Molecular characterisation of Alfalfa mosaic virus isolates in potato from the Tokat province, Türkiye

Abstract

The Alfalfa mosaic virus (AMV) was detected in potato fields in the Tokat province. The coat protein (CP) sequences of AMV isolates from the Tokat province were determined and compared with sequences of reference AMV isolates from GenBank. Total nucleic acid (TNA) was extracted from plants with positive results according to serological test results. Then, reverse-transcription polymerase chain reaction (RT-PCR) was performed using primer pair specific to partial the coat protein region, and positive PCR products were sent for sequence analysis in both directions. Two Turkish AMV isolates (AMV-PN3-5 and AMV-PN3-6) had a 96-99% nt homology amongst themselves, according to nucleotides (nt) sequence analysis. Based on the phylogenetic tree obtained from 24 AMV isolates from GenBank for both sequences, the two Turkish AMV isolates were clustered in subgroup I containing Iranian, Canadian, Turkish, Korean, and Serbian isolates, at the nucleotide level. Sequence comparison showed that these two isolates of AMV shared 96% to 99.7% sequence similarity with the twenty-six reported isolates of AMV obtained from GenBank. This is the first report on the genetic variability of AMV isolates infecting potato crops in the Tokat province.

Coat protein of alfalfa mosaic alfamovirus (AMV) from Türkiye: genetic inference and in silico docking analysis for potential antiphytoviral purposes

“…The phylogenetic tree related these isolates to other Turkish isolates from Van and Iğdır provinces with 3 major groups (Güller et al, 2022). Topkaya (2022) reported the presence of AMV by PCR amplification based on the CP gene from potato plants in the Tokat province, Türkiye. The two sequences (700 bp) obtained showed phylogenetic affinity in subgroup I, consisting of isolates from Iran, Canada, Türkiye, Korea, and Serbia.…”

“…AMV-infected pepper plants were reported in Samsun by Arli-Sökmen et al (2005), in Adana by Çetinkıran and Baloğlu (2011), and in Kahramanmaraş by Demir (2005). In addition, the presence of AMV in Türkiye was molecularly shown with RT-PCR in parsley in Konya , potato in Tokat (Topkaya, 2022), and alfalfa in Bingöl and Van (Usta and Güller, 2020;Güller et al, 2022). AMV was also reported in the provinces of Manisa, Balıkesir, and Burdur from different plant origins Kılıç and Yardımcı, 2015).…”