Comparison of genetic variation of 3′UTR region of Beet black scorch virus in Khorasan isolates with the other isolates from Iran and the world

Document Type : Research Paper

Authors

1 Sugar Beet Research Department, Khorasan Razavi Agricultural and Natural Resources Research and Education Center, AREEO, Mashhad, Iran.

2 Associate Professor, Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran

3 Associate Professor, Sugar Beet Seed Institute, Agricultural Research, Education, and Extension Organization (AREEO), Karadj, Iran

Abstract

Beet black scorch virus is one of the soil-borne sugar beet viruses in Iran. In this research work, we collected 80 samples of sugar beet farms in Razavi and Northern Khorasan Provinces. After extraction of their total RNA, the 3'UTR region of the virus genome was amplified to 315 nucleotides using reverse transcription polymerase chain reaction using specific primers. The 3'UTR of six different isolates was sequenced following cloning and then submitted to NCBI. Phylogenetic analysis based on nucleotide sequences of the 3'UTR region showed that the entire world isolates could be classified into two main groups II and I and each one was divided into two subgroups. Isolates of this study were grouped with 23 isolates from Iran in subgroup IA and Four isolates from Khorasan province were placed in the IB subgroup. Four Iranian BBSV isolates from the West were grouped in the subgroup GIIA. All Chinese isolates and the European isolates together with the USA isolate clustered in subgroup GIIB. The results of nucleotide comparison of six isolates showed that although no mutation occurred at position 3477 (uridine instead of guanine), However, in position 3398, adenine replaced guanine (similar to 60% of Iranian isolates) and in position 3393, uridine was substituted for cytosine only in Fariman isolates (MW274750). The results of comparing the average nucleotide identity of 3'UTR isolates in this study showed that they are identical to Iranian isolates in the range from 97.75% to 97.98%. Nevertheless, they had the least identity with Kermanshah isolates (92.52%).

Keywords

References

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Iranian Journal of Plant Protection Science
Volume 52, Issue 2
February 2022
Pages 135-147

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History

  • Receive Date: 02 August 2020
  • Revise Date: 12 January 2021
  • Accept Date: 21 December 2021

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