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Figure 1. Molecular and ecological integration of stress physiology in Allium crops. Schematic overview of the multiscale mechanisms underlying stress responses in Allium species. The central node represents integrated Allium stress physiology, linking molecular, physiological, and ecological processes. Four interconnected domains are illustrated: (1) Abiotic stress screening, highlighting early-stage predictive traits for salinity tolerance and biomass-based selection approaches; (2) Combined stress dynamics, emphasizing the temporal effects of sequential abiotic and biotic stresses (e.g., pre-vs. post-infection waterlogging) on physiological outcomes; (3) Molecular defense architecture, depicting the dual isoallicin system involving cytosolic and vacuolar alliinases (ALL) and lachrymatory factor synthase (LFS), enabling both constitutive and inducible defense responses; and (4) Pathobiome and physiological disorders, illustrating microbiome restructuring and non-infectious abnormalities that affect yield and storage quality. The bottom panel outlines future research directions, including multi-omics integration, biomarker development, microbiome engineering, and climate-resilient breeding strategies. Arrows indicate functional interconnections among these domains, reflecting the dynamic and integrated nature of stress adaptation in Allium crops.Salinity is one of the most severe abiotic constraints limiting onion productivity, particularly in salt-affected soils and irrigated systems. Kasar et al. (2026) conducted a large-scale screening of 116 onion genotypes at the germination stage to establish a reliable protocol for assessing salinity tolerance (Kale et al., 2024). By identifying 150 mM NaCl as an optimal discriminatory concentration and integrating morphological parameters with multivariate analyses, including principal component analysis and membership function modeling, the authors categorized genotypes into graded tolerance groups ranging from highly tolerant to highly sensitive. Importantly, total fresh weight under saline conditions emerged as a robust and practical screening trait. This work provides breeders with a reproducible early-stage selection framework and highlights that seedling-stage performance may serve as a predictive indicator of longterm field resilience. The study reinforces the importance of integrating quantitative modeling approaches into physiological screening for climate-resilient breeding.Climate change increasingly exposes crops to overlapping stress events, necessitating investigation beyond single-stress paradigms. Salunkhe et al. (2025) examined the interaction between waterlogging and anthracnose disease caused by Colletotrichum gloeosporioides species complex in onion (Salunkhe et al., 2025). Their study revealed that stress timing critically shapes disease outcomes. Post-infection waterlogging significantly intensified disease severity, reduced chlorophyll and carotenoid content, decreased relative water content, elevated membrane injury, and triggered strong antioxidant responses (SOD and APX). In contrast, pre-infection waterlogging partially suppressed pathogen establishment, suggesting hypoxia-induced defense priming. These findings demonstrate that stress sequencing determines physiological exhaustion versus tolerance, emphasizing the importance of temporal context in stress physiology. This work contributes to a growing body of evidence that cross-tolerance and stress priming are central mechanisms in plant adaptation. For Allium crops cultivated in monsoon climates or poorly drained soils, understanding such stress interactions is essential for both management strategies and breeding programs.Chemical Defense Architecture: The Isoallicin System A defining feature of Allium species is their sulfur-based defense chemistry. Cho et al. (2024) provided a comprehensive "isoallicin-omics" analysis of onion defense metabolism using genomic, transcriptomic, and metabolomic approaches (Cho et al., 2024). Mining the DHW30006 onion genome, the authors identified 64 alliinase (ALL) genes and 29 lachrymatory factor synthase (LFS) genes, key enzymes in isoallicin and lachrymatory factor biosynthesis. A particularly significant discovery was the presence of two functional categories of alliinases: vacuolar signal peptide-containing ALLs and cytosolic non-SP ALLs. This dual system suggests a layered defense strategy. Cytosolic alliinases maintain a basal production of isoallicin in intact tissues, functioning as a phytoanticipin defense, while vacuolar alliinases amplify isoallicin production upon tissue damage. Traditionally, isoallicin production was considered exclusively damageinduced. This study redefines the system as both constitutive and inducible, reflecting a sophisticated spatial and temporal regulation of defense metabolism. Such diversification of gene families and subcellular compartmentalization underscores the evolutionary adaptation of Allium crops to biotic stress.Disease outcomes are increasingly understood within the context of the plant microbiome. Jayasinghe et al. (2024) investigated fungal community composition associated with leaf blight of Welsh onion in Taiwan using ITS1 amplicon sequencing (Jayasinghe et al., 2024). Their results revealed that leaf blight is a disease complex primarily involving Stemphylium and Colletotrichum, alongside shifts in phyllosphere and rhizosphere fungal communities. Symptomatic plants exhibited altered alphadiversity patterns and restructured co-occurrence networks, supporting the "pathobiome" concept in which multiple taxa interact to drive disease progression. Rather than a single causal agent, disease emerges from community-level interactions shaped by environmental conditions and host physiology. This systems-level perspective opens new avenues for microbiome-based diagnostics and disease management strategies. It also aligns with broader ecological frameworks, recognizing that stress responses extend beyond host gene expression to encompass microbial assemblages.Beyond abiotic and biotic stresses, physiological disorders represent a major yet underappreciated constraint on Allium production. Kale et al. (2024) provided the first comprehensive review and bibliometric assessment of physiological disorders in onion and garlic, including premature bolting, sprouting, doubles, watery scale, thick neck, and rubberization (Kale et al., 2024). Their analysis revealed increasing scientific attention over recent decades but persistent knowledge gaps in linking environmental triggers, genetic regulation, and management strategies. Physiological disorders can account for substantial yield and storage losses, yet they remain insufficiently integrated into molecular and breeding frameworks. By combining bibliometric visualization with critical assessment, the authors underscore the need to bridge agronomic practices, environmental modeling, and molecular physiology to mitigate these non-infectious abnormalities.