Gallus gallus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA120343 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The parents and progeny of the I X III genetic cross were genotyped using the ToxoGeneChip in order to generate a more detailed genetic map. We also used the genomic hybridization data to look for copy number variations (CNV) and segmental duplications.
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Project description:Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 2)
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Project description:Validation experiment of copy number variations identified by next-generation sequencing in chickens (part 1)
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Project description:Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory regions. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as model animal for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosome regions that segregate for important agricultural and disease phenotypes. NimbleGen 385k whole genome tiling arrays were used to map CNVs in the chicken. This study has identified 96 CNVs in three lines of chickens (broiler, Leghorn and Rhode Island red). These CNVs encompass 16 Mb (1.3%) of the chicken genome. Twenty six CNVs were found in two or more animals. Smaller sized CNVs mostly affect none coding sequences while larger CNV regions involve genes, for example prolactin receptor, aldose reductase and zinc finger proteins, suggesting chicken CNVs potentially affect agricultural or disease related traits.
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Project description:An initial comparative map of copy number variations in the goat (Capra hircus) genome
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Project description:Segmental copy number variations (CNVs) in the human genome are associated with developmental disorders and susceptibility to human diseases. More importantly, these variations may represent a major genetic component of our phenotypic diversity. In this study, using a whole genome array CGH assay, we identified 3,654 autosomal segmental CNVs, of which 800 appeared at a frequency of at least 3%. 77% of these frequent CNVs are novel. In the 95 individuals analyzed, the most diverse genomes differed by at least 9 Mb in size or varied by at least 266 loci in content. Approximately 68% of the 800 polymorphic regions overlap with genes, reflecting human diversity in senses (smell, hearing, taste, and sight), Rhesus phenotype, metabolism, and disease susceptibility. Intriguingly, 14 polymorphic regions harbor 21 of the known human microRNAs, raising the possibility of microRNAs’ contribution to phenotypic diversity in humans. This in depth survey of CNVs across the human genome provides a valuable baseline for studies involving human genetics. Keywords: array CGH, segmental copy number variations (CNVs)
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Project description:Here we describe the initial analysis of copy number variations in cattle selected for resistance or susceptibility to intestinal nematodes
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Project description:Chromosomal segmental copy number variation (CNV) has been recently recognized as a very important source of genetic variability. Some CNV loci involve genes or conserved regulatory regions. Compelling evidence indicates that CNVs impact genome functions. The chicken is a very important farm animal species which has also served as model animal for biological and biomedical research for hundreds of years. A map of CNVs in chickens could facilitate the identification of chromosome regions that segregate for important agricultural and disease phenotypes. NimbleGen 385k whole genome tiling arrays were used to map CNVs in the chicken. This study has identified 96 CNVs in three lines of chickens (broiler, Leghorn and Rhode Island red). These CNVs encompass 16 Mb (1.3%) of the chicken genome. Twenty six CNVs were found in two or more animals. Smaller sized CNVs mostly affect none coding sequences while larger CNV regions involve genes, for example prolactin receptor, aldose reductase and zinc finger proteins, suggesting chicken CNVs potentially affect agricultural or disease related traits. Blood DNA isolated from Cornish Rock, Leghorn and Rhode Island Red birds. Cy5 labeled DNA from a Cornish Rock male used as reference was mixed with Cy3 labeled DNA samples was then hybridized to the 385K chicken tiling array. Fluorescence intensity data were normalized with qspline algorithm and ratio data were analyzed with the circular binary segmentation algorithm from Olshen et al. Copy number variation calls were made if the averaged Log2 ratio of a segment was shifted by 0.3 from the baseline.
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