Rapid and Directional Improvement of Elite Rice Variety via Combination of Genomics and Multiplex Genome Editing

High yield and superior quality are the main goals pursued by breeders for crop improvement. However, both of them are complex agronomic traits controlled by multiple genes, so the simultaneous improvement of these traits via sexual recombination is time-consuming and direction-uncontrolled. In this study, to solve this dilemma, we introduced the comparative genomic analysis based multiplex genome editing system (CG-MGE), a method for rapid and directional improvement of multiple traits. Application of this method, association analysis between genotypes and phenotypes was carried out to mine excellent alleles; subsequently, the rare excellent alleles of Gn1a, GW2, TGW3, and Chalk5 were simultaneously created by multiplex genome editing and successfully improved the plant architecture, grain yield, and quality of a widely cultivated elite rice variety. Overall, this study provides a method for rapid and directional improvement of crops, and the application of the CG-MGE will be helpful to accelerate rational design breeding.