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.

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.

Passion fruit (Passiflora edulis) production is significantly limited by sporadic cold stress events in unfavorable years. The existence of cultivars with varying cold tolerance offers opportunities for genetic improvement of this high-value crop. To elucidate the molecular basis of cold adaption in passion fruit, we conducted an integrated transcriptomic and metabolomic analysis comparing cold-tolerant and cold-sensitive passion fruit cultivars under low-temperature stress. Our multi-omics approach revealed that cold tolerance is associated with significant reprogramming of key pathways, particularly sphingolipid metabolism, phenylpropanoid metabolism, and terpene metabolism. We further validated that exogenous application of the key metabolites within these pathways, sphinganine, chlorogenic acid, rutin, and three terpenoids enhanced cold tolerance in cold sensitive cultivars. Conversely, virus-induced gene silencing (VIGS) of core biosynthetic genes (e.g., PesSPT, PesKDSR, PesHCT, PesFG2) in these pathways compromised cold resistance, leading to increased oxidative damage and more severe phenotypic injury. This study provides comprehensive insights into the molecular networks underlying cold tolerance in passion fruit, highlighting potential candidate genes and metabolites. Our findings establish a crucial foundation for future molecular breeding strategies aimed at improving cold resistance in this profitable horticultural crop.