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Partenaires :Fabien Nogué, IJPB Versailles ; Pierre-Marc Delaux, LRSV Toulouse, coordinateurs ;IBMP Strasbourg, RDP Lyon, AGAP Montpellier, GAFL Avignon, IPS2 Saclay, BFP Bordeaux, Pépinière viticole Mercier, Limagrain,

Coordinateur : Annabelle Déjardin

Personnel BioForA impliqué : Annabelle Déjardin, Gilles Pilate, Justine Corret, Françoise Laurans

Autre personnel impliqué: 

Financement : ANR - PEPR Sélection Végétale

Budget : 110 000 euros (budget total 2 millions euros)

Résumé :

Since its discovery in 2012, CRISPR-Cas technology has rapidly supplanted all other methods for genome editing due to its ease of use, reliable design and high efficiency. Thanks to a large international research effort, the technology has been greatly improved over the last decade to meet the needs of scientists and breeders, enlarging their toolkit for creating new varieties. However, we are still far from the ideal situation where any type of modification can be routinely introduced at any position in the genome of any plant species. The main objective of the TYPEX project is to enable the French community of scientists and breeders to master the extremely precise editing of the plant genome of a large number of model and crop species. At the moment efficient and precise genome editing is hampered by two main limitations, (1) inherent features of genome editing tools limiting their versatility and/or efficiency and (2) the efficient regeneration of fertile plants after the introduction and action of the CRISPR-Cas module into plant cells, which varies enormously between species and between varieties within a given species.
Recently, a new CRISPR-based strategy has been developed, named Prime Editing, a ‘search-and-replace’ genome editing technology that mediates a variety of edits, including all 12 types of base substitution, small sequence insertions, deletions, and replacements. Since it was first reported in human and yeast cells, this method has been applied to few plant species. Findings from these studies indicate that substantial improvement in Prime Editing methods is needed before they can be routinely used in plant breeding. The first objective of the TYPEX project will be to develop tools and general rules for efficient Prime Editing in plants. Three plants, Marchantia, Physcomitrium, and Arabidopsis, will be used in parallel to improve Prime Editing in the frame of the TYPEX project. Classical CRISPR-Cas strategies are used in routine in these model plants. Several key parameters associated with the Prime Editing efficiency, such as, reverse transcriptase type, experimental condition, pegRNA design, will be potential targets for improvement with different strategies developed for their optimization. Because the strategies of transformation used for these very divergent models are different, improvements made in the three plants will be very complementary and more easily transferable to a majority of plants, including crops. The strategy for improvement of Prime Editing is based on a Design/Built/Test/Learn (DBTL) cycle strategy in the three model species. The final goal is to build a shared capacity for Prime Editing/genome editing with a platform in charge of gene synthesis, cloning nomenclature and collection of optimized CRISPR modules. The platform will distribute to the participants of the project the different modules/protocols to be used for optimized editing. This will be part of the second objective of the project that is to deploy Prime Editing in a diverse range of crop plant species. For this purpose, the general rules developed on model species will be extensively tested on a number of plants where classical CRISPR-Cas strategy is already feasible and that are major crops for French agriculture. The third objective will be to permit Prime Editing in crops that are not yet amenable to routine techniques of transformations, such as prunus and eucalyptus trees, pea or common bean. For this purpose, new strategies of delivery of the CRISPR Cas modules will be deployed to overcome this major technological barrier; based on optimized design, the Prime Editing should then work smoothly in these species.
In a nutshell, the TYPEX project will strongly enhance the capacity of French R&D actors to obtain any desired genome modification in any crop species and foster the French research community for gene function analysis and bioengineering.