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A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna Dukić, Marinela; Berner, Daniel; Roesti, Marius; Haag, Christoph R; Ebert, Dieter

Abstract

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.

Item Metadata

Title
A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna
Creator
Dukić, Marinela; Berner, Daniel; Roesti, Marius; Haag, Christoph R; Ebert, Dieter
Contributor
University of British Columbia. Biodiversity Research Centre
Publisher
BioMed Central
Date Issued
2016-10-13
Description
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.
Subject
Crossover; Daphnia magna; Linkage map; RAD-sequencing; Recombination breakpoints; Recombination rate
Genre
Article
Type
Text
Language
eng
Date Available
2017-12-14
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0362015
URI
http://hdl.handle.net/2429/64017
Affiliation
Science, Faculty of; Other UBC; Non UBC; Zoology, Department of
Citation
BMC Genetics. 2016 Oct 13;17(1):137
Publisher DOI
10.1186/s12863-016-0445-7
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
The Author(s).
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Attribution 4.0 International (CC BY 4.0)