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.

Passion fruit (Passiflora edulis) possesses a complex aroma and is widely grown in tropical and subtropical areas. Here, we conducted the de novo assembly, annotation and comparison of purple (P. edulis Sims) and yellow passion fruit (P. edulis f. flavicarpa) reference genomes using PacBio, Illumina and Hi-C technologies. Notably, we discovered evidence of recent whole-genome duplication events in P. edulis genomes. Comparative analysis revealed 7.6∼8.1 million single nucleotide polymorphisms, one million insertions/deletions, and over 142 Mb presence/absence variations among different P. edulis genomes. During the ripening of yellow passion fruit, metabolites related to flavor, aroma, and color were substantially accumulated or changed. Through joint analysis of genomic variations, differentially expressed genes, and accumulated metabolites, we explored candidate genes associated with flavor, aroma and color distinctions. Flavonoid biosynthesis pathways, anthocyanin biosynthesis pathways and related metabolites are pivotal factors affecting the coloration of passion fruit, and terpenoids metabolites accumulated more in purple passion fruit. Finally, by heterologous expression in yeast (Saccharomyces cerevisiae), we functionally characterized 12 terpene synthases (TPSs). Our findings revealed that certain TPS homologues in both yellow and purple passion fruit varieties produce identical terpene products, while others yield distinct compounds or even lose their functionality. These discoveries revealed the genetic and metabolic basis of unique characteristics in aroma and flavor between the two passion fruit varieties. This study provides resources for better understanding the genome architecture and accelerating genetic improvement of passion fruits.

Cassava is a crucial crop that makes a significant contribution to ensuring human food security. However, high-quality telomere-to-telomere cassava genomes have not been available up to now, which has restricted the progress of haploid molecular breeding for cassava. In this study, we constructed two nearly complete haploid resolved genomes and an integrated, telomere-to-telomere gap-free reference genome of an excellent cassava variety, ‘Xinxuan 048’, thereby providing a new high-quality genomic resource. Furthermore, the evolutionary history of several species within the Euphorbiaceae family was revealed. Through comparative analysis of haploid genomes, it was found that two haploid genomes had extensive differences in linear structure, transcriptome features, and epigenetic characteristics. Genes located within the highly divergent regions and differentially expressed alleles are enriched in the functions of auxin response and the starch synthesis pathway. The high heterozygosity of cassava ‘Xinxuan 048’ leads to rapid trait segregation in the first selfed generation. This study provides a theoretical basis and genomic resource for molecular breeding of cassava haploids.

Metabolomics, representing the biochemical phenotype of cells or tissues, serves as an intrinsic factor underlying the differences in plant traits. Recent advances in multi-omics technologies have significantly deepened our understanding of plant metabolic diversity, enabling researchers to dissect complex biochemical networks at unprecedented levels of detail. This review explores the integration of metabolomics with genomics, transcriptomics, proteomics, epigenomics, microbiomics, and other omics approaches, emphasizing the power of these combined approaches in unraveling the molecular mechanisms underlying plant adaptation, stress resistance, and phenotypic variation. Through a critical analysis of representative case studies across diverse crops, we demonstrate how multi-omics strategies facilitate the identification of key metabolic pathways and regulatory networks for crop improvement. We also discuss current challenges in data integration, metabolite coverage, and the functional characterization of unknown compounds, and propose future directions for overcoming these limitations. Addressing these challenges will require both the enhanced resolution and sensitivity of analytical techniques, as well as more robust frameworks for data integration and interpretation. By overcoming these challenges, the convergence of metabolomics with other omics disciplines will continue to expand our understanding of plant biology, offering novel insights and innovation in crop breeding and sustainable agriculture.

Passion fruit (Passiflora edulis) is an economically important fruit worldwide. However, heat stress severely threatens its production, particularly in tropical and subtropical regions. To elucidate the molecular and metabolic mechanisms underlying heat tolerance, comparative physiological, transcriptomic, and metabolomic analyses were conducted between two yellow passion fruit cultivars: heat-tolerant ‘Summer Queen’ (F2) and heat-sensitive ‘Qinmi 9’ (QM9). Physiological evaluations demonstrated that QM9 exhibited significantly lower heat tolerance than F2, manifesting as severe leaf wilting, impaired photosynthetic efficiency, and elevated reactive oxygen species (ROS) accumulation. F2 exhibited distinct metabolic and transcriptional adaptations under heat stress, particularly in purine metabolism and flavonoid biosynthesis. Metabolites such as glutamine, xanthine, luteoloside, and trifolin were enriched in F2, alongside the upregulation of genes like adenosine kinase (AK), xanthine dehydrogenase (XDH), guanine deaminase (GDA), and flavonoid 3′-hydroxylase (F3′H). Weighted gene co-expression network analysis (WGCNA) highlighted strong associations between these pathways and transcription factors (e.g., MYB, HSF, WRKY), suggesting their pivotal roles in heat adaptation. Exogenous application of xanthine and trifolin markedly enhanced heat tolerance in passion fruit. Furthermore, knockdown of PeGDA and PeXDH markedly altered the heat tolerance of F2. These findings reveal that elevated metabolites in purine metabolism and flavonoid biosynthesis enhance heat tolerance in passion fruit, offering new insights into the molecular mechanisms of heat tolerance and potential targets for breeding climate-resilient passion fruit varieties.