Article

Multi-omics approaches in plant biology: decoding agronomic traits for sustainable agriculture

Muhammad Usama YounasKey Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou 225009, ChinaShimin ZuoJoint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, ChinaMuhammad QasimMicroelement Research Center, College of Resources and Agricultural University, Wuhan, Hubei, 430070, ChinaIrshad AhmadJoint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, ChinaZhiming FengJoint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, 225009, ChinaShakal Khan KoraiDepartment of Grassland, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaUsman ZulfiqarDepartment of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur 63100, PakistanTukhtaboeva FeruzaDepartment of Microbiology, Virology and Immunology, Kokond University Andijan Branch, Andijan 170619, UzbekistanIsmoilov IbrokhimDepartment of Genetics and Biotechnology, Andijan State University, University St‑129, Andijan 170100, UzbekistanTabarak MalikDivision of Research and Development, Lovely Professional University, 144411 Phagwara, India

2025en

ABI

Abstract

• Integration of multi-omics data provides a comprehensive understanding of the genetic, epigenetic, and metabolic bases of key agronomic traits in plants. • Multi-omics strategies are driving innovations in crop improvement, sustainable agriculture, and optimized farming practices. • Emerging tools and interdisciplinary collaborations are essential for addressing complex biological challenges through holistic, multi-omics approaches. The emergence of multi-omics technologies has transformed our understanding of molecular mechanisms governing key traits across diverse plant species. Multi-omics approaches, including genomics, transcriptomics, metabolomics, and microbiome profiling, have provided unprecedented insights into the molecular basis of crop resilience and productivity. In rice, integrated genomics and metabolomics have identified key loci and metabolic pathways that control grain yield and nutritional quality. In maize, transcriptomic and genomic analyses have identified networks regulating flowering time and drought tolerance. In wheat, epigenomic and transcriptomic approaches have uncovered regulators of cold stress adaptation. These studies underscore the potential of multi-omics in linking molecular variation with complex agronomic traits, thereby providing a foundation for crop improvement. Emerging layers such as lipidomics, immunomics, glycomics, and RNomics further expand integrative potential, while advanced trait-analysis frameworks (GWAS, TWAS, WGCNA) offer practical pathways for breeding, resilience, and biofortification. We also discuss emerging trends and emphasize the role of advanced tools and interdisciplinary collaborations in addressing current scientific challenges. Together, these insights present a holistic perspective on advancing plant biology and agricultural innovation.

Identifiers

DOI: 10.1016/j.stress.2025.101118

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