Evolutionary Changes in Tomato Yellow Leaf Curl Virus Associated with Widespread Ty-1 Use in Japan

Tomato yellow leaf curl virus (TYLCV) is a major global threat to tomato production. In Japan, TYLCV Israel (IL) and Mild (Mld) strains have predominated since 1996, and resistance breeding has relied extensively on Ty-1. To assess whether long-term deployment of Ty-1 has shaped viral evolution, we conducted the first nationwide, multiyear survey of TYLCV diversity in Japan. From 2022 to 2025, 294 symptomatic samples were collected from 13 prefectures, of which 203 tested positive for TYLCV. Phylogenetic analyses of 182 partial TYLCV sequences revealed that although most isolates clustered within the canonical IL or Mld strains, distinct noncanonical Mld isolates have emerged and persisted regionally. Full-length genome sequencing showed that representative noncanonical isolates (Rec71 and Rec103) are recombinants between TYLCV-Mld and honeysuckle yellow vein virus, with recombination breakpoints in the intergenic region and replication-associated genes. Virus infectious clone assays demonstrated that Rec103 is highly virulent (equivalent to IS76-like isolate) and Ty-1-mediated resistance is only partially effective. In contrast, Ty-2 effectively conferred resistance against Rec103, despite its putative major parent, TYLCV-Mld, being known to overcome Ty-2 resistance. Given the widespread cultivation of Ty-1-bearing varieties in Japan, these findings provide evidence of host resistance-driven viral adaptation. Collectively, our results reveal ongoing TYLCV evolution under host genetic selection and highlight the evolutionary risks of relying on a single resistance gene, underscoring the importance of diversified, strategically deployed resistance sources for durable, robust disease management. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.