Detection and characterization of viroids causing diseases in peach and nectarine production areas in Adana-Mersin provinces by molecular methods

This thesis was conducted with the aim of detecting viroids in the peach and nectarine production areas of Adana and Mersin provinces using molecular methods, identifying the detected viroid agents, and revealing the biological characteristics and pathogenic effects of these viroids. During the surveys conducted between 2022 and 2024, a total of 190 samples were collected, with 92 from Adana (53 nectarine, 39 peach) and 98 from Mersin (90 nectarine, 8 peach), which were used in the thesis. The presence of Peach latent mosaic viroid (Pelamoviroid latenspruni, PLMVd) was detected in 23 samples using RT-PCR and RT-qPCR tests, while no Hop stunt viroid (Hostuviroid impedihumuli, HSVd) was detected in any of the samples. According to the RT-PCR results, a 339 bp band was obtained for PLMVd, and the infection rate in nectarine samples from Adana was 18.87%, in peach samples 10.26%, while in Mersin, the infection rate was 6.67% in nectarine samples and 37.5% in peach samples. Overall, the infection rate of PLMVd in the collected samples was calculated to be 12.11%. In some selected infected samples, the distribution of PLMVd in different plant tissues (root, leaf, shoot, flower, fruit) was investigated, and it was found to be more concentrated in shoot and leaf tissues. Additionally, in order to examine the distribution of PLMVd in trees, positive results were obtained from leaf samples collected from four different directions (north, south, east, west) of selected infected peach (Ufo-flattened peach) and nectarine (Patagonia) trees, which were subjected to RT-PCR. According to Real-Time PCR results, the PLMVd concentration varied between the samples. Phylogenetic analyses revealed that the full genome PLMVd isolates sequenced from Adana and Mersin provinces showed 88%-91% genetic similarity with other PLMVd isolates worldwide selected from the GenBank. Secondary structure analyses conducted with selected PLMVd isolates showed that the RNA structure had a hammerhead-like (hammerhead) and highly branched structure, and these structures were similar to international references. In each of these structures, one hammerhead structure and a total of 11 loops and 11 pseudoknots were found. Additionally, conserved 4-bp nucleotide sequences were observed in the hammerhead structure, and it was observed that an HHH (kissing hairpin) type 8th pseudoknot could be formed. In biological diagnosis studies, symptoms such as mosaic, albinism, chlorosis, deformation, wrinkling, curling, and narrowing of leaves were observed on the leaves of the test plants (Prunus persica GF-677 and Prunus persica Garnem), and the presence of the detected PLMVd agent was also confirmed biologically.