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 themare complex agronomic traits controlled by multiple genes, so the simultaneous improvement of these traits via sexual recombinationis time-consuming and direction-uncontrolled. In this study, to solve this dilemma, we introduced the comparative genomic analysisbased multiplex genome editing system (CG-MGE), a method for rapid and directional improvement of multiple traits. Applicationof this method, association analysis between genotypes and phenotypes was carried out to mine excellent alleles; subsequently, therare excellent alleles ofGn1a,GW2,TGW3, andChalk5were simultaneously created by multiplex genome editing and successfullyimproved the plant architecture, grain yield, and quality of a widely cultivated elite rice variety. Overall, this study provides a methodfor rapid and directional improvement of crops, and the application of the CG-MGE will be helpful to accelerate rational design breeding.