Clemson professor’s research focuses on identifying unintended effects of genetic engineering process in crops

December 9, 2024

Clemson University Department of Genetics and Biochemistry Professor Hong Luo has received a $650,000 grant from the U.S. Department of Agriculture to study the unintended consequences of three site-specific DNA recombination systems commonly used to genetically engineer target crops.

With the world's growing population and less land being available for farming, it's more important than ever to increase nutritional quality and crop yield of food crops.

One way that is done is by genetically modifying a plant by introducing a foreign gene (called a transgene) from another organism, essentially giving the plant a new trait not naturally present in its genome. It often enhances a plant's resistance to pests, diseases or environmental stresses, or to improve its nutritional value. Another way of improving plant traits is to modify the genes the target plants already have through gene-editing technology to modify the DNA sequence of a gene that controls a particular trait.

Potential hazard

But when foreign genes are introduced into target crops using the transgenic approach or by manipulating endogenous gene expression in target crops using genome editing for trait modification, some unneeded DNA may end up permanently residing in the host genomes of the final transgenic products. That raises questions of potential hazards or adverse effects to the host, environment and human health.

"The unnecessary DNA that gets into the transgenic plants with the target gene need to be removed," Luo said.

One way to remove them is by using site-specific DNA recombinases. Site-specific recombinases recognize specific DNA sequences by flanking the desirable gene with target sequences that the recombinase can recognize and excise.

Previous research by Luo showed that when some recombination genes that come from bacteria are introduced into plants for use in removing unwanted DNA, they also impacted plant characteristics. Sometimes they enhanced plant growth, and other times they hindered it.

"This is a very interesting phenomena. Over the years, we've been using recombinase to remove unnecessary DNA from the transgenic products to make sure that they will be environmentally safe, but we didn't realize using the recombinase for this purpose came with this kind of side effects," he said.

Three genes, two species

In this study, Luo will study three different recombinase genes - Cre, FLP and PhiC31 - in creeping bentgrass, an economically and environmentally important monocot perennial grass species, and in Arabidopsis, a dicot model plant.

His lab will investigate whether there are unintended off-target effects to host genomes, epigenomes and phenotypes and whether they negatively or positively affect plant traits and present hazards to the environment.

"This will give us an idea about what aspects those recombinases impact in which particular plant species," he said.

During the research, Luo will profile the whole genome gene expression in transgenic plants and nontransgenic plants to compare which genes and biological pathways have changed.

The research will provide information for regulatory agencies to assess site-specific recombination system-related biotechnology strategies developed for transgene excision and containment, he said. The research could also identify which site-specific recombination systems work best in various species to increase yield while preventing unintended environmental problems.

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