Programmable genome engineering and gene modifications for plant biodesign

Jialin Liu; Ruixiang Zhang; Nan Chai; Liying Su; Zhiye Zheng; Taoli Liu; Ziming Guo; Yuanhao Ma; Yongyao Xie; Xianrong Xie; Qiupeng Lin; Letian Chen; Yao-Guang Liu; Qinlong Zhu

doi:10.1016/j.xplc.2025.101427

Programmable genome engineering and gene modifications for plant biodesign

Plant Commun. 2025 Jun 24:101427. doi: 10.1016/j.xplc.2025.101427. Online ahead of print.

Authors

Affiliations

¹ Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China.
² Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
³ Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China. Electronic address: zhuql@scau.edu.cn.

PMID: 40566685
DOI: 10.1016/j.xplc.2025.101427

Abstract

Plant science has entered a transformative era with genome editing by enabling precise DNA alterations to address global challenges such as climate adaptability and food safety. These alterations are primarily driven by the integration of three modular components that can be activated or suppressed: DNA-targeting modules, effector modules, and control modules. The field has evolved from protein-centric systems (zinc finger nucleases and transcription activator-like effector nucleases) to RNA-focused platforms (CRISPR-Cas and other nucleases), which facilitate diverse control over genetic and epigenetic contexts. The modular design of DNA-targeting modules paired with effector domains, with or without inducible systems, provides scientists with superior precision in regulating transcription and altering chromatin states. The present review article examines these three modules and highlights various optimization methods. Additionally, it outlines innovative tools such as optogenetic systems and receptor-integrated systems that enable spatiotemporal control of genome editor expression. These modular instruments overcome traditional boundaries and allow scientists to create plants with favorable characteristics, decipher complex gene networks, and adopt sustainable farming practices.

Keywords: CRISPR-Cas; genome engineering; inducible control systems; synthetic biology; transcriptional/epigenetic regulation.

Publication types

Review