Abstracts (first author)
Unlocking poor quality Daphnia samples by SNP genotyping
In order to track temporal-evolutionary changes in the plakton communities, as an important issue remains the proper identification of species and their hybrids. For the analyses of Daphnia longispina complex, microsatellie genotyping is a commonly used method. However, we found these length-based markers unsuitable when analyzing poor quality samples. Therefore the historical, formaldehyde preserved samples remain inaccessible. To overcome this problem, we propose SNP based genotyping, due to possibility of shorter fragment amplification. Furthermore, this method allows not only high-throughput genotyping, but the calibration among laboratories is also relatively precise. Therefore, we aim to develop a reliable method to identify species of the D. longispina complex and their hybrids by SNP genotyping. By comparing the transcriptome of D. galeata with D. pulex genome (wfleabase.org) we are identifying genes and their chromosomal location in order to obtain multi-loci markers, and corresponding primers are then being designed. After the sequencing and alignment of these genes for each species in the complex (D. cucullata, D. galeata and D. longispina), candidate SNPs are being identified. For the small scale confirmation of the diagnostic value of these candidate SNPs, we are sequencing a set of genetically well-defined clones from species and hybrids originating from diverse locations across Europe. For the large-scale screenings we are optimizing multiplex PCR reaction of short amplicons and SNP detection via SnaPshot Multiplex kit. To validate the results, we are applying the developed assay for the samples, which were previously analyzed with microsatellite markers. By multi-locus SNP genotyping we will be able to assess the population structures in long-term formaldehyde preserved samples of a hybridizing species complex.