The advancement of multi-omics tools has revolutionized the study of complex biological systems, providing comprehensive insights into the molecular mechanisms underlying critical traits across various organisms. By integrating data from genomics, transcriptomics, metabolomics, and other omics platforms, researchers can systematically identify and characterize biological elements that contribute to phenotypic traits. This review delves into recent progress in applying multi-omics approaches to elucidate the genetic, epigenetic, and metabolic networks associated with key traits in plants. We emphasize the potential of these integrative strategies to enhance crop improvement, optimize agricultural practices, and promote sustainable environmental management. Furthermore, we explore future prospects in the field, underscoring the importance of cutting-edge technological advancements and the need for interdisciplinary collaboration to address ongoing challenges. By bridging various omics platforms, this review aims to provide a holistic framework for advancing research in plant biology and agriculture.

Alpinia officinarum Hance is a medicinal and edible plant whose secondary metabolites possess significant pharmacological value. However, the lack of genomic resources has hindered a comprehensive understanding of this species and constrained its breeding efforts. In this study, we integrated PacBio HiFi, Illumina paired-end (PE), and high-throughput chromosome conformation capture (Hi-C) sequencing data to construct the first haplotype-resolved, chromosome-level reference genome of A. officinarum Hance. The resulting assembly achieved a contig N50 of 51.42 Mb, with the two haplotypes spanning 2.08 Gb and 1.99 Gb, respectively, and anchored onto 48 chromosomes. Repetitive sequences accounted for 82.04% and 81.02% of the two haplotypes, respectively, and 31,605 and 31,438 protein-coding genes were predicted, respectively. This high-quality genomic resource provides a solid foundation for genomic and genetic studies of A. officinarum Hance and related Zingiberaceae species, and also facilitates future haplotype-based breeding efforts.