Battle against hot pepper disease heats up
First isolated from chili peppers in the 1920s, the pathogen Phytophthora capsici has been plaguing the global hot pepper industry ever since. The fungus-like organism causes a root rot disease that severely limits pepper yields, and attempts to manage it are hampered by its persistence in soil and the difficulty of controlling it with pesticides.
Now a team from University of California, Davis has found a candidate gene that encodes natural resistance to P. capsici in peppers. They’ve also identified DNA “markers” that can detect the gene in different pepper populations with complete accuracy.
Having the gene and markers should speed efforts to breed P. capsici resistance into pepper, says UC Davis hot pepper breeder, Allen Van Deynze, giving the $30-billion industry a much-needed new tool in the fight against root rot.
The research, led by Van Deynze and UC Davis doctoral student Zeb Rehrig, was published yesterday (June 30) in the journal The Plant Genome.
The gene, called CaDMR1, is located on the P5 chromosome of pepper—a spot where breeders already knew a significant source of P. capsici resistance existed, Van Deynze says. But until now, no one had been able to hone in on the exact gene or on markers for targeting it so precisely. And the markers really are the key, Van Deynze adds. “The gene is knowledge and you can start making hypotheses about how it works. But the immediate tool [for breeding] is the marker.”
That is, when breeders make crosses between populations of parent plants, they can use markers to identify those specific seedlings among the offspring that carry the resistance gene. The alternative is to test the plants themselves for their ability to fight off the pathogen—a much more time-consuming and expensive process. “So the marker allows you to screen many, many more seedlings and larger populations,” Van Deynze says. “And that’s how you get increased genetic gain [in resistance] per generation.”
To locate the gene, Van Deynze and Rehrig started by screening a population of chili pepper plants that varied in their resistance to P. capsici, and whose genomes had been mapped with about 30,000 genetic markers. At the end of this step, the scientists had identified about a dozen markers that were strongly associated with the peppers’ ability to fend off a P. capsici infection.
Van Deynze and Rehrig then tested the peppers against 20 P. capsici samples from across Mexico, New Mexico, New Jersey, California, Michigan and Tennessee to figure out which genetic regions conferred resistance to the greatest number of P. capsici isolates. Finally, they leveraged the recently completed pepper genome sequence to examine specific genes within these regions until they pinpointed CaDMR1.
The project in many ways was an “alignment of the stars,” Van Deynze says. “We had all this genomic information, we had good genetic data, and we were working on a problem that all the major breeding programs have been targeting in pepper.” Plus, he and Rehrig got the chance to teach the next generation about plant breeding. Working with the UC Davis Student Farm, his research group took 2,000 students through a program in which they learned about chili pepper diversity and its use in breeding, as well as how to make crosses between plants and describe the offspring, “just like a breeder would do,” he says.
Van Deynze hopes the students took from the experience what he’s learned from working on the pepper problem. “It’s a fun time,” he says, “to be in agriculture.”
The research was funded through a UC Davis Department of Plant Sciences Graduate Student Research grant and a USDA/NIFA Plant Breeding and Education grant.