For millennia, tomatoes have undergone a continuous evolution shaped by natural mutations, but the course of their genetic destiny took an unprecedented turn when humans intervened. Through centuries of selective breeding and meticulous trait selection, we have crafted tomatoes to suit our preferences. Today, the advent of CRISPR genome editing allows us to take control of this evolutionary process, creating crop mutations that enhance desirable traits. However, a recent study conducted by plant geneticists and computational scientists at Cold Spring Harbor Laboratory (CSHL) has delved into the intricate world of plant breeding and the impact of natural and CRISPR mutations on tomato size predictability.
In their research, published in Science, CSHL Professor and HHMI Investigator Zachary Lippman and Associate Professor David McCandlish posed a fundamental question: can different natural and engineered mutations have similar effects on tomato size, depending on the presence of other gene mutations? To answer this question, they decided to turn back the evolutionary clock.
Using the precision of CRISPR, they introduced a series of mutations into the SlCLV3 gene, which is known for its natural ability to increase fruit size. These mutations were then combined with alterations in genes that interact with SlCLV3. In total, they created 46 distinct tomato strains, each with unique combinations of mutations.
The findings were revealing. It became apparent that the effects of SlCLV3 mutations on tomato size were more predictable when specific accompanying mutations were present. While mutations in one gene consistently produced expected changes in tomato size, mutations in another gene yielded unpredictable outcomes. Intriguingly, the most advantageous effects came from two mutations that had arisen thousands of years ago and played a central role in the domestication of tomatoes.
The study, led by CSHL School of Biological Sciences graduate Lyndsey Aguirre, highlighted the significance of contextual factors when introducing new crop mutations. Zachary Lippman emphasized this point, stating, “Is genome editing a way to quickly bring in consumer benefits—better flavor, nutrition? The answer is probably yes. The question is how predictable is it going to be.”
The research by Lippman and McCandlish underscores the need to reevaluate the role of background mutations, particularly as we venture into creating more highly engineered organisms. David McCandlish commented, “The field will have to grapple with this as we start to make more highly engineered organisms. Once you start making 10, 20 mutations, the probability of having unanticipated results may increase.”
In the grand narrative of evolution, written in numerous languages we are still deciphering, plant genetics and computational biology provide two vital means of understanding this intricate text. Lippman and McCandlish hope that their collaborative interpretation of this complex interplay will guide science in meeting future challenges and enable humanity to adapt crops to the ever-evolving needs of society.