Yi Li, professor of horticultural plant biotechnology in the College of Agriculture, Health and Natural Resources (CAHNR), has received a $650,000 grant from the U.S. Department of Agriculture to study the effects of simultaneously making multiple edits in plant genomes.
CRISPR/Cas-mediated gene editing, which emerged in 2013, is a powerful technology that enables the development of healthier and more resilient food crops by creating new traits without introducing foreign genes from other plants or organisms. This approach has been used to enhance drought tolerance, nutritional quality, and disease resistance in various crop species.
While this technology has advanced rapidly over the past decade, scientists still do not fully understand the unintended effects of simultaneously making multiple genetic modifications within a single plant genome, a process known as “multiplex genome editing.”
Li’s laboratory has been working on genome editing in turfgrass species, and multiplex genome editing is also among their research interests, aimed at developing varieties with enhanced resilience to environmental stresses.
Multiplex genome editing is a highly desirable strategy for the agricultural industry because many traits are controlled by multiple genes rather than a single one. In addition, producers often want to introduce several beneficial traits, such as pest resistance, environmental resilience, and improved nutritional quality, which requires the simultaneous editing of multiple genes within a single plant genome.
“Many beneficial traits are controlled by multiple genes in real-world plants,” Li says. “Therefore, if we can manipulate several genes simultaneously within the same genome of a single plant, we can develop beneficial traits much more effectively and efficiently.”
The more extensively you modify a plant’s genome at once, the greater the likelihood of unintended chromosomal effects, which could lead to negative consequences for the plant.
“The concern is that multiplex genome editing may also cause unintended effects, such as chromosomal rearrangements, large deletions, translocations, or alterations in epigenetic regulation, which could unintentionally affect gene expression,” Li says. “These changes may lead to undesirable consequences in plant growth and development, or even alter the toxin levels and nutritional composition of food crops.”
With this grant, Li will investigate both what the consequences of multiplex gene editing are and at what threshold they are likely triggered.
Previously, a landmark study conducted by Professor Yiping Qi at the University of Maryland demonstrated that multiplex gene editing can induce unintended chromosomal alterations. However, that study investigated the effects of editing at 50 genomic sites simultaneously, an exceptionally high number of targeted genes. Li’s research, by contrast, will focus on a smaller number of edits, using a carefully controlled experimental design that more accurately reflects real-world applications in crop improvement.
“In the end, this study may reveal that the simultaneous manipulation of about ten genes, for example, can be achieved with minimal unintended effects on chromosomal structure and epigenetic regulation,” Li says. “However, we may discover that when more than twenty genes are edited at once, the risk of unintended genomic alterations and downstream biological consequences increases substantially.”
Li will use the tomato, a model plant whose genome and epigenome have been fully characterized, as the experimental system for this study.
“The tomato itself is a very important horticultural crop,” Li says.
His lab will use a variety of techniques to identify DNA-level mutations and structural variants, transcriptional changes, and changes to DNA methylation and other types of epigenetic modifications. These approaches will provide a comprehensive view of the alterations resulting from multiplex genome editing.
In addition to moving science forward, this work will help federal regulators determine what kind of information producers of multiplex gene edited plants need to provide to ensure they meet quality and safety standards.
“This research should provide valuable information to regulatory agencies as they determine what types of data should be required from crops edited at multiple genetic loci simultaneously when evaluating their deregulation and approval,” Li says.
