EAGER: Targeted and specific elimination of plant chromosomes

In this rapidly changing and drying world, the rapid breeding and development of climate-adapted crop varieties is a necessary foundation of US national competitiveness and sustainability. This proposal takes genome editing by CRISPR from its preponderant use of modification or alteration of one or few genes, to a novel tool for genome-scale alterations that are urgently needed to accelerate breeding. The development of this novel technology can impact the breeding of multiple crops, including allopolyploid ones, such as wheat, canola, and peanut, that can be notoriously challenging due to their genomic complexity, but are critical components of US’s staple foods. In terms of outreach, undergraduate and graduate students will be trained in advanced plant genomics and molecular biology in the context of this project. Additionally, it will provide opportunities for exposing underrepresented groups to STEM-related work through dissemination of the concepts, methods and societal implications of this work through publications, presentations and / or outreach videos geared towards the general public and, specifically, younger audiences. The strategy entails targeting CRISPR to hand-picked sets of chromosomal sequences, so that “immune” chromosomes survive, while targeted chromosomes are eliminated. This results in individuals with specific, desirable chromosome sets, such as those from a given parent. The objectives are to demonstrate and optimize accession-specific chromosome elimination and to engineer elimination of a parental chromosome set in tomato, effectively resulting in haploid induction. Using both the model arabidopsis and the crop tomato, the work involves development of methods for identification of accession- and chromosome-specific CRISPR targets, for rapid validation of these targets, and for engineering of genotype- and karyotype-specific drives. Genome-scale alterations of crop genomes through Targeted Elimination of Chromosomes (TEC), could potentially enable broad application of haploid induction, manipulation of allopolyploid genome, and selection of specific genome-wide haplotypic configurations in hybrid progeny. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.