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The Basel Daphnia magna QTL panel

The Basel Daphnia magna QTL panel is a F2 breeding panel, which allows us to find regions in the genome of D. magna, which are associated with phenotypic traits. Any phenotypic trait can be mapped, disregarding if the trait is a single locus trait (mendelian trait) or a quantitative genetic trait (hence QTL: quantitative trait loci). The panel is based on a cross between a Finnish and a German clone of D. magna. The resulting F1 hybrid clone was selfed to produce hundreds of F2 clones, which form the basis of this panel.

The genetic material of the panel

QTL panel

The QTL panel is based on two parental clones, which were selected from a larger set of 14 clones from different European locations. The two clones chosen were selected because of the large phenotypic differences detected for many traits in experiments under controlled conditions and because of the ease with which it was possible to conduct genetic crosses. The two chosen clones are: The Xinb3 clone (the Finish Clone) and the Iinb1 clone (the Munich Clone).


The genetic map

To map phenotypes on the genome a genetic map is required, which is based on the same genetic material. Therefore we produced genetic maps for the F2 panel. These maps are refined from time to time to increase the map density and the number of F2 clones included.

unviable_egg

red draft

The Egg bearing infertility phenotype (top) and the Infertile red dwarf phenotype (bottom) the first two phenotypes mapped with the QTL panel. The lower animal is about 1.5 mm long.


How to use the panel?

This panel is an open source panel and can be used by everybody. We generally arrange this in form of a collaboration between you and our group. Testing for a specific phenotypic trait and running the analysis takes from 6 to 12 months. These are the steps:


Getting started

If you want to work with the panel, send an email to Dieter Ebert. We will send you the two parent clones of the panel (and if needed, about 10 of the F2 clones). You test these clones for phenotypic traits and if significant differences are seen between the two parents (or among the F2 clones), we can discuss how to screen all or parts of the F2 clones for this phenotype(s).

To work with the panel you need to be equipped to work with large number of Daphnia clones under controlled conditions. If this is not possible, one needs to design a nested approach, in which a sub-set of clones is tested first and based on this first information further selected sub-sets of clones are selected. This works well for traits with major QTLs, but is hardly meaningful for traits with several minor QTLs.

The analysis of the data requires some level of statistical experience to crunch the data. We use and provide R scripts for the analyses.

We are maintaining a database with all phenotypic traits tested on the F2 clones. Therefore, we request that any further traits quantified are submitted to our database. The aim of this database is to perform comprehensive analyses with the combined datasets. If you are interested in making use of this resource, get in touch with Dieter Ebert.


Traits mapped so far

Over the last years we mapped or plan to map the following traits in the QTL panel.

Trait category Trait Investigator Current state of the project
Recessive deleterious mutations Infertile red dwarf phenotype Jarkko Routtu (Ebert lab) Routtu et al 2010. BMC Genomics; Routtu et al, 2014, BMC Genomics
Recessive deleterious mutations Egg bearing infertility phenotype Jarkko Routtu (Ebert lab) Routtu et al 2010. BMC Genomics; Routtu et al, 2014, BMC Genomics
Host-parasite interaction Spore production of Hamiltosporidium tvaerminnensis after vertical infection Jarkko Routtu (Ebert lab) Routtu & Ebert 2015, Heredity
Host-parasite interaction Spore production of Hamiltosporidium tvaerminnensis after horizontal infection Jarkko Routtu (Ebert lab) Routtu & Ebert 2015, Heredity
Host-parasite interaction Long term persistence of Hamiltosporidium tvaerminnensis in monoclonal D. magna populations Michelle Krebs (Ebert lab) paper in prep.
Host-parasite interaction Resistance to Pasteuria ramosa (locus A) Jarkko Routtu (Ebert lab) Routtu & Ebert 2015, Heredity
Host-parasite interaction Resistance to Pasteuria ramosa (locus D) Gilberto Bento (Ebert lab) in preparation
Host-parasite interaction Second line of defense against Pasteuria ramosa Matt Hall (Ebert lab) paper in prep.
Host-parasite interaction Spore production of Pasteuria ramosa Matt Hall (Ebert lab) paper in prep.
Life-history Resting egg production Anne Roulin (Ebert lab) Roulin et al. 2013. Mol. Ecology
Life-history Male production Anne Roulin (Ebert lab) Roulin et al. 2013. Mol. Ecology
Life-history diverse life history traits Matt Hall (Ebert lab) Routtu et al, 2014, BMC Genomics
Life-history ephippia hatching Till Czypionka (De Meester lab) data collection
Physiology Salt tolerance (3 different traits) Michael Pfrender lab analysis
Physiology RNA/DNA ratio with and without exposure to fish smell Luc DeMeester lab analysis
Behaviour phototactic behavior with and without exposure to fish smell Luc DeMeester lab Routtu et al, 2014, BMC Genomics
Behaviour digging behaviour of Daphnia in sediments Roberto Arbore (Ebert lab) Arbore et al (submitted)


History of the Basel Daphnia magna QTL panel

The beginning of our QTL goes back to 2005, when Isabelle Colson joined the group. Isabelle took part in the initial phenotypic screening of the candidate parent clones and she performed the selfing of the Finish and the Munich clones. The F1 and the F2 clones were produced in 2006/7. In parallel Isabelle had developed a set of microsatellites, starting from an EST library of D. magna. Thus, all microsats were associated with coding genes (Colson et al 2009, BMC Research Notes). When Isabelle moved to a faculty position in the UK, Jarkko Routtu joined the group and continued with the project. Jarkko genotypes 214 F2 clones for 29 of our microsats, which we had found to be polymorphic across the parents and the F1 clones. Meanwhile, Bastiaan Jansen from the group of Luc De Mester in Leuven, Belgium, typed the F2 clones for another set of 80 microsats. The combined dataset of 109 microsats resulted in the first generation genetic map (Routtu et al. 2010).

Having a map at hand, the QTL panel was ready to be used to map phenotypic traits. The first traits mapped where two deleterious mutations, which happened to segregate in our panel. Isabelle Colson had observed that among the hatchlings of the sexual eggs produced by the F1 clone, two sterile phenotype occurred. Both of them would reach adulthood, but were unable to produce viable offspring. One of them we called Red Dwarf, because the animals remaind relatively small and had a reddish colour. The other looks normal and even produces asexual eggs, but they do not develop (egg bearing infertility phenotype). Both traits turned out to be caused by single recessive deleterious loci.

Since then we mapped more than 20 other traits, being related to host-parasite interactions, behaviour, life-history and physiology. To keep the panel going, it was necessary to have support from dedicated technicians. These were Nicolas Boileau, Tim Jaenike, Nicole Kalberer and Kristina Muller.

The next bigger enterprise was the construction of a Nimblegene SNP array to type more markers. We were able to obtain 1,324 SNPs of good quality markers for the second generation map. The new map was produced by Jarkko Routtu, which improved our efforts to map phenotypic traits tremendously. We can now locate QTLs within 1.1 cM. At the same time, Matt Hall increased the panel to about 360 F2 clones, which improved the quality of the map further.

Marinela Dukic is currently producing a new map version which is based on RADseq SNP markers. This map will include about 4000 SNPs, but is based only on about 50 F2 clones.