Study of Potato Virus Y Isolates Commonly Occurring in Different Regions of the Russian Federation Using New Molecular Markers

Abstract

The paper reports the study which was carried out to investigate the genetic polymorphism of potato virus Y isolates using new marker sequences. The work was performed in 2022–2023. PVY isolates collected in 2017 from domestic and foreign varieties grown in different regions of the Russian Federation and preselected for serotype were used for analysis. Three loci were selected as potential markers with high phylogenetic information content, namely, the coat protein gene (Cp), the 5'-untranslated region of NTR, and the VPg protein gene, which covalently binds to the 5'-end of RNA and acts as a transcription regulator. Highest amplification efficiency (100% of the cDNA samples tested) was achieved using the NTR fragment. It was also the most phylogenetically informative: a comparative analysis of the studied sequences showed the presence of 23.8 and 15% variable and phylogenetically informative positions, respectively. The phylogenetic tree constructed on the basis of the comparative analysis of the NTR marker sequences included several clusters supported by high bootstrap values. The clusters encompassed the isolates from the following subgroups: PVY^NTN—Red Scarlett (III), Red Scarlett (5-4), and Dunya (7-12); PVY^N:O—Pomdor, Zagadka, and Nida; PVY^O/C—Picasso, Favorit (III), CH991 131 (8-2), Floris (7-14), and Romano (5-3), and PVY^Wilga—Red Scarlett (6-10) and Kenza, as well as the type strains belonging to these subgroups, the marker sequences of which being deposited in the NCBI database. An isolate from the potato variety Zhukovsky rannii (5-2) showed an intermediate position between the necrotic and ordinal clusters, forming a separate branch and not grouping with any of the type strains on the phylogenetic tree based on the marker nucleotide sequences of the NTR locus. Sequencing analysis generally confirmed the initial serological identification of the tested samples demonstrating the predominance of the necrotic and recombinant groups of strains.