Genetic diversity of Raspberry leaf blotch emaravirus in red raspberries from Serbia

Darko Jevremović, Aleksandar Leposavić, Svetlana A Paunović

Abstract


Raspberry leaf blotch emaravirus (RLBV) is a recently characterised virus infecting raspberries reported in several European countries. RLBV causes yellow blotching, the distortion of leaf margins, and the twisting of raspberry leaves. For a long time, similar symptoms were attributed to the feeding damage caused by raspberry leaf and bud mite (Phyllocoptes gracilis). From 2014−2017, a large-scale survey was conducted in Serbia to investigate the degree of association of the observed symptoms with the RLBV infection. A total of 98 symptomatic and asymptomatic samples were collected from 30 locations. All collected samples were tested on the RLBV presence by reverse transcription and polymerase chain reaction (RT-PCR) using three sets of RNA-specific primers targeting RNA-1, RNA-3, and RNA-5 of the RLBV genome. RT-PCR analysis revealed high incidence of RLBV in tested samples (68.7%). RLBV was confirmed in raspberries ‘Fertödi Zamatos’, ‘Glen Ample’, ‘Meeker’, ‘Polana’, ‘Tulameen’ and ‘Willamette’. Twenty-one isolates were selected for sequencing the portion of the nucleocapsid (NC) gene. The nucleotide sequences of the isolates showed 93.2−100% identity. Phylogenetic analysis confirmed significant genetic variability of the Serbian RLBV isolates based on the nucleocapsid-encoding sequences and revealed the existence of two main clusters. Phylogenetic analysis of the 45 RLBV sequences from Finland, Slovakia, Scotland, and this study also confirmed the existence of two main clusters of isolates.


Keywords


Rubus idaeus L.; RLBV; RT-PCR; molecular diversity, phylogenetic analysis

Full Text:

PDF HTML XML

References


Dobrivojević K, Petanović R, 1985. Eriophyd raspberry leaf mite, Phyllocoptes gracilis (Nal.) (Eriophyoidea, Acarina), an insufficiently known pest in Yugoslavia. Zaštita Bilja 36 (3): 254-260.

Dong L, Lemmetty A, Latvala S, Samuilova O, Valkonen JPT, 2016. Occurrence and genetic diversity of Raspberry leaf blotch virus (RLBV) infecting cultivated and wild Rubus species in Finland. Ann Appl Biol 168 (1): 122-132. https://doi.org/10.1111/aab.12247

Dulić-Marković I, Ranković M, 1997. Virusne bolesti maline u Jugoslaviji. Jugoslovensko Voćarstvo 31 (119/120): 253-257.

Gratwick M, 1992. Raspberry leaf and bud mite. In: Crop pests in the UK; Gratwick M (ed.), pp: 350-353. Springer, Netherlands. https://doi.org/10.1007/978-94-011-1490-5_70

Hall TA, 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser (Oxf) 41: 95-98.

Jevremović D, Leposavić A, Paunović AS, 2016. Raspberry leaf blotch virus - A common raspberry pathogen in Serbia. J Mt Agric Balk 19 (3): 147-156.

Kumar S, Stecher G, Tamura K, 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33 (7): 1870-1874. https://doi.org/10.1093/molbev/msw054

Kumar S, Subbarao BL, Hallan V, 2017. Molecular characterisation of emaraviruses associated with Pigeonpea sterility mosaic disease. Scientific Reports 7: 11831. https://doi.org/10.1038/s41598-017-11958-8

Li R, Mock R, Huang Q, Abad J, Hartung J, Kinard G, 2008. A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. J Virol Methods 154 (1): 48-55. https://doi.org/10.1016/j.jviromet.2008.09.008

Lu Y, McGavin W, Cock PJA, Schnettler E, Yan F, Chen J, MacFarlane S, 2015. Newly identified RNAs of raspberry leaf blotch virus encoding a related group of proteins. J Gen Vir 96 (11): 3432-3439. https://doi.org/10.1099/jgv.0.000277

Martin RR, MacFarlane S, Sabanadzovic S, Quito D, Poudel B, Tzanetakis IE, 2013. Viruses and virus diseases of Rubus. Plant Dis 97 (2): 168-182. https://doi.org/10.1094/PDIS-04-12-0362-FE

McGavin WJ, Mitchell C, Cock PJ, Wright KM, MacFarlane SA, 2012. Raspberry leaf blotch virus, a putative new member of the genus Emaravirus, encodes a novel genomic RNA. J Gen Virol 93 (2): 430-437. https://doi.org/10.1099/vir.0.037937-0

Milenković S, Marčić D, 2011. Raspberry leaf and bud mite (Phyllocoptes gracilis) in Serbia: the pest status and control options. Acta Hortic 946: 253-256. https://doi.org/10.17660/ActaHortic.2012.946.40

OEPP/EPPO, 2009. PM 4/10(2): Certification scheme for Rubus. EPPO Bull 39 (3): 271-277. https://doi.org/10.1111/j.1365-2338.2009.02308.x

Petrović S, Leposavić A, Jevremović D, 2017. Raspberry - The management, processing and marketing. Sci Pomol Soc of Serbia, Čačak. 258 pp.




DOI: 10.5424/sjar/2019171-13861