Research Highlights

Research Highlights
Genomic Tools to Enable Trait Discovery and Deployment - Genome Editing Methods

By Robert Stupar, University of Minnesota

Genome editing methodologies offer great promise for trait enhancement in all crop species. However, each species faces unique challenges when adopting these methods. Even with CRISPR-Cas9, the most successful platform to date, efficient implementation and customized applications are required in order fulfill that promise. This project will develop enabling technologies specifically for soybean genome editing, that will optimize the development of new traits and make these tools more accessible to a wider range of soybean researchers. 

There are several challenges that are particular to soybean. The first challenge is the efficiency of soybean regeneration. When a novel gene or a gene edit is introduced to a plant, it is generally introduced into a single cell. That cell is then treated with nutrients that allow it to divide and eventually become an entire new plant. Even in the best cases, this process of regeneration is not very efficient; so many attempts are required to get a new plant that expresses the desired genetic modification. In soybean, the process is complicated by the fact that only some genotypes (cultivars) are easily regenerated. Ideally, conducting the desired genetic modifications in modern, high yielding, elite commercial soybean would be preferable. However, because of this challenge, the modifications often have to be made in older lines (such as Williams 82) which are then crossed with elite soybeans to make a new commercial variety. This project will address this challenge by making plant regeneration more efficient and more general for a variety of different genotypes.

Another challenge is that the CRISPR-Cas9 system itself is not very efficient. The easiest modifications to make with the system are small cuts in the DNA that result in a non-functioning gene (also called a knock out). It is more difficult to make precise changes or to replace a small segment of undesired DNA with a segment of desired DNA. As with regeneration, if efficiency is low, more and more attempts need to be made in order to achieve the desired result. This increases the time and cost needed to introduce new traits. This project is experimenting with ways to increase this efficiency, particularly when precise changes that do not eliminate gene function, but instead change it, need to be made. 

Lastly, entirely new ways of changing gene expression are being investigated. Building on past genomic research, some funded by USB, the researchers are looking beyond just DNA sequences to find methods that will turn up or turn down gene function and expression. One could envision this as turning on a faucet. You always get water coming out, but depending on how far you turn the knob you can get more or less water. A method to precisely determine the timing and/or amount of gene expression could be very powerful.

This project was funded by USB for $104,999 in 2019, and is a part of the iPOP (innovative project) called Genomic Tools to Enable Trait Discovery. Once developed, these tools will protected by patents where appropriate, and could then be licensed or otherwise made available to public and private researchers.

Figure 1. Protoplast isolation and transformation using green-fluorescent protein. In this project, the protoplast system is being optimized to improve transformation and regeneration. 

This project was funded by the soybean checkoff. To find research related to this research highlight or to see other checkoff research projects, please visit the National Soybean Checkoff Research Database.