Diversity of plum pox virus in plum orchards in Serbia

BGPI : équipe 6 European Community’s Seven Framework Programme (FP7/2007-2013) under Grant Agreement n°204429 SharCo project and project TR-31064 from the Serbian Ministry of Education and ScienceInternational audienceSerbia is a leading plum producing country in Europe with more than 41 million of bearing trees . For almost 80 years, Plum pox virus (PPV) is a threat for the stone fruit production in Serbia. So far, three major out of seven strains were reported: PPV-M, PPV-D and PPV-Rec. Material for this study was collected during three year period (2008-2010). A total number of 265 samples were collected from 84 plum orchards in 12 Serbian districts. Two to four trees showing clear sharka symptoms were randomly chosen and sampled from each orchard. Strain-typing was performed by IC-RT-PCR method with PPV-M and PPV-D specific primers targeting two genomic regions of PPV. Additionally, 39 isolates from different locations were selected for sequencing fragments located in C-tеr NIb―N-tеr CP part of CP region and C-ter P3-6K1-N- ter CI region. The most prevalent strain in analyzed samples was PPV-Rec (53.5%), followed by PPV-D (27.9%) and PPV-M (5.4%). Mixed infections were found in 13.2% of samples. All types of mixed infections were detected: PPV-M+PPV-D, PPV-M+PPV-Rec and PPV-D+PPV-Rec. The highest incidence among mixed infections was PPV-D+PPV-Rec combination - 67.6%. For the first time, natural triple infection was confirmed in one sample (PPV-M+PPV-D+PPV-Rec). In 37 orchards only one PPV strain was found; in 42 orchards two strains and all three strains were detected in 5 orchards. The most prevalent strain was PPV-Rec that was found in 69 orchards (in single and mixed infections) in all districts. On the contrary, PPV-M strain was found only in 15 orchards. Obtained results confirmed earlier assumption on the long term presence of PPV-Rec strain on plum in Serbia. Phylogenetic analysis of selected isolates confirmed strain-typing results. Further analysis showed the absence of geographical genetic differentiation of isolates that suggest the intensive gene flow between districts through contaminated planting material in the past