Novel diversity in emerging crops with gene editing by chemical mutagenesis and CRISPR

New crops have the potential to improve the climate resilience of agriculture, to supply biobased materials to reduce fossil oil use and CO2-emissions, and to enable a transition to plant-based protein diets. However, these crops have not been fully domesticated and the lack of investment in their genetic improvement leaves them as "emerging and underexposed crops".

This project aims to fast-track the use of modern breeding tools in two emerging and underexposed crops:

1) quinoa, a species with high abiotic stress tolerance to salinity and drought, and gluten-free grains with a high and balanced content of essential amino acids; 

2) white lupin, a robust leguminous species adapted to temperate climates that exhibits protein and oil contents comparable to those of soy.

This project will speed-up the creation of new genetic variation and varieties in these crops. Mutant populations will be created, and gene editing tools (CRISPR) will be developed to target antinutritional factors. Other targets include enhancing the quality of primary and secondary products. Key genes in the pathways of these traits are known, and some examples in these crops already have been created by WR using reverse genetics screens. Also, forward mutation screens will be used to find mutants with either increased or impaired abiotic stress tolerance to find genes underlying resilience to abiotic stresses. Finally, mutation breeding and gene editing will be used to create new possibilities for making F1-hybrids.

Two routes to creating F1-hybrid systems will be targeted:

1) finding lines with delayed male flowering to be used as maternal lines in an F1, but which can be multiplied by selfing;

2) simplifying the use of cytoplasmic male sterility (CMS) in cases where CMS is available, but restorer/maintainer lines are lacking.

In quinoa, restorer gene loci are known, and knockout lines of those genes will be tested for suitability as maintainer lines. The core innovation in this project to be developed for these new crops is the development of classical mutation breeding and gene editing CRISPR/CAS9 strategies in combination with advanced phenotyping, sequencing technologies, and (heuristic) gene function knowledge. Bioinformatics tools for the analysis of sequence data to find rare mutations and to predict gene function knowledge will also be a key innovation of the project. The plant materials from mutation breeding can be used within the legal framework of the European Union. To facilitate the practical use of mutants produced with CRISPR/CAS9, we aim to develop a transient expression of CRISPR/CAS9 that leads to mutants but not to integration of transgenic elements into the genome of the plant.