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With Molecular "Green Thumb" Live in the Lab: Genome Editing as a New Tool for Plant Breeding

Author Dr. Ilka Ottleben

At the Julius Kühn Institute, the Federal Research Institute for Cultivated Plants in Germany, a young working group is trying to specifically modify the genetic material of plants, through genome editing. In this way, they also want to investigate possible risks of this technology. LAB Worldwide visited the team for one day.

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Fig. 1: At the Julius Kühn Institute (JKI), Federal Research Center for Cultivated Plants in Quedlinburg, some researchers are trying to change the DNA of cultivated plants such as soy bean via genome editing in order to scientifically investigate the "new breeding technique" and potential risks.
Fig. 1: At the Julius Kühn Institute (JKI), Federal Research Center for Cultivated Plants in Quedlinburg, some researchers are trying to change the DNA of cultivated plants such as soy bean via genome editing in order to scientifically investigate the "new breeding technique" and potential risks.
(Source: Ottleben / LABORPRAXIS)

It somewhat resembles the vault of a bank: it is narrow and slightly stuffy, and no daylight enters. The electronically-secured door prevents unauthorized access. The Institute for the Safety of Biotechnological Processes at the Julius Kühn Institute (JKI) in Quedlinburg stores treasures of a completely different nature in the most valuable possessions of those who want them safely stored in a bank. Not in safes, but in culture cabinets. Close to close they fill the room down to the last centimeter.

Only when doctoral student Katharina Unkel opens the doors do they reveal something whose value cannot be measured primarily in money but rather in work, knowledge and potential: carrots, potatoes, chicory and soya are stored here. Not the tubers, beans & Co. but hundreds of small plants, green "tissue clots", tiny cuttings of leaves or roots of these cultivated plants. Well sealed in transparent culture vessels, on milky-white culture media and under artificial daylight. Or they are not visible to the naked eye in the form of individual plant cells.

Genome Editing in Plant Breeding

All these plants, tissues and cells have something special in common: the sequence of their genetic information was specifically modified by "genome editing" (GE), a technique that has progressed enormously quickly since the CRISPR/Cas method was published by Emmanuelle Charpentier and Jennifer Doudna in 2012, whereby it is becoming increasingly sophisticated. The working group around Dr. Thorben Sprink that works here and is based at the JKI working area "New Breeding Techniques" is dealing with it. Using sequence-specific nucleases such as Cas9 (CRISPR associated protein 9), it allows DNA sequences to be specifically "edited". This opens up numerous new application possibilities and raises all kinds of hopes. Plant breeding has also discovered the technology for itself, in particular because it can make variety breeding faster, more targeted and thus also cheaper.

The first plants produced with this technique are already entering onto the market. However, does the process and its further development also entail risks? One of the tasks of the plant biotechnologist Sprink is to evaluate this scientifically. Together with his colleagues, the 30-year-old research group leader has been conducting basic and applied research in the field of sequence-specific nucleases since May 2017.

Additional Information
LP-Info: Genome Editing: The method

The term genome editing (GE) summarizes new molecular biology techniques that incorporate mutations at defined sites of a DNA sequence, e.g. change individual bases (point mutation) or insert longer sequences or remove. Thus, e.g. Genes are switched off specifically. The basis is formed by sequence-specific nucleases such as Cas9 (CRISPR associated protein 9) or TALEN (transcription activator-like effector nuclease). The CRISPR / Cas9 system consists of

  • a molecular "probe", the single-guide RNA, which finds exactly the target site for a mutation in the genome,
  • and the so-called "gene scissors" Cas9 coupled to these "pilots", which cuts the DNA double strand exactly at this point.
  • Cellular repair systems repair the severed DNA strand but usually make small mistakes: A (wanted) mutation arises.

DNA changes are the basis of every breed. Conventional plant breeding needs about 7 to 10 generations to a new variety. GE could shorten this process to 1 or 2 generations. Mutagenesis methods that are widely used today, such as irradiation, produce DNA changes completely undirected, whereas GE is precise

The Mission: Research, Evaluation, Consulting

Not least to contribute to advise the Federal Government independently and quickly on current issues concerning the so-called "New Breeding Techniques". This is one of the tasks of the JKI, the only Federal Research Institute for Cultivated Plants in Germany, in addition to the legally-assigned evaluation tasks. "Research - Evaluate - Consult": this is how the independent higher federal authority describes its work in relation to cultivated plants and "this triad is also really what is reflected in my daily work", states Sprink. Does it research differently against this background? "The requests that often have to be processed at short notice certainly require a certain degree of flexibility. At the same time my work is extremely exciting and varied. One notices quite directly what is going on in politics and society and wonders "how one can help from a scientific point of view".

The countless plants and cultures in his laboratory's culture cabinets are an important basis for the necessary expertise. They originate from the independent research projects of his staff, focusing on the technique of genome editing and in which "the first thing is usually to establish genome editing in the respective culture, to investigate which method is most efficient for changing the culture and – very importantly in terms of risk research – to see whether off-targets occur, i.e. whether one sees undesirable or unexpected effects in areas other than the desired areas of the genome," explains Sprink.

Additional Information
LP-Info: Current projects

Currently in the AG Sprink among others these independent research projects on genome editing in the following crops are edited:

Dr. Jochen Menz: Post Doc; EU project to improve industrial chicory (see text)

Enikö Lörincz-Besenyei: Joint project with the DSMZ to stabilize the yield of potatoes under high temperatures

Dr. Janina Metje-Sprink: Post-doc; Cooperation project with Instituto Nacional de Investigación Agropecuaria in Uruguay to improve soybean production

Katharina Unkel: PhD student, Faster variety breeding of carrots (see text)

Dominik Modrzejewski: PhD student, ElsaGEA Project on the Theory of Genome Editing (see text)

Targets: Improve or Accelerate

However, the targets in the genome of the respective plant are deliberately selected: for example, Katharina Unkel tries to use CRISPR/Cas9 in her doctoral thesis to specifically insert mutations within a certain gene of the carrot that could induce haploidie. Such carrots would have a single set of chromosomes instead of a double set and thus they would have a decisive advantage for further breeding, given that their genes would behomozygous. Indeed, such a condition is otherwise only reached after years of crossbreeding. "With carrots, it easily takes 15 to 18 years. GE-induced haploidie induction could shorten this process to two to four years," explains Unkel. "With other crops that are difficult to propagate, such as fruit trees or wine, it can easily take 20 to 50 years to cultivate a new variety," adds Sprink.

Her colleague, Post-Doc Jochen Menz, is working on an EU project aimed at increasing the industrial benefit of the difficult-to-grow, self-incompatible chicory by genome editing. His focus is on risk and safety assessment. "We want to change industrial chicory in such a way that it either forms more inulin, which is widely used, for example, as a sugar substitute in food production, or optionally less inulin but more terpenes, which are under discussion to have anti-tumor properties," explains Menz.