Harnessing 'junk' tomato genes could help speed-breed improved crops

September 23 , 2019

A family of 'jumping tomato genes' once dismissed as 'junk DNA' could greatly boost breeding programs, new research suggests.

A study has found they could be used to accelerate crop breeding for traits such as improved drought resistance.

Researchers from Cambridge University have discovered that drought stress triggers the activity of a family of jumping genes. These were previously known to contribute to fruit shape and color in tomatoes.

Their characterization of the gene family (Rider retrotransposons) is also present and potentially active in other crops. This means it is a potential source of new trait variations that could help plants better cope with more extreme conditions.

"Transposons carry huge potential for crop improvement," said Dr Matthias Benoit, the paper's lead author.

"They are powerful drivers of trait diversity, and while we have been harnessing these traits to improve our crops for generations, we are now starting to understand the molecular mechanisms involved."

Jumping genes are mobile snippets of DNA code that can copy themselves into new positions within the genome. They can change, disrupt or amplify genes, or have no effect at all.

Discovered in corn kernels by Nobel prize-winning scientist Barbara McClintock in the 1940s, only now are scientists realizing that transposons are not junk at all but actually play an important role in the evolutionary process, and in altering gene expression and the physical characteristics of plants.

Using the jumping genes already present in plants to generate new characteristics would be a significant leap forward from traditional breeding techniques. They could make it possible to rapidly generate new traits in crops to make harvesting more efficient and maximize yield.

These new traits could then be refined and optimized by gene targeting technologies.

"In a large population size, such as a tomato field, in which transposons are activated in each individual we would expect to see an enormous diversity of new traits," said Dr Hajk Drost, a co-author of the paper.

"By controlling this 'random mutation' process within the plant we can accelerate this process to generate new phenotypes that we could not even imagine."

Today's gene targeting technologies are very powerful. But they often require some functional understanding of the underlying gene to yield useful results.

Jumping gene activity is a native tool already present within the plant, which can be harnessed to generate new phenotypes or resistances and complement gene targeting efforts.

Using jumping genes offers a transgene-free method of breeding that acknowledges the current EU legislation on genetically modified organisms.

The work also revealed that Rider is present in several plant species, including economically important crops such as rapeseed, beetroot and quinoa.

This wide abundance encourages further investigations into how it can be activated in a controlled way, or reactivated or re-introduced into plants that currently have mute jumping gene elements so that their potential can be regained.

Such an approach has the potential to significantly reduce breeding time compared to traditional methods.

"Identifying that Rider activity is triggered by drought suggests that it can create new gene regulatory networks that would help a plant respond to drought," said Benoit.

"This means we could harness Rider to breed crops that are better adapted to drought stress by providing drought responsiveness to genes already present in crops. This is particularly significant in times of global warming, where there is an urgent need to breed more resilient crops."

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