MOLECULAR GENETICS AND GENOME EDITING IN RICE (ORYZA SATIVA L.): INTEGRATING GENE DISCOVERY, FUNCTIONAL GENOMICS AND CRISPR-BASED PRECISION BREEDING

Abstract

Rice is a major crop for which productivity and quality are being challenged by climate change, the development of new 
biotic stressors and pests, and the need for sustainable resource use. Through advances in molecular genetics and genomics, 
there may be greater opportunities to identify key genes and alleles controlling this large range of important agronomic traits. 
This review summarizes the potential pathways through which genomic resources, gene discovery, functional genomics and 
genome editing (based on CRISPR technology) can be integrated to accelerate rice improvement. Using examples, the role of 
reference genomes, pan-genomes, genome resequencing, genome-wide association studies, quantitative trait loci mapping, 
and genomic selection in the discovery of candidate loci for yield, plant architecture, stress tolerance, disease resistance, and 
grain quality are discussed. In addition, principles in using transcriptomics, reverse genetics, gene-regulatory networks and 
multi-omics to prioritize candidates and infer gene function are considered, as well as the latest approaches in genome
editing: CRISPR/Cas9, Cas12a, base editing, prime editing, multiplex editing, and promoter editing for yield, stress, and 
quality enhancements. Although most advances have been made, translation into the field is still predicted to be limited by 
genotype-dependent transformation and regeneration, off-target effects, editing efficiency, background effects, pleiotropy, 
and validation on a large scale in the field. An integrated gene-to-cultivar framework for linking genomic discovery and 
multi-omics evidence with functional validation, specific genome modification, molecular characterization, and multi
environmental field evaluation is proposed. Combining such methods with traditional breeding and genomic selection may 
help to develop productive, resilient, and high-quality rice cultivars adapted to various target environments and farmer and 
consumer priorities.