Fougere Gregory C, Xu Dong, Gaiero Jonathan R, McCreary Cara, Marchand Geneviève, Despres Charles, Wang Aiming, Fall Mamadou Lamine, Griffiths Jonathan S
London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada.
Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada.
Viruses. 2025 May 12;17(5):696. doi: 10.3390/v17050696.
Tomato brown rugose fruit virus (ToBRFV) is a recently emerged viral pathogen in the genus first observed in 2014 in the Middle East that has since spread worldwide, causing significant losses in greenhouse tomato production. ToBRFV is easily mechanically transmitted and can escape the durable resistance gene, facilitating its global spread. Seed companies have identified novel sources of resistance and introduced these resistance traits into commercial cultivars. The identity, number, and mechanisms of these putative novel resistance genes are largely unknown but could be exerting selective pressures on ToBRFV. Here, we report 15 new ToBRFV genomic sequences from Canadian greenhouse production systems in susceptible and novel resistant or tolerant cultivars collected since 2023. We combined these sequences with five other Canadian ToBRFV genomes previously deposited in Genbank and a further five consensus sequences derived from metagenomic-based wastewater monitoring sequence data and conducted phylogenetic analysis. Most Canadian sequences grouped together when compared with 332 publicly available international sequences, but several isolates appeared distantly related, suggesting multiple introductions to Canadian production systems. High sequence identity between samples suggest movement of ToBRFV between independent greenhouses, highlighting areas where biosecurity can be improved. Several novel non-synonymous polymorphisms identified in the p126 and movement protein (MP) open reading frames (ORFs) were unique to Canadian sequences and associated with infection of novel resistant tomato cultivars. Many polymorphisms in the p126 ORF are located in a region of the protein associated with resistance-breaking isolates of tomato mosaic virus and ToBRFV, but have not been previously reported. Four novel polymorphisms in MP were also identified and do not appear to be associated with sites previously identified as interacting with and could be related to other unknown resistance genes. Together, these results confirm the difficulties in preventing the transmission of ToBRFV, identify putative adaptations to novel and existing resistance genes, and emphasize the urgent need for the cloning and characterization of these new sources of resistance to ToBRFV.
番茄褐色皱纹果病毒（ToBRFV）是该属中一种最近出现的病毒病原体，2014年首次在中东被发现，此后已传播到全球，给温室番茄生产造成重大损失。ToBRFV易于通过机械传播，并且能够避开持久的抗性基因，这促进了它在全球的传播。种子公司已经鉴定出新型抗性来源，并将这些抗性性状引入商业栽培品种中。这些假定的新型抗性基因的身份、数量和作用机制在很大程度上尚不清楚，但可能正在对ToBRFV施加选择压力。在此，我们报告了自2023年以来从加拿大温室生产系统中收集的、来自易感以及新型抗性或耐性品种的15条新的ToBRFV基因组序列。我们将这些序列与之前保存在Genbank中的另外5个加拿大ToBRFV基因组以及另外5条源自基于宏基因组的废水监测序列数据的共有序列相结合，并进行了系统发育分析。与332条公开可用的国际序列相比，大多数加拿大序列聚集在一起，但有几个分离株似乎关系较远，这表明ToBRFV多次传入加拿大生产系统。样本之间的高序列同一性表明ToBRFV在独立温室之间传播，突出了生物安全可以改进的领域。在p126和运动蛋白（MP）开放阅读框（ORF）中鉴定出的几个新型非同义多态性是加拿大序列所特有的，并且与新型抗性番茄品种的感染有关。p126 ORF中的许多多态性位于与番茄花叶病毒和ToBRFV的抗性突破分离株相关的蛋白质区域，但此前尚未见报道。还鉴定出MP中的4个新型多态性，似乎与先前确定为与……相互作用的位点无关，可能与其他未知抗性基因有关。总之，这些结果证实了预防ToBRFV传播的困难，确定了对新型和现有抗性基因的假定适应性，并强调了迫切需要克隆和表征这些新的ToBRFV抗性来源。
