Building Tools for Plant Genome Editing

Researchers and plant breeders are diligently working to secure global food security. While the population increases, the amount of arable land is decreasing. Climate change is also contributing to the growing uncertainty about future food supplies due to its impact on crop yields. Yet, all is not lost. My research at University of Maryland is addressing this problem at a fundamental level by improving the gene editing toolkits that are at the center of cutting-edge research to develop high-yield and climate-resilient crops.

Plant scientists breed plants by altering the genetic material in plant cells. Deoxyribonucleic acid (DNA) contains hereditary information that can be thought of as the instructions for making a protein. DNA is transcribed into ribonucleic acid (RNA), with RNA translated into proteins that can enhance or worsen certain plant trait(s). In other words, instructions for a plant to germinate and produce crops are stored in DNA and transferred through RNA to proteins that can be thought of as the machinery that enables a plant to grow. By modifying the instructions at the DNA or RNA level, we can modify plant traits such as drought resistance or yield.

Simon Sretenovic in lab.

The technologies that enable these changes are called genome editing technologies. Throughout history, several genome editing technologies have been developed. For example, mutagenesis exposes plant seeds to chemicals or radiation to randomly change the instructions stored in DNA. Several grain crops, like wheat and maize varieties producing higher yields were created in the 1950s using this technique. Transgenic technologies introduce genes from other organisms into plant genomes to facilitate new plant traits. Bt corn is a plant created in 1996 using this technique for defense against insect pests.

Mutagenic and transgenic technologies can be thought of as toolkits used by plant breeders. For example, a sculptor would have large hammers at his disposal to drastically reshape a sculpture. The latest amongst genome editing technologies, CRISPR-Cas toolkit, is in many ways more like a watchmaker’s toolkit compared to sculptor’s toolkit. Rather than a hammer, the watchmaker may have a small screwdriver to loosen and pick up a stuck screw without changing any other tiny components of the wristwatch. Using the CRISPR toolkit, plant genomes are altered in a targetable way with minimal damage to any non-targeted part of the genome.

Though an improvement on prior toolkits, CRISPR technology still has drawbacks. For example, not all information within a plant genome can be edited and certain CRISPR tools have proven unreliable. As a result, several researchers have tried to engineer a CRIPSPR toolkit to improve performance. This is where my contribution comes in as a graduate researcher in Dr. Yiping Qi’s lab at the University of Maryland-College Park. We tested several engineered CRISPR-Cas toolkits, prepared by other researchers for genome editing of mammalian cells, in plants. We found that one toolkit element (called SpRY-Cas9) demonstrated drastically expanded targeting scope to almost every target site tested. In other words, it could edit even hard to reach information buried within plant genome. By repurposing enzymes, which are able to modify plant genomes, from various organisms we hope to produce novel CRISPR tools that provide a valuable addition to the existing CRISPR toolbox.

Sretenovic in lab with colleague.

As a Ph.D. student I have had the pleasure of receiving a FFAR Fellowship. The FFAR Fellows program is a carefully curated experience providing a plethora of opportunities to hone non-technical skills through virtual sessions as well as in person residential sessions. In my opinion, non-technical skills like communication, situation-awareness and teamwork skills are equally important to technical skills as they help us get projects done. As a FFAR Fellow, I have been working with Inari Agriculture and Syngenta on genome editing technologies. It has been a great opportunity to gain insights into how research is conducted in industrial settings.

I find research a very fulfilling endeavor when the experimental results are promising, but oftentimes something either doesn’t work or the results leave me wanting for more. During those times, I like to remind myself of the mission to contribute a small part towards optimizing and developing novel genome editing toolkits. Such technologies can be used to accelerate breeding of high yield crops resistant against climate change and ultimately ensuring global food security.

Sretenovic in lab with colleague.