First Report of TYLCV-IS141, a Tomato Yellow Leaf Curl Virus Recombinant Infecting Tomato Plants Carrying the Ty-1 Resistance Gene in Sardinia (Italy)

Abstract

HomePlant DiseaseVol. 103, No. 6First Report of TYLCV-IS141, a Tomato Yellow Leaf Curl Virus Recombinant Infecting Tomato Plants Carrying the Ty-1 Resistance Gene in Sardinia (Italy) PreviousNext DISEASE NOTES OPENOpen Access licenseFirst Report of TYLCV-IS141, a Tomato Yellow Leaf Curl Virus Recombinant Infecting Tomato Plants Carrying the Ty-1 Resistance Gene in Sardinia (Italy)M. Granier, L. Tomassoli, A. Manglli, M. Nannini, M. Peterschmitt, and C. UrbinoM. GranierCIRAD, UMR BGPI, F-34398 Montpellier, France; Search for more papers by this author, L. TomassoliConsiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca, Difesa e Certificazione CREA-DC, I00156 Rome, Italy; and Search for more papers by this author, A. ManglliConsiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca, Difesa e Certificazione CREA-DC, I00156 Rome, Italy; and Search for more papers by this author, M. NanniniAgris Sardegna, IT 09123 Cagliari, ItalySearch for more papers by this author, M. PeterschmittCIRAD, UMR BGPI, F-34398 Montpellier, France; Search for more papers by this author, and C. Urbino†Corresponding author: C. Urbino; E-mail Address: cica.urbino@cirad.frhttp://orcid.org/0000-0002-6215-9389CIRAD, UMR BGPI, F-34398 Montpellier, France; Search for more papers by this authorAffiliationsAuthors and Affiliations M. Granier1 L. Tomassoli2 A. Manglli2 M. Nannini3 M. Peterschmitt1 C. Urbino1 † 1CIRAD, UMR BGPI, F-34398 Montpellier, France; 2Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Centro di ricerca, Difesa e Certificazione CREA-DC, I00156 Rome, Italy; and 3Agris Sardegna, IT 09123 Cagliari, Italy Published Online:22 Mar 2019https://doi.org/10.1094/PDIS-09-18-1558-PDNAboutSections ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinked InRedditEmailWechat Tomato yellow leaf curl virus (TYLCV), tomato yellow leaf curl Sardinia virus (TYLCSV), and interspecies recombinants derived from them were detected in tomato (Solanum lycopersicum) in Italy (Panno et al. 2018). Cultivars carrying the Ty-1 gene are a key component in the control of tomato yellow leaf curl disease (TYLCD); Ty-1 prevents symptom expression and reduces virus accumulation. During a survey in September 2016 in Sardinia (Italy), symptomatic infections typical of TYLCD were observed on tomato plants of the resistant cultivar Parioli, in commercial greenhouses of the province of Cagliari, suggesting infection with TYLCV/TYLCSV recombinants (Belabess et al. 2015; Panno et al. 2018) or betasatellite (Conflon et al. 2018), which were both associated with the break of Ty-1 resistance. Total DNA was extracted from leaf samples of three symptomatic and one nonsymptomatic plants collected in a single greenhouse. Using polymerase chain reaction (PCR) tests, all four samples were positive for the presence of the Ty-1 gene at the heterozygous state (Verlaan et al. 2011) but negative for the presence of betasatellite DNA (Briddon et al. 2002). According to multiplex PCR tests (Belabess et al. 2015), the nonsymptomatic sample was negative for the detection of TYLCV, TYLCSV, and TYLCV/TYLCSV recombinants; one symptomatic sample was positive for all three types of genomes, and the other two were positive for TYLCSV and TYLCV/TYLCSV recombinants. These latter two DNA extracts were used in rolling circle amplification (RCA). To select recombinant genomes for cloning, the RCA product was digested with SacI, because this restriction site is unique in TYLCV and absent in TYLCSV genomes. A 2.8-kb restricted fragment was cloned in the SacI-linearized plasmid pBC, and three clones, obtained from the two DNA extracts, were sequenced. The three sequenced genomes had 2,773 nucleotides (nt) and shared 99% identity to each other. Like TYLCV-IL-[IT:Sic23:16], a TYLCV/TYLCSV recombinant recently detected from Ty-1 resistant plants sampled in Sicily in 2016 (Panno et al. 2018), the Sardinian genomes were composed mostly of a TYLCV-IL sequence, except 124 nt (nt 16 to 139) between the origin or replication and the ATG codon of the V2 gene, which were derived from TYLCSV. The highest nt identity of the TYLCSV sequence was detected with a TYLCSV isolate from Sicily, accession no. Z28390 (92%), and that of the TYLCV sequence was detected with TYLCV-IL-[IT:Sic:04], DQ144621 (98%). Because the sequence identity of Sardinian and Sicilian recombinants was higher than 94% (97.6%), they were considered to belong to the same group of TYLCV-IL isolates previously named TYLCV-IS141 (Belabess et al. 2018). For the sake of clarity, we propose to give this name to all recombinants with the same recombination event. Thus, the sequence deposited to GenBank (MH817479) was called TYLCV-IS141 (TYLCV-IL-[IT:Sar IS141:16]). Because this recombinant was detected in coinfection with TYLCSV or TYLCV, it cannot be stated that it caused TYLCD symptoms on resistant plants. Moreover, these symptoms were not observed during the following year. However, TYLCV-IS141 recombinants were already detected from plants collected in 2012 and 2016 in Sicily (Belabess et al. 2015, 2018; Panno et al. 2018), and it was found to be positively selected in Ty-1 resistant plants (Belabess et al. 2018). Further samplings are needed to estimate the prevalence of TYLCV-IS141 recombinants in Sardinia and Sicily and to test their fitness in Ty-1 resistant plants.The author(s) declare no conflict of interest.