Xingzhu Feng

Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China
Author    Correspondence author
Rice Genomics and Genetics, 2025, Vol. 16, No. 4   
Received: 28 Jun., 2025    Accepted: 12 Aug., 2025    Published: 28 Aug., 2025

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Functional genomics is an important approach to analyzing the gene functions and complex biological processes of rice. CRISPR interference (CRISPRi) technology has become an efficient, reversible and highly specific gene regulatory tool by using Cas9 (dCas9), which lacks cutting activity, to target and bind to DNA with single-guide RNA (sgRNA), thereby inhibiting gene transcription without causing double-strand breaks. This study systematically introduces the principle and composition of the CRISPRi system, including the dCas9 variant, the design strategy of sgRNA and its transcriptional inhibition mechanism. It reviews the latest progress of CRISPRi in the construction and optimization of rice platforms, and focuses on discussing its application in gene silencing, systematic research of gene families, and combined transcriptome and metabolome analysis. Meanwhile, through typical cases such as flowering time regulation, grain quality improvement and stress resistance enhancement, the application value of CRISPRi in the research of important traits of rice was demonstrated. This study also analyzed the advantages of this technology over the traditional CRISPR-Cas9, as well as the current technical bottlenecks (such as off-target effects, differences in silencing efficiency) and possible directions for improvement. This study aims to comprehensively summarize the research strategies of rice functional genomics based on CRISPRi, identify key challenges, and propose future development directions to accelerate molecular breeding and precise trait improvement of rice.

CRISPRi; Rice; Functional genomics; Gene silencing; Molecular breeding