The economic value of the saffron stigma is primarily due to three crucial apocarotenoids: crocin, picrocrocin, and safranal, which contribute to its color, flavor, and aroma. These compounds make saffron highly valuable in various industries. Plant viruses like the cucumber mosaic virus (CMV) and turnip mosaic virus (TuMV) are significant threats to agricultural crops worldwide, causing economic losses. To elucidate the influence of viral stress on the quality of saffron, morphological, physiological, biochemical, and molecular indexes were assessed. Under the stress of both viruses, typical viral symptoms appeared. The lowest contents of leaf pigments, flowering performance, petal anthocyanin, greenness, and photosynthesis properties were observed in plants infected with CMV and TuMV. According to high-performance liquid chromatography (HPLC) analysis, CMV inoculation led to the highest reduction in crocin and safranal content, while inducing the highest increase in picrocrocin compared to the mock treatment. Gene expression analysis involved in the biosynthesis of crucial secondary metabolites showed a high correlation with the content of each metabolite. CMV inoculation resulted in the lowest expression of CsALDH31l and the highest expression of CsUGT709G1 compared with the mock treatment. Our findings demonstrate the association between virus stress and changes in the metabolism of the saffron medicinal plant.

Saffron ( Crocus sativus L.), valued for its culinary and medicinal properties, is increasingly affected by viral infections that compromise its biochemical integrity and market quality. This study investigates the impact of cucumber mosaic virus (CMV; Cucumovirus CMV ) and turnip mosaic virus (TuMV; Potyvirus rapae ) on saffron’s antioxidant profile, flavonoid content, and physiological parameters. Sixteen traits were quantified, including enzymatic antioxidants (CAT, POD, PPO, PAL), non-enzymatic markers (Trolox, vitamin C, proline), total flavonoids and phenolics, gas exchange parameters (Ci, Cond, VpdL), and morphological indicators. Principal component analysis (PCA) revealed that antioxidant-related traits contributed strongly to the first principal component (F1), explaining 78.29% of the total variance. Viral infection led to elevated antioxidant enzyme activity and flavonoid accumulation, alongside reduced stomatal conductance and altered water vapor dynamics. These findings suggest that CMV and TuMV induce oxidative stress responses and metabolic shifts that may affect saffron’s nutritional and sensory quality. Integrative biochemical profiling offers a valuable approach for assessing viral impact and guiding crop management strategies.

Saffron (Crocus sativus L.) is a high-value crop vulnerable to potyvirus infections threatening its yield and quality. In this study, we combined Oxford Nanopore long-read sequencing with exploratory transcriptomic profiling to characterize the saffron virome and to describe expression profiles associated with two distinct infection histories: (i) saffron plants experimentally inoculated with cucumber mosaic virus (CMV; Cucumovirus CMV) and turnip mosaic virus (TuMV; Potyvirus rapae) under controlled greenhouse conditions, and (ii) saffron plants naturally infected by diverse viruses. We identified six plant-infecting viral families in both conditions, including Potyviridae, Geminiviridae, Caulimoviridae, Tymoviridae, Aspiviridae, and Partitiviridae. Transcriptomic profiling revealed distinct expression profiles associated with each infection background. Given the limitations of the experimental design, gene expression differences are interpreted descriptively. We describe pathway enrichments associated with antiviral responses. Naturally infected plants exhibited a broad-spectrum, tolerance-based response characterized by the upregulation of photosynthesis-related genes, calcium-mediated signaling components, and stress-responsive transcription factors. In contrast, virus-inoculated plants activated a targeted antiviral program involving RNA silencing, autophagy, ubiquitin-mediated proteolysis, and hormonal regulation. Both GO and KEGG enrichment analyses supported these findings, highlighting photosynthesis and metabolic flexibility in naturally infected plants versus hypersensitive response, RNA surveillance, and lignin biosynthesis in virus-inoculated plants. This work provides a comprehensive view of the saffron virome and offers a hypothesis-generating overview of transcriptional responses associated with natural versus experimental virus infections. These findings advance the understanding of the saffron virome and provide a valuable resource for breeding virus-resistant cultivars.

Saffron (Crocus sativus L.) is increasingly challenged by viral infections, yet the physiological links between viral stress and defense-associated metabolic responses remain insufficiently resolved. This study examined whether cucumber mosaic virus (CMV) and turnip mosaic virus (TuMV) are associated with coordinated changes in antioxidant defense, phenylpropanoid-related metabolism, gas-exchange traits, and flower biomass in saffron grown under controlled greenhouse conditions. Sixteen biochemical and physiological traits were quantified, including catalase (CAT), peroxidase (POD), polyphenol oxidase (PPO), phenylalanine ammonia-lyase (PAL), total phenolics, flavonoids, Trolox-equivalent antioxidant capacity, vitamin C, proline, carbohydrate content, stomatal conductance, intercellular CO2 concentration, vapor pressure deficit at leaf level, leaf temperature, Ci/Ca, and flower dry weight. Principal component analysis showed that antioxidant enzymes, non-enzymatic antioxidants, and secondary-metabolite traits were positively associated with the major axis of variation, whereas carbohydrate content, stomatal conductance, vapor pressure deficit, and flower dry weight were negatively associated. Hierarchical clustering further separated virus-infected plants from mock controls and highlighted coordinated enrichment of antioxidant and phenylpropanoid-associated traits under infection. Together, the trait pattern supports a physiology-based interpretation in which CMV and TuMV infection are associated with oxidative-defense activation, PAL-linked phenylpropanoid reprogramming, and a defense-growth tradeoff in saffron. These findings provide a physiology-centered framework for understanding how viral infection alters functional traits in this economically important non-model crop.

The economic value of saffron stigma is primarily due to three crucial apocarotenoids: crocin, picrocrocin, and safranal, which contribute to its color, flavor and aroma. These compounds make saffron highly sought after in various industries. Plant viruses like Cucumber mosaic virus (CMV) and Turnip mosaic virus (TuMV) are significant threats to agricultural crops worldwide, causing economic losses. To elucidate the influence of viral stress on the quality of saffron, morphological, physiological, biochemical and molecular indexes were assessed. Under the stress of both viruses, typical viral symptoms appeared. The lowest content of leaf pigments, flowering performance, petal anthocyanin, greenness and photosynthesis properties were observed in plants infected with CMV and TuMV. According to High performance liquid chromatography (HPLC) analysis, CMV inoculation led to the highest reduction in crocin and safranal content, while inducing the highest increase in picrocrocin compared to the mock treatment. Gene expression analysis involved in the biosynthesis of crucial secondary metabolites showed a high correlation with the content of each metabolite. CMV inoculation caused the lowest expression of CsALDH31l and the highest expression of CsUGT709G1 compared to the mock. Our findings demonstrate the associations between virus stress and changes in the metabolism of the saffron medicinal plant.