Multilocus Genotyping of ‘Candidatus Phytoplasma Solani’ Associated with Grapevine Bois Noir in Iran

SIMPLE SUMMARY: Understanding the epidemiological cycle of Bois noir (BN) associated with ‘Candidatus Phytoplasma solani’ is vital to managing the disease effectively. The genotyping of ‘Ca. P. solani’ strains, according to tuf, vmp1, and stamp genes, contributes to a better knowledge of the geographical distribution of BN. In this study, we provide information on the molecular variants of ‘Ca. P. solani’ in Iranian vineyards. We observed six known vmp1 variants and discovered two new ones, V24 and V27. This information is useful for future investigations to more accurately understand the epidemiological cycle(s) of BN in Iranian vineyards, contributing to the management of the disease. ABSTRACT: Grapevine Bois noir (BN) is associated with ‘Candidatus Phytoplasma solani’. It has been recorded in vineyards throughout Europe as well as in different countries in Asia, where it now constitutes a threat to Iranian viticulture. BN is strictly dependent on ‘Ca. P. solani’ strains, wild host plants, and insect vectors. The molecular typing of ‘Ca. P. solani’, based on the nonribosomal gene tuf and the two hypervariable markers vmp1 and stamp, is valuable for the reconstruction and clarification of the pathways of BN spread. In this study, an RFLP analysis was performed on the vmp1 gene, and a single-nucleotide polymorphism analysis confirmed new vmp types in ‘Ca. P. solani’. A stamp gene phylogenetic analysis allowed us to distinguish between the new genotype infections in the grapevines and the ‘weeds’ Convolvulus arvensis and Erigeron bonariensis in Iranian vineyards, highlighting the close genetic relatedness of the strains of ‘Ca. P. solani’ found in Iran and Azerbaijan. The most common genotype in the grapevines was tuf b/V24/stamp III, which was associated with C. arvensis. This information contributes toward the identification of further routes of introduction of ‘Ca. P. solani’ in Iran to sustain the control measures for the management of BN.