating the toxicity to grazing animals? It was a question Schardl set out to answer two decades ago.

“When I started here, almost 21 years ago now, we knew rather little about the endophyte biology,” said Schardl. “It wasn’t very long after the endophyte being in there was even discovered. There was a suspicion that ergot alkaloids produced by the endophytes were the toxins that were causing the problems with the livestock. Yet at that time, no one knew what genes were responsible for the machinery that synthesizes the alkaloids.”

Hypothesizing that preventing ergot alkaloid production would preserve the benefits to the grasses but remove the toxicity to the animals, Schardl and his team set about to isolate a key gene necessary for alkaloid production. “I must say we had a lot of help, a lot of collaboration with people all around the world on this particular objective,” he said.

The tall fescue endophyte is genetically complex, so researchers first focused on the simpler genetics of the endophyte in perennial ryegrass. By eliminating a particular gene in a test called a “gene knockout,” it could be determined if ergot alkaloid production was affected.

“Before we did that test, we could never be absolutely certain we’d found the right gene,” Schardl said. “So we did that test and yes, indeed, it eliminated alkaloid production in that system. So now what we’re doing is we’re trying to do the same thing with the tall fescue endophyte. And we’re moving in that direction at, I hope, a relentless pace.”

Up until now, it’s been a long process. In the tradition of scientific research, every door opened by Schardl’s work has revealed not only an answer but a new set of questions. The seemingly straightforward task of turning off a gene could have repercussions on other systems in either the fungus or the grass, including affecting the grass’ ability to battle insects and nematodes or survive drought. For that reason Schardl collaborates with other researchers at UK and West Virginia University. UK researchers working with Schardl include chemist Bob Grossman, entomologist Dan Potter, agronomists Tim Phillips and Lowell Bush, and computer scientist Jerzy Jaromczyk.

The research is picking up speed. Helping to increase that pace is Schardl’s current project, mapping the genome of a model endophyte, funded by a grant from the National Science Foundation and the U. S. Department of Agriculture.

“One of the things that we wanted to do was to really get an idea of the entire genetic makeup of an endophyte,” Schardl said. “This started to become possible with genomics, with the ability to go through such DNA sequencing at a reasonable cost to actually determine the code for the entire genetic makeup of an organism.”

Estimating that mapping the entire genome will take a mere six months, Schardl is philosophic when comparing this to the length of time he has already spent.

“It’s almost a bit depressing that we’ve worked for about 18 years now on finding the genes for synthesis of these ergot alkaloids and we’ve found, oh about two dozen genes for synthesis of various alkaloids. And now we just sequenced an entire genome,” he said. “If we only had that technology when I started. But the way science is, of course, is you struggle to get incremental progress that leads to the technological developments that speed it up. It’s like when you’re accelerating your car from the stoplight. You start off very slow. You don’t just instantly go to 60 miles an hour. You build up from there and that’s the way it’s been. Six months to 10,000 genes.”

Schardl’s team at UK is one of only five in the world focusing on endophytes at the molecular genetic level. There is a group at West Virginia University, two laboratories in New Zealand and one in Australia. Their research feeds the work of countless scientists who are researching other aspects of the fungus’s biology, from their natural ecology to managing them in a beef or dairy production system.

“At this point, as of this year, we believe the endophyte research community has gotten all the genes for all four of the known alkaloids produced by endophytes. There’s the temptation to say ‘OK, we’re done.’ But then we look at the genome and say no, no, there’s a whole set of other stuff in here that’s going to be important.”

Important to livestock producers, entomologists, and plant growers, to name only a few of those who stand to be affected by Schardl’s research into the secrets of a fungus.

“We hope it will open up doors,” said Schardl, “so that other laboratories that have not been looking at the genetics of the endophytes will be tempted to do that or will be able to use the genetics of the endophytes to help them in their studies of other aspects of the biology.”