Genome Engineering in Rice: Applications, Advancements and Future Perspectives

Abstract

Rice (Oryza sativa L.) is one of the essential cereal crops for the majority of the world’s population. However, we need to ensure a continuous supply and enhanced the productivity of this crop in the purview of global climate change and increasing world population. Several crop improvement strategies, including genetic engineering and molecular breeding, have been routinely used to develop varieties superior in stress tolerance and yield. However, each one of them has limitations. Genome engineering or genome editing using targeted nucleases is recently being deployed as a key strategy to improve rice and other crops which promises a significant improvement in yield without the requirement of additional agricultural land in the future. Targeted genome editing using artificial nucleases has largely revolutionized the field of crops’ genome modification. Several studies recently used Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) to successfully modulate genes in a precise and predictable manner in plants for gene function studies and crop improvement programmes. These techniques open up new prospects to develop improved plant lines by adding important traits or by removing undesirable traits. The ability of these technologies to perform targeted and efficient modifications in genome sequence will undoubtedly lead to novel developments in plants, including crop plants. Moreover, due to the non-insertion of foreign DNA, this technique is socially acceptable and may help to alleviate regulatory issues associated with genetically modified plants. In this review, we describe the recent advancement in the CRISPR/Cas9 system and also highlight the strengths and weaknesses of this technology in comparison to the other two well-established genome editing platforms (ZFNs and TALENs). We have also discussed the small size new protein named CasX, its DNA cleavage characteristics, and its advantages over other CRISPR-Cas genome-editing enzymes. These technologies are mostly used for substitution of targeted gene fragments and insertion of exogenous DNA sequences into specific genomic location in crop plants that offer great potential for genetic improvement and breeding of rice.