Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Comparative genomic hybridsation of genomic DNA from a male and a female duck to the Roche NimbleGen chicken whole genome oligonucleotide array

ABSTRACT: Comparative genomic hybridsation of genomic DNA from a male and a female duck to the Roche NimbleGen chicken whole genome oligonucleotide array

ORGANISM(S): Anas platyrhynchos

SUBMITTER: Darren Griffin

PROVIDER: E-TABM-921 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis.

Skinner Benjamin M BM Robertson Lindsay B W LB Tempest Helen G HG Langley Elizabeth J EJ Ioannou Dimitris D Fowler Katie E KE Crooijmans Richard P M A RP Hall Anthony D AD Griffin Darren K DK Völker Martin M

BMC genomics 20090805

<h4>Background</h4>The availability of the complete chicken (Gallus gallus) genome sequence as well as a large number of chicken probes for fluorescent in-situ hybridization (FISH) and microarray resources facilitate comparative genomic studies between chicken and other bird species. In a previous study, we provided a comprehensive cytogenetic map for the turkey (Meleagris gallopavo) and the first analysis of copy number variants (CNVs) in birds. Here, we extend this approach to the Pekin duck ( ...[more]

PMID: 19656363

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Project description:MarekM-bM-^@M-^Ys disease virus (MDV) is an oncovirus causing tumor disease known as MarekM-bM-^@M-^Ys disease (MD) in chicken. Breeding of chickens genetically resistant to MD is considered a vital augment to better control MD. To find the mechanism underlying the genetic resistance to MD, a genomic structural variation, copy number variation (CNV), was examined in inbred MD-resistant and -susceptible chicken lines by using the comparative genomic hybridization (CGH) technique. A total of 45 copy number variation regions (CNVRs) were found spanning across 3,297,038 bp in length of the chicken genome in 4 lines of chickens. Ten CNVRs were selectively confirmed with quantitative real-time PCR. The comparison between the resistant and susceptible chicken lines revealed 28 differentially presented CNVRs, which are functionally involved in immune response, cell proliferation in midbrain, G-protein coupled receptor signaling pathway, and protein-glutamine gamma-glutamyltransferase activity. Two CNVRs that are related with MD-resistance and M-bM-^@M-^Ssusceptibility were also found transmitted to descendent recombinant congenic lines that differ in susceptibility to MD. A positive correlation was identified between the CNVRs and gene expression, indicating the importance of gene expression dosage in disease resistance. We also found the overlapping between the CNVR region and the MarekM-bM-^@M-^Ys disease trait related quantitative trait loci (QTLs). In conclusion, our data provided additional information elucidating one of possible mechanisms underlying of genetic resistance to MD. The findings may eventually lead to better strategies for genetic improvement of resistance to MD in poultry. L63: highly resistant to MD; L72: highly susceptible to MD; RCS-L: moderate resistant to MD; RCS-M: moderate susceptible to MD Red blood cell DNAs were isolated from L63, L72, RCS-L and RCS-M and then labeled with Cy3. DNA from Red Junglefowl was labeled with Cy5 as reference and mixed with Cy3 labeled DNA, then hybridized to the 385K chicken tiling array. The hybridization, normalization and segmentation analysis were performed by NimbleGen Systems Inc. (Madison, USA). A detailed description of their technical specifics can be found on http://www.nimblegen.com/products/lit/lit.html. Briefly, the segments with five or more probes having a mean log2 ratio greater than M-BM-10.5 (0.5_5) were chosen as candidate CNVs.

Dataset Information

Comparative genomic hybridsation of genomic DNA from a male and a female duck to the Roche NimbleGen chicken whole genome oligonucleotide array

Publications

Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis.

Similar Datasets

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