Identification of tandem repeats loci for prospective Xylella fastidiosa subsp. pauca genotyping

Abstract: Olive Quick Decline Syndrome (OQDS) by Xylella fastidiosa subsp. pauca is one of the most alarming epidemic bacterial outbreak in the world. It has started in the Apulia region in 2013 but, despite huge efforts in control the pathogen, it has continued to spread and could theoretically affect olive grows not only in Mediterranean area, but wherever suitable environmental conditions exist. This research is aimed to develop a molecular tool suitable not only to diagnose the disease, but also effective in providing information about the origin of the pathogen, its population dynamics and diffusion pathways. This aim has been approached by VNTR (Variable Number of Tandem Repeats) analysis, a very sensitive method for bacterial genotyping, which is also rapid, cost-effective, and highly repeatable. It is worth pointing out that this method has formerly proven effective on different X. fastidiosa subspecies and on different host plants. Firstly, the already published TRs were tested in silico on the genome of X. fastidiosa subsp. pauca strain De Donno. In addition, new TR loci were identified and related primers were designed. All the potential TR loci were then amplified on the DNA of few isolates from the Italian outbreak. The preliminary genotyping results obtained are encouraging, and the prospective value of the assay in tracing OQDS strains is discussed.