Open Access Research article

The first-generation Daphnia magna linkage map

Jarkko Routtu1*, Bastiaan Jansen2, Isabelle Colson13, Luc De Meester2 and Dieter Ebert1

Author Affiliations

1 Zoologisches Institut, Evolutionsbiologie, Universität Basel, Vesalgasse 1, 4051 Basel, Switzerland

2 Katholieke Universiteit Leuven, Charles de Bériotstraat 32, 3000 Leuven, Belgium

3 Bangor University, Bangor LL57 2DG, UK

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BMC Genomics 2010, 11:508  doi:10.1186/1471-2164-11-508

Published: 22 September 2010



Daphnia magna is a well-established model species in ecotoxicology, ecology and evolution. Several new genomics tools are presently under development for this species; among them, a linkage map is a first requirement for estimating the genetic background of phenotypic traits in quantitative trait loci (QTL) studies and is also very useful in assembling the genome. It also enables comparative studies between D. magna and D. pulex, for which a linkage map already exists.


Here we describe the first genetic linkage map of D. magna. We generated 214 F2 (intercross) clonal lines as the foundation of the linkage analysis. The linkage map itself is based on 109 microsatellite markers, which produced ten major linkage groups ranging in size from 31.1 cM to 288.5 cM. The total size of this linkage map extends to 1211.6 Kosambi cM, and the average interval for the markers within linkage groups is 15.1 cM. The F2 clones can be used to map QTLs for traits that differ between the parental clones. We successfully mapped the location of two loci with infertility alleles, one inherited from the paternal clone (Iinb1) and the other from the maternal clone (Xinb3).


The D. magna linkage map presented here provides extensive coverage of the genome and a given density of markers that enable us to detect QTLs of moderate to strong effects. It is similar in size to the linkage map of D. pulex.