A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna

Background: Recombination rate is an essential parameter for many genetic analyses. Recombination rates are highly variable across species, populations, individuals and different genomic regions. Due to the profound influence that recombination can have on intraspecific diversity and interspecific divergence, characterization of recombination rate variation emerges as a key resource for population genomic studies and emphasises the importance of high-density genetic maps as tools for studying genome biology. Here we present such a high-density genetic map for Daphnia magna, and analyse patterns of recombination rate across the genome. Results: A F2 intercross panel was genotyped by Restriction-site Associated DNA sequencing to construct the third-generation linkage map of D. magna. The resulting high-density map included 4037 markers covering 813 scaffolds and contigs that sum up to 77 % of the currently available genome draft sequence (v2.4) and 55 % of the estimated genome size (238 Mb). Total genetic length of the map presented here is 1614.5 cM and the genome-wide recombination rate is estimated to 6.78 cM/Mb. Merging genetic and physical information we consistently found that recombination rate estimates are high towards the peripheral parts of the chromosomes, while chromosome centres, harbouring centromeres in D. magna, show very low recombination rate estimates. Conclusions: Due to its high-density, the third-generation linkage map for D. magna can be coupled with the draft genome assembly, providing an essential tool for genome investigation in this model organism. Thus, our linkage map can be used for the on-going improvements of the genome assembly, but more importantly, it has enabled us to characterize variation in recombination rate across the genome of D. magna for the first time. These new insights can provide a valuable assistance in future studies of the genome evolution, mapping of quantitative traits and population genetic studies.Science, Faculty ofOther UBCNon UBCZoology, Department ofReviewedFacult

Additional file 1: Figure S1. of A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna

A flow chart of the genetic map construction process. For a detailed description, see Methods section “Linkage analysis”. (PDF 84 kb

Additional file 2: of A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna

The framework and composite map of Daphnia magna. Listed information include the names of RAD markers; marker alignment position to D. magna genome assembly v2.4; marker assignment as a representative of a segregation pattern (“FRAME” marker), significance level of the segregation ratio distortion (SRD) for each marker based on the p-value of Chi-square test for a difference between the observed and the expected Mendelian ratio (p < 0.1 *, p < 0.05 **, p < 0.01 ***, p < 0.005 ****, p < 0.001 *****, p < 0.0005 ******, p < 0.0001 *******); the number of the linkage group; the position of the marker within the linkage group (in cM, Kosambi corrected); genotype data used for the construction of genetic map. (XLSX 1401 kb

How to Make Outpatient Healthcare Data in Germany Available for Research in the Dynamic Course of Digital Transformation

There is increasing interest on re-use of outpatient healthcare data for research, as most medical diagnosis and treatment is provided in the ambulatory sector. One of the early projects to bring primary data from German ambulatory care into clinical research technically, organizationally and in compliance with legal demands has been the RADAR project, that is based on a broad consent and has used the then available practice information system's interfaces to extract and transfer data to a research repository. In course of the digital transformation of the German healthcare system, former standards are abandoned and new interoperability standards, interfaces and regulations on secondary use of patient data are defined, however with slow adoption by Health-IT systems. Therefore, it is of importance for all initiatives that aim at using ambulatory healthcare data for research, how to access this data in an efficient and effective way

DOOR

Cover design is in memoriam of the author’s father who received this picture from his colleagues. The image resembles the image of the detective Havank, which is also the name of the finger print database in the Netherlands