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CRISPR: rapid and targeted varietal improvement

24/10/2018 - François-Xavier Branthôme - Lire en français
Physalis, groundcherry, Inca berry, Cape gooseberry, poha berry, golden berry...

Few people can recognize the taste of the physalis fruit; with its long spread-out branches and its sporadically ripening fruit, the plant is not suited to large-scale industrial cultivation.
This could change thanks to a gene editing tool called CRISPR ("Clustered Regularly Interspaced Short Palindromic Repeats"). Professor Lippman, a researcher at the Howard Hughes Medical Institute and the Cold Spring Harbor Laboratory (CSHL), leads a team that has accumulated extensive knowledge of the tomato plant and of the genes that control its growth. The team used CRISPR, a genetic engineering tool with big potential, to create physalis plants with a compact plant structure, a manageable size, and that produce fruit that is larger and more abundant.
To date, no traditional selection process had undertaken a systematic approach to the cultivation of physalis. But due to the close proximity of physalis with the tomato, Lippmann's team had accurate and abundant data regarding the genes that control the growth and flowering of the plant. "We knew of some clear targets to improve the plant's architecture, fruit production, and fruit size."»

In the October 2018 issue of Nature Plants, the researchers described the effects of the alterations they carried out by CRISPR on three genes of the physalis plant. Lippman's team was able to achieve and demonstrate a modification in the production of a hormone regulating the blossoming process, which led to more compact plants, producing fruit that is gathered in clusters rather than isolated. A modification carried out on another blossom-regulating hormone had an effect on the density of fruit production, with plants carrying a CRISPR-generated mutation of this gene producing up to 50% more fruit on one given length of stalk, compared to non-modified plants. The third mutation led to an increase in the number of sections containing seeds within each fruit, resulting in an increase in the overall size of the fruit
Lippman's team worked on other aspects as well, in order to adapt the plant to large-scale production. In less than two years, the team produced improvements that would have taken far longer with traditional selection methods. But the researchers are also thinking beyond the results they obtained with physalis, and considering much wider implications: "This is pretty good proof that with gene editing, you can think about bringing other wild plants or orphan crops into agricultural production," concluded Lippman.

Using a wild variety to increase the lycopene content
The same CRISPR tools were used by a team of Brazilian, American and German scientists, who announced early October that they had produced a super tomato that is particularly rich in lycopene, thanks to CRISPR-Cas9 gene editing technology. As well as achieving desired modifications, they obtained conclusive results in record time: one generation was enough for the researchers, who were working on a wild variety from South America called Solanum pimpinellifolium, in order to use CRISPR-Cas9 to carry out a number of very precise modifications on a few targeted genes. 

The choice of the wild variety Solanum pimpinellifolium solanacea, which looks very different from the cultivated tomato plants that are currently grown by the industry, was part of a voluntary approach to break away from the genetic material that is available on the "market", allowing scientists to "reinitialize", in a way, the work being carried out in the field of variety development. In this way, the researchers of the team led by Professor Jörg Kudla, from the University of Muenster, were also able to dispense with the negative effects of traditional selection practiced over the past decades, particularly with regard to the reduction in genetic diversity and the loss of useful features of wild genetic material.
The fruit of S. pimpinellifolium is very small, but extremely rich in flavor and, in particular, much richer in lycopene. The manipulations carried out on six fundamental genes in order to domesticate the plant and improve the agricultural yield resulted in a plant that is more compact, with fruit that is three times bigger than the wild fruit and of a more oblong shape, and the number of fruits in each cluster is ten times higher than the original variety.

"This domestication process is entirely new, insofar as it helps to preserve the genetic potential and the particularly desirable features of the wild varieties whilst also obtaining – in a very short space of time – a variety that presents the most useful characteristics for cultivation," explained Professor Kudla. This new tomato is also and mostly remarkable for its lycopene content, which is twice as high as the lycopene level in the wild variety and about five times higher than it is in most varieties of table-tomatoes or processing tomatoes. ”This is a decisive innovation which cannot be achieved by any conventional breeding process with currently cultivated tomatoes," concluded Professor Kudla. ”From a health point of view, the tomato we have created probably has an additional value in comparison with conventional cultivated tomatoes and other vegetables, which only contain lycopene in very limited quantities.”»

The hurdle of legislation
Gene-edited crops must be subject to the same stringent regulations as conventional genetically modified (GM) organisms, Europe’s highest court ruled on 25 July.
The decision, handed down by the Court of Justice of the European Union (ECJ) in Luxembourg, is a major setback for proponents of gene-edited crops, including many scientists. They had hoped that organisms created using relatively new, precise gene-editing technologies such as CRISPR–Cas9 would be exempted from existing European law that has limited the planting and sale of GM crops. 
Instead, the ECJ ruled that crops created using these technologies are subject to a 2001 directive. That law was developed for older breeding techniques, and it imposes high hurdles for developing GM crops for food. 
It is an important judgment, and it’s a very rigid judgment,” says Kai Purnhagen, a legal scholar and researcher at Wageningen University in the Netherlands, who specializes in European and international law. “It means for all the new inventions such as CRISPR–Cas9 food, you would need to go through the lengthy approval process of the European Union.” That is likely to hinder investment in crop research using these tools in the EU, says Purnhagen. “From a practical perspective, I don’t think this will be at all of interest for business,” he adds.

The ruling is “tremendously disappointing”, says Nigel Halford, a crop geneticist at Rothamsted Research in Harpenden, UK. Gene-editing techniques will still be used as a research tool in developing crops, he states, but he doubts that companies in Europe will have much appetite to develop them. “They are not going to invest in a technology they see not having any commercial application,” Halford says. 

Environmental organization Friends of the Earth, meanwhile, applauded the Court’s decision in a statement. It also called for all products made through gene editing to be regulated, assessed for their health and environmental impacts, and clearly labeled.

Sources:,, Diariodelweb,,

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