Identification and molecular characterization of some virus and viroid diseases in walnut and pistachio trees in the Southeastern Anatolia Region

Surveys were conducted in walnut and pistachio plantations in the Southeastern Anatolia Region in 2021–2022 for this thesis study. 230 walnut and 649 pistachio samples were collected as a result of these surveys; the provinces of Şanlıurfa provided 283 and 29 walnut samples, Diyarbakır provided 78 and 133 walnut samples, Siirt provided 185 and 18 walnut samples, and Batman provided 103 and 50 walnut samples. Real-Time RT-PCR analysis was used to investigate the presence of Cherry leaf roll nepovirus (CLRV), Plum pox potyvirus (PPV), Peach latent mosaic pelamoviroid (PLMVd), and Hop stunt hostuviroid (HSVd) in the collected pistachio samples and Pistacia emaravirus B (PiVB) in the walnut samples. Real-Time RT-PCR tests revealed that of 649 pistachio samples, 14.7% had HSVd and 5.4% had PLMVd infection. Furthermore, mixed infections of PLMVd and HSVd were present in 0.9% of the samples. PiVB was not detected in any of the tested samples. Among the 230 walnut samples examined, 11.3% had HSVd, 12.6% had PPV, 42.2% had CLRV, and 5.7% had PLMVd. Additionally, 7.8% of the samples had PPV+CLRV, 1.3% had PPV+HSVd, and 0.4% had mixed infections with PPV+PLMVd, 1.3% had HSVd+PLMVd, 2.2% had HSVd+CLRV, 2.2% had PLMVd+CLRV, and 0.4% had HSVd+CLRV+PLMVd factors. Molecular characterization studies were carried out by randomly cloning one PLMVd, HSVd, CLRV, and PPV isolate from the isolates detected as single infections in each province. Nucleic acid sequences from the isolates revealed similarities with other isolates found worldwide, with rates ranging from 89.5–100% for HSVd isolates, 87.1–98.6% for CLRV isolates, and 91.4–99.3% for PPV isolates. These similarities were found in the isolates from which nucleic acid sequences were obtained. This study reports the first-ever detection of PLMVd in pistachios and HSVd in walnuts. Molecular evidence for PPV was discovered in walnuts for the first time ever.