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.

Background: Perennial ryegrass (Lolium perenne L.), a widely cultivated turfgrass and forage species in Europe and North America, exhibits rapid growth and notable salt tolerance. The high-affinity potassium transporter (HKT) gene family has been implicated in salt stress responses across multiple plant species. However, whether the salt tolerance of L. perenne is closely associated with its HKT gene family remains unclear. Methods and Results: In this study, we systematically identified HKT family members in the L. perenne genome. Five HKT genes were identified and classified into three subfamilies. Among these, LpHKT1a–c exhibited canonical class I features with a conserved serine (S) residue in the P1 domain, whereas LpHKT2 belonged to class II, characterized by a glycine (G) residue in the same domain. Notably, LpHKT3 formed a distinct subfamily with a truncated structure and divergent P1/P2 domains, suggesting potential non-canonical functions. LpHKT1a likely lacked the P4 domain. Promoter analysis revealed that all five LpHKT genes contain multiple stress-related cis-acting elements. Real-time quantitative reverse transcription polymerase chain reaction results showed that LpHKT1b/c and LpHKT2 were highly expressed in both roots and leaves. Under low-concentration NaCl stress (25 mM), the expression of these three genes significantly increased by 8- to 12-fold at 6–12 h post-treatment (vs. control). Ion accumulation analysis demonstrated a rapid increase in Na⁺ levels following NaCl treatment, whereas K⁺ concentrations initially remained stable but significantly increased after 24 h. Conclusions: Combined with the cellular localization of LpHKT1c predominantly in the xylem, these findings suggest that LpHKT genes may be involved in Na⁺ and K⁺ transport in roots. This study represents the first genome-wide identification of the HKT gene family in L. perenne, providing critical insights into the molecular mechanisms underlying its salt tolerance and offering valuable genetic resources for molecular breeding aimed at enhancing stress resilience.

Background: Domain of Unknown Function 1645 (DUF1645) is a conserved but poorly characterized plant gene family whose evolutionary history and roles in stress adaptation remain unclear. We performed an integrated genomic, evolutionary, transcriptomic, and Quantitative Trait Locus (QTL) characterization of the DUF1645 family in rice (Oryza sativa). Methods and Results: We identified 14 intronless, non-redundant OsDUF1645 genes distributed across eight chromosomes. Phylogenetic and collinearity analyses suggested that family expansion within Poaceae involved ancestral segmental and localized tandem duplication events. Promoter analysis identified stress- and phytohormone-responsive cis-acting elements, including ABRE, MBS, and MeJA-associated motifs. Public transcriptome datasets revealed diverse OsDUF1645 expression patterns under abiotic and hormonal treatments. Integration with the Quantitative Trait Loci Annotation Rice Online (Q-TARO) QTLome identified physical co-localization of multiple OsDUF1645 loci with stress- and agronomic-trait QTLs, including salinity-, drought-, root architecture-, and water-deficit-associated regions. On Chromosome 1, OsDUF1645.1, OsDUF1645.2, OsDUF1645.3, and OsDUF1645.4 overlapped QTL intervals associated with salinity-related physiological traits, including Na⁺ uptake and Na⁺ balance, and drought-related root traits. On Chromosome 5, the tandemly arranged OsDUF1645.8, OsDUF1645.9, and OsDUF1645.10 co-localized with QTLs related to root architecture and water-deficit responses. qRT-PCR validation under salinity, osmotic stress, and cadmium exposure confirmed distinct stress-responsive expression profiles; OsDUF1645.6 exhibited broad multi-stress responsiveness, whereas OsDUF1645.3 was downregulated under several conditions. Conclusions: The OsDUF1645 family exhibits substantial functional diversification, supported by distinct regulatory architectures, expression profiles, and QTL associations. These findings provide a framework for prioritizing OsDUF1645 candidates for functional validation and their potential application in molecular breeding and development of climate-resilient rice cultivars.

Bread wheat (Triticum aestivum L.) increasingly encounters combinations of abiotic stresses that interact in time and whose effects are not predictable from single-stress responses. We define yield-stable resilience as the capacity to maintain grain yield under compound climate extremes without a significant penalty in yield or quality under favourable conditions; both components are required, and a line that tolerates stress while losing yield potential does not satisfy the definition. This critical review addresses three dimensions: the temporal architecture of stress across development; the biological control layers that run from perception through recovery to stress memory; and the precision-engineering strategies enabled by genome editing. We argue that field-level yield stability is rarely achieved by constitutively overexpressing or deleting a single stress-response gene. Instead, stress-integration networks must be engineered in a context-dependent, dosage-aware manner. To explain why single-gene solutions fall short, we examine molecular and physiological trade-offs, including water conservation versus transpirational cooling, photoprotection versus carbon acquisition, and stay-green versus remobilization. Stress-memory mechanisms, which range from chromatin modifications to persistent signalling states, offer a route to primed protection, but causal validation in wheat remains largely absent. The hexaploid wheat genome affords distinctive engineering opportunities through homoeologue-dosage control, promoter tuning and tissue-specific regulation. We propose an evidence-gated pathway that proceeds from mechanism to calibrated editing, to biologically realistic stress testing, to multi-environment yield testing, and finally to equitable deployment, and we treat breeding integration, introgression, recurrent selection and precision editing as a single pipeline rather than as competing alternatives.