New genomic techniques approved in EU

Approval of NGTs at the European parliament

New genomic techniques (NGT) have been debated for months at the European parliament. On February the 7th the mandate has passed in Strasbourg with 307 votes in favour, 263 against and 41 abstentions.

The objective is to enhance sustainability and resilience in the food system by developing improved plant varieties through NGTs. These varieties should be climate resilient, pest resistant, and offer higher yields with fewer fertilizers and pesticides. NGT plants are to remain prohibited in organic production  until further notice.

Currently, all plants obtained through new genomic techniques are regulated as genetically modified organisms (GMOs). The Parliament supports a proposal to create two categories for NGT plants with different rules:

1. NGT 1 plants might involve techniques like CRISPR-Cas9 where precise changes are made to the DNA sequence, but the alterations are limited in scope and mimic naturally occurring genetic variations. Deemed equivalent to conventional ones, they are be exempt from GMO legislation. Such new genomic techniques are thus considered equivalent to conventional plants.

2. NGT 2 plants are those where the genomic alterations are more substantial. These could include more complex modifications, such as the introduction of genes from unrelated species or significant rearrangements of the genome. Most GMO legislation requirements are to be maintained for these new genomic techniques.

What are new genomic techniques ?

GMOs are often mentioned when we talk about genomics. But there are other flagship technologies, such as genome-editing techniques, the famous new genomic techniques. The most talked-about is the Crispr-Cas9 method, known as "molecular scissors". First presented in 2012, it won the 2020 Nobel Prize for Chemistry from French geneticist and microbiologist Emmanuelle Charpentier, in association with American Jennifer Doudna.

How do new genomic techniques work ?

The schema is simple, it takes place at the level of the long ribbons of DNA in the shape of a double helix, containing all the genes that predetermine the characteristics of an individual.

These genes are coded, as in computing, with identified base sequences. This is where the Crispr-Cas9 "scissors" come into play, via two essential elements.

The first is a strand of RNA, and the second is an enzyme, Cas9, which is capable of "cutting" the DNA ribbon at a precise point, between two well-identified bases.

So, quite simply, this system will make it possible to inactivate a problematic gene or replace it with a healthy copy. A mutation has occurred, but the cell has been left to repair the DNA itself.

A diversity of new genomic techniques

NGTs are not limited to Crispr-cas9. Gene editing techniques differ above all in the nature of the scissors used. The first discoveries date back to before 2005, with zinc finger nucleases (ZFNs).

These special enzymes are capable of detecting specific DNA segments and cutting them. In this way, they can lead to the targeted insertion or deletion of a nucleotide, resulting in the appearance or disappearance of a trait. Another mechanism, Talens (Transcription activator-like effector nuclease), was identified in 2009 in Xanthomonas bacteria. Tale motifs, made up of a succession of peptides capable of interacting with specific DNA sequences in the host plant, were identified. The researchers then combined this genetic identification mechanism with a nuclease capable of cutting the DNA strand.

Successful examples of new genomic techniques

A revolution is underway in the world of plant breeding. Through targeted mutations alone, researchers can conduct their work faster and without the need for foreign genes. Success stories of new genomic techniques are pouring in from all four corners of the globe, and other projects are looking very promising:

• In the United States, the first food product derived from a plant improved by genome editing is Calyno soybean oil (Calyxt). Its characteristic feature is its high fatty acid content, close to that of olive oil.

• In Japan, start-up Sanatech Seed has created a variety of "Sicilian red tomato", Gaba, so named because it is rich in a certain neurotransmitter, gamma-aminobutyric acid, which plays a central role in brain function and blood pressure regulation.

• In China, researchers have long been striving to breed wheat varieties resistant to powdery mildew, a disease responsible for heavy losses in these latitudes. The problem for plant breeders is the complexity of the soft wheat genome. Unlike human DNA, which has diploid chromosomes, wheat has hexaploid chromosomes. This means that the same gene is present in three or six copies, and must therefore be neutralized three or six times. Using the Talen method, Chinese researchers succeeded in simultaneously mutating three Mlo genes carried by three chromosomes in the three wheat genomes. Note that this same feat would have been illusory in traditional breeding, the probability of such a spontaneous mutation being 10-27 . Put another way, the breeder would have had a one-in-a-billion-in-a-billion chance of seeing the mutation occur.

• Other success stories include potyvirus-resistant cucumbers (Israel), browning-free avocados (USA), citrus fruit resistant to bacterial canker (USA), mildew-resistant grapevines (Chile), tomatoes with a slightly spicy taste (Brazil), fruit trees soon to be free of scab and mildew, mildew-free potatoes.... The list of countries adopting regulations favorable to NBT-derived varieties continues to grow: USA, China, Argentina, Brazil, Chile, Colombia, Australia, Canada, Japan, Nigeria... Even the UK, barely out of the EU, has decided in 2021 to authorize field trials of plants (this is wheat) selected by NBT, and to relax regulations.

Data technology to make the most of new genomic techniques

The Excel spreadsheet is no longer enough for plant breeders, a fortiori for those using new genomic techniques. A plant breeding software tailored for new genomic techniques provides specialized tools for managing, analyzing, and collaborating on their specific data:

• Efficient Data Integration: The software can integrate data from various sources, providing a holistic view of the new genomic techniques editing process and its outcomes.

• Customizable Workflows: Researchers can create and customize workflows specific to new genomic techniques data analysis, streamlining the process and adapting to the unique requirements of NGT1.

• Data Traceability: Plant breeding software can ensure traceability of CRISPR edits, helping researchers track and document each modification for regulatory compliance and intellectual property purposes.

• Collaborative Tools: Collaboration features in the software enable efficient teamwork among researchers working on new genomic techniques projects, allowing them to share and discuss data securely.

In summary, plant breeding software offers a comprehensive solution for managing, analyzing, and collaborating on the diverse data involved in new genomic techniques research, contributing to more efficient and effective plant breeding programs.

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Source of the images:

Cover Photo: experimental wheat in Germany, DANIEL PILAR/LAIF/REDUX

Nobel prize : MIGUEL RIOPA / AFP

Schemes of Crispr-Cas9 : The Nobel Prize in Chemistry 2020 by Emmanuelle Charpentier & Jennifer A. Doudna : Genetic scissors: a tool for rewriting the code of life

Illustration of people harvesting produce and examining floating DNA strands in an open farm field : YO HOSOYAMADA

Visual representation of how gene silencing and editing with CRISPR works : Science in the News, Harvard

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