Identification and functional verification of resistance genes against Lily bulb virus-1 (LbV-1) in Lilium: Insight from sRNA sequencing and transcriptomic profiling.

Lilium is an economically important genus widely cultivated for ornamental and commercial use. In this study, we report the identification and characterization of a novel mitovirus, designated Lily Bulb Virus-1 (LbV-1), detected in commercial lily bulb stocks. This virus represents a previously uncharacterized member of the mitochondrial RNA virus group associated with lily crops. A survey of 50 commercially cultivated lily bulbs, including Lilium longiflorum varieties, revealed LbV-1 infection in a single cultivar, indicating a low but detectable incidence under the tested conditions. Although infected plants exhibited no visible symptoms during in vitro cultivation, the presence of LbV-1 was confirmed through PCR amplification, small RNA (sRNA) sequencing, transmission electron microscopy (TEM), and mechanical inoculation assays. A total of 9122,220 unique sRNA reads were identified, with 21-22 nt virus-derived small RNAs mapping to the LbV-1 genome, supporting active host-virus interaction. Additionally, transcriptome-based analyses indicated efficient bulb-mediated transmission, with an infection rate of up to 45% in progeny plants. Comparative transcriptomic analysis of infected and healthy bulbs yielded over 30 million high-quality reads, resulting in the assembly of 3671,77 transcripts and 168,004 unigenes with an average length of 1445 bp. Differential expression analysis identified eight candidate genes (Li-PCP, Li-DUF, Li-UBD, Li-FRC, Li-CF, Li-APD, Li1-UN, and Li7-UN) that were significantly upregulated in response to LbV-1 infection and validated across three developmental stages using RT-qPCR. Functional analysis demonstrated that seven of these genes enhanced viral resistance when expressed in susceptible lily plants. These findings provide new insights into the molecular biology, transmission dynamics, and host defense responses associated with LbV-1. This study highlights the importance of systematic screening of commercial lily bulb stocks to prevent the unnoticed spread of latent viral infections and to safeguard sustainable lily production systems.