Tissue-Specific Transcriptomic Responses and Viral Accumulation in Lily Cultivars Infected with Cucumber Mosaic Virus

Cucumber mosaic virus (CMV) threatens lily production by reducing floral quality and enabling carry-over via infected planting stock. To explore tissue-specific host responses, we analyzed a legacy, single-replicate RNA-seq dataset from two cultivars, ‘Cancun’ and ‘Connecticut King’ (CK), profiling leaf (source) and bulb (sink) tissues at 0 and 28 days post-inoculation (dpi), alongside leaf DAS-ELISA. Principal component analysis indicated that tissue identity dominated the transcriptome (PC1 = 47.7%), with CMV treatment driving within-tissue shifts over time. Exploratory Gene Ontology/KEGG summaries and a focused marker panel revealed a consistent split: in leaves, genes linked to jasmonate/WRKY-associated defense (e.g., WRKY40/41/51/53; AOS/OPR1/2; CYP74A/DDE2) tended to show higher expression at 28 dpi, whereas cell-wall/transport-related terms were reduced; in bulbs, transcripts associated with photosynthetic/organellar maintenance (LHCB/CAB, HCF107) and β-amylase-linked carbohydrate turnover were more prominent, with comparatively limited elevation of canonical defense modules. Leaf ELISA trajectories were compatible with this framework: CK showed a transient peak at 14 dpi followed by a decline at 24 dpi, whereas ‘Cancun’ increased progressively. Taken together, the concordance among ordination, enrichment patterns, marker behavior, and leaf titers in this non-replicated dataset is consistent with a working model in which stronger or earlier leaf responses may contribute to partial containment and reduced systemic accumulation. We propose a compact leaf marker set (WRKY40/41/51/53; AOS/OPR1/2; CYP74A/DDE2) and bulb candidates (β-amylase; LHCB/CAB/HCF107) as hypothesis-generating indicators of containment and sink maintenance. These tissue-resolved patterns provide a descriptive framework and a starting point for future validation by qPCR and replicated RNA-seq across additional cultivars, with the long-term goal of informing selection and stock hygiene in lily production.