Over thousands of years, tomatoes have naturally mutated during evolution, and humans have subsequently selected the traits they prefer. Now, CRISPR genome editing technology can achieve more precise changes. Researchers at Cold Spring Harbor Laboratory studied the predictability of growing tomatoes using natural mutations and CRISPR-induced mutations. Their results suggest that "background" mutations from evolutionary and agricultural history can have a significant impact on the outcome of engineered mutations. This emphasizes the need to understand and consider these background mutations when introducing new genetic alterations.
Over tens of thousands of years, evolution has shaped the tomato through natural mutations. After humans entered the field of tomato cultivation, they spent centuries cultivating tomatoes and selecting their favorite traits. Now, CRISPR genome editing technology allows us to create new crop mutations that further improve traits. However, no single mutation, whether natural or engineered, works alone.
Each mutation operates within a sea of thousands of so-called "background" mutations. These changes are the product of evolutionary and agricultural history. What if just one mutation could drastically change the expected results of an engineered mutation?
Now, a Cold Spring Harbor Laboratory (CSHL) plant geneticist and a computational scientist have teamed up to explore the predictability of natural and CRISPR mutations in plant breeding. To do this, they turned back the evolutionary clock.
CSHL professor and HHMI researcher Zachary Lippman and associate professor David McCandlish wanted to know whether different natural and engineered mutations would have similar effects on tomato size, depending on the presence of two other genetic mutations. They used CRISPR technology to create a series of mutations in the SlCLV3 gene. (Natural mutations in this gene are known to increase fruit size.) They then combined these mutations with mutations in other genes that work with SlCLV3.
Cold Spring Harbor Laboratory scientists collected more than 40 tomato lines with natural and engineered mutations that affect fruit size. These strains were grown for several years in various areas including Florida and Cold Spring Harbor, New York. Image credit: Lipman Laboratory/Cold Spring Harbor Laboratory
They created a total of 46 tomato lines with different combinations of mutations. They found that the effects of the SlCLV3 mutation were more predictable when certain other mutations were also present. Mutations in one gene produce predictable changes in tomato size, but mutations in another gene produce random results. Notably, the most beneficial effects involved two mutations that emerged thousands of years ago and are central to tomato domestication.
McCandlish and Lipman's new research may help us better understand genetic predictability. But one thing is for sure. When introducing new crop mutations, context matters. Lipman explained:
"Can genome editing rapidly deliver benefits to consumers -- better flavor and nutrition? The answer is probably yes. The question is how predictable it will be."
Collection of tomatoes with different combinations of artificial and natural mutations. These mutations affect the number of stromules (or seed bags), resulting in varying fruit sizes. Lyndsey Aguirre, a CSHL School of Biological Sciences graduate, leads the project. Image credit: Lipman Laboratory/Cold Spring Harbor Laboratory
The work of McCandlish and Lipman suggests that the role of background mutations needs to be reassessed. "As we start making more highly engineered organisms, the field is going to have to grapple with this problem," McCandlish said. "Once you start making 10, 20 mutations, the chance of unexpected results may increase."
The Book of Evolution was written in a variety of languages, many of which we are still learning. Plant genetics and computational biology offer two ways to decipher the text. Lipman and McCandlish hope their collaborative interpretation will help science meet the challenge. Going forward, this may also help humans adapt crops to meet evolving social needs.