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83 results for “SNP analysis”
Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes
<p>Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The Siamese cobra (<i>Naja kaouthia</i>) exhibits ZZ/ZW heteromorphic sex chromosomes. The W sex chromosome contains a large number of repeats and shares several amniote sex chromosomal linkages. In conjunction with recent advances in high-throughput sequencing, Diversity Arrays Technology (DArTseq™) provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 perfectly sex-linked loci, 90 loci showed partial homology with several amniote sex chromosomal linkages, and 89 loci were homologous to transposable elements, which suggests that recombination suppression may be the crucial step in snake sex chromosome differentiation. Two loci were confirmed as W-specific nucleotides in females but not in males in the population examined by PCR amplification; one of the two loci (locus id: 100002617) was further amplified in females of the Indochinese spitting cobra (<i>N. siamensis</i>) but not in the other 22 snake species examined. Female-specific DArT markers were identified in Siamese cobra. These loci might result from a sex chromosome differentiation process between Z and W and involve putative sex-determination regions in Siamese cobra. Short sequences derived from DArTseq™ technology also shared linkage homologies among amniote sex chromosomes, which supports the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex chromosomal linkages. The locus (id: 100002617) shared in <i>N. kaouthia</i> and <i>N. siamensis</i>, but among 22 other snake species, indicates inheritance from a common ancestor as synapomorphic loci in the <i>Naja</i> lineage. The ease of use of the DArT markers and DArTseq™ platform provides a useful strategy for future research on sex chromosome evolution in snakes.</p>
Data from: An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits
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.
Data from: Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip
Elucidating the genetic basis of fitness-related traits is a major goal of molecular ecology. Traits subject to sexual selection are particularly interesting, as non-random mate choice should deplete genetic variation and thereby their evolutionary benefits. We examined the genetic basis of three sexually selected morphometric traits in bighorn sheep (Ovis canadensis): horn length, horn base circumference, and body mass. These traits are of specific concern in bighorn sheep as artificial selection through trophy hunting opposes sexual selection. Specifically, horn size determines trophy status and, in most North American jurisdictions, if an individual can be legally harvested. Using between 7,994–9,552 phenotypic measures from the long-term individual-based study at Ram Mountain (Alberta, Canada), we first showed that all three traits are heritable (h2 = 0.15–0.23). We then conducted a genome-wide association study (GWAS) utilizing a set of 3,777 SNPs typed in 76 individuals using the Ovine Infinium® HD SNP BeadChip. We found suggestive association for body mass at a single locus (OAR9_91647990). The absence of strong associations with SNPs suggests that the traits are likely polygenic. These results represent a step forward for characterizing the genetic architecture of fitness related traits in sexually dimorphic ungulates.
Genome-wide SNP analysis of male and female rice field frogs, Hoplobatrachus rugulosus, supports a non-genetic sex determination system
<p>Sex determination systems (SDSs) in anurans are diverse and have undergone independent evolutionary transitions among species. The mode of sexual reproduction of the rice field frog (<i>Hoplobatrachus rugulosus</i>), an economically viable edible amphibian species, is not well known. Previous studies have proposed that threshold temperature conditions may determine sex in these frogs. To elucidate the SDS in <i>H. rugulosus</i>, we karyotyped 10 male and 12 female frogs, and performed fluorescence <i>in situ</i> hybridization combined with<b> </b>sequencing analyses using DArTseq™. Our results revealed a highly conserved karyotype with no sex chromosome heteromorphism, and the sequencing analyses did not identify any consistent sex-linked loci, supporting the hypothesis of temperature-dependent sex determination. The results of this study, and others, on SDSs in the rice field frog and related species also provides support for the theory that heteromorphic sex chromosomes may lead to an evolutionary trap that prevents variable SDSs. These findings add important information to the body of knowledge on <i>H. rugulosus</i> and are likely to have a significant impact on the productivity and economic success of rice field frog farming.</p>
Supplementary material 1 from: Giangregorio P, Mucci N, Norman AJ, Pedrotti L, Filacorda S, Molinari P, Spong G, Davoli F (2023) Performance of SNP markers for parentage analysis in the Italian Alpine brown bear using non-invasive samples. Nature Conservation 53: 105-123. https://doi.org/10.3897/natureconservation.53.86739
Genetic and field data
Genome-wide SNP analysis of male and female rice field frogs, Hoplobatrachus rugulosus, supports a non-genetic sex determination system
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Data from: Development of a 44K SNP Assay focussing on the analysis of a varroa specific defense behavior in honey bees (Apis mellifera carnica)
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Data from: Genomic analysis of morphometric traits in bighorn sheep using the Ovine Infinium® HD SNP BeadChip
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Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes
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Data from: An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits
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Affymetrix SNP array data for analysis of peanut agronomic traits
GEO Series GSE197103. Arachis hypogaea. 333 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
SNP array analysis has facilitated the identification of novel chromosomal alterations associated with disease and SNPs related to Adverse Drug Reactions in neuroblastoma
GEO Series GSE288908. Homo sapiens. 45 samples. Type: Genome variation profiling by SNP array.
50K SNP Copy Number Analysis of Ovarian Carcinomas
GEO Series GSE13813. Homo sapiens. 118 samples. Type: Genome variation profiling by SNP array.
Evaluating the restoration of DNA derived from archival formalin-fixed paraffin embedded tissues for genomic profiling by SNP-CGH analysis
GEO Series GSE43406. Homo sapiens. 43 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays [Omni1-Quad]
GEO Series GSE48482. Homo sapiens. 55 samples. Type: SNP genotyping by SNP array.
Paired copy number analysis of DLBCL Diffuse Large B Cell Lymphoma [SNP 6.0 Array]
GEO Series GSE71389. Homo sapiens. 62 samples. Type: Genome variation profiling by SNP array.
SNP array analysis of neuroblastoma tumors
GEO Series GSE8333. Homo sapiens. 44 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays [Illumina Quad610 Beadchip]
GEO Series GSE48483. Homo sapiens. 67 samples. Type: SNP genotyping by SNP array.
CGH + SNP microarray analysis in consanguineous family with ovarian dysgenesis
GEO Series GSE62347. Homo sapiens. 6 samples. Type: Genome variation profiling by genome tiling array; Genome variation profiling by SNP array.
SNP analysis of human induced pluripotent stem cells
GEO Series GSE31035. Homo sapiens. 12 samples. Type: SNP genotyping by SNP array.
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International Brain Laboratory public data
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OpenNeuro
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