Developing multiplex assays for crayfish detection using eDNA and ddPCR

The use of environmental DNA (eDNA) for crayfish detection has increased worldwide. The number of projects and publications significant rise with the use of techniques such as PCR, qPCR and ddPCR, as well as the increasing use of next-generation sequencing technologies like Nanopore and Illumina. The choice of technology and tools is influenced mainly by research objectives, researcher expertise and available funding. At INBO, we aim to develop an eDNA-based monitoring system for the detection of nine crayfish species in Belgium. Our approach begins with and in-silico study using sequences and primers available in the literature. Subsequently, new sequences will be generated for the target individuals to design specific-target primers and probes. These primers will be tested individually and in combination, culminating in a multiplex assay in a ddPCR for crayfish detection from environmental samples.