ArticleBMC genomics2014
An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 51 citations in OpenAlex.
- Polymorphisms ofFoods (Basel, Switzerland) · 2024Article
- Article
- QTL study reveals candidate genes underlying host resistance in a Red Queen model system.PLoS genetics · 2023Article
- Review
- Genetic Polymorphisms ofGenes · 2022Article
- Identification ofFrontiers in genetics · 2022Article
- Identification ofGenes · 2021Article
- A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host Resistance.Molecular biology and evolution · 2021Article
- Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome ofInternational journal of molecular sciences · 2020Article
- Article
- Epigenetic, transcriptional and phenotypic responses in two generations ofEnvironmental epigenetics · 2019Article
- Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns.Evolution letters · 2018Article
- Differential gene transcription across the life cycle in Daphnia magna using a new all genome custom-made microarray.BMC genomics · 2018Article
- Identification of General Patterns of Sex-Biased Expression inG3 (Bethesda, Md.) · 2018Article
- Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes.Molecular ecology · 2018Article
- Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia.Genome biology and evolution · 2017Article
- Transition from Environmental to Partial Genetic Sex Determination in Daphnia through the Evolution of a Female-Determining Incipient W Chromosome.Molecular biology and evolution · 2017Article
- The genetic basis of resistance and matching-allele interactions of a host-parasite system: The Daphnia magna-Pasteuria ramosa model.PLoS genetics · 2017Article
- A high-density genetic map reveals variation in recombination rate across the genome of Daphnia magna.BMC genetics · 2016Article
- Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.Scientific data · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 9 institutions in 7 countries.
Funding
Abstract
backgroundAlthough 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.
resultsUsing 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.
conclusionsThe 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.