Exploring the hemp virome and assessing hemp germplasm for resistance to an emerging pathogen

Abstract

Hemp (Cannabis sativa L., <0.3% tetrahydrocannabidiol, THC) as a crop has been widely adopted throughout the United States. However, there is little support or guidance on disease identification and management for growers. This study aimed to describe the diversity and distribution of viruses infecting hemp in Colorado and determine if there is genetic resistance to pathogens in hemp. Throughout 2021 and 2022, leaf tissues from symptomatic and asymptomatic plants were sampled during three phenological stages (early vegetative, late vegetative, and mature flowering) in four regions of Colorado. High Throughput Sequencing (HTS) revealed a total of seven viruses across both years from 48 pooled samples: alfalfa mosaic virus, beet curly top virus (BCTV), cannabis cryptic virus, cannabis sativa mitovirus 1, grapevine line pattern virus, opuntia umbra-like virus, and tomato bushy stunt virus. These viruses had >97% nucleotide identity to their nearest GenBank accessions. As the growing season progressed, viral incidence and the number of viral species increased. We observed similar and unique viromes between individual cultivars from the same field. Given the prevalence of BCTV in the virome and its prevalence across the western United States, 13 genotypes of hemp were screened for resistance to this pathogen. Two genotypes (4587 and 4710) had a lower BCTV copy number and disease index than others. Our study provides initial evidence of the diversity of viral communities in hemp across Colorado and provides impetus for developing accurate detection methods and screening for host resistance.