Improved Virus Screening of Horticultural Crops Using a Double-stranded RNA Sequencing-Based Approach

Global economic impact of pathogenic plant viruses is valued at $60 billion. In the US for appleand cherry alone these losses total up to $678 million annually. Detection of viruses is a criticalpriority to mitigate spread of diseases that threaten horticultural crop health fruit yield andquality. The current methods for virus diagnostics are low-throughput and limited to detection ofindividual viruses with established sequence information. In contrast double-stranded RNAsequencing (dsRNAseq) is capable of screening large numbers of samples for all viruses in asingle workflow. NuPhY's USDA SBIR Phase I application will evaluate the feasibility ofusing a dsRNAseq-based platform for broad-spectrum high-throughput virus screening inhorticultural crops.During Phase I we aim to develop an accurate rapid cost-effective dsRNAseq-based system ofbroad-spectrum tree fruit virus detection. The first objective will establish virus detection limits(sensitivity) of dsRNAseq in infected cherry tissues and determine the optimal tissue type forsequencing-based analysis using Little Cherry Virus as a case study. The second objective willoptimize the high-throughput dsRNAseq workflow and establish a customized data analysispipleline through testing of infected and healthy tissues from cherry apple and pear trees.NuPhY's proposed work aligns with the USDA SBIR program goals because it entails theinnovation optimization and provision of an agriculturally-related manufacturing technologythat can quickly be deployed as a service to US tree fruit growers and nursery managers.Ultimately our technological solution will pre-emptively mitigate economic losses associatedwith viral pathogens while enhancing efficiency and sustainability within US horticultureindustries.