Caltech researchers develop new gene-directing technology – Pasadena Now

Palmer amaranth invades a field of soybeans. Credit: United Soybean Board

Weeds are an annoying irritant to most home gardeners, but in large agricultural settings, weeds can pose an especially deadly problem. For example, Amaranthus palmeri, known as the Palmer pig, has evolved in many areas to be completely resistant to modern herbicides, enabling it to take over fields of corn, soybeans and other important crops. To make pigweed susceptible to herbicides again, you would need to change its genetics.

The spread of a specific genetic trait through a population, even if that trait does not benefit those who carry it, is the purpose of a “gene motif.” Gene drives can be used for many different applications. These fall into two broad categories: population modification and population suppression. Population modification can make mosquitoes immune to malaria, and therefore unable to spread, or make a crop more heat tolerant in anticipation of climate change. Population suppression can be used to bring about the local reduction or elimination of a weed or invasive species. But any gene-editing program must have strict controls built in to keep the modifications localized to a specific area and to prevent other species from accidentally inheriting the modified genes.

Now, Caltech researchers have developed a new gene-boosting technology called ClvR (pronounced “cleaver”), that can be customized specifically for plant species, preventing accidental gene modification in cross-pollination situations. More importantly, the technology can be designed to be self-limiting, spreading only the desired genes for a limited number of generations, thus limiting their spread in time and space. The work is the first gene drive generated in plants and the first to enable species-specific modification, as well as the first to act at the level of plant sex cells.

A paper describing the new study appears in the journal Plants of nature on June 17. The research was conducted in the laboratory of Bruce Hay, professor of biology and biological engineering.

How can you genetically engineer a plant so that its offspring will definitely have a particular gene of interest? During the breeding of plants and animals, one of the two copies of a gene present in a parent is randomly inherited by an offspring. Gene drive tilts the rates of inheritance in favor of one of these copies: the one in which the DNA responsible for the gene drive behavior resides. This results in its spreading at high frequency in the population over time.

ClvR ensures that the genes of interest are passed on by affecting the sex cells or gametes of a plant. of ClvRthe system uses CRISPR/Cas9 gene editing technology to ensure that if a gamete does not contain the desired gene, it will not survive. That way, any future offspring will come from gametes with the desired gene.

The system works using a so-called “toxin/antidote” paradigm. Cas9 (“toxin”) is programmed to destroy, in the adult stage, a gene necessary for the survival of the gamete, essentially ensuring its death. But the catch is that ClvR-bearing gametes are also equipped with an undamaged version of the same target gene (“Rescue” or “antidote”), which functions as an antidote to a poison, leading to the survival of ClvR-bearing gametes . That Rescue—key to gamete survival—is also linked to a cargo gene, the gene of interest that a researcher wants to propagate in the plant population. In other words, the cargo gene hitchhikes along with the Rescue gene. This ensures that only gametes containing both will survive – essentially forcing the cargo gene into the population.

“There are two ways to win a race: To be better than all the other competitors or to outdo all the other competitors,” says Hay. In this case, the ClvR system attracts all other competing chromosomes that can be inherited by the offspring ensuring that only sex cells with the desired load survive.

Importantly, ClvR the system is customizable for different circumstances. The toxin and antidote genes can be chosen to be specific to the desired plant species, so if the genetic information is transferred to another species, nothing will happen. Furthermore, the “cargo” gene can be engineered for various purposes—for example, this gene can resensitize pigweeds to herbicides or make an endangered plant more heat-tolerant or disease-resistant—a form of evolutionary rescue. Finally, the ClvR system can also be engineered to bring about local suppression or elimination of a weed or invasive species through the creation of a high frequency of sterile females, which leads to a population collapse.

“The ClvR system provides a general, species-specific tool for altering the genetics of plant populations in ways that can contribute to global challenges such as food security and resilience in endangered native species and ecologies threatened by invasive species and climate change,” says Hay “We are excited to collaborate with others on these issues.”

The paper is titled “Snapping and rescuing gamete killers create conditions for gene induction in plants.” Former postdoctoral researcher (now research scientist) Georg Oberhofer is the lead author of the study. In addition to Oberhofer and Hay, Caltech co-authors are research technician Michelle L. Johnson, former graduate student Tobin Ivy (PhD ’24) and director of the Caltech Genomics Facility Igor Antoshechkin. Funding was provided by the Caltech Center for Evolutionary Science, the Resnick Sustainability Institute, the National Institutes of Health, and the US Department of Agriculture.