High-throughput sequencing in plant disease management: a comprehensive review of benefits, challenges, and future perspectives

Abstract

High-throughput sequencing (HTS) has instigated a paradigm shift in plant pathology, showcasing its transformative role in the management of plant diseases. As a powerful tool, HTS aids in identifying pathogens and enhances disease management strategies by detecting novel and emerging pathogens, tracking disease outbreaks, and contributing to developing disease-resistant cultivars. Despite these benefits, the implementation of HTS faces obstacles due to the complexity of data interpretation and economic factors that affect its widespread adoption. This comprehensive review summarizes the strengths, limitations, and opportunities associated with using HTS in managing plant diseases. The article also delves into the prospects of HTS, incorporating technological advancements, synergy with complementary methodologies, capacity-building initiatives, and the development of best practices and guidelines. By acknowledging and addressing these obstacles while harnessing the full capabilities of HTS, we advocate for a refined approach to managing plant diseases. This approach is critical for ensuring global food security, especially in the context of a growing global population and climate change.

Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding

“…The HTS technology has emerged as a valuable tool that facilitates the identification of phytopathogenic organisms and enhances disease management approaches. HTS enables the detection of novel and emerging pathogens, facilitates the tracking of disease outbreaks, and contributes to the development of disease-resistant cultivars [ 42 , 43 ].…”

Plant NLR immunity activation and execution: a biochemical perspective

“…Plant disease outbreaks remain the major threat to food production across continents, with losses caused by pathogens and pests reducing crop yields globally by approximately 30% each year [ 1 ]. New microbial strains which colonize and damage crops can now be detected more efficiently using high-throughput sampling, next-generation DNA sequencing technologies and epidemiology modelling [ 2 ]. Nevertheless, the spread of disease agents, exacerbated by global trade and a changing climate, presents a huge challenge for modern agriculture [ 1 , 3 ].…”