Applications and Future Prospects of Plant Multi-Omics Technologies in Precision Agriculture

Against the backdrop of global population growth, intensifying climate change, and limited arable land, ensuring food security and promoting sustainable agriculture have become critical issues. The limitations of conventional agricultural systems are becoming increasingly apparent, creating an urgent need for innovation driven by science and technology. In this context, plant multi-omics technologies serve as the foundational data and technical cornerstone of systems biology and precision agriculture. Integrating multi-level data from genomics, transcriptomics, proteomics, metabolomics, epigenomics, and microbiomics offers substantial advantages for systematically understanding and improving plants. Unlike previous reviews that mainly catalog omics technologies or focus on individual crops, this review adopts a unified discovery-to-translation framework and critically evaluates the strength of evidence across applications. This review focuses on cutting-edge applications of multi-omics in three key areas: improving the traits of cereal crops (rice, wheat and maize), remediating soil health, and innovating products such as biofertilizers and biostimulants for agriculture. We systematically explore the roles of multi-omics in accelerating breeding processes, deciphering complex agronomic traits, restoring soil ecosystems, and constructing intelligent decision-support systems. The review also examines current challenges, including the complexity of data integration and the difficulties of predicting genotype-by-environment interactions. Furthermore, it outlines future directions involving deeper convergence with artificial intelligence, high-throughput phenomics, and digital twins. In summary, plant multi-omics technology is a vital tool for unravelling the mysteries of plant life and is also a key enabler of intelligent, precise and sustainable agricultural transformation.