Incidence and genetic diversity of raspberry bushy dwarf virus ( RBDV ) in Rubus spp. in Turkey

• Published in: Annals of applied biology Vol. 183; no. 3; pp. 209 - 219
• Main Authors: Çağlayan, Kadriye, Ördek, Kivilcim, Gazel, Mona, Elçi, Eminur, Roumi, Vahid, Lamovšek, Janja, Mavrič Pleško, Irena
• Format: Journal Article
• Language: English
• Published: Oxford Wiley Subscription Services, Inc 01.11.2023
• Subjects: Coat protein; Comparative analysis; Dwarf disease; Fruits; Gene sequencing; Genetic diversity; Genetic variance; Genomes; Idaeovirus rubi; Movement protein; Nucleotide sequence; Nucleotides; Phylogeny; Plant virus diseases; Plant viruses; Proteins; Ribonucleic acid; RNA; Rubus; Viruses; Turkey
• ISSN: 0003-4746; 1744-7348
• DOI: 10.1111/aab.12847

Abstract Raspberry bushy dwarf virus (RBDV), recently renamed to Idaeovirus rubi , is one of the most common viruses infecting Rubus species worldwide but there is still a limited number of genome sequences available in the GenBank database and the majority of the sequences include partial sequences of RNA‐1 and RNA‐2. The distribution and incidence of RBDV in main raspberry and blackberry growing provinces in Turkey were monitored during 2015–2019 and 537 Rubus spp. samples were tested by both DAS‐ELISA and RT‐PCR. Among the tested samples, 36 samples tested positive for RBDV by DAS‐ELISA and 67 samples by RT‐PCR. There was relatively low nucleotide diversity among the Turkish isolates. Turkish isolates shared 93%–97.7%, 84.3%–98.9%, and 85%–99.2% nucleotide sequence identities with available sequences in the GenBank, in partial RNA‐1, movement protein (MP) and coat protein (CP) genes, respectively. In the phylogenetic tree constructed for RNA‐1, MP, and CP sequences, all Turkish raspberry isolates were clustered in a distinct clade. However, the blackberry isolates showed considerable variation in nucleotide sequences and were placed in three distinct groups. The divergent blackberry isolates showed high variability in MP (84.5%–89.3%) and CP (85.5%–89.7%) regions and were placed in a distinct group. The rest of blackberry isolates clustered together with sweet cherry RBDV isolates adjacent to the grapevine clade or together with raspberry isolates. The comparative analysis conducted on three RNA segments of RBDV highlighted the high sequence diversity of Turkish RBDV isolates. This study also emphasizes the importance of regular monitoring of RBDV infections in Turkey, with special regard to those Rubus spp. and grapevine accessions employed in conservation and selection programmes. In particular, the presence of new RBDV genetic variants and infection of Rubus species must be taken into account to choose a correct detection protocol and management strategy.