CRISPR: Overcoming its obstacles in plant research

By Jenna Gallegos

January 7, 2020

CRISPR is an extremely powerful gene editing tool that has already made huge waves in plant research. We can potentially use CRISPR to make hardier crops, engineer produce in ways that directly benefit consumers and address climate change. But while CRISPR is often described as “cut and paste” for genes, the actual process is not that simple. Scientists still face several obstacles associated with using CRISPR in plant research, including regulatory hurdles.

Editing many chromosomes at once

CRISPR was originally discovered in bacteria, where it evolved as a defense mechanism against viruses. We’ve gotten very good at using CRISPR in its native organisms and close relatives. Moving CRISPR into more complex organisms with larger genomes has come with its own set of challenges. While bacteria have a single circular genome, the genomes of other organisms are sorted into multiple chromosomes (23 for humans).

Plants have a unique genetic feature that makes them particularly difficult to engineer. While humans and most animals only have two copies of each chromosome, some plants have many more. For example, wheat is hexaploid (6 copies) and strawberries can have variable copy numbers up to 10. This feature, called polyploidy, makes plants particularly difficult to engineer, because the likelihood of editing the target gene in every copy goes down as the number of chromosome copies goes up.

Scientists are working on a number of different modifications to the traditional CRISPR workflow, so that it is more likely that multiple copies of the same gene will be edited at once. Unfortunately, these changes are also likely to result in more off-target effects.

Off-target effects

Another challenge in using CRISPR in all species is managing off-target effects. Off- target effects occur when additional regions of the genome, beyond the target gene, are edited. Although the extent and impacts of off-target effects have been heavily debated in the scientific community, off-target effects to some extent are certainly a concern.

The issue of off-target effects merits a separate discussion for plants because traditional and mutational breeding — the two alternatives to using CRISPR in plant research — both produce a massive amount of off-target changes.

Imagine a plant breeder has discovered a gene for disease resistance in a native plant. In order to get that disease resistance gene into a crop plant the traditional way, the researcher would cross the native plant with the crop.

When a native plant is crossed with a crop plant, their genomes are shuffled randomly. The plant breeder will have to cross breed the hybrid plant back to the crop parent dozens of times to get a disease-resistant plant that resembles the original crop. Even then, scores of unwanted and unknown changes will persist.

As an alternative to this slow process, plant breeders will often expose the crop plant to a chemical that causes mutations in a process known as mutational breeding. Researchers will then select the resulting mutant plant that has the desired disease-resistant trait. However, the plant will have incurred many other random and unknown mutations.

Alternatively, the plant breeder could use CRISPR to engineer the crop plant to have the same genetic disease resistance as the native relative. Other, off-target effects may have occurred, but the changes will be far less frequent than those introduced by traditional or mutational breeding. Therefore, compared to older methods of crop improvement, CRISPR produces far less off-target effects.

Regulatory environment

Changes introduced by CRISPR are sometimes so subtle that they could have occurred naturally, making them indistinguishable from natural mutations. For this reason, the United States Department of Agriculture (USDA) has elected not to regulate CRISPR-edited plants in the same way that more traditional genetically engineered plants are regulated. This decision has already had a positive impact on the amount of CRISPR-related research in plants in the United States.

Europe has decided to regulate CRISPR quite differently. There, CRISPR edited crops will be regulated like transgenic crops. In transgenic crops, a novel genetic element, such as a gene from another plant or bacteria, or an extra copy of one of the plant’s own genes, has been introduced. While it is technically possible for transgenic crops to arise in nature, it is much less likely than a mutation to the plant’s own native genes.

Experts agree that this ruling is likely to have detrimental effects on CRISPR-related plant research in Europe, prompting leading scientists and others to call for a reassessment of the decision. Remarkably, the EU regulates mutational breeding with much more leniency than CRISPR, despite the capacity for larger genetic changes.