A new study on tomatoes from Cold Spring Harbor Laboratory (CSHL) has yielded important results, providing the strongest evidence to date for explaining the differences in vine morphology among different tomato varieties and revealing the key role of recessive mutations. This discovery is of great significance for both agricultural breeding and medical treatment, and is expected to help scientists optimize plant breeding techniques and improve clinical treatment methods.
Recessive mutations are differences in DNA that usually require simultaneous changes in other genes to affect plant physiological traits. Cold Spring Harbor Laboratory Professor Zachary Lippman, Associate Professor David McCandlish, and Professor Yuval Eshed from the Weizmann Institute of Science jointly studied the effects of recessive mutations on plant traits.
Their latest research, published in the journal Nature, shows that interactions between recessive mutations can increase or decrease the number of reproductive branches in tomato plants, thereby affecting the number of fruits, seeds, and flowers. This interaction involves paralogous genes. Lippman explained that paralogs arise through gene duplication during evolution and are a major feature of genetic networks. They can buffer each other to prevent gene mutations from affecting traits. This study found that combinations of natural and artificially induced recessive mutations in two pairs of paralogs can affect tomato branching in multiple ways.
A key part of the project was the pan-genome sequencing of global Solanaceae plants (including cultivated and wild tomatoes) completed by Lippman and his colleagues. Unlike a genome that covers only one species, the pan-genome covers DNA sequences and traits from multiple species. Through whole-genome sequencing, Lippman's laboratory identified naturally occurring hidden mutations in key genes controlling branching. His postdoctoral researcher Sophia Zebell used CRISPR technology to design other hidden mutations and counted the number of flower cluster branches in more than 35,000 clusters across 216 tomato plants.
Subsequently, postdoctoral researcher Carlos Martí-Gómez from McCandlish's laboratory used computer models to predict how specific mutation combinations in plants would alter branching numbers. Lippman said that it is now possible to design hidden mutations in crops such as tomatoes to change important agricultural traits such as yield.
In addition, the modeling in this study has many other applications. McCandlish stated that side effects are common when creating mutations or using drugs that simulate mutation effects. By mapping side effect profiles, it is possible to select methods that control target traits while minimizing adverse side effects. This means that the research not only points the way for cultivating higher-quality crops but also brings hope for developing more effective drugs.
