Resistance-Breaking Tomato Spotted Wilt Virus Variant that Recently Occurred in Pepper in South Korea is a Genetic Reassortant

Tomato spotted wilt virus (TSWV) is a destructive viral pathogen in various crops, including pepper. Although the single dominant gene Tsw has been utilized in pepper breeding to confer resistance to TSWV, the occurrence of TSWV variants that overcome Tsw-mediated resistance has been reported in various countries after several years of growing resistant cultivars. In this study, we determined the complete genome sequence of a resistance-breaking TSWV variant (TSWV-YI) that recently emerged in pepper in South Korea. TSWV-YI infected all of the resistant pepper cultivars tested. The phylogenetic and recombination analyses of the complete TSWV-YI genome sequence showed that it is a reassortant that acquired its L and M RNA segments from the existing South Korean TSWV population and its S RNA in an isolate from another country. Given that TSWV-YI is a resistance-breaking variant, it appears that reassortment of the S RNA led to the emergence of this variant that breaks the Tsw gene in pepper grown in South Korea. Our results suggest that resistance-breaking TSWV variants are a potential threat to pepper production in South Korea and that strategies to manage these variants should be developed to ensure sustainable pepper production.

Automated summary

This study identified a breakthrough TSWV variant (TSWV-YI) in pepper crops in South Korea, with phylogenetic and recombination analyses showing it to be a reassortant variant incorporating RNA segments from both local and foreign sources. The emergence of TSWV-YI, which infected previously resistant pepper cultivars, highlights the potential threat of resistance-breaking variants to sustainable pepper production in South Korea, necessitating the development of management strategies.