Genome Editing Database Helps Researchers Pull Together to Advance Agriculture

CRISPR technology has received significant media attention in recent months regarding its future potential applications in humans. What is perhaps less widely known is that genome editing, now including CRISPR/Cas9 engineering, has been used for decades to modify and improve plants, allowing for increased crop yields in agriculture and the introduction of novel desirable traits in plants that can enhance food production.

The Boyce Thompson Institute's Plant Genome Editing Database has been created by scientists to encourage sharing of data from experiments where CRISPR/Cas9 technology, along with other approaches to gene editing, have been used to study economically important traits. We spoke to Zhangjun Fei and David Stern from the institute to learn more.

Karen Steward (KS): Can you tell us a bit about how the Plant Genome Editing Database was established and how it is run and managed? Why is it important that such databases are readily available?

Zhangjun Fei (ZF): CRISPR/Cas has been widely used to generate mutants in diverse plant species, which results in large amounts of data that are very useful but not easily accessible to the research community. To this end, we have developed the Plant Genome Editing Database, which provides a central repository for efficiently managing these plant mutant data, as well as to provide a platform for sharing the data and mutants with the research community. With the comprehensive CRISPR/Cas-generated mutant information archived in the Plant Genome Editing Database, the database will lead to more efficient use of resources by reducing unnecessary duplicate experiments and catalyzing collaborations among research institutions. We encourage researchers who generate plant mutants using genome editing technologies to submit their data to the database for sharing. Meanwhile, our groups are also collecting plant mutant data from literature, which will be deposited in the database for easy access and sharing.

KS: Can you highlight some of what you would consider to be the biggest success stories in terms of how plant genome editing has impacted the food industry?

David Stern (DS): For now, to my knowledge, there is one gene-edited product on the market, which is a “healthier” soybean oil marketed by Calyxt. There have been several press releases about that in the past two weeks. However, there is a great deal in the pipeline.

KS: How has the availability of CRISPR/Cas9 gene editing improved agricultural research over traditional genome editing techniques?

DS: To understand basic mechanisms of plant growth, development, nutrition and disease resistance, scientists for decades have sought to alter plants and observe their properties under laboratory or field conditions. The precision of gene editing is extremely attractive as a way to alter a plant’s genome without disturbing other genes or introducing “foreign” DNA. Legacy methods used to create transgenic plants, often involve the introduction of bacterial DNA along with the gene or genes of interest.

Molly Campbell (MC): In the genetic editing of plants, what traits are typically considered to be the most valuable and why?

ZF: The most valuable traits include those related to crop yield and quality, as well as biotic and abiotic stress tolerances. Improvement of these traits can increase the value of a crop, reduce the stress placed on the environment, and help crops persist in the face of challenges due to climate change.

MC: To date, how many plants have been generated using the CRISPR/Cas 9 technology and documented in the database?

ZF: In the database, currently we have archived more than 400 CRISPR/Cas-generated mutants from tomatoes. We invite researchers from around the world to submit their mutant data generated in any plant species using any genome editing technologies.

MC: What challenges currently exist in the genetic editing of plants? How do you envision overcoming these challenges?

ZF: One challenge of gene editing is making changes to the genome in the wrong spots, which may cause unwanted or deleterious changes in the genome. To overcome this challenge, novel technologies are constantly being developed to minimize such off-target effects. Additionally, with the advances of sequencing technologies, mutants can be checked for off-target edits using whole genome sequencing, and we can select those without off-targets. Another challenge is the lack of efficient transformation systems for some crops, which could make genome editing technologies difficult to be applied to.

Zhangjun Fei and David Stern were speaking to Karen Steward and Molly Campbell, Science Writers at Technology Networks.