Just like humans, each individual tomato has a unique set of genetic variations that affect gene expression. Millions of small genetic variations make it difficult to predict the effects that specific mutations will have on different types of tomatoes.
For the investigation, Professor Zach Lippman and his team used CRISPR, a highly accurate gene-editing technique, on two tomato genes that control fruit size. The researchers generated over 60 tomato mutants by removing little pieces of DNA in areas near the genes that control their expression.
While individual mutations did not change the size of the tomatoes at all, others slightly increased the size. Meanwhile, a few synergistic combinations of mutations caused a dramatic, unpredicted increase in fruit size.
“The real Holy Grail in all this for crop breeding is predictability. If I mutate this sequence, I’m going to get this effect. Because there is this sea of other variants that nature has accumulated nearby the mutation that you’re engineering, as well as scattered throughout the genome, many of which could be influencing the specific mutation that you’re creating,” said Professor Lippman.
The range of interactions for any two mutations represents the results of a single mutation occurring in different genetic backgrounds. This is comparable to what is found in some human diseases, where certain pre-existing mutations provide protection from disease-causing mutations.
The researchers will continue investigating how individual and combined mutations affect certain crop traits.
Professor Lippman hopes to study enough measurable interactions to make breeding more predictable and efficient. He noted that his research could lead to the creation of new tomato varieties and the improvement of existing ones.
The study is published in the journal Nature Plants.