Development of genetic markers to facilitate genetic studies in the Lyme disease tick, Ixodes scapularis (Acari: Ixodidae)

Ixodes scapularisis the arthropod vector of the Borrelia burgdorferi bacterium, the causative agent of Lyme Disease (LD). There are 24,000 new cases of LD reported each year. LD can be successfully treated if caught early, but there are no effective treatments for later stages of LD. The I. scapularis genome has been sequenced and assembled in an attempt to identify new approaches to control this tick. Ixodes genome assembly is extremely fragmented due in part by the high level of polymorphism present in the tick colony that was used to sequence the genome. We are developing a range of genetic markers as an approach to construct a genetic map for Ixodes and as tools to study population structures of this tick in the US. We used eTRA (Exact Tandem Repeats Analyzer) software to analyze 367,000 Ixodes BAC end sequences for microsatellite repeats. More than 240,000 microsatellites were identified from 152,000 BAC end sequences and are being tested on Ixodes for polymorphism. The POLYBAYES program was used to analyze single nucleotide polymorphisms (SNPs) in ESTs aligned to assembled Ixodes scaffolds. To date, we have identified 874 SNPs from 108 tentative consensus sequences (TCs). Current efforts are focused on establishing the suitability of SNP markers associated with genes that may play a role in tick-host-pathogen interactions. In future work, we will use our collection of genetic markers to resolve population structures of Ixodes in the upper Midwest and East coast and to perform association mapping to identify genes associated with tick-Borrelia competence.