Notre Dame, IN, United States
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Routtu J.,Tel Aviv University | Hall M.D.,Monash University | Albere B.,University of New Hampshire | Beisel C.,ETH Zurich | And 11 more authors.
BMC Genomics | Year: 2015

Background: Although Daphnia is increasingly recognized as a model for ecological genomics and biomedical research, there is, as of yet, no high-resolution genetic map for the genus. Such a map would provide an important tool for mapping phenotypes and assembling the genome. Here we estimate the genome size of Daphnia magna and describe the construction of an SNP array based linkage map. We then test the suitability of the map for life history and behavioural trait mapping. The two parent genotypes used to produce the map derived from D. magna populations with and without fish predation, respectively and are therefore expected to show divergent behaviour and life-histories. Results: Using flow cytometry we estimated the genome size of D. magna to be about 238 mb. We developed an SNP array tailored to type SNPs in a D. magna F2 panel and used it to construct a D. magna linkage map, which included 1,324 informative markers. The map produced ten linkage groups ranging from 108.9 to 203.6 cM, with an average distance between markers of 1.13 cM and a total map length of 1,483.6 cM (Kosambi corrected). The physical length per cM is estimated to be 160 kb. Mapping infertility genes, life history traits and behavioural traits on this map revealed several significant QTL peaks and showed a complex pattern of underlying genetics, with different traits showing strongly different genetic architectures. Conclusions: The new linkage map of D. magna constructed here allowed us to characterize genetic differences among parent genotypes from populations with ecological differences. The QTL effect plots are partially consistent with our expectation of local adaptation under contrasting predation regimes. Furthermore, the new genetic map will be an important tool for the Daphnia research community and will contribute to the physical map of the D. magna genome project and the further mapping of phenotypic traits. The clones used to produce the linkage map are maintained in a stock collection and can be used for mapping QTLs of traits that show variance among the F2 clones. © 2014 Routtu et al.; licensee BioMed Central Ltd.

PubMed | Lawrence Berkeley National Laboratory, University of Edinburgh, University of Bayreuth, Indiana University and 9 more.
Type: | Journal: Scientific data | Year: 2016

The full exploration of gene-environment interactions requires model organisms with well-characterized ecological interactions in their natural environment, manipulability in the laboratory and genomic tools. The waterflea Daphnia magna is an established ecological and toxicological model species, central to the food webs of freshwater lentic habitats and sentinel for water quality. Its tractability and cyclic parthenogenetic life-cycle are ideal to investigate links between genes and the environment. Capitalizing on this unique model system, the STRESSFLEA consortium generated a comprehensive RNA-Seq data set by exposing two inbred genotypes of D. magna and a recombinant cross of these genotypes to a range of environmental perturbations. Gene models were constructed from the transcriptome data and mapped onto the draft genome of D. magna using EvidentialGene. The transcriptome data generated here, together with the available draft genome sequence of D. magna and a high-density genetic map will be a key asset for future investigations in environmental genomics.

Rull J.,Institute Ecologia Ac | Aluja M.,Institute Ecologia Ac | Feder J.L.,Galvin Life Science Center
Biological Journal of the Linnean Society | Year: 2010

Across its range in North America, four geographically separated, ecologically and genetically diverged populations of hawthorn (Crataegus)-infesting Rhagoletis pomonella (Diptera: Tephritidae) flies inhabit the Eje Volcánico Trans Mexicano (EVTM), the Sierra Madre Oriental (SMO), the Chiapas Highlands (CHIS) and the USA. Here, we tested whether these four populations are reproductively isolated by any intrinsic, nonhost-related, pre- or postmating barriers to gene flow. Crossing experiments suggested that a low level of host-independent prezygotic isolation may exist between hawthorn flies from EVTM and the three other populations, but only with respect to a slight reduction in copulation duration in EVTM matings. Some evidence for postmating isolation was found, again primarily involving EVTM crossed to SMO, CHIS and US flies. Certain crosses produced no (SMO male × EVTM female) or few (EVTM male × CHIS female; CHIS male × SMO female) F1 hybrid offspring. F2 crosses were generally fertile, except for US male × CHIS female matings. Inherent reproductive isolation therefore appears to be quantitative rather than absolute between populations, as the possibility for gene flow exists through at least some combinations of mating among EVTM, SMO, CHIS and US flies. Our results are consistent with a recently advanced hypothesis that episodic introgression from Mexico into the USA has played a role in providing genetic variation, facilitating sympatric host race formation and the adaptive radiation of the R. pomonella sibling species' complex in the USA. © 2010 The Linnean Society of London.

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