Genome-wide Investigation of Genetic Diversity in the Poultry Red Mite, Dermanyssus Gallinae, From European Farms Utilising a NGS-Multiplex Platform

The poultry red mite ( Dermanyssus gallinae ), an obligatory blood feeding ectoparasite, is primarily associated with egg laying hens where it is estimated to cause losses of ~€230 million per annum from European farmers. Current control strategies, including the use of acaricidal chemicals and desiccant dusts, are often ineffective and there is widespread resistance to acaricides across Europe. Alternative methods to control D. gallinae are urgently required and strategies include development of recombinant subunit vaccines and discovery of new potential acaricides. These strategies will benefit hugely from knowledge of the extent and rates of occurrence of genetic diversity within D. gallinae populations. In this study, genetic diversity of mites harvested from the UK and from sites across mainland Europe was studied at inter- and intra-farm levels. To achieve this, the genome analysis toolkit (GATK) best practices pipeline for single nucleotide polymorphism (SNP) and insertion/deletion variant calling was modified to be self-validating and used to identify 32,599 D. gallinae SNPs by comparing transcriptomic sequences (derived from mites harvested in Germany, Schicht et al.) with a D. gallinae genome assembly (derived from mites harvested in Scotland, Burgess et al.). Dermanyssus gallinae populations were sampled from 22 UK farms and 57 farms from 15 countries in mainland Europe. Analysis of 144 high-quality SNP markers across 117 pooled D. gallinae samples showed high spatial genetic diversity with significant linkage disequilibrium. Revisiting a subset of farms revealed notable temporal changes in genetic diversity.