Hop Latent Viroid (HLVd) causes significant yield losses in cannabis cultivation, yet natural variation in cultivar tolerance remains poorly understood. The objective of this portion of our research was to identify molecular and transcriptomic features associated with natural HLVd tolerance in Jamaican Lion (JL) using a new chromosome-scale genome assembly and transcriptomic profiling.

To accomplish this, we scaffolded the publicly available JL genome to chromosome scale and performed comprehensive annotation using RNA-seq data from the Cannabis Pangenome Project, Cannabis Expression Atlas, and HLVd-challenged tissue samples from Medicinal Genomics. This approach captured inducibly expressed plant resistance genes often missed in standard annotations. Our updated assembly enabled precise identification of candidate resistance genes and their chromosomal context—a critical advancement over the previous contig-level JL assemblies.

Differential expression analysis of root and meristem tissues from HLVd-inoculated versus non-inoculated JL clones confirmed that HLVd localizes primarily in root tissues. We identified differentially expressed pathways including components of general pathogen defense responses and secondary metabolism. For example, in the roots of plants two weeks after HLVd inoculation, genes in the anthocyanin biosynthesis pathway were enriched, suggesting a role for this secondary metabolite pathway in viroid defense.

These findings provide the first chromosome-scale genomic resource for studying HLVd tolerance in cannabis and for identifying specific molecular targets for breeding programs. Based on our analyses, natural variation in secondary metabolite production is correlated with host tolerance and may be a key factor in cultivar-specific resistance.

Learning Objectives:

• New chromosome-scale genome assembly enables precise identification of HLVd resistance genes in Jamaican Lion
  
  
• Secondary metabolite variation offers molecular targets for breeding HLVd-tolerant cultivars