Abstract
BackgroundRecombination 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.ResultsA 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.ConclusionsDue 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0445-7) contains supplementary material, which is available to authorized users.
Highlights
Recombination rate is an essential parameter for many genetic analyses
Linkage map The genetic map of D. magna constructed in this study includes 4037 markers (Additional file 1), assigned to ten Linkage group (LG) that correspond to the ten chromosomes of D. magna (n = 10). 952 clusters of co-segregating markers were identified, and only one marker from each cluster was used to assemble a framework map
LGs were numbered according to their genetic length estimated in this study; not exactly corresponding to the previously published D. magna linkage maps [17, 18]
Summary
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. There is accumulating evidence for large amounts of variation in recombination rate across species, populations, individuals, and different genomic regions [5, 7, 9]. Considering the profound influence that the recombination landscape can have on genome-wide genetic variation and diversity, analysis of the recombination rate emerge as a key resource for population and evolutionary genomics studies, emphasising the importance of high-density genetic maps as essential tools for studying many features of genome biology
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