Cultivating Resistance

Sneaky parasitic weeds may steal genes from the plants they are attacking and use those genes against the host plant, according to a team of scientists.

In a study, researchers detected 52 incidences of the nonsexual transfer of DNA—known as horizontal gene transfer, or HGT—from a host plant to members of a parasitic plant family known as the broomrapes, said Claude dePamphilis, professor of biology, Penn State. The transferred genes then became functional in the parasitic species. Although considered rare in plants and other complex species, HGT may thus occur in some parasitic plants, an insight that could lead to better methods of controlling parasitic plants that threaten agriculture, he added.

"These parasitic plants that we study from the broomrape family include some of the world's most devastating agricultural weeds," said dePamphilis. "The HGT discovery is really part of our effort to try to better understand how parasitic plants work and how we can better control them. Our hope is that we can use this information to find the best strategies to generate, or breed, resistant host plants."

dePamphilis in greenhouse

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Claude dePamphilis, professor of biology in Penn State's Eberly College of Science, displays a broomrape, a parasitic plant growing from grindella, in a greenhouse adjacent to Buckhout Laboratory.

Image: Bill Zimmerman

The researchers, who released their findings Oct. 24, 2016, in the Proceedings of the National Academy of Sciences, suggest that the transfer could boost the parasitic plant's ability to invade their hosts and overcome defenses the host creates to try to ward off attacks. HGT may also help reduce the risk of infection for the parasites.

While horizontal gene transfers in less complex species, such as bacteria, are common, most evolution in more complex organisms is driven by the sexual exchange of DNA, along with mutation and natural selection. However, the researchers suggest that the close feeding connections of parasitic plants with their hosts may increase the chances of intact genes traveling from the host to the parasite's genome where it can quickly become functional.

"Parasitic plants seem to have a far greater rate of horizontal gene transfer than non-parasitic plants and we think this is because of their very intimate connection with their host," said dePamphilis.

The roots of the parasite contact and enter the host, and then begin extracting water, sugars, mineral nutrients and even nucleic acids, including DNA and RNA, he added.

"So, they are stealing genes from their host plants, incorporating them into the genome and then turning those genes back around, very often, as a weapon against the host."—Claude dePamphilis

Farmers throughout the world struggle with these types of parasitic plants, which are so numerous in some areas of the world that they become a major source of crop loss. In Sub-Saharan Africa, for example, Striga—or witchweed—is one of the most damaging sources of agricultural loss, according to dePamphilis.

To detect HGT in the plants, the researchers used data generated by their collaborative research effort funded by the U.S. National Science Foundation—the Parasitic Plant Genome Project—to generate evolutionary histories for thousands of genes in the parasitic plants, said dePamphilis.

The researchers focused on transcriptomes—expressed gene sequences—of three parasitic plants: Triphysaria versicolor, also called yellowbeak owl's-clover; Striga hermonthica, or giant witchweed; and Phelipanche aegyptiaca, called Egyptian broomrape, as well as the nonparasitic plant Lindenbergia philippensis, and genome sequences from 22 other nonparasitic plants.

Because the researchers considered mRNA, which can move between hosts and their parasites, as a possible source of the transfers, they tested and re-tested the data to rule out the experimental host as the source of the genetic material. Instead, they found that the foreign sequences had been derived from entire genes of past host plants and incorporated into the parasitic plant genomes.

Future research may investigate the mechanism of horizontal gene transfer to help engineer improved plant defenses against parasitic attacks, dePamphilis said.

"Our hope is that we can use this information to find the best strategies to generate, or breed, resistant host plants."—Claude dePamphilis

Primary authors along with dePamphilis are Zhenzhen Yang, postdoctoral scholar in biology at Penn State and Yeting Zhang, former doctoral student in genetics at Penn State and now a postdoctoral fellow, Rutgers University. The researchers also worked with James H. Westwood, professor of plant pathology, physiology and weed science and Christopher R. Clarke, postdoctoral research fellow, both of Virginia Tech; John I. Yoder, professor of plant sciences and Siming Liu, postdoctoral scholar, both of University of California Davis; Michael P. Timko, professor of biology and Chun Su, graduate student in biology, both of University of Virginia; Eric Wafula, bioinformatics programmer, Loren A. Honaas, postdoctoral scholar in biology, now at the U.S. Department of Agriculture, Huiting Zhang, doctoral student in plant biology, Sam Jones, doctoral student, plant biology, Paula E. Ralph, technician, biology; Naomi S. Altman, professor of statistics and Stephan C. Schuster, professor of biochemistry and molecular biology, all of Penn State.

The U.S. National Science Foundation, the National Institute of Food and Agriculture Project of the U.S. Department of Agriculture, and the Huck Institutes of the Life Sciences supported this work.

Top image: Huitting Zhang, a Penn State Ph.D. candidate studying plant biology, examines a sample of parasitic plants in the research team's laboratory. Image: Bill Zimmerman